diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 487600e24..97f1229e5 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -81,10 +81,10 @@ jobs: build_type: Debug build_python: ON build_qt_antimony: OFF - libroadrunner_deps_owner: [ "sys-bio" ] - libroadrunner_deps_repo: [ "libroadrunner-deps" ] - libroadrunner_deps_name: [ "libroadrunner-deps" ] - libroadrunner_deps_release_version: [ "v2.3.4" ] + antimony_deps_owner: [ "sys-bio" ] + antimony_deps_repo: [ "libroadrunner-deps" ] + antimony_deps_name: [ "antimony-deps" ] + antimony_deps_release_version: [ "v2.3.5" ] python_version: [ "3.13" ] runs-on: ${{ matrix.platform.os_name }} @@ -180,7 +180,7 @@ jobs: if: matrix.platform.os_type != 'windows' uses: actions/cache@main with: - path: ${RUNNER_WORKSPACE}/.ccache + path: ${{ runner.workspace }}/.ccache key: ${{ runner.os }}-${{ steps.ccache_cache_timestamp.outputs.timestamp }} @@ -224,28 +224,35 @@ jobs: shell: bash run: | cd ${RUNNER_WORKSPACE} - mkdir -p ${{ matrix.libroadrunner_deps_name }}-binaries - cd ${{ matrix.libroadrunner_deps_name }}-binaries + mkdir -p ${{ matrix.antimony_deps_name }}-binaries + cd ${{ matrix.antimony_deps_name }}-binaries if [ "${{ matrix.platform.os_type }}" == 'windows' ]; then compiler_version=$(ls "C:\Program Files\Microsoft Visual Studio") - binary_file_name=${{ matrix.libroadrunner_deps_name }}-${{ matrix.platform.os_type }}-msvc${compiler_version}-${host_architecture}-${{ matrix.platform.build_type }} + binary_file_name=${{ matrix.antimony_deps_name }}-${{ matrix.platform.os_type }}-msvc${compiler_version}-${host_architecture}-${{ matrix.platform.build_type }} elif [ "${{ matrix.platform.os_type }}" == 'macos' ]; then os_version=$(sw_vers -productVersion | cut -d '.' -f 1) - binary_file_name=${{ matrix.libroadrunner_deps_name }}-${{ matrix.platform.os_type }}-${os_version}-${host_architecture}-${{ matrix.platform.build_type }} + binary_file_name=${{ matrix.antimony_deps_name }}-${{ matrix.platform.os_type }}-${os_version}-${host_architecture}-${{ matrix.platform.build_type }} elif [ "${{ matrix.platform.os_type }}" == 'ubuntu' ]; then os_version=$(lsb_release -rs | cut -d '.' -f 1) - binary_file_name=${{ matrix.libroadrunner_deps_name }}-${{ matrix.platform.os_type }}-${os_version}-${host_architecture}-${{ matrix.platform.build_type }} + binary_file_name=${{ matrix.antimony_deps_name }}-${{ matrix.platform.os_type }}-${os_version}-${host_architecture}-${{ matrix.platform.build_type }} elif [ "${{ matrix.platform.os_type }}" == 'manylinux' ]; then os_name="${{ matrix.platform.name }}" os_name_without_build_type="${os_name%%-*}" - binary_file_name=${{ matrix.libroadrunner_deps_name }}-${os_name_without_build_type}-${host_architecture}-${{ matrix.platform.build_type }} + binary_file_name=${{ matrix.antimony_deps_name }}-${os_name_without_build_type}-${host_architecture}-${{ matrix.platform.build_type }} fi - curl -LO "https://github.com/${{ matrix.libroadrunner_deps_owner }}/${{ matrix.libroadrunner_deps_repo }}/releases/download/${{ matrix.libroadrunner_deps_release_version }}/$binary_file_name.zip" + curl -LO "https://github.com/${{ matrix.antimony_deps_owner }}/${{ matrix.antimony_deps_repo }}/releases/download/${{ matrix.antimony_deps_release_version }}/$binary_file_name.zip" unzip -q $binary_file_name.zip rm $binary_file_name.zip - echo ANT_DEPENDENCIES_INSTALL_PREFIX="-DANT_DEPENDENCIES_INSTALL_PREFIX=${RUNNER_WORKSPACE}/${{ matrix.libroadrunner_deps_name }}-binaries" >> "${GITHUB_ENV}" + if [ -d "$binary_file_name" ]; then + mv "$binary_file_name"/* . + rmdir "$binary_file_name" + fi + + echo ANT_DEPENDENCIES_INSTALL_PREFIX="-DANT_DEPENDENCIES_INSTALL_PREFIX=${RUNNER_WORKSPACE}/${{ matrix.antimony_deps_name }}-binaries" >> "${GITHUB_ENV}" + + #if [ "${{ matrix.platform.os_type }}" == 'windows' ]; then - # echo EXPAT_LIBRARY="-DEXPAT_LIBRARY=${RUNNER_WORKSPACE}/${{ matrix.libroadrunner_deps_name }}-binaries/lib/${{ matrix.platform.expat_lib_name }}" >> "${GITHUB_ENV}" + # echo EXPAT_LIBRARY="-DEXPAT_LIBRARY=${RUNNER_WORKSPACE}/${{ matrix.antimony_deps_name }}-binaries/lib/${{ matrix.platform.expat_lib_name }}" >> "${GITHUB_ENV}" #fi - name: Install Qt @@ -280,7 +287,6 @@ jobs: -DCMAKE_C_COMPILER_LAUNCHER=${COMPILER_LAUNCHER} \ -DCMAKE_CXX_COMPILER_LAUNCHER=${COMPILER_LAUNCHER} \ -DCMAKE_BUILD_TYPE=${{ matrix.platform.build_type }} \ - -DUSE_UNIVERSAL_BINARIES=OFF \ -DCMAKE_OSX_ARCHITECTURES=${{ matrix.platform.arch }} \ -DCMAKE_INSTALL_PREFIX="${RUNNER_WORKSPACE}/install-antimony" \ ${ANT_DEPENDENCIES_INSTALL_PREFIX} \ @@ -304,32 +310,17 @@ jobs: # Valgrind is Linux-only (no Windows support, weak/no Apple Silicon # support), so this only runs on one leg of the matrix rather than - # across every platform/config combination. See MEMORYCHECK_* in the - # root CMakeLists.txt and valgrind.supp for the suppressions file. - # - # This runs automatically on every push/PR, against the release build - # (which has -g added just for this leg -- see "Configure CMake for - # Antimony" above -- so it's still symbol-rich) so it's much faster - # than a full debug-build run and still gives usable stack traces, at - # the cost of somewhat less precise line numbers due to optimization - # (inlining etc.), and a small risk that -O3 could eliminate a - # provably-dead allocation an unoptimized debug build wouldn't. + # across every platform/config combination. # # For a slower but fully accurate debug-build memcheck run (e.g. to # dig into something this one flagged), trigger # .github/workflows/valgrind-debug-memcheck.yml manually from the - # Actions tab -- see the comment at the top of that file for why it's - # a separate workflow rather than another leg here. + # Actions tab. # # `ctest -T memcheck` only prints a per-test defect *count* to the # console -- the actual valgrind report (stack traces, "definitely # lost" byte counts, etc.) goes to a per-test log file instead: - # Testing/Temporary/MemoryChecker..log, one per test. Rather - # than running every test as one opaque block and only finding out - # what broke at the very end, run them in numbered chunks (via - # `ctest -I ,`) and print any defects from each chunk - # immediately after it finishes, so problems surface within minutes - # rather than at the end of the whole run. + # Testing/Temporary/MemoryChecker..log, one per test. - name: Run Antimony tests under valgrind (memcheck), in chunks if : matrix.platform.name == 'ubuntu-latest-release' shell: bash @@ -396,14 +387,18 @@ jobs: run: | cd ${RUNNER_WORKSPACE}/install-antimony/bindings/python if [ "${{ matrix.platform.os_type }}" == 'windows' ]; then - ${{env.python_exe}} -m pip install setuptools wheel - ${{env.python_exe}} setup.py bdist_wheel + ${{env.python_exe}} -m pip install setuptools wheel build + ${{env.python_exe}} -m build --wheel --no-isolation --outdir dist elif [ "${{ matrix.platform.os_type }}" == 'manylinux' ]; then - python${{ matrix.python_version }} -m pip install --trusted-host pypi.org --trusted-host pypi.python.org --trusted-host files.pythonhosted.org setuptools wheel - python${{ matrix.python_version }} setup.py bdist_wheel + python${{ matrix.python_version }} -m pip install --root-user-action=ignore --trusted-host pypi.org --trusted-host pypi.python.org --trusted-host files.pythonhosted.org setuptools wheel build + python${{ matrix.python_version }} -m build --wheel --no-isolation --outdir dist + elif [ "${{ matrix.platform.os_type }}" == 'macos' ]; then + export MACOSX_DEPLOYMENT_TARGET="$(sw_vers -productVersion | cut -d '.' -f 1).0" + python${{ matrix.python_version }} -m pip install setuptools wheel build + python${{ matrix.python_version }} -m build --wheel --no-isolation --outdir dist else - python${{ matrix.python_version }} -m pip install setuptools wheel - python${{ matrix.python_version }} setup.py bdist_wheel + python${{ matrix.python_version }} -m pip install setuptools wheel build + python${{ matrix.python_version }} -m build --wheel --no-isolation --outdir dist fi - name: Rename Python wheel artifacts @@ -436,3 +431,61 @@ jobs: with: name: ${{env.python_wheel_artifacts_name}} path: ${{env.python_wheel_artifacts_file}} + + # The SBML Test Suite round-trip only runs on one leg of the matrix, + # same reasoning as valgrind above: it's slow, and doesn't need to run + # on every OS/config combination to be useful. macos-14-release is + # chosen since ubuntu-latest-release is already dedicated to valgrind. + - name: Build Antimony Python wheel for SBML Test Suite round-trip + if: matrix.platform.name == 'macos-14-release' + shell: bash + run: | + cd ${RUNNER_WORKSPACE}/install-antimony/bindings/python + python${{ matrix.python_version }} -m pip install setuptools wheel build + python${{ matrix.python_version }} -m build --wheel --no-isolation --outdir dist-sbml-test-suite + python${{ matrix.python_version }} -m pip install dist-sbml-test-suite/antimony*.whl + python${{ matrix.python_version }} -m pip install -r "${GITHUB_WORKSPACE}/src/bindings/python/sbml_test_suite/requirements.txt" + + - name: Download SBML Test Suite semantic cases + if: matrix.platform.name == 'macos-14-release' + shell: bash + env: + GH_TOKEN: ${{ github.token }} + run: | + cd "${RUNNER_WORKSPACE}" + mkdir -p sbml-test-suite + asset_url=$(gh api repos/sbmlteam/sbml-test-suite/releases/latest \ + --jq '.assets[] | select(.name | startswith("semantic_tests")) | .browser_download_url') + if [ -z "$asset_url" ]; then + echo "::error::Failed to find a semantic_tests asset in the latest sbml-test-suite release." + exit 1 + fi + echo "Downloading ${asset_url}" + curl -fL "$asset_url" -o sbml-test-suite/semantic_tests.zip + unzip -q sbml-test-suite/semantic_tests.zip -d sbml-test-suite/extracted + # -quit makes find stop after the first match itself, rather than + # relying on a downstream `head -n 1` to cut it off -- piping into + # head closes the pipe early and GNU find treats that broken pipe + # as a fatal write error instead of exiting quietly. + settings_file=$(find "${RUNNER_WORKSPACE}/sbml-test-suite/extracted" -name '*-settings.txt' -print -quit) + if [ -z "$settings_file" ]; then + echo "::error::No *-settings.txt files found under sbml-test-suite/extracted -- unexpected archive layout." + exit 1 + fi + cases_dir=$(dirname "$settings_file") + echo "SBML_TEST_SUITE_DIR=$(dirname "$cases_dir")" >> "${GITHUB_ENV}" + + - name: Run SBML Test Suite round-trip tests + if: matrix.platform.name == 'macos-14-release' + shell: bash + run: | + cd "${GITHUB_WORKSPACE}/src/bindings/python/sbml_test_suite" + python${{ matrix.python_version }} -m pytest -ra --junitxml="${RUNNER_WORKSPACE}/sbml-test-suite-results.xml" \ + --sbml-test-suite-dir="${SBML_TEST_SUITE_DIR}" + + - name: Upload SBML Test Suite round-trip results + if: always() && matrix.platform.name == 'macos-14-release' + uses: actions/upload-artifact@main + with: + name: sbml-test-suite-results + path: ${{ runner.workspace }}/sbml-test-suite-results.xml diff --git a/.github/workflows/valgrind-debug-memcheck.yml b/.github/workflows/valgrind-debug-memcheck.yml index e17fd05dc..b6a3d2062 100644 --- a/.github/workflows/valgrind-debug-memcheck.yml +++ b/.github/workflows/valgrind-debug-memcheck.yml @@ -99,7 +99,7 @@ jobs: - name: Cache ccache files uses: actions/cache@main with: - path: ${RUNNER_WORKSPACE}/.ccache + path: ${{ runner.workspace }}/.ccache key: ${{ runner.os }}-debug-memcheck-${{ steps.ccache_cache_timestamp.outputs.timestamp }} diff --git a/CMakeLists.txt b/CMakeLists.txt index 24afeee28..b6294bdbc 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -11,8 +11,8 @@ project(libantimony) # Set up version information. # SET(LIBANTIMONY_VERSION_MAJOR 3) -SET(LIBANTIMONY_VERSION_MINOR 1) -SET(LIBANTIMONY_VERSION_PATCH ".3") +SET(LIBANTIMONY_VERSION_MINOR 2) +SET(LIBANTIMONY_VERSION_PATCH ".0") SET(LIBANTIMONY_VERSION_RELEASE "") @@ -31,7 +31,12 @@ endif() # C++14 minimum: required by the vendored GoogleTest 1.16.x (see # src/test/googletest/README.md), which uses std::make_index_sequence # and friends internally. -set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++14") +# MSVC doesn't understand the GNU-style -std= flag (and already +# defaults to a sufficiently modern standard), so only add it for +# GCC/Clang to avoid a D9002 "unknown option" warning on every file. +if(NOT MSVC) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++14") +endif() include (InstallRequiredSystemLibraries) include (CMakeTestCCompiler) @@ -77,8 +82,11 @@ set(CMAKE_BUILD_TYPE "RelWithDebInfo" CACHE STRING "Choose the type of build, op # which language bindings should be build option(WITH_CELLML "Generate CellML translations" OFF ) +mark_as_advanced(WITH_CELLML) +if(WITH_CELLML) + message(FATAL_ERROR "The ability to export Antimony to CellML is not currently functional.") +endif() option(WITH_QTANTIMONY "Generate QTAntimony" ON ) -option(WITH_SWIG "Regenerate SWIG-based language bindings." OFF ) option(WITH_PYTHON "Generate Python language bindings." OFF) if (WITH_PYTHON) option(PYTHON_SYSTEM_INSTALL "Install the python bindings using setup.py and distutils. May require admin privileges." OFF ) @@ -290,36 +298,6 @@ set(LIBANTIMONY_LIBS ${LIBANTIMONY_LIBS} ${CMAKE_DL_LIBS} ) message(STATUS "Antimony libs: ${LIBANTIMONY_LIBS}") -############################################################################### -# -# If WITH_SWIG is selected, we need to find swig -# -if(WITH_SWIG) - find_program(SWIG_EXECUTABLE - NAMES swig - PATHS - "c:/Program Files (x86)/Swig" - c:/Program Files/Swig - c:/Program Files/swigwin-3.0.10 - c:/Program Files/swigwin-4.0.2 - /usr/local/bin - /opt/local/bin - /usr/bin - DOC "The file name of the swig executable." - ) - find_package(SWIG) - set(SWIG_EXTRA_ARGS "" CACHE STRING "Extra arguments to SWIG" ) -endif(WITH_SWIG) - -if(WITH_SWIG) - message(STATUS " Using SWIG = ${SWIG_EXECUTABLE}") - - if (SWIG_FOUND AND SWIG_VERSION VERSION_LESS "2.0.4") - message(WARNING " You are using swig version ${SWIG_VERSION} while we recommend at least version 2.0.4.") - endif() - -endif() - if(WITH_PYTHON) message(STATUS " Using Python = ${PYTHON_EXECUTABLE}") endif() diff --git a/QTAntimony_src/QTAntimony.cpp b/QTAntimony_src/QTAntimony.cpp index 735f57f42..844e1df2e 100644 --- a/QTAntimony_src/QTAntimony.cpp +++ b/QTAntimony_src/QTAntimony.cpp @@ -11,6 +11,8 @@ #include #include #include +#include +#include #ifdef Q_OS_WIN #ifndef WIN32_LEAN_AND_MEAN @@ -107,7 +109,7 @@ void QTAntimony::DisplayWindow(QMainWindow* t) { } QRect desk = desktop()->availableGeometry(focus); if (focus==NULL) { - desk = desktop()->availableGeometry(desktop()->primaryScreen()); + desk = QGuiApplication::primaryScreen()->availableGeometry(); QRect window; window.setTop(desk.height()/8); window.setBottom(desk.height()*7/8); diff --git a/QTAntimony_src/Tutorial.xxd b/QTAntimony_src/Tutorial.xxd index 81a143844..edb878593 100644 --- a/QTAntimony_src/Tutorial.xxd +++ b/QTAntimony_src/Tutorial.xxd @@ -503,1854 +503,1816 @@ const static unsigned char ___doc_AntimonyTutorial_htm[] = { 0x3c, 0x68, 0x32, 0x20, 0x69, 0x64, 0x3d, 0x22, 0x63, 0x68, 0x61, 0x6e, 0x67, 0x65, 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___doc_AntimonyTutorial_htm_len = 105654; diff --git a/README.md b/README.md index 82d493665..409779bfc 100644 --- a/README.md +++ b/README.md @@ -9,9 +9,11 @@ PyPI - Downloads Funding Funding - Funding + Funding + Funding + Funding - + # Summary Antimony is a human-readable, human-writable modular model definition language, letting you create SBML models with a simple text interface, i.e. @@ -42,6 +44,94 @@ Other binaries are available from https://github.com/sys-bio/antimony/releases -Antimony depends on the libSBML and SBMLNetwork libraries. The currently-used versions of each will always be available from https://github.com/sys-bio/libroadrunner-deps/. +Antimony depends on the libSBML and SBMLNetwork libraries. The currently-used versions of each will always be available from https://github.com/sys-bio/libroadrunner-deps/releases/. Antimony has been supported by NIH/NIGMS Grants GM081070, GM123032, and NIBIB EB028887. + + +# Building from Source + +Here we describe how to build libAntimony from source. *Note: if these instructions don't work for any reason, look at [the github build instructions](https://github.com/sys-bio/antimony/blob/develop/.github/workflows/main.yml), which will always be up-to-date out of necessity.* + +## Install Required Build Tools + +Install [CMake](https://cmake.org/). On Windows, you also need to install **Visual Studio** with the **Desktop development with C++** workload, which enables you to run CMake from an MSVC x64 development environment. + +To build the Python bindings, install Python and ensure that CMake can locate it. + +To build the QtAntimony (the standalone Antimony editor), install Qt 5.15 (or a later version of Qt5) and ensure that CMake can locate it. + +If you are actually developing Antimony, you will need the [Bison](https://www.gnu.org/software/bison/) parser to re-generate [src/antimony.tab.cpp](https://github.com/sys-bio/antimony/blob/develop/src/antimony.tab.cpp) from [src/antimony.ypp](https://github.com/sys-bio/antimony/blob/develop/src/antimony.ypp) when the latter changes. + +## Download Prebuilt Dependencies + +Download the latest version of prebuilt Antimony dependencies that match your operating system, and build type from the [libroadrunner-deps releases page](https://github.com/sys-bio/libroadrunner-deps/releases). Make sure you get the 'release' version if you are building the release version of Antimony. + +If no pre-built dependencies match your operating system, you'll need to find libsbml with the released packages enabled (in particular: comp, fbc, and distrib) and SBMLNetwork. Libsbml in turn requires an XML library; we recommend using expat. A CMake system that builds these and a few others is available at [libroadrunner-deps](https://github.com/sys-bio/libroadrunner-deps/); see that repository (and its github build files) for more information. + +## Obtain Antimony Source Code + +Clone the Antimony repository and enter the source directory: + +```bash +git clone https://github.com/sys-bio/antimony.git +cd antimony +``` + +## Configure with CMake + +From the command line (i.e. PowerShell in an MSVC x64 development environment, or a terminal window in MacOS or Linux), enter the following. Replace `/path/to/libroadrunner-deps-install` with the location of the extracted prebuilt dependencies. + +### Windows +``` +cmake -S . -B build-antimony ` + -DCMAKE_INSTALL_PREFIX="./install-antimony" ` + -DANT_DEPENDENCIES_INSTALL_PREFIX="C:/path/to/libroadrunner-deps-install" ` + -DCMAKE_BUILD_TYPE=Release ` + -DWITH_PYTHON=ON ` + -DWITH_QTANTIMONY=OFF ` + -DWITH_GTEST=OFF +``` + +### MacOS/Linux +``` +cmake -S . -B build-antimony \ + -DCMAKE_INSTALL_PREFIX="./install-antimony" \ + -DANT_DEPENDENCIES_INSTALL_PREFIX="/path/to/libroadrunner-deps-install" \ + -DCMAKE_BUILD_TYPE=Release \ + -DWITH_PYTHON=ON \ + -DWITH_QTANTIMONY=OFF \ + -DWITH_GTEST=OFF +``` + +### Making changes + +The above represents a typical build, but modifications are available: +* If you want to compile for a different architecture than the environment where you're running CMake, use (for example) `-A x86` or `DCMAKE_OSX_ARCHITECTURES="$(uname -m)` +* If you do want to build QTAntimony, change WITH_QTANTIMONY to ON, and set QT5_DIR to the location of the CMake files where you installed QT5 (i.e. `Qt5.15.16/5.15.16/msvc2019_64/lib/cmake/Qt5`). +* If you don't want the python bindings, change WITH_PYTHON to OFF. +* If you want to build the tests, change WITH_GTEST to ON + +## Build and Install + +### Windows + +```powershell +cmake --build build-antimony --config Release --target install --parallel +``` + +### macOS and Linux + +```bash +cmake --build build-antimony --target install --parallel +``` + +### Location of files + +The compiled files will be installed in the `install-antimony` directory. This directory should now include: + +- Antimony libraries in `lib`, +- Public C/C++ header files in `include`, +- If `WITH_PYTHON=ON`, Python bindings in `bindings/python`. This directory can be used to build a Python wheel (see [these instructions](https://packaging.python.org/en/latest/flow/#the-built-distributions-wheels)), +- If `WITH_QTANTIMONY=ON`, the QtAntimony graphical application in `bin`. + diff --git a/doc/AntimonyTutorial.docx b/doc/AntimonyTutorial.docx index 6fb04463d..6b3f84d89 100644 Binary files a/doc/AntimonyTutorial.docx and b/doc/AntimonyTutorial.docx differ diff --git a/doc/AntimonyTutorial.htm b/doc/AntimonyTutorial.htm index 9e660b307..906dcaead 100644 --- a/doc/AntimonyTutorial.htm +++ b/doc/AntimonyTutorial.htm @@ -123,6 +123,14 @@

Background

interfaces.

Change Log

+

The 3.2 release cleaned up the build system, increased efficiency, +and fixed numerous bugs, mostly discovered through converting SBML Test +Suite models to Antimony and back to SBML, and ensuring that a +simulation of the round-tripped model matched a simulation of the +original model. The entirety of the SBML Test Suite (with the exception +of ‘fast’ reactions, now deprecated in SBML) now successfully round-trip +through Antimony without loss of information (though some things may +change structurally for hierarchical models).

The 3.1 release changed FBC support to version 3 of that package, changing how FBC constraints were translated to SBML (but not changing how they were declared in Antimony), and adding support for gene @@ -747,14 +755,47 @@

Substance-only species

Now, whenever ‘S1’ is used in the model, it is a reference to the species amount, and not its concentration. Defining an initial amount is also changed:

-

S1 = 2.5;

+
S1 = 2.5;

This will set the initial amount to 2.5, not the initial concentration. If you wish to set the initial concentration instead, use the compartment:

-

S1 = 3.1*C

+
S1 = 3.1*C

Because a concentration times the compartment volume yields an amount, in this formulation, ‘3.1’ is set as the initial concentration.

+

Named stoichiometries

+

A stoichiometry in a reaction may be given an ID instead of a number, +and that ID may be set later:

+
J0: n A -> B; k1*A^n
+n = 3
+

The id of the stoichiometry may now be changed by other model +constructs: events, rate rules, and assignment rules may all use the +value as a target:

+
J0: n A -> m B; k1*A^n
+n := time/3
+m = 1
+at A < 3: m = 2
+

This also gives the stoichiometry an ID that can be given a value +directly (or be tracked) by some simulators (such as roadrunner).

+

If you want to use the same ID for multiple stoichiometries, this can +be done straightforwardly:

+
J0: n A -> n B; k1*A^n
+n = 3
+

However! When translated to SBML, every stoichiometry must have a +unique ID. Therefore, an assignment rule will be created to set the +value of B’s stoichiometry to ‘n’. Effectively, the model will +become:

+
J0: n A -> J0_B_stoich B; k1*A^n
+n = 3
+J0_B_stoich := n
+

This is mathematically identical, but some simulators may balk at an +assignment rule to a stoichiometry, as this is a feature of SBML that +not everyone supports. If this happens, just name all your +stoichiometries uniquely:

+
J0: n A -> m B; k1*A^n
+n = 3
+m = 3
+

and remember to change them both at the same time.

Modules

Antimony input files may define several different models, and may use previously-defined models as parts of newly-defined models. Each diff --git a/doc/AntimonyTutorial.md b/doc/AntimonyTutorial.md index 8f03af1ec..9aaca53e5 100644 --- a/doc/AntimonyTutorial.md +++ b/doc/AntimonyTutorial.md @@ -104,6 +104,8 @@ be used in other contexts as well. Its main features include: ## Change Log +The 3.2 release cleaned up the build system, increased efficiency, and fixed numerous bugs, mostly discovered through converting SBML Test Suite models to Antimony and back to SBML, and ensuring that a simulation of the round-tripped model matched a simulation of the original model. The entirety of the SBML Test Suite (with the exception of 'fast' reactions, now deprecated in SBML) now successfully round-trip through Antimony without loss of information (though some things may change structurally for hierarchical models). + The 3.1 release changed FBC support to version 3 of that package, changing how FBC constraints were translated to SBML (but not changing how they were declared in Antimony), and adding support for gene products, gene @@ -848,16 +850,51 @@ Now, whenever ‘S1’ is used in the model, it is a reference to the species amount, and not its concentration. Defining an initial amount is also changed: -S1 = 2.5; + S1 = 2.5; This will set the initial amount to 2.5, not the initial concentration. If you wish to set the initial concentration instead, use the compartment: -S1 = 3.1*C + S1 = 3.1*C Because a concentration times the compartment volume yields an amount, in this formulation, '3.1' is set as the initial concentration. +### Named stoichiometries + +A stoichiometry in a reaction may be given an ID instead of a number, and that ID may be set later: + + J0: n A -> B; k1*A^n + n = 3 + +The id of the stoichiometry may now be changed by other model constructs: events, rate rules, and assignment rules may all use the value as a target: + + J0: n A -> m B; k1*A^n + n := time/3 + m = 1 + at A < 3: m = 2 + +This also gives the stoichiometry an ID that can be given a value directly (or be tracked) by some simulators (such as roadrunner). + +If you want to use the same ID for multiple stoichiometries, this can be done straightforwardly: + + J0: n A -> n B; k1*A^n + n = 3 + +However! When translated to SBML, every stoichiometry must have a unique ID. Therefore, an assignment rule will be created to set the value of B's stoichiometry to 'n'. Effectively, the model will become: + + J0: n A -> J0_B_stoich B; k1*A^n + n = 3 + J0_B_stoich := n + +This is mathematically identical, but some simulators may balk at an assignment rule to a stoichiometry, as this is a feature of SBML that not everyone supports. If this happens, just name all your stoichiometries uniquely: + + J0: n A -> m B; k1*A^n + n = 3 + m = 3 + +and remember to change them both at the same time. + ### Modules Antimony input files may define several different models, and may use diff --git a/doc/AntimonyTutorial.pdf b/doc/AntimonyTutorial.pdf index c3673e8a3..a94819879 100644 Binary files a/doc/AntimonyTutorial.pdf and b/doc/AntimonyTutorial.pdf differ diff --git a/doc/examples/biomodels/BIOMD0000000001_url.txt b/doc/examples/biomodels/BIOMD0000000001/BIOMD0000000001_url.txt similarity index 94% rename from doc/examples/biomodels/BIOMD0000000001_url.txt rename to doc/examples/biomodels/BIOMD0000000001/BIOMD0000000001_url.txt index 66e0e6337..70f0bc824 100644 --- a/doc/examples/biomodels/BIOMD0000000001_url.txt +++ b/doc/examples/biomodels/BIOMD0000000001/BIOMD0000000001_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000001() // Compartments and Species: @@ -27,7 +27,7 @@ model *BIOMD0000000001() React16: ILL -> DLL; comp1*(kf_16*ILL - kr_16*DLL); // Events: - RemovalACh: at time > t2: kf_13 = 0, kf_8 = 0, kf_4 = 0, kf_1 = 0, kf_12 = 0, kf_7 = 0, kf_3 = 0, kf_0 = 0; + RemovalACh: at time > t2: kf_0 = 0, kf_3 = 0, kf_7 = 0, kf_12 = 0, kf_1 = 0, kf_4 = 0, kf_8 = 0, kf_13 = 0; // Species initializations: BLL = 0; @@ -154,22 +154,39 @@ model *BIOMD0000000001() kf_16.sboTerm = 35 kr_16.sboTerm = 38 React0.sboTerm = 177 + React0.kineticLaw.sboTerm = 80 React1.sboTerm = 177 + React1.kineticLaw.sboTerm = 80 React2.sboTerm = 181 + React2.kineticLaw.sboTerm = 80 React3.sboTerm = 177 + React3.kineticLaw.sboTerm = 80 React4.sboTerm = 177 + React4.kineticLaw.sboTerm = 80 React5.sboTerm = 181 + React5.kineticLaw.sboTerm = 80 React6.sboTerm = 181 + React6.kineticLaw.sboTerm = 80 React7.sboTerm = 177 + React7.kineticLaw.sboTerm = 80 React8.sboTerm = 177 + React8.kineticLaw.sboTerm = 80 React9.sboTerm = 181 + React9.kineticLaw.sboTerm = 80 React10.sboTerm = 181 + React10.kineticLaw.sboTerm = 80 React11.sboTerm = 181 + React11.kineticLaw.sboTerm = 80 React12.sboTerm = 177 + React12.kineticLaw.sboTerm = 80 React13.sboTerm = 177 + React13.kineticLaw.sboTerm = 80 React14.sboTerm = 181 + React14.kineticLaw.sboTerm = 80 React15.sboTerm = 181 + React15.kineticLaw.sboTerm = 80 React16.sboTerm = 181 + React16.kineticLaw.sboTerm = 80 // CV terms: comp1 identity "http://identifiers.org/go/GO:0031594" diff --git a/doc/examples/biomodels/BIOMD0000000002_url.txt b/doc/examples/biomodels/BIOMD0000000002/BIOMD0000000002_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000002_url.txt rename to doc/examples/biomodels/BIOMD0000000002/BIOMD0000000002_url.txt index b91281eee..23a169639 100644 --- a/doc/examples/biomodels/BIOMD0000000002_url.txt +++ b/doc/examples/biomodels/BIOMD0000000002/BIOMD0000000002_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000002() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000003_url.txt b/doc/examples/biomodels/BIOMD0000000003/BIOMD0000000003_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000003_url.txt rename to doc/examples/biomodels/BIOMD0000000003/BIOMD0000000003_url.txt index 92ccf0d81..895e8d5c9 100644 --- a/doc/examples/biomodels/BIOMD0000000003_url.txt +++ b/doc/examples/biomodels/BIOMD0000000003/BIOMD0000000003_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000003() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000004_url.txt b/doc/examples/biomodels/BIOMD0000000004/BIOMD0000000004_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000004_url.txt rename to doc/examples/biomodels/BIOMD0000000004/BIOMD0000000004_url.txt index 05ff9a885..81a39fde2 100644 --- a/doc/examples/biomodels/BIOMD0000000004_url.txt +++ b/doc/examples/biomodels/BIOMD0000000004/BIOMD0000000004_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000004() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000005_url.txt b/doc/examples/biomodels/BIOMD0000000005/BIOMD0000000005_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000005_url.txt rename to doc/examples/biomodels/BIOMD0000000005/BIOMD0000000005_url.txt index f13deef74..b4ecbbef3 100644 --- a/doc/examples/biomodels/BIOMD0000000005_url.txt +++ b/doc/examples/biomodels/BIOMD0000000005/BIOMD0000000005_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000005() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000006_url.txt b/doc/examples/biomodels/BIOMD0000000006/BIOMD0000000006_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000006_url.txt rename to doc/examples/biomodels/BIOMD0000000006/BIOMD0000000006_url.txt index 002d24465..9ecd60b83 100644 --- a/doc/examples/biomodels/BIOMD0000000006_url.txt +++ b/doc/examples/biomodels/BIOMD0000000006/BIOMD0000000006_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000006() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000007_url.txt b/doc/examples/biomodels/BIOMD0000000007/BIOMD0000000007_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000007_url.txt rename to doc/examples/biomodels/BIOMD0000000007/BIOMD0000000007_url.txt index 35e611622..62e35362d 100644 --- a/doc/examples/biomodels/BIOMD0000000007_url.txt +++ b/doc/examples/biomodels/BIOMD0000000007/BIOMD0000000007_url.txt @@ -1,14 +1,14 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000007() // Compartments and Species: compartment Cell; substanceOnly species UbE in Cell, UbE2 in Cell, Wee1 in Cell, Cdc25 in Cell; substanceOnly species G2K in Cell, R in Cell, G1K in Cell, IE in Cell, PG2 in Cell; - substanceOnly species G1R in Cell, G2R in Cell, PG2R in Cell, $SPF in Cell; - substanceOnly species $MPF in Cell, $IEB in Cell, $UbEB in Cell, $UbE2B in Cell; - substanceOnly species $Wee1B in Cell, $Cdc25B in Cell, $Rum1Total in Cell; - substanceOnly species $Cdc13Total in Cell, $Cig2Total in Cell; + substanceOnly species G1R in Cell, G2R in Cell, PG2R in Cell, SPF in Cell; + substanceOnly species MPF in Cell, $IEB in Cell, $UbEB in Cell, $UbE2B in Cell; + substanceOnly species $Wee1B in Cell, $Cdc25B in Cell, Rum1Total in Cell; + substanceOnly species Cdc13Total in Cell, Cig2Total in Cell; // Assignment Rules: SPF := Cig1 + alpha*G1K + MPF; @@ -58,7 +58,7 @@ model *BIOMD0000000007() // Events: Start: at 60 after SPF >= 0.1: kp = kp/2; - Division: at UbE <= 0.1: Mass = Mass/2, kp = 2*kp; + Division: at UbE <= 0.1: kp = 2*kp, Mass = Mass/2; // Species initializations: UbE = 0.11; diff --git a/doc/examples/biomodels/BIOMD0000000008_url.txt b/doc/examples/biomodels/BIOMD0000000008/BIOMD0000000008_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000008_url.txt rename to doc/examples/biomodels/BIOMD0000000008/BIOMD0000000008_url.txt index 628d663eb..f7100bbfc 100644 --- a/doc/examples/biomodels/BIOMD0000000008_url.txt +++ b/doc/examples/biomodels/BIOMD0000000008/BIOMD0000000008_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000008() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000009_url.txt b/doc/examples/biomodels/BIOMD0000000009/BIOMD0000000009_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000009_url.txt rename to doc/examples/biomodels/BIOMD0000000009/BIOMD0000000009_url.txt index 977cdaf6e..2df169799 100644 --- a/doc/examples/biomodels/BIOMD0000000009_url.txt +++ b/doc/examples/biomodels/BIOMD0000000009/BIOMD0000000009_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000009() // Compartments and Species: @@ -9,8 +9,8 @@ model *BIOMD0000000009() species KKPase in compartment_, E1_KKK in compartment_, E2_P_KKK in compartment_; species P_KKK_KK in compartment_, P_KKK_P_KK in compartment_, PP_KK_K in compartment_; species PP_KK_P_K in compartment_, KKPase_PP_KK in compartment_, KKPase_P_KK in compartment_; - species KPase_PP_K in compartment_, KPase_P_K in compartment_, $K_PP_norm in compartment_; - species $KK_PP_norm in compartment_, $KKK_P_norm in compartment_, $rel_K_PP_max in compartment_; + species KPase_PP_K in compartment_, KPase_P_K in compartment_, K_PP_norm in compartment_; + species KK_PP_norm in compartment_, KKK_P_norm in compartment_, rel_K_PP_max in compartment_; // Assignment Rules: K_PP_norm := (PP_K + KPase_PP_K)/(PP_K + P_K + K + PP_KK_K + PP_KK_P_K + KPase_PP_K + KPase_P_K); diff --git a/doc/examples/biomodels/BIOMD0000000010_url.txt b/doc/examples/biomodels/BIOMD0000000010/BIOMD0000000010_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000010_url.txt rename to doc/examples/biomodels/BIOMD0000000010/BIOMD0000000010_url.txt index 85869ecfd..f66f8494c 100644 --- a/doc/examples/biomodels/BIOMD0000000010_url.txt +++ b/doc/examples/biomodels/BIOMD0000000010/BIOMD0000000010_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000010() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000011_url.txt b/doc/examples/biomodels/BIOMD0000000011/BIOMD0000000011_url.txt similarity index 72% rename from doc/examples/biomodels/BIOMD0000000011_url.txt rename to doc/examples/biomodels/BIOMD0000000011/BIOMD0000000011_url.txt index 289265b58..176dc7d2a 100644 --- a/doc/examples/biomodels/BIOMD0000000011_url.txt +++ b/doc/examples/biomodels/BIOMD0000000011/BIOMD0000000011_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MAPK_in_Solution() // Compartments and Species: @@ -278,73 +278,70 @@ model *MAPK_in_Solution() model notes ``` # MAPK cascade in solution (no scaffold) -| | -||--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| :- | -| | -| | This model describes a basic 3- stage Mitogen Activated Protein Kinase (MAPK) cascade in solution. This cascade is typically expressed as RAF= =>MEK==>MAPK (alternative forms are K3==>K2==> K1 and KKK==>KK==>K) . The input signal is RAFK (RAF Kinase) and the output signal is MAPKpp ( doubly phosphorylated form of MAPK) . RAFK phosphorylates RAF once to RAFp. RAFp, the phosphorylated form of RAF induces two phoshporylations of MEK, to MEKp and MEKpp. MEKpp, the doubly phosphorylated form of MEK, induces two phosphorylations of MAPK to MAPKp and MAPKpp. | | +| Description | +|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| This model describes a basic 3- stage Mitogen Activated Protein Kinase (MAPK) cascade in solution. This cascade is typically expressed as RAF= =>MEK==>MAPK (alternative forms are K3==>K2==> K1 and KKK==>KK==>K) . The input signal is RAFK (RAF Kinase) and the output signal is MAPKpp ( doubly phosphorylated form of MAPK) . RAFK phosphorylates RAF once to RAFp. RAFp, the phosphorylated form of RAF induces two phoshporylations of MEK, to MEKp and MEKpp. MEKpp, the doubly phosphorylated form of MEK, induces two phosphorylations of MAPK to MAPKp and MAPKpp. | -| | -||----------------------------|----------------------------------------| -| :- | :- | -| | -| | a10 = 5. | MAPKPH + MAPKpp -> MAPKppMAPKPH | | -| | a1 = 1. | RAF + RAFK -> RAFRAFK | | -| | a2 = 0.5 | RAFp + RAFPH -> RAFpRAFPH | | -| | a3 = 3.3 | MEK + RAFp -> MEKRAFp | | -| | a4 = 10. | MEKp + MEKPH -> MEKpMEKPH | | -| | a5 = 3.3 | MEKp + RAFp -> MEKpRAFp | | -| | a6 = 10. | MEKPH + MEKpp -> MEKppMEKPH | | -| | a7 = 20. | MAPK + MEKpp -> MAPKMEKpp | | -| | a8 = 5. | MAPKp + MAPKPH -> MAPKpMAPKPH | | -| | a9 = 20. | MAPKp + MEKpp -> MAPKpMEKpp | | -| | d10 = 0.4 | MAPKppMAPKPH -> MAPKPH + MAPKpp | | -| | d1 = 0.4 | RAFRAFK -> RAF + RAFK | | -| | d2 = 0.5 | RAFpRAFPH -> RAFp + RAFPH | | -| | d3 = 0.42 | MEKRAFp -> MEK + RAFp | | -| | d4 = 0.8 | MEKpMEKPH -> MEKp + MEKPH | | -| | d5 = 0.4 | MEKpRAFp -> MEKp + RAFp | | -| | d6 = 0.8 | MEKppMEKPH -> MEKPH + MEKpp | | -| | d7 = 0.6 | MAPKMEKpp -> MAPK + MEKpp | | -| | d8 = 0.4 | MAPKpMAPKPH -> MAPKp + MAPKPH | | -| | d9 = 0.6 | MAPKpMEKpp -> MAPKp + MEKpp | | -| | k10 = 0.1 | MAPKppMAPKPH -> MAPKp + MAPKPH | | -| | k1 = 0.1 | RAFRAFK -> RAFK + RAFp | | -| | k2 = 0.1 | RAFpRAFPH -> RAF + RAFPH | | -| | k3 = 0.1 | MEKRAFp -> MEKp + RAFp | | -| | k4 = 0.1 | MEKpMEKPH -> MEK + MEKPH | | -| | k5 = 0.1 | MEKpRAFp -> MEKpp + RAFp | | -| | k6 = 0.1 | MEKppMEKPH -> MEKp + MEKPH | | -| | k7 = 0.1 | MAPKMEKpp -> MAPKp + MEKpp | | -| | k8 = 0.1 | MAPKpMAPKPH -> MAPK + MAPKPH | | -| | k9 = 0.1 | MAPKpMEKpp -> MAPKpp + MEKpp | | -| | -||--------------|--------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| :- | :- | :- | -| | -| | MAPK | 0.3 | MAPK'[t] == d7\*MAPKMEKpp[t] + k8\*MAPKpMAPKPH[t] -  a7\*MAPK[t]\*MEKpp[t] | | -| | MAPKMEKpp | 0 | MAPKMEKpp'[t] == -(d7\*MAPKMEKpp[t]) - k7\*MAPKMEKpp[t]  + a7\*MAPK[t]\*MEKpp[t] | | -| | MAPKp | 0 | MAPKp'[t] == k7\*MAPKMEKpp[t] - a8\*MAPKp[t]\*MAPKPH[t]  + d8\*MAPKpMAPKPH[t] + d9\*MAPKpMEKpp[t] + k10\* MAPKppMAPKPH[t] - a9\*MAPKp[t]\*MEKpp[t] | | -| | MAPKPH | 0.3 | MAPKPH'[t] == -(a8\*MAPKp[t]\*MAPKPH[t]) + d8\*MAPKpMAPKPH[ t] + k8\*MAPKpMAPKPH[t] - a10\*MAPKPH[t]\*MAPKpp[t] +  d10\*MAPKppMAPKPH[t] + k10\*MAPKppMAPKPH[t] | | -| | MAPKpMAPKPH | 0 | MAPKpMAPKPH'[t] == a8\*MAPKp[t]\*MAPKPH[t] - d8\* MAPKpMAPKPH[t] - k8\*MAPKpMAPKPH[t] | | -| | MAPKpMEKpp | 0 | MAPKpMEKpp'[t] == -(d9\*MAPKpMEKpp[t]) - k9\*MAPKpMEKpp[t]  + a9\*MAPKp[t]\*MEKpp[t] | | -| | MAPKpp | 0 | MAPKpp'[t] == k9\*MAPKpMEKpp[t] - a10\*MAPKPH[t]\*MAPKpp[t]  + d10\*MAPKppMAPKPH[t] | | -| | MAPKppMAPKPH | 0 | MAPKppMAPKPH'[t] == a10\*MAPKPH[t]\*MAPKpp[t] - d10\* MAPKppMAPKPH[t] - k10\*MAPKppMAPKPH[t] | | -| | MEK | 0.2 | MEK'[t] == k4\*MEKpMEKPH[t] + d3\*MEKRAFp[t] -  a3\*MEK[t]\*RAFp[t] | | -| | MEKp | 0 | MEKp'[t] == -(a4\*MEKp[t]\*MEKPH[t]) + d4\*MEKpMEKPH[t]  + k6\*MEKppMEKPH[t] + d5\*MEKpRAFp[t] + k3\*MEKRAFp[ t] - a5\*MEKp[t]\*RAFp[t] | | -| | MEKPH | 0.2 | MEKPH'[t] == -(a4\*MEKp[t]\*MEKPH[t]) + d4\*MEKpMEKPH[t]  + k4\*MEKpMEKPH[t] - a6\*MEKPH[t]\*MEKpp[t] + d6\* MEKppMEKPH[t] + k6\*MEKppMEKPH[t] | | -| | MEKpMEKPH | 0 | MEKpMEKPH'[t] == a4\*MEKp[t]\*MEKPH[t] - d4\*MEKpMEKPH[t]  - k4\*MEKpMEKPH[t] | | -| | MEKpp | 0 | MEKpp'[t] == d7\*MAPKMEKpp[t] + k7\*MAPKMEKpp[t] +  d9\*MAPKpMEKpp[t] + k9\*MAPKpMEKpp[t] - a7\*MAPK[t]\* MEKpp[t] - a9\*MAPKp[t]\*MEKpp[t] - a6\*MEKPH[t]\*MEKpp[t]  + d6\*MEKppMEKPH[t] + k5\*MEKpRAFp[t] | | -| | MEKppMEKPH | 0 | MEKppMEKPH'[t] == a6\*MEKPH[t]\*MEKpp[t] - d6\*MEKppMEKPH[ t] - k6\*MEKppMEKPH[t] | | -| | MEKpRAFp | 0 | MEKpRAFp'[t] == -(d5\*MEKpRAFp[t]) - k5\*MEKpRAFp[t]  + a5\*MEKp[t]\*RAFp[t] | | -| | MEKRAFp | 0 | MEKRAFp'[t] == -(d3\*MEKRAFp[t]) - k3\*MEKRAFp[t] +  a3\*MEK[t]\*RAFp[t] | | -| | RAF | 0.4 | RAF'[t] == -(a1\*RAF[t]\*RAFK[t]) + k2\*RAFpRAFPH[t] +  d1\*RAFRAFK[t] | | -| | RAFK | 0.1 | RAFK'[t] == -(a1\*RAF[t]\*RAFK[t]) + d1\*RAFRAFK[t] +  k1\*RAFRAFK[t] | | -| | RAFp | 0 | RAFp'[t] == d5\*MEKpRAFp[t] + k5\*MEKpRAFp[t] +  d3\*MEKRAFp[t] + k3\*MEKRAFp[t] - a3\*MEK[t]\*RAFp[t]  - a5\*MEKp[t]\*RAFp[t] - a2\*RAFp[t]\*RAFPH[t] + d2\* RAFpRAFPH[t] + k1\*RAFRAFK[t] | | -| | RAFPH | 0.3 | RAFPH'[t] == -(a2\*RAFp[t]\*RAFPH[t]) + d2\*RAFpRAFPH[t]  + k2\*RAFpRAFPH[t] | | -| | RAFpRAFPH | 0 | RAFpRAFPH'[t] == a2\*RAFp[t]\*RAFPH[t] - d2\*RAFpRAFPH[t]  - k2\*RAFpRAFPH[t] | | -| | RAFRAFK | 0 | RAFRAFK'[t] == a1\*RAF[t]\*RAFK[t] - d1\*RAFRAFK[t] -  k1\*RAFRAFK[t] | | +| Rate constant       | Reaction | +|:---------------------------|:---------------------------------------| +| a10 = 5. | MAPKPH + MAPKpp -> MAPKppMAPKPH | +| a1 = 1. | RAF + RAFK -> RAFRAFK | +| a2 = 0.5 | RAFp + RAFPH -> RAFpRAFPH | +| a3 = 3.3 | MEK + RAFp -> MEKRAFp | +| a4 = 10. | MEKp + MEKPH -> MEKpMEKPH | +| a5 = 3.3 | MEKp + RAFp -> MEKpRAFp | +| a6 = 10. | MEKPH + MEKpp -> MEKppMEKPH | +| a7 = 20. | MAPK + MEKpp -> MAPKMEKpp | +| a8 = 5. | MAPKp + MAPKPH -> MAPKpMAPKPH | +| a9 = 20. | MAPKp + MEKpp -> MAPKpMEKpp | +| d10 = 0.4 | MAPKppMAPKPH -> MAPKPH + MAPKpp | +| d1 = 0.4 | RAFRAFK -> RAF + RAFK | +| d2 = 0.5 | RAFpRAFPH -> RAFp + RAFPH | +| d3 = 0.42 | MEKRAFp -> MEK + RAFp | +| d4 = 0.8 | MEKpMEKPH -> MEKp + MEKPH | +| d5 = 0.4 | MEKpRAFp -> MEKp + RAFp | +| d6 = 0.8 | MEKppMEKPH -> MEKPH + MEKpp | +| d7 = 0.6 | MAPKMEKpp -> MAPK + MEKpp | +| d8 = 0.4 | MAPKpMAPKPH -> MAPKp + MAPKPH | +| d9 = 0.6 | MAPKpMEKpp -> MAPKp + MEKpp | +| k10 = 0.1 | MAPKppMAPKPH -> MAPKp + MAPKPH | +| k1 = 0.1 | RAFRAFK -> RAFK + RAFp | +| k2 = 0.1 | RAFpRAFPH -> RAF + RAFPH | +| k3 = 0.1 | MEKRAFp -> MEKp + RAFp | +| k4 = 0.1 | MEKpMEKPH -> MEK + MEKPH | +| k5 = 0.1 | MEKpRAFp -> MEKpp + RAFp | +| k6 = 0.1 | MEKppMEKPH -> MEKp + MEKPH | +| k7 = 0.1 | MAPKMEKpp -> MAPKp + MEKpp | +| k8 = 0.1 | MAPKpMAPKPH -> MAPK + MAPKPH | +| k9 = 0.1 | MAPKpMEKpp -> MAPKpp + MEKpp | + + +| Variable | IC   | ODE | +|:-------------|:-------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| MAPK | 0.3 | MAPK'[t] == d7\*MAPKMEKpp[t] + k8\*MAPKpMAPKPH[t] -  a7\*MAPK[t]\*MEKpp[t] | +| MAPKMEKpp | 0 | MAPKMEKpp'[t] == -(d7\*MAPKMEKpp[t]) - k7\*MAPKMEKpp[t]  + a7\*MAPK[t]\*MEKpp[t] | +| MAPKp | 0 | MAPKp'[t] == k7\*MAPKMEKpp[t] - a8\*MAPKp[t]\*MAPKPH[t]  + d8\*MAPKpMAPKPH[t] + d9\*MAPKpMEKpp[t] + k10\* MAPKppMAPKPH[t] - a9\*MAPKp[t]\*MEKpp[t] | +| MAPKPH | 0.3 | MAPKPH'[t] == -(a8\*MAPKp[t]\*MAPKPH[t]) + d8\*MAPKpMAPKPH[ t] + k8\*MAPKpMAPKPH[t] - a10\*MAPKPH[t]\*MAPKpp[t] +  d10\*MAPKppMAPKPH[t] + k10\*MAPKppMAPKPH[t] | +| MAPKpMAPKPH | 0 | MAPKpMAPKPH'[t] == a8\*MAPKp[t]\*MAPKPH[t] - d8\* MAPKpMAPKPH[t] - k8\*MAPKpMAPKPH[t] | +| MAPKpMEKpp | 0 | MAPKpMEKpp'[t] == -(d9\*MAPKpMEKpp[t]) - k9\*MAPKpMEKpp[t]  + a9\*MAPKp[t]\*MEKpp[t] | +| MAPKpp | 0 | MAPKpp'[t] == k9\*MAPKpMEKpp[t] - a10\*MAPKPH[t]\*MAPKpp[t]  + d10\*MAPKppMAPKPH[t] | +| MAPKppMAPKPH | 0 | MAPKppMAPKPH'[t] == a10\*MAPKPH[t]\*MAPKpp[t] - d10\* MAPKppMAPKPH[t] - k10\*MAPKppMAPKPH[t] | +| MEK | 0.2 | MEK'[t] == k4\*MEKpMEKPH[t] + d3\*MEKRAFp[t] -  a3\*MEK[t]\*RAFp[t] | +| MEKp | 0 | MEKp'[t] == -(a4\*MEKp[t]\*MEKPH[t]) + d4\*MEKpMEKPH[t]  + k6\*MEKppMEKPH[t] + d5\*MEKpRAFp[t] + k3\*MEKRAFp[ t] - a5\*MEKp[t]\*RAFp[t] | +| MEKPH | 0.2 | MEKPH'[t] == -(a4\*MEKp[t]\*MEKPH[t]) + d4\*MEKpMEKPH[t]  + k4\*MEKpMEKPH[t] - a6\*MEKPH[t]\*MEKpp[t] + d6\* MEKppMEKPH[t] + k6\*MEKppMEKPH[t] | +| MEKpMEKPH | 0 | MEKpMEKPH'[t] == a4\*MEKp[t]\*MEKPH[t] - d4\*MEKpMEKPH[t]  - k4\*MEKpMEKPH[t] | +| MEKpp | 0 | MEKpp'[t] == d7\*MAPKMEKpp[t] + k7\*MAPKMEKpp[t] +  d9\*MAPKpMEKpp[t] + k9\*MAPKpMEKpp[t] - a7\*MAPK[t]\* MEKpp[t] - a9\*MAPKp[t]\*MEKpp[t] - a6\*MEKPH[t]\*MEKpp[t]  + d6\*MEKppMEKPH[t] + k5\*MEKpRAFp[t] | +| MEKppMEKPH | 0 | MEKppMEKPH'[t] == a6\*MEKPH[t]\*MEKpp[t] - d6\*MEKppMEKPH[ t] - k6\*MEKppMEKPH[t] | +| MEKpRAFp | 0 | MEKpRAFp'[t] == -(d5\*MEKpRAFp[t]) - k5\*MEKpRAFp[t]  + a5\*MEKp[t]\*RAFp[t] | +| MEKRAFp | 0 | MEKRAFp'[t] == -(d3\*MEKRAFp[t]) - k3\*MEKRAFp[t] +  a3\*MEK[t]\*RAFp[t] | +| RAF | 0.4 | RAF'[t] == -(a1\*RAF[t]\*RAFK[t]) + k2\*RAFpRAFPH[t] +  d1\*RAFRAFK[t] | +| RAFK | 0.1 | RAFK'[t] == -(a1\*RAF[t]\*RAFK[t]) + d1\*RAFRAFK[t] +  k1\*RAFRAFK[t] | +| RAFp | 0 | RAFp'[t] == d5\*MEKpRAFp[t] + k5\*MEKpRAFp[t] +  d3\*MEKRAFp[t] + k3\*MEKRAFp[t] - a3\*MEK[t]\*RAFp[t]  - a5\*MEKp[t]\*RAFp[t] - a2\*RAFp[t]\*RAFPH[t] + d2\* RAFpRAFPH[t] + k1\*RAFRAFK[t] | +| RAFPH | 0.3 | RAFPH'[t] == -(a2\*RAFp[t]\*RAFPH[t]) + d2\*RAFpRAFPH[t]  + k2\*RAFpRAFPH[t] | +| RAFpRAFPH | 0 | RAFpRAFPH'[t] == a2\*RAFp[t]\*RAFPH[t] - d2\*RAFpRAFPH[t]  - k2\*RAFpRAFPH[t] | +| RAFRAFK | 0 | RAFRAFK'[t] == a1\*RAF[t]\*RAFK[t] - d1\*RAFRAFK[t] -  k1\*RAFRAFK[t] | + Generated by Cellerator Version 1.4.3 (6-March-2004) using Mathematica 5.0 for Mac OS X (November 19, 2003), March 6, 2004 12:18:07, using (PowerMac, PowerPC,Mac diff --git a/doc/examples/biomodels/BIOMD0000000012_url.txt b/doc/examples/biomodels/BIOMD0000000012/BIOMD0000000012_url.txt similarity index 89% rename from doc/examples/biomodels/BIOMD0000000012_url.txt rename to doc/examples/biomodels/BIOMD0000000012/BIOMD0000000012_url.txt index a41577119..cd9681284 100644 --- a/doc/examples/biomodels/BIOMD0000000012_url.txt +++ b/doc/examples/biomodels/BIOMD0000000012/BIOMD0000000012_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000012() // Compartments and Species: @@ -31,6 +31,14 @@ model *BIOMD0000000012() Reaction11: => Y; a0_tr + a_tr*KM^n/(KM^n + PX^n); Reaction12: => Z; a0_tr + a_tr*KM^n/(KM^n + PY^n); + // Interactions: + _I0: X -o Reaction4; ; + _I1: Y -o Reaction5; ; + _I2: Z -o Reaction6; ; + _I3: PZ -( Reaction10; ; + _I4: PX -( Reaction11; ; + _I5: PY -( Reaction12; ; + // Species initializations: PX = 0; PY = 0; @@ -112,14 +120,23 @@ model *BIOMD0000000012() ps_a.sboTerm = 186 ps_0.sboTerm = 485 Reaction1.sboTerm = 179 + Reaction1.kineticLaw.sboTerm = 49 Reaction2.sboTerm = 179 + Reaction2.kineticLaw.sboTerm = 49 Reaction3.sboTerm = 179 + Reaction3.kineticLaw.sboTerm = 49 Reaction4.sboTerm = 184 + Reaction4.kineticLaw.sboTerm = 49 Reaction5.sboTerm = 184 + Reaction5.kineticLaw.sboTerm = 49 Reaction6.sboTerm = 184 + Reaction6.kineticLaw.sboTerm = 49 Reaction7.sboTerm = 179 + Reaction7.kineticLaw.sboTerm = 49 Reaction8.sboTerm = 179 + Reaction8.kineticLaw.sboTerm = 49 Reaction9.sboTerm = 179 + Reaction9.kineticLaw.sboTerm = 49 Reaction10.sboTerm = 183 Reaction11.sboTerm = 183 Reaction12.sboTerm = 183 @@ -273,26 +290,25 @@ given in the article by simple rules were introduced. The parameters given in the article were: -| | -||------------------------------------------------------------------------:|---------------------|---------------------------|| -| | promotor strength (full) ( *tps_active* ): | 0.5 | transcripts/(promotor\*s) | | -| | mRNA half life, τ 1/2,mRNA : | 2 | min | | -| | protein half life, τ 1/2,prot : | 10 | min | | -| | K M : | 40 | monomers/cell | | -| | Hill coefficient n: | 2 | | | +| promotor strength (repressed) ( *tps_repr* ): | 5\*10 -4 | transcripts/(promotor\*s) | +| promotor strength (full) ( *tps_active* ): | 0.5 | transcripts/(promotor\*s) | +| mRNA half life, τ 1/2,mRNA : | 2 | min | +| protein half life, τ 1/2,prot : | 10 | min | +| K M : | 40 | monomers/cell | +| Hill coefficient n: | 2 | | + From these the following constants can be derived: -| | -||----------------------------------------------------------------------:|--------------------------------------------------------------------------------------------------------------------|----------------------------------------|| -| | mRNA decay rate ( *kd_mRNA* ): | *ln(2)/ τ 1/2,mRNA* | = 0.347 min -1 | | -| | protein decay rate ( *kd_prot* ): | *ln(2)/ τ 1/2,prot* | | -| | transcription rate ( *a_tr* ): | *tps_active\*60* | = 29.97 transcripts/min | | -| | transcription rate (repressed) ( *a0_tr* ): | *tps_repr\*60* | = 0.03 transcripts/min | | -| | translation rate ( *k_tl* ): | *eff\*kd_mRNA* | = 6.93 proteins/(mRNA\*min) | | -| | α : | *a_tr\*eff\*τ 1/2,prot /(ln(2)\*K M ) * | = 216.4 proteins/(promotor\*cell\*Km) | | -| | α 0 : | *a0_tr\*eff\*τ 1/2,prot /(ln(2)\*K M ) * | = 0.2164 proteins/(promotor\*cell\*Km) | | -| | β : | *k_dp/k_dm* | = 0.2 | | +| average mRNA lifetime ( *t_ave* ): | *τ 1/2,mRNA /ln(2) * | = 2.89 min | +| mRNA decay rate ( *kd_mRNA* ): | *ln(2)/ τ 1/2,mRNA* | = 0.347 min -1 | +| protein decay rate ( *kd_prot* ): | *ln(2)/ τ 1/2,prot* | +| transcription rate ( *a_tr* ): | *tps_active\*60* | = 29.97 transcripts/min | +| transcription rate (repressed) ( *a0_tr* ): | *tps_repr\*60* | = 0.03 transcripts/min | +| translation rate ( *k_tl* ): | *eff\*kd_mRNA* | = 6.93 proteins/(mRNA\*min) | +| α : | *a_tr\*eff\*τ 1/2,prot /(ln(2)\*K M ) * | = 216.4 proteins/(promotor\*cell\*Km) | +| α 0 : | *a0_tr\*eff\*τ 1/2,prot /(ln(2)\*K M ) * | = 0.2164 proteins/(promotor\*cell\*Km) | +| β : | *k_dp/k_dm* | = 0.2 | Annotation by the Kinetic Simulation Algorithm Ontology (KiSAO): diff --git a/doc/examples/biomodels/BIOMD0000000013_url.txt b/doc/examples/biomodels/BIOMD0000000013/BIOMD0000000013_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000013_url.txt rename to doc/examples/biomodels/BIOMD0000000013/BIOMD0000000013_url.txt index 324f1c36c..8653174d8 100644 --- a/doc/examples/biomodels/BIOMD0000000013_url.txt +++ b/doc/examples/biomodels/BIOMD0000000013/BIOMD0000000013_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *untitled() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000014_url.txt b/doc/examples/biomodels/BIOMD0000000014/BIOMD0000000014_url.txt similarity index 59% rename from doc/examples/biomodels/BIOMD0000000014_url.txt rename to doc/examples/biomodels/BIOMD0000000014/BIOMD0000000014_url.txt index 89b6d7fd5..53eeb0ac3 100644 --- a/doc/examples/biomodels/BIOMD0000000014_url.txt +++ b/doc/examples/biomodels/BIOMD0000000014/BIOMD0000000014_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MAPK_in_Scaffold() // Compartments and Species: @@ -1641,413 +1641,409 @@ model *MAPK_in_Scaffold() model notes ``` # MAPK cascade on a scaffold -| | -||---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| :- | -| | -| | Levchenko, A., Bruck, J., Sternberg, P.W. (2000) .Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties. Proc. Natl. Acad. Sci. USA 97(11):5818-5823. [ http://www.pnas.org/cgi/content/abstract/97/11/5818 ](http://www.pnas.org/cgi/content/abstract/97/11/5818) | | +| Citation | +|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| Levchenko, A., Bruck, J., Sternberg, P.W. (2000) .Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties. Proc. Natl. Acad. Sci. USA 97(11):5818-5823. [ http://www.pnas.org/cgi/content/abstract/97/11/5818 ](http://www.pnas.org/cgi/content/abstract/97/11/5818) | -| | -||------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| :- | -| | -| | This model describes a basic 3-stage Mitogen Activated Protein Kinase (MAPK). Kinases in solution are written as K[3,J], K[2,J], K[1,J] for MAPKKK, MAPKK, and MAPK, respectively, J indicates the phosphorylation level, J=0,1 for K3 and J=0,1,2 for K2 and K1. Scaffolds have three slots, for MAPK, MAPKK, and MAPKKK, respectively. Bound and free scaffold are denoted as S[i,j,k], where i, j, and k indicate the binding of K[1,i], K[2,j] and K[3,k] in their respective slots. Here i,j=-1,0,1,or,2 and k=-1,0,or,1. A value of -1 means the slot is empty, 0 means the unphorphorylated kinase is bound, 1 means the singly phosphorylated kinase is bound, and 2 means the doubly phosphorylated kinase is bound. Thus S[1,-1,2] is a scaffold with K[3,1] bound in the first slot and K[1,2] in the third slot, while the second slot is empty.Note: Indices X[I,J,K] are translated into the unindexed variable X_I_J_K and so forth in the SBML. Negative indices are translated as mI, etc, thus S[1,-1,2] becomes S_1_m1_2. | | -| | -||----------------------------|------------------------------------------------------------| -| :- | :- | -| | -| | a10 = 5. | MAPKP + K[1, 2] -> K_MAPKP[1, 2] | | -| | a1 = 1. | RAFK + K[3, 0] -> K_RAFK[3, 0] | | -| | a2 = 0.5 | RAFP + K[3, 1] -> K_RAFP[3, 1] | | -| | a3 = 3.3 | K[2, 0] + K[3, 1] -> K_K[2, 0, 3,  1] | | -| | a4 = 10. | MEKP + K[2, 1] -> K_MEKP[2, 1] | | -| | a5 = 3.3 | K[2, 1] + K[3, 1] -> K_K[2, 1, 3,  1] | | -| | a6 = 10. | MEKP + K[2, 2] -> K_MEKP[2, 2] | | -| | a7 = 20. | K[1, 0] + K[2, 2] -> K_K[1, 0, 2,  2] | | -| | a8 = 5. | MAPKP + K[1, 1] -> K_MAPKP[1, 1] | | -| | a9 = 20. | K[1, 1] + K[2, 2] -> K_K[1, 1, 2,  2] | | -| | d10 = 0.4 | K_MAPKP[1, 2] -> MAPKP + K[1, 2] | | -| | d1 = 0.4 | K_RAFK[3, 0] -> RAFK + K[3, 0] | | -| | d1a = 0 | S_RAFK[0, 0, 0] -> RAFK + S[0, 0, 0] | | -| | d1a = 0 | S_RAFK[0, -1, 0] -> RAFK + S[0, -1,  0] | | -| | d1a = 0 | S_RAFK[0, 1, 0] -> RAFK + S[0, 1, 0] | | -| | d1a = 0 | S_RAFK[0, 2, 0] -> RAFK + S[0, 2, 0] | | -| | d1a = 0 | S_RAFK[-1, 0, 0] -> RAFK + S[-1, 0,  0] | | -| | d1a = 0 | S_RAFK[1, 0, 0] -> RAFK + S[1, 0, 0] | | -| | d1a = 0 | S_RAFK[-1, -1, 0] -> RAFK + S[-1, -1,  0] | | -| | d1a = 0 | S_RAFK[-1, 1, 0] -> RAFK + S[-1, 1,  0] | | -| | d1a = 0 | S_RAFK[1, -1, 0] -> RAFK + S[1, -1,  0] | | -| | d1a = 0 | S_RAFK[1, 1, 0] -> RAFK + S[1, 1, 0] | | -| | d1a = 0 | S_RAFK[-1, 2, 0] -> RAFK + S[-1, 2,  0] | | -| | d1a = 0 | S_RAFK[1, 2, 0] -> RAFK + S[1, 2, 0] | | -| | d1a = 0 | S_RAFK[2, 0, 0] -> RAFK + S[2, 0, 0] | | -| | d1a = 0 | S_RAFK[2, -1, 0] -> RAFK + S[2, -1,  0] | | -| | d1a = 0 | S_RAFK[2, 1, 0] -> RAFK + S[2, 1, 0] | | -| | d1a = 0 | S_RAFK[2, 2, 0] -> RAFK + S[2, 2, 0] | | -| | d2 = 0.5 | K_RAFP[3, 1] -> RAFP + K[3, 1] | | -| | d3 = 0.42 | K_K[2, 0, 3, 1] -> K[2, 0] + K[3,  1] | | -| | d4 = 0.8 | K_MEKP[2, 1] -> MEKP + K[2, 1] | | -| | d5 = 0.4 | K_K[2, 1, 3, 1] -> K[2, 1] + K[3,  1] | | -| | d6 = 0.8 | K_MEKP[2, 2] -> MEKP + K[2, 2] | | -| | d7 = 0.6 | K_K[1, 0, 2, 2] -> K[1, 0] + K[2,  2] | | -| | d8 = 0.4 | K_MAPKP[1, 1] -> MAPKP + K[1, 1] | | -| | d9 = 0.6 | K_K[1, 1, 2, 2] -> K[1, 1] + K[2,  2] | | -| | k10 = 0.1 | K_MAPKP[1, 2] -> MAPKP + K[1, 1] | | -| | k1 = 0.1 | K_RAFK[3, 0] -> RAFK + K[3, 1] | | -| | k1 = 0.1 | S_RAFK[0, 0, 0] -> RAFK + S[0, 0, 1] | | -| | k1 = 0.1 | S_RAFK[0, -1, 0] -> RAFK + S[0, -1,  1] | | -| | k1 = 0.1 | S_RAFK[0, 1, 0] -> RAFK + S[0, 1, 1] | | -| | k1 = 0.1 | S_RAFK[0, 2, 0] -> RAFK + S[0, 2, 1] | | -| | k1 = 0.1 | S_RAFK[-1, 0, 0] -> RAFK + S[-1, 0,  1] | | -| | k1 = 0.1 | S_RAFK[1, 0, 0] -> RAFK + S[1, 0, 1] | | -| | k1 = 0.1 | S_RAFK[-1, -1, 0] -> RAFK + S[-1, -1,  1] | | -| | k1 = 0.1 | S_RAFK[-1, 1, 0] -> RAFK + S[-1, 1,  1] | | -| | k1 = 0.1 | S_RAFK[1, -1, 0] -> RAFK + S[1, -1,  1] | | -| | k1 = 0.1 | S_RAFK[1, 1, 0] -> RAFK + S[1, 1, 1] | | -| | k1 = 0.1 | S_RAFK[-1, 2, 0] -> RAFK + S[-1, 2,  1] | | -| | k1 = 0.1 | S_RAFK[1, 2, 0] -> RAFK + S[1, 2, 1] | | -| | k1 = 0.1 | S_RAFK[2, 0, 0] -> RAFK + S[2, 0, 1] | | -| | k1 = 0.1 | S_RAFK[2, -1, 0] -> RAFK + S[2, -1,  1] | | -| | k1 = 0.1 | S_RAFK[2, 1, 0] -> RAFK + S[2, 1, 1] | | -| | k1 = 0.1 | S_RAFK[2, 2, 0] -> RAFK + S[2, 2, 1] | | -| | k1a = 100 | RAFK + S[0, 0, 0] -> S_RAFK[0, 0, 0] | | -| | k1a = 100 | RAFK + S[0, -1, 0] -> S_RAFK[0, -1,  0] | | -| | k1a = 100 | RAFK + S[0, 1, 0] -> S_RAFK[0, 1, 0] | | -| | k1a = 100 | RAFK + S[0, 2, 0] -> S_RAFK[0, 2, 0] | | -| | k1a = 100 | RAFK + S[-1, 0, 0] -> S_RAFK[-1, 0,  0] | | -| | k1a = 100 | RAFK + S[1, 0, 0] -> S_RAFK[1, 0, 0] | | -| | k1a = 100 | RAFK + S[-1, -1, 0] -> S_RAFK[-1, -1,  0] | | -| | k1a = 100 | RAFK + S[-1, 1, 0] -> S_RAFK[-1, 1,  0] | | -| | k1a = 100 | RAFK + S[1, -1, 0] -> S_RAFK[1, -1,  0] | | -| | k1a = 100 | RAFK + S[1, 1, 0] -> S_RAFK[1, 1, 0] | | -| | k1a = 100 | RAFK + S[-1, 2, 0] -> S_RAFK[-1, 2,  0] | | -| | k1a = 100 | RAFK + S[1, 2, 0] -> S_RAFK[1, 2, 0] | | -| | k1a = 100 | RAFK + S[2, 0, 0] -> S_RAFK[2, 0, 0] | | -| | k1a = 100 | RAFK + S[2, -1, 0] -> S_RAFK[2, -1,  0] | | -| | k1a = 100 | RAFK + S[2, 1, 0] -> S_RAFK[2, 1, 0] | | -| | k1a = 100 | RAFK + S[2, 2, 0] -> S_RAFK[2, 2, 0] | | -| | k2 = 0.1 | K_RAFP[3, 1] -> RAFP + K[3, 0] | | -| | k3 = 0.1 | K_K[2, 0, 3, 1] -> K[2, 1] + K[3,  1] | | -| | k3 = 0.1 | S[0, 0, 1] -> S[0, 1, 1] | | -| | k3 = 0.1 | S[-1, 0, 1] -> S[-1, 1, 1] | | -| | k3 = 0.1 | S[1, 0, 1] -> S[1, 1, 1] | | -| | k3 = 0.1 | S[2, 0, 1] -> S[2, 1, 1] | | -| | k4 = 0.1 | K_MEKP[2, 1] -> MEKP + K[2, 0] | | -| | k5 = 0.1 | K_K[2, 1, 3, 1] -> K[2, 2] + K[3,  1] | | -| | k5a = 0.1 | S[0, 1, 1] -> S[0, 2, 1] | | -| | k5a = 0.1 | S[-1, 1, 1] -> S[-1, 2, 1] | | -| | k5a = 0.1 | S[1, 1, 1] -> S[1, 2, 1] | | -| | k5a = 0.1 | S[2, 1, 1] -> S[2, 2, 1] | | -| | k6 = 0.1 | K_MEKP[2, 2] -> MEKP + K[2, 1] | | -| | k7 = 0.1 | K_K[1, 0, 2, 2] -> K[1, 1] + K[2,  2] | | -| | k7 = 0.1 | S[0, 2, 0] -> S[1, 2, 0] | | -| | k7 = 0.1 | S[0, 2, -1] -> S[1, 2, -1] | | -| | k7 = 0.1 | S[0, 2, 1] -> S[1, 2, 1] | | -| | k8 = 0.1 | K_MAPKP[1, 1] -> MAPKP + K[1, 0] | | -| | k9 = 0.1 | K_K[1, 1, 2, 2] -> K[1, 2] + K[2,  2] | | -| | k9a = 0.1 | S[1, 2, 0] -> S[2, 2, 0] | | -| | k9a = 0.1 | S[1, 2, -1] -> S[2, 2, -1] | | -| | k9a = 0.1 | S[1, 2, 1] -> S[2, 2, 1] | | -| | koff = 0.5 | S[0, 0, 0] -> K[1, 0] + S[-1, 0,  0] | | -| | koff = 0.5 | S[0, 0, 0] -> K[2, 0] + S[0, -1,  0] | | -| | koff = 0.5 | S[0, 0, 0] -> K[3, 0] + S[0, 0,  -1] | | -| | koff = 0.5 | S[0, 0, -1] -> K[1, 0] + S[-1, 0,  -1] | | -| | koff = 0.5 | S[0, 0, 1] -> K[1, 0] + S[-1, 0,  1] | | -| | koff = 0.5 | S[0, 0, -1] -> K[2, 0] + S[0, -1,  -1] | | -| | koff = 0.5 | S[0, 0, 1] -> K[2, 0] + S[0, -1,  1] | | -| | koff = 0.5 | S[0, -1, 0] -> K[1, 0] + S[-1, -1,  0] | | -| | koff = 0.5 | S[0, 1, 0] -> K[1, 0] + S[-1, 1,  0] | | -| | koff = 0.5 | S[0, -1, 0] -> K[3, 0] + S[0, -1,  -1] | | -| | koff = 0.5 | S[0, 1, 0] -> K[3, 0] + S[0, 1,  -1] | | -| | koff = 0.5 | S[0, -1, -1] -> K[1, 0] + S[-1, -1,  -1] | | -| | koff = 0.5 | S[0, -1, 1] -> K[1, 0] + S[-1, -1,  1] | | -| | koff = 0.5 | S[0, 1, -1] -> K[1, 0] + S[-1, 1,  -1] | | -| | koff = 0.5 | S[0, 1, 1] -> K[1, 0] + S[-1, 1,  1] | | -| | koff = 0.5 | S[0, 2, 0] -> K[1, 0] + S[-1, 2,  0] | | -| | koff = 0.5 | S[0, 2, 0] -> K[3, 0] + S[0, 2,  -1] | | -| | koff = 0.5 | S[0, 2, -1] -> K[1, 0] + S[-1, 2,  -1] | | -| | koff = 0.5 | S[0, 2, 1] -> K[1, 0] + S[-1, 2,  1] | | -| | koff = 0.5 | S[-1, 0, 0] -> K[2, 0] + S[-1, -1,  0] | | -| | koff = 0.5 | S[1, 0, 0] -> K[2, 0] + S[1, -1,  0] | | -| | koff = 0.5 | S[-1, 0, 0] -> K[3, 0] + S[-1, 0,  -1] | | -| | koff = 0.5 | S[1, 0, 0] -> K[3, 0] + S[1, 0,  -1] | | -| | koff = 0.5 | S[-1, 0, -1] -> K[2, 0] + S[-1, -1,  -1] | | -| | koff = 0.5 | S[-1, 0, 1] -> K[2, 0] + S[-1, -1,  1] | | -| | koff = 0.5 | S[1, 0, -1] -> K[2, 0] + S[1, -1,  -1] | | -| | koff = 0.5 | S[1, 0, 1] -> K[2, 0] + S[1, -1,  1] | | -| | koff = 0.5 | S[-1, -1, 0] -> K[3, 0] + S[-1, -1,  -1] | | -| | koff = 0.5 | S[-1, 1, 0] -> K[3, 0] + S[-1, 1,  -1] | | -| | koff = 0.5 | S[1, -1, 0] -> K[3, 0] + S[1, -1,  -1] | | -| | koff = 0.5 | S[1, 1, 0] -> K[3, 0] + S[1, 1,  -1] | | -| | koff = 0.5 | S[-1, 2, 0] -> K[3, 0] + S[-1, 2,  -1] | | -| | koff = 0.5 | S[1, 2, 0] -> K[3, 0] + S[1, 2,  -1] | | -| | koff = 0.5 | S[2, 0, 0] -> K[2, 0] + S[2, -1,  0] | | -| | koff = 0.5 | S[2, 0, 0] -> K[3, 0] + S[2, 0,  -1] | | -| | koff = 0.5 | S[2, 0, -1] -> K[2, 0] + S[2, -1,  -1] | | -| | koff = 0.5 | S[2, 0, 1] -> K[2, 0] + S[2, -1,  1] | | -| | koff = 0.5 | S[2, -1, 0] -> K[3, 0] + S[2, -1,  -1] | | -| | koff = 0.5 | S[2, 1, 0] -> K[3, 0] + S[2, 1,  -1] | | -| | koff = 0.5 | S[2, 2, 0] -> K[3, 0] + S[2, 2,  -1] | | -| | kon = 10 | K[1, 0] + S[-1, 0, 0] -> S[0, 0,  0] | | -| | kon = 10 | K[1, 0] + S[-1, 0, -1] -> S[0, 0,  -1] | | -| | kon = 10 | K[1, 0] + S[-1, 0, 1] -> S[0, 0,  1] | | -| | kon = 10 | K[1, 0] + S[-1, -1, 0] -> S[0, -1,  0] | | -| | kon = 10 | K[1, 0] + S[-1, 1, 0] -> S[0, 1,  0] | | -| | kon = 10 | K[1, 0] + S[-1, -1, -1] -> S[0, -1,  -1] | | -| | kon = 10 | K[1, 0] + S[-1, -1, 1] -> S[0, -1,  1] | | -| | kon = 10 | K[1, 0] + S[-1, 1, -1] -> S[0, 1,  -1] | | -| | kon = 10 | K[1, 0] + S[-1, 1, 1] -> S[0, 1,  1] | | -| | kon = 10 | K[1, 0] + S[-1, 2, 0] -> S[0, 2,  0] | | -| | kon = 10 | K[1, 0] + S[-1, 2, -1] -> S[0, 2,  -1] | | -| | kon = 10 | K[1, 0] + S[-1, 2, 1] -> S[0, 2,  1] | | -| | kon = 10 | K[2, 0] + S[0, -1, 0] -> S[0, 0,  0] | | -| | kon = 10 | K[2, 0] + S[0, -1, -1] -> S[0, 0,  -1] | | -| | kon = 10 | K[2, 0] + S[0, -1, 1] -> S[0, 0,  1] | | -| | kon = 10 | K[2, 0] + S[-1, -1, 0] -> S[-1, 0,  0] | | -| | kon = 10 | K[2, 0] + S[1, -1, 0] -> S[1, 0,  0] | | -| | kon = 10 | K[2, 0] + S[-1, -1, -1] -> S[-1, 0,  -1] | | -| | kon = 10 | K[2, 0] + S[-1, -1, 1] -> S[-1, 0,  1] | | -| | kon = 10 | K[2, 0] + S[1, -1, -1] -> S[1, 0,  -1] | | -| | kon = 10 | K[2, 0] + S[1, -1, 1] -> S[1, 0,  1] | | -| | kon = 10 | K[2, 0] + S[2, -1, 0] -> S[2, 0,  0] | | -| | kon = 10 | K[2, 0] + S[2, -1, -1] -> S[2, 0,  -1] | | -| | kon = 10 | K[2, 0] + S[2, -1, 1] -> S[2, 0,  1] | | -| | kon = 10 | K[3, 0] + S[0, 0, -1] -> S[0, 0,  0] | | -| | kon = 10 | K[3, 0] + S[0, -1, -1] -> S[0, -1,  0] | | -| | kon = 10 | K[3, 0] + S[0, 1, -1] -> S[0, 1,  0] | | -| | kon = 10 | K[3, 0] + S[0, 2, -1] -> S[0, 2,  0] | | -| | kon = 10 | K[3, 0] + S[-1, 0, -1] -> S[-1, 0,  0] | | -| | kon = 10 | K[3, 0] + S[1, 0, -1] -> S[1, 0,  0] | | -| | kon = 10 | K[3, 0] + S[-1, -1, -1] -> S[-1, -1,  0] | | -| | kon = 10 | K[3, 0] + S[-1, 1, -1] -> S[-1, 1,  0] | | -| | kon = 10 | K[3, 0] + S[1, -1, -1] -> S[1, -1,  0] | | -| | kon = 10 | K[3, 0] + S[1, 1, -1] -> S[1, 1,  0] | | -| | kon = 10 | K[3, 0] + S[-1, 2, -1] -> S[-1, 2,  0] | | -| | kon = 10 | K[3, 0] + S[1, 2, -1] -> S[1, 2,  0] | | -| | kon = 10 | K[3, 0] + S[2, 0, -1] -> S[2, 0,  0] | | -| | kon = 10 | K[3, 0] + S[2, -1, -1] -> S[2, -1,  0] | | -| | kon = 10 | K[3, 0] + S[2, 1, -1] -> S[2, 1,  0] | | -| | kon = 10 | K[3, 0] + S[2, 2, -1] -> S[2, 2,  0] | | -| | kpoff = 0.05 | S[0, 0, 1] -> K[3, 1] + S[0, 0,  -1] | | -| | kpoff = 0.05 | S[0, 1, 0] -> K[2, 1] + S[0, -1,  0] | | -| | kpoff = 0.05 | S[0, 1, -1] -> K[2, 1] + S[0, -1,  -1] | | -| | kpoff = 0.05 | S[0, 1, 1] -> K[2, 1] + S[0, -1,  1] | | -| | kpoff = 0.05 | S[0, -1, 1] -> K[3, 1] + S[0, -1,  -1] | | -| | kpoff = 0.05 | S[0, 1, 1] -> K[3, 1] + S[0, 1,  -1] | | -| | kpoff = 0.05 | S[0, 2, 0] -> K[2, 2] + S[0, -1,  0] | | -| | kpoff = 0.05 | S[0, 2, -1] -> K[2, 2] + S[0, -1,  -1] | | -| | kpoff = 0.05 | S[0, 2, 1] -> K[2, 2] + S[0, -1,  1] | | -| | kpoff = 0.05 | S[0, 2, 1] -> K[3, 1] + S[0, 2,  -1] | | -| | kpoff = 0.05 | S[1, 0, 0] -> K[1, 1] + S[-1, 0,  0] | | -| | kpoff = 0.05 | S[1, 0, -1] -> K[1, 1] + S[-1, 0,  -1] | | -| | kpoff = 0.05 | S[1, 0, 1] -> K[1, 1] + S[-1, 0,  1] | | -| | kpoff = 0.05 | S[-1, 0, 1] -> K[3, 1] + S[-1, 0,  -1] | | -| | kpoff = 0.05 | S[1, 0, 1] -> K[3, 1] + S[1, 0,  -1] | | -| | kpoff = 0.05 | S[1, -1, 0] -> K[1, 1] + S[-1, -1,  0] | | -| | kpoff = 0.05 | S[1, 1, 0] -> K[1, 1] + S[-1, 1,  0] | | -| | kpoff = 0.05 | S[-1, 1, 0] -> K[2, 1] + S[-1, -1,  0] | | -| | kpoff = 0.05 | S[1, 1, 0] -> K[2, 1] + S[1, -1,  0] | | -| | kpoff = 0.05 | S[1, -1, -1] -> K[1, 1] + S[-1, -1,  -1] | | -| | kpoff = 0.05 | S[1, -1, 1] -> K[1, 1] + S[-1, -1,  1] | | -| | kpoff = 0.05 | S[1, 1, -1] -> K[1, 1] + S[-1, 1,  -1] | | -| | kpoff = 0.05 | S[1, 1, 1] -> K[1, 1] + S[-1, 1,  1] | | -| | kpoff = 0.05 | S[-1, 1, -1] -> K[2, 1] + S[-1, -1,  -1] | | -| | kpoff = 0.05 | S[-1, 1, 1] -> K[2, 1] + S[-1, -1,  1] | | -| | kpoff = 0.05 | S[1, 1, -1] -> K[2, 1] + S[1, -1,  -1] | | -| | kpoff = 0.05 | S[1, 1, 1] -> K[2, 1] + S[1, -1,  1] | | -| | kpoff = 0.05 | S[-1, -1, 1] -> K[3, 1] + S[-1, -1,  -1] | | -| | kpoff = 0.05 | S[-1, 1, 1] -> K[3, 1] + S[-1, 1,  -1] | | -| | kpoff = 0.05 | S[1, -1, 1] -> K[3, 1] + S[1, -1,  -1] | | -| | kpoff = 0.05 | S[1, 1, 1] -> K[3, 1] + S[1, 1,  -1] | | -| | kpoff = 0.05 | S[1, 2, 0] -> K[1, 1] + S[-1, 2,  0] | | -| | kpoff = 0.05 | S[-1, 2, 0] -> K[2, 2] + S[-1, -1,  0] | | -| | kpoff = 0.05 | S[1, 2, 0] -> K[2, 2] + S[1, -1,  0] | | -| | kpoff = 0.05 | S[1, 2, -1] -> K[1, 1] + S[-1, 2,  -1] | | -| | kpoff = 0.05 | S[1, 2, 1] -> K[1, 1] + S[-1, 2,  1] | | -| | kpoff = 0.05 | S[-1, 2, -1] -> K[2, 2] + S[-1, -1,  -1] | | -| | kpoff = 0.05 | S[-1, 2, 1] -> K[2, 2] + S[-1, -1,  1] | | -| | kpoff = 0.05 | S[1, 2, -1] -> K[2, 2] + S[1, -1,  -1] | | -| | kpoff = 0.05 | S[1, 2, 1] -> K[2, 2] + S[1, -1,  1] | | -| | kpoff = 0.05 | S[-1, 2, 1] -> K[3, 1] + S[-1, 2,  -1] | | -| | kpoff = 0.05 | S[1, 2, 1] -> K[3, 1] + S[1, 2,  -1] | | -| | kpoff = 0.05 | S[2, 0, 0] -> K[1, 2] + S[-1, 0,  0] | | -| | kpoff = 0.05 | S[2, 0, -1] -> K[1, 2] + S[-1, 0,  -1] | | -| | kpoff = 0.05 | S[2, 0, 1] -> K[1, 2] + S[-1, 0,  1] | | -| | kpoff = 0.05 | S[2, 0, 1] -> K[3, 1] + S[2, 0,  -1] | | -| | kpoff = 0.05 | S[2, -1, 0] -> K[1, 2] + S[-1, -1,  0] | | -| | kpoff = 0.05 | S[2, 1, 0] -> K[1, 2] + S[-1, 1,  0] | | -| | kpoff = 0.05 | S[2, 1, 0] -> K[2, 1] + S[2, -1,  0] | | -| | kpoff = 0.05 | S[2, -1, -1] -> K[1, 2] + S[-1, -1,  -1] | | -| | kpoff = 0.05 | S[2, -1, 1] -> K[1, 2] + S[-1, -1,  1] | | -| | kpoff = 0.05 | S[2, 1, -1] -> K[1, 2] + S[-1, 1,  -1] | | -| | kpoff = 0.05 | S[2, 1, 1] -> K[1, 2] + S[-1, 1,  1] | | -| | kpoff = 0.05 | S[2, 1, -1] -> K[2, 1] + S[2, -1,  -1] | | -| | kpoff = 0.05 | S[2, 1, 1] -> K[2, 1] + S[2, -1,  1] | | -| | kpoff = 0.05 | S[2, -1, 1] -> K[3, 1] + S[2, -1,  -1] | | -| | kpoff = 0.05 | S[2, 1, 1] -> K[3, 1] + S[2, 1,  -1] | | -| | kpoff = 0.05 | S[2, 2, 0] -> K[1, 2] + S[-1, 2,  0] | | -| | kpoff = 0.05 | S[2, 2, 0] -> K[2, 2] + S[2, -1,  0] | | -| | kpoff = 0.05 | S[2, 2, -1] -> K[1, 2] + S[-1, 2,  -1] | | -| | kpoff = 0.05 | S[2, 2, 1] -> K[1, 2] + S[-1, 2,  1] | | -| | kpoff = 0.05 | S[2, 2, -1] -> K[2, 2] + S[2, -1,  -1] | | -| | kpoff = 0.05 | S[2, 2, 1] -> K[2, 2] + S[2, -1,  1] | | -| | kpoff = 0.05 | S[2, 2, 1] -> K[3, 1] + S[2, 2,  -1] | | -| | kpon = 0 | K[1, 1] + S[-1, 0, 0] -> S[1, 0,  0] | | -| | kpon = 0 | K[1, 1] + S[-1, 0, -1] -> S[1, 0,  -1] | | -| | kpon = 0 | K[1, 1] + S[-1, 0, 1] -> S[1, 0,  1] | | -| | kpon = 0 | K[1, 1] + S[-1, -1, 0] -> S[1, -1,  0] | | -| | kpon = 0 | K[1, 1] + S[-1, 1, 0] -> S[1, 1,  0] | | -| | kpon = 0 | K[1, 1] + S[-1, -1, -1] -> S[1, -1,  -1] | | -| | kpon = 0 | K[1, 1] + S[-1, -1, 1] -> S[1, -1,  1] | | -| | kpon = 0 | K[1, 1] + S[-1, 1, -1] -> S[1, 1,  -1] | | -| | kpon = 0 | K[1, 1] + S[-1, 1, 1] -> S[1, 1,  1] | | -| | kpon = 0 | K[1, 1] + S[-1, 2, 0] -> S[1, 2,  0] | | -| | kpon = 0 | K[1, 1] + S[-1, 2, -1] -> S[1, 2,  -1] | | -| | kpon = 0 | K[1, 1] + S[-1, 2, 1] -> S[1, 2,  1] | | -| | kpon = 0 | K[1, 2] + S[-1, 0, 0] -> S[2, 0,  0] | | -| | kpon = 0 | K[1, 2] + S[-1, 0, -1] -> S[2, 0,  -1] | | -| | kpon = 0 | K[1, 2] + S[-1, 0, 1] -> S[2, 0,  1] | | -| | kpon = 0 | K[1, 2] + S[-1, -1, 0] -> S[2, -1,  0] | | -| | kpon = 0 | K[1, 2] + S[-1, 1, 0] -> S[2, 1,  0] | | -| | kpon = 0 | K[1, 2] + S[-1, -1, -1] -> S[2, -1,  -1] | | -| | kpon = 0 | K[1, 2] + S[-1, -1, 1] -> S[2, -1,  1] | | -| | kpon = 0 | K[1, 2] + S[-1, 1, -1] -> S[2, 1,  -1] | | -| | kpon = 0 | K[1, 2] + S[-1, 1, 1] -> S[2, 1,  1] | | -| | kpon = 0 | K[1, 2] + S[-1, 2, 0] -> S[2, 2,  0] | | -| | kpon = 0 | K[1, 2] + S[-1, 2, -1] -> S[2, 2,  -1] | | -| | kpon = 0 | K[1, 2] + S[-1, 2, 1] -> S[2, 2,  1] | | -| | kpon = 0 | K[2, 1] + S[0, -1, 0] -> S[0, 1,  0] | | -| | kpon = 0 | K[2, 1] + S[0, -1, -1] -> S[0, 1,  -1] | | -| | kpon = 0 | K[2, 1] + S[0, -1, 1] -> S[0, 1,  1] | | -| | kpon = 0 | K[2, 1] + S[-1, -1, 0] -> S[-1, 1,  0] | | -| | kpon = 0 | K[2, 1] + S[1, -1, 0] -> S[1, 1,  0] | | -| | kpon = 0 | K[2, 1] + S[-1, -1, -1] -> S[-1, 1,  -1] | | -| | kpon = 0 | K[2, 1] + S[-1, -1, 1] -> S[-1, 1,  1] | | -| | kpon = 0 | K[2, 1] + S[1, -1, -1] -> S[1, 1,  -1] | | -| | kpon = 0 | K[2, 1] + S[1, -1, 1] -> S[1, 1,  1] | | -| | kpon = 0 | K[2, 1] + S[2, -1, 0] -> S[2, 1,  0] | | -| | kpon = 0 | K[2, 1] + S[2, -1, -1] -> S[2, 1,  -1] | | -| | kpon = 0 | K[2, 1] + S[2, -1, 1] -> S[2, 1,  1] | | -| | kpon = 0 | K[2, 2] + S[0, -1, 0] -> S[0, 2,  0] | | -| | kpon = 0 | K[2, 2] + S[0, -1, -1] -> S[0, 2,  -1] | | -| | kpon = 0 | K[2, 2] + S[0, -1, 1] -> S[0, 2,  1] | | -| | kpon = 0 | K[2, 2] + S[-1, -1, 0] -> S[-1, 2,  0] | | -| | kpon = 0 | K[2, 2] + S[1, -1, 0] -> S[1, 2,  0] | | -| | kpon = 0 | K[2, 2] + S[-1, -1, -1] -> S[-1, 2,  -1] | | -| | kpon = 0 | K[2, 2] + S[-1, -1, 1] -> S[-1, 2,  1] | | -| | kpon = 0 | K[2, 2] + S[1, -1, -1] -> S[1, 2,  -1] | | -| | kpon = 0 | K[2, 2] + S[1, -1, 1] -> S[1, 2,  1] | | -| | kpon = 0 | K[2, 2] + S[2, -1, 0] -> S[2, 2,  0] | | -| | kpon = 0 | K[2, 2] + S[2, -1, -1] -> S[2, 2,  -1] | | -| | kpon = 0 | K[2, 2] + S[2, -1, 1] -> S[2, 2,  1] | | -| | kpon = 0 | K[3, 1] + S[0, 0, -1] -> S[0, 0,  1] | | -| | kpon = 0 | K[3, 1] + S[0, -1, -1] -> S[0, -1,  1] | | -| | kpon = 0 | K[3, 1] + S[0, 1, -1] -> S[0, 1,  1] | | -| | kpon = 0 | K[3, 1] + S[0, 2, -1] -> S[0, 2,  1] | | -| | kpon = 0 | K[3, 1] + S[-1, 0, -1] -> S[-1, 0,  1] | | -| | kpon = 0 | K[3, 1] + S[1, 0, -1] -> S[1, 0,  1] | | -| | kpon = 0 | K[3, 1] + S[-1, -1, -1] -> S[-1, -1,  1] | | -| | kpon = 0 | K[3, 1] + S[-1, 1, -1] -> S[-1, 1,  1] | | -| | kpon = 0 | K[3, 1] + S[1, -1, -1] -> S[1, -1,  1] | | -| | kpon = 0 | K[3, 1] + S[1, 1, -1] -> S[1, 1,  1] | | -| | kpon = 0 | K[3, 1] + S[-1, 2, -1] -> S[-1, 2,  1] | | -| | kpon = 0 | K[3, 1] + S[1, 2, -1] -> S[1, 2,  1] | | -| | kpon = 0 | K[3, 1] + S[2, 0, -1] -> S[2, 0,  1] | | -| | kpon = 0 | K[3, 1] + S[2, -1, -1] -> S[2, -1,  1] | | -| | kpon = 0 | K[3, 1] + S[2, 1, -1] -> S[2, 1,  1] | | -| | kpon = 0 | K[3, 1] + S[2, 2, -1] -> S[2, 2,  1] | | +| Description | +|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| This model describes a basic 3-stage Mitogen Activated Protein Kinase (MAPK). Kinases in solution are written as K[3,J], K[2,J], K[1,J] for MAPKKK, MAPKK, and MAPK, respectively, J indicates the phosphorylation level, J=0,1 for K3 and J=0,1,2 for K2 and K1. Scaffolds have three slots, for MAPK, MAPKK, and MAPKKK, respectively. Bound and free scaffold are denoted as S[i,j,k], where i, j, and k indicate the binding of K[1,i], K[2,j] and K[3,k] in their respective slots. Here i,j=-1,0,1,or,2 and k=-1,0,or,1. A value of -1 means the slot is empty, 0 means the unphorphorylated kinase is bound, 1 means the singly phosphorylated kinase is bound, and 2 means the doubly phosphorylated kinase is bound. Thus S[1,-1,2] is a scaffold with K[3,1] bound in the first slot and K[1,2] in the third slot, while the second slot is empty.Note: Indices X[I,J,K] are translated into the unindexed variable X_I_J_K and so forth in the SBML. Negative indices are translated as mI, etc, thus S[1,-1,2] becomes S_1_m1_2. | + + +| Rate constant       | Reaction | +|:---------------------------|:-----------------------------------------------------------| +| a10 = 5. | MAPKP + K[1, 2] -> K_MAPKP[1, 2] | +| a1 = 1. | RAFK + K[3, 0] -> K_RAFK[3, 0] | +| a2 = 0.5 | RAFP + K[3, 1] -> K_RAFP[3, 1] | +| a3 = 3.3 | K[2, 0] + K[3, 1] -> K_K[2, 0, 3,  1] | +| a4 = 10. | MEKP + K[2, 1] -> K_MEKP[2, 1] | +| a5 = 3.3 | K[2, 1] + K[3, 1] -> K_K[2, 1, 3,  1] | +| a6 = 10. | MEKP + K[2, 2] -> K_MEKP[2, 2] | +| a7 = 20. | K[1, 0] + K[2, 2] -> K_K[1, 0, 2,  2] | +| a8 = 5. | MAPKP + K[1, 1] -> K_MAPKP[1, 1] | +| a9 = 20. | K[1, 1] + K[2, 2] -> K_K[1, 1, 2,  2] | +| d10 = 0.4 | K_MAPKP[1, 2] -> MAPKP + K[1, 2] | +| d1 = 0.4 | K_RAFK[3, 0] -> RAFK + K[3, 0] | +| d1a = 0 | S_RAFK[0, 0, 0] -> RAFK + S[0, 0, 0] | +| d1a = 0 | S_RAFK[0, -1, 0] -> RAFK + S[0, -1,  0] | +| d1a = 0 | S_RAFK[0, 1, 0] -> RAFK + S[0, 1, 0] | +| d1a = 0 | S_RAFK[0, 2, 0] -> RAFK + S[0, 2, 0] | +| d1a = 0 | S_RAFK[-1, 0, 0] -> RAFK + S[-1, 0,  0] | +| d1a = 0 | S_RAFK[1, 0, 0] -> RAFK + S[1, 0, 0] | +| d1a = 0 | S_RAFK[-1, -1, 0] -> RAFK + S[-1, -1,  0] | +| d1a = 0 | S_RAFK[-1, 1, 0] -> RAFK + S[-1, 1,  0] | +| d1a = 0 | S_RAFK[1, -1, 0] -> RAFK + S[1, -1,  0] | +| d1a = 0 | S_RAFK[1, 1, 0] -> RAFK + S[1, 1, 0] | +| d1a = 0 | S_RAFK[-1, 2, 0] -> RAFK + S[-1, 2,  0] | +| d1a = 0 | S_RAFK[1, 2, 0] -> RAFK + S[1, 2, 0] | +| d1a = 0 | S_RAFK[2, 0, 0] -> RAFK + S[2, 0, 0] | +| d1a = 0 | S_RAFK[2, -1, 0] -> RAFK + S[2, -1,  0] | +| d1a = 0 | S_RAFK[2, 1, 0] -> RAFK + S[2, 1, 0] | +| d1a = 0 | S_RAFK[2, 2, 0] -> RAFK + S[2, 2, 0] | +| d2 = 0.5 | K_RAFP[3, 1] -> RAFP + K[3, 1] | +| d3 = 0.42 | K_K[2, 0, 3, 1] -> K[2, 0] + K[3,  1] | +| d4 = 0.8 | K_MEKP[2, 1] -> MEKP + K[2, 1] | +| d5 = 0.4 | K_K[2, 1, 3, 1] -> K[2, 1] + K[3,  1] | +| d6 = 0.8 | K_MEKP[2, 2] -> MEKP + K[2, 2] | +| d7 = 0.6 | K_K[1, 0, 2, 2] -> K[1, 0] + K[2,  2] | +| d8 = 0.4 | K_MAPKP[1, 1] -> MAPKP + K[1, 1] | +| d9 = 0.6 | K_K[1, 1, 2, 2] -> K[1, 1] + K[2,  2] | +| k10 = 0.1 | K_MAPKP[1, 2] -> MAPKP + K[1, 1] | +| k1 = 0.1 | K_RAFK[3, 0] -> RAFK + K[3, 1] | +| k1 = 0.1 | S_RAFK[0, 0, 0] -> RAFK + S[0, 0, 1] | +| k1 = 0.1 | S_RAFK[0, -1, 0] -> RAFK + S[0, -1,  1] | +| k1 = 0.1 | S_RAFK[0, 1, 0] -> RAFK + S[0, 1, 1] | +| k1 = 0.1 | S_RAFK[0, 2, 0] -> RAFK + S[0, 2, 1] | +| k1 = 0.1 | S_RAFK[-1, 0, 0] -> RAFK + S[-1, 0,  1] | +| k1 = 0.1 | S_RAFK[1, 0, 0] -> RAFK + S[1, 0, 1] | +| k1 = 0.1 | S_RAFK[-1, -1, 0] -> RAFK + S[-1, -1,  1] | +| k1 = 0.1 | S_RAFK[-1, 1, 0] -> RAFK + S[-1, 1,  1] | +| k1 = 0.1 | S_RAFK[1, -1, 0] -> RAFK + S[1, -1,  1] | +| k1 = 0.1 | S_RAFK[1, 1, 0] -> RAFK + S[1, 1, 1] | +| k1 = 0.1 | S_RAFK[-1, 2, 0] -> RAFK + S[-1, 2,  1] | +| k1 = 0.1 | S_RAFK[1, 2, 0] -> RAFK + S[1, 2, 1] | +| k1 = 0.1 | S_RAFK[2, 0, 0] -> RAFK + S[2, 0, 1] | +| k1 = 0.1 | S_RAFK[2, -1, 0] -> RAFK + S[2, -1,  1] | +| k1 = 0.1 | S_RAFK[2, 1, 0] -> RAFK + S[2, 1, 1] | +| k1 = 0.1 | S_RAFK[2, 2, 0] -> RAFK + S[2, 2, 1] | +| k1a = 100 | RAFK + S[0, 0, 0] -> S_RAFK[0, 0, 0] | +| k1a = 100 | RAFK + S[0, -1, 0] -> S_RAFK[0, -1,  0] | +| k1a = 100 | RAFK + S[0, 1, 0] -> S_RAFK[0, 1, 0] | +| k1a = 100 | RAFK + S[0, 2, 0] -> S_RAFK[0, 2, 0] | +| k1a = 100 | RAFK + S[-1, 0, 0] -> S_RAFK[-1, 0,  0] | +| k1a = 100 | RAFK + S[1, 0, 0] -> S_RAFK[1, 0, 0] | +| k1a = 100 | RAFK + S[-1, -1, 0] -> S_RAFK[-1, -1,  0] | +| k1a = 100 | RAFK + S[-1, 1, 0] -> S_RAFK[-1, 1,  0] | +| k1a = 100 | RAFK + S[1, -1, 0] -> S_RAFK[1, -1,  0] | +| k1a = 100 | RAFK + S[1, 1, 0] -> S_RAFK[1, 1, 0] | +| k1a = 100 | RAFK + S[-1, 2, 0] -> S_RAFK[-1, 2,  0] | +| k1a = 100 | RAFK + S[1, 2, 0] -> S_RAFK[1, 2, 0] | +| k1a = 100 | RAFK + S[2, 0, 0] -> S_RAFK[2, 0, 0] | +| k1a = 100 | RAFK + S[2, -1, 0] -> S_RAFK[2, -1,  0] | +| k1a = 100 | RAFK + S[2, 1, 0] -> S_RAFK[2, 1, 0] | +| k1a = 100 | RAFK + S[2, 2, 0] -> S_RAFK[2, 2, 0] | +| k2 = 0.1 | K_RAFP[3, 1] -> RAFP + K[3, 0] | +| k3 = 0.1 | K_K[2, 0, 3, 1] -> K[2, 1] + K[3,  1] | +| k3 = 0.1 | S[0, 0, 1] -> S[0, 1, 1] | +| k3 = 0.1 | S[-1, 0, 1] -> S[-1, 1, 1] | +| k3 = 0.1 | S[1, 0, 1] -> S[1, 1, 1] | +| k3 = 0.1 | S[2, 0, 1] -> S[2, 1, 1] | +| k4 = 0.1 | K_MEKP[2, 1] -> MEKP + K[2, 0] | +| k5 = 0.1 | K_K[2, 1, 3, 1] -> K[2, 2] + K[3,  1] | +| k5a = 0.1 | S[0, 1, 1] -> S[0, 2, 1] | +| k5a = 0.1 | S[-1, 1, 1] -> S[-1, 2, 1] | +| k5a = 0.1 | S[1, 1, 1] -> S[1, 2, 1] | +| k5a = 0.1 | S[2, 1, 1] -> S[2, 2, 1] | +| k6 = 0.1 | K_MEKP[2, 2] -> MEKP + K[2, 1] | +| k7 = 0.1 | K_K[1, 0, 2, 2] -> K[1, 1] + K[2,  2] | +| k7 = 0.1 | S[0, 2, 0] -> S[1, 2, 0] | +| k7 = 0.1 | S[0, 2, -1] -> S[1, 2, -1] | +| k7 = 0.1 | S[0, 2, 1] -> S[1, 2, 1] | +| k8 = 0.1 | K_MAPKP[1, 1] -> MAPKP + K[1, 0] | +| k9 = 0.1 | K_K[1, 1, 2, 2] -> K[1, 2] + K[2,  2] | +| k9a = 0.1 | S[1, 2, 0] -> S[2, 2, 0] | +| k9a = 0.1 | S[1, 2, -1] -> S[2, 2, -1] | +| k9a = 0.1 | S[1, 2, 1] -> S[2, 2, 1] | +| koff = 0.5 | S[0, 0, 0] -> K[1, 0] + S[-1, 0,  0] | +| koff = 0.5 | S[0, 0, 0] -> K[2, 0] + S[0, -1,  0] | +| koff = 0.5 | S[0, 0, 0] -> K[3, 0] + S[0, 0,  -1] | +| koff = 0.5 | S[0, 0, -1] -> K[1, 0] + S[-1, 0,  -1] | +| koff = 0.5 | S[0, 0, 1] -> K[1, 0] + S[-1, 0,  1] | +| koff = 0.5 | S[0, 0, -1] -> K[2, 0] + S[0, -1,  -1] | +| koff = 0.5 | S[0, 0, 1] -> K[2, 0] + S[0, -1,  1] | +| koff = 0.5 | S[0, -1, 0] -> K[1, 0] + S[-1, -1,  0] | +| koff = 0.5 | S[0, 1, 0] -> K[1, 0] + S[-1, 1,  0] | +| koff = 0.5 | S[0, -1, 0] -> K[3, 0] + S[0, -1,  -1] | +| koff = 0.5 | S[0, 1, 0] -> K[3, 0] + S[0, 1,  -1] | +| koff = 0.5 | S[0, -1, -1] -> K[1, 0] + S[-1, -1,  -1] | +| koff = 0.5 | S[0, -1, 1] -> K[1, 0] + S[-1, -1,  1] | +| koff = 0.5 | S[0, 1, -1] -> K[1, 0] + S[-1, 1,  -1] | +| koff = 0.5 | S[0, 1, 1] -> K[1, 0] + S[-1, 1,  1] | +| koff = 0.5 | S[0, 2, 0] -> K[1, 0] + S[-1, 2,  0] | +| koff = 0.5 | S[0, 2, 0] -> K[3, 0] + S[0, 2,  -1] | +| koff = 0.5 | S[0, 2, -1] -> K[1, 0] + S[-1, 2,  -1] | +| koff = 0.5 | S[0, 2, 1] -> K[1, 0] + S[-1, 2,  1] | +| koff = 0.5 | S[-1, 0, 0] -> K[2, 0] + S[-1, -1,  0] | +| koff = 0.5 | S[1, 0, 0] -> K[2, 0] + S[1, -1,  0] | +| koff = 0.5 | S[-1, 0, 0] -> K[3, 0] + S[-1, 0,  -1] | +| koff = 0.5 | S[1, 0, 0] -> K[3, 0] + S[1, 0,  -1] | +| koff = 0.5 | S[-1, 0, -1] -> K[2, 0] + S[-1, -1,  -1] | +| koff = 0.5 | S[-1, 0, 1] -> K[2, 0] + S[-1, -1,  1] | +| koff = 0.5 | S[1, 0, -1] -> K[2, 0] + S[1, -1,  -1] | +| koff = 0.5 | S[1, 0, 1] -> K[2, 0] + S[1, -1,  1] | +| koff = 0.5 | S[-1, -1, 0] -> K[3, 0] + S[-1, -1,  -1] | +| koff = 0.5 | S[-1, 1, 0] -> K[3, 0] + S[-1, 1,  -1] | +| koff = 0.5 | S[1, -1, 0] -> K[3, 0] + S[1, -1,  -1] | +| koff = 0.5 | S[1, 1, 0] -> K[3, 0] + S[1, 1,  -1] | +| koff = 0.5 | S[-1, 2, 0] -> K[3, 0] + S[-1, 2,  -1] | +| koff = 0.5 | S[1, 2, 0] -> K[3, 0] + S[1, 2,  -1] | +| koff = 0.5 | S[2, 0, 0] -> K[2, 0] + S[2, -1,  0] | +| koff = 0.5 | S[2, 0, 0] -> K[3, 0] + S[2, 0,  -1] | +| koff = 0.5 | S[2, 0, -1] -> K[2, 0] + S[2, -1,  -1] | +| koff = 0.5 | S[2, 0, 1] -> K[2, 0] + S[2, -1,  1] | +| koff = 0.5 | S[2, -1, 0] -> K[3, 0] + S[2, -1,  -1] | +| koff = 0.5 | S[2, 1, 0] -> K[3, 0] + S[2, 1,  -1] | +| koff = 0.5 | S[2, 2, 0] -> K[3, 0] + S[2, 2,  -1] | +| kon = 10 | K[1, 0] + S[-1, 0, 0] -> S[0, 0,  0] | +| kon = 10 | K[1, 0] + S[-1, 0, -1] -> S[0, 0,  -1] | +| kon = 10 | K[1, 0] + S[-1, 0, 1] -> S[0, 0,  1] | +| kon = 10 | K[1, 0] + S[-1, -1, 0] -> S[0, -1,  0] | +| kon = 10 | K[1, 0] + S[-1, 1, 0] -> S[0, 1,  0] | +| kon = 10 | K[1, 0] + S[-1, -1, -1] -> S[0, -1,  -1] | +| kon = 10 | K[1, 0] + S[-1, -1, 1] -> S[0, -1,  1] | +| kon = 10 | K[1, 0] + S[-1, 1, -1] -> S[0, 1,  -1] | +| kon = 10 | K[1, 0] + S[-1, 1, 1] -> S[0, 1,  1] | +| kon = 10 | K[1, 0] + S[-1, 2, 0] -> S[0, 2,  0] | +| kon = 10 | K[1, 0] + S[-1, 2, -1] -> S[0, 2,  -1] | +| kon = 10 | K[1, 0] + S[-1, 2, 1] -> S[0, 2,  1] | +| kon = 10 | K[2, 0] + S[0, -1, 0] -> S[0, 0,  0] | +| kon = 10 | K[2, 0] + S[0, -1, -1] -> S[0, 0,  -1] | +| kon = 10 | K[2, 0] + S[0, -1, 1] -> S[0, 0,  1] | +| kon = 10 | K[2, 0] + S[-1, -1, 0] -> S[-1, 0,  0] | +| kon = 10 | K[2, 0] + S[1, -1, 0] -> S[1, 0,  0] | +| kon = 10 | K[2, 0] + S[-1, -1, -1] -> S[-1, 0,  -1] | +| kon = 10 | K[2, 0] + S[-1, -1, 1] -> S[-1, 0,  1] | +| kon = 10 | K[2, 0] + S[1, -1, -1] -> S[1, 0,  -1] | +| kon = 10 | K[2, 0] + S[1, -1, 1] -> S[1, 0,  1] | +| kon = 10 | K[2, 0] + S[2, -1, 0] -> S[2, 0,  0] | +| kon = 10 | K[2, 0] + S[2, -1, -1] -> S[2, 0,  -1] | +| kon = 10 | K[2, 0] + S[2, -1, 1] -> S[2, 0,  1] | +| kon = 10 | K[3, 0] + S[0, 0, -1] -> S[0, 0,  0] | +| kon = 10 | K[3, 0] + S[0, -1, -1] -> S[0, -1,  0] | +| kon = 10 | K[3, 0] + S[0, 1, -1] -> S[0, 1,  0] | +| kon = 10 | K[3, 0] + S[0, 2, -1] -> S[0, 2,  0] | +| kon = 10 | K[3, 0] + S[-1, 0, -1] -> S[-1, 0,  0] | +| kon = 10 | K[3, 0] + S[1, 0, -1] -> S[1, 0,  0] | +| kon = 10 | K[3, 0] + S[-1, -1, -1] -> S[-1, -1,  0] | +| kon = 10 | K[3, 0] + S[-1, 1, -1] -> S[-1, 1,  0] | +| kon = 10 | K[3, 0] + S[1, -1, -1] -> S[1, -1,  0] | +| kon = 10 | K[3, 0] + S[1, 1, -1] -> S[1, 1,  0] | +| kon = 10 | K[3, 0] + S[-1, 2, -1] -> S[-1, 2,  0] | +| kon = 10 | K[3, 0] + S[1, 2, -1] -> S[1, 2,  0] | +| kon = 10 | K[3, 0] + S[2, 0, -1] -> S[2, 0,  0] | +| kon = 10 | K[3, 0] + S[2, -1, -1] -> S[2, -1,  0] | +| kon = 10 | K[3, 0] + S[2, 1, -1] -> S[2, 1,  0] | +| kon = 10 | K[3, 0] + S[2, 2, -1] -> S[2, 2,  0] | +| kpoff = 0.05 | S[0, 0, 1] -> K[3, 1] + S[0, 0,  -1] | +| kpoff = 0.05 | S[0, 1, 0] -> K[2, 1] + S[0, -1,  0] | +| kpoff = 0.05 | S[0, 1, -1] -> K[2, 1] + S[0, -1,  -1] | +| kpoff = 0.05 | S[0, 1, 1] -> K[2, 1] + S[0, -1,  1] | +| kpoff = 0.05 | S[0, -1, 1] -> K[3, 1] + S[0, -1,  -1] | +| kpoff = 0.05 | S[0, 1, 1] -> K[3, 1] + S[0, 1,  -1] | +| kpoff = 0.05 | S[0, 2, 0] -> K[2, 2] + S[0, -1,  0] | +| kpoff = 0.05 | S[0, 2, -1] -> K[2, 2] + S[0, -1,  -1] | +| kpoff = 0.05 | S[0, 2, 1] -> K[2, 2] + S[0, -1,  1] | +| kpoff = 0.05 | S[0, 2, 1] -> K[3, 1] + S[0, 2,  -1] | +| kpoff = 0.05 | S[1, 0, 0] -> K[1, 1] + S[-1, 0,  0] | +| kpoff = 0.05 | S[1, 0, -1] -> K[1, 1] + S[-1, 0,  -1] | +| kpoff = 0.05 | S[1, 0, 1] -> K[1, 1] + S[-1, 0,  1] | +| kpoff = 0.05 | S[-1, 0, 1] -> K[3, 1] + S[-1, 0,  -1] | +| kpoff = 0.05 | S[1, 0, 1] -> K[3, 1] + S[1, 0,  -1] | +| kpoff = 0.05 | S[1, -1, 0] -> K[1, 1] + S[-1, -1,  0] | +| kpoff = 0.05 | S[1, 1, 0] -> K[1, 1] + S[-1, 1,  0] | +| kpoff = 0.05 | S[-1, 1, 0] -> K[2, 1] + S[-1, -1,  0] | +| kpoff = 0.05 | S[1, 1, 0] -> K[2, 1] + S[1, -1,  0] | +| kpoff = 0.05 | S[1, -1, -1] -> K[1, 1] + S[-1, -1,  -1] | +| kpoff = 0.05 | S[1, -1, 1] -> K[1, 1] + S[-1, -1,  1] | +| kpoff = 0.05 | S[1, 1, -1] -> K[1, 1] + S[-1, 1,  -1] | +| kpoff = 0.05 | S[1, 1, 1] -> K[1, 1] + S[-1, 1,  1] | +| kpoff = 0.05 | S[-1, 1, -1] -> K[2, 1] + S[-1, -1,  -1] | +| kpoff = 0.05 | S[-1, 1, 1] -> K[2, 1] + S[-1, -1,  1] | +| kpoff = 0.05 | S[1, 1, -1] -> K[2, 1] + S[1, -1,  -1] | +| kpoff = 0.05 | S[1, 1, 1] -> K[2, 1] + S[1, -1,  1] | +| kpoff = 0.05 | S[-1, -1, 1] -> K[3, 1] + S[-1, -1,  -1] | +| kpoff = 0.05 | S[-1, 1, 1] -> K[3, 1] + S[-1, 1,  -1] | +| kpoff = 0.05 | S[1, -1, 1] -> K[3, 1] + S[1, -1,  -1] | +| kpoff = 0.05 | S[1, 1, 1] -> K[3, 1] + S[1, 1,  -1] | +| kpoff = 0.05 | S[1, 2, 0] -> K[1, 1] + S[-1, 2,  0] | +| kpoff = 0.05 | S[-1, 2, 0] -> K[2, 2] + S[-1, -1,  0] | +| kpoff = 0.05 | S[1, 2, 0] -> K[2, 2] + S[1, -1,  0] | +| kpoff = 0.05 | S[1, 2, -1] -> K[1, 1] + S[-1, 2,  -1] | +| kpoff = 0.05 | S[1, 2, 1] -> K[1, 1] + S[-1, 2,  1] | +| kpoff = 0.05 | S[-1, 2, -1] -> K[2, 2] + S[-1, -1,  -1] | +| kpoff = 0.05 | S[-1, 2, 1] -> K[2, 2] + S[-1, -1,  1] | +| kpoff = 0.05 | S[1, 2, -1] -> K[2, 2] + S[1, -1,  -1] | +| kpoff = 0.05 | S[1, 2, 1] -> K[2, 2] + S[1, -1,  1] | +| kpoff = 0.05 | S[-1, 2, 1] -> K[3, 1] + S[-1, 2,  -1] | +| kpoff = 0.05 | S[1, 2, 1] -> K[3, 1] + S[1, 2,  -1] | +| kpoff = 0.05 | S[2, 0, 0] -> K[1, 2] + S[-1, 0,  0] | +| kpoff = 0.05 | S[2, 0, -1] -> K[1, 2] + S[-1, 0,  -1] | +| kpoff = 0.05 | S[2, 0, 1] -> K[1, 2] + S[-1, 0,  1] | +| kpoff = 0.05 | S[2, 0, 1] -> K[3, 1] + S[2, 0,  -1] | +| kpoff = 0.05 | S[2, -1, 0] -> K[1, 2] + S[-1, -1,  0] | +| kpoff = 0.05 | S[2, 1, 0] -> K[1, 2] + S[-1, 1,  0] | +| kpoff = 0.05 | S[2, 1, 0] -> K[2, 1] + S[2, -1,  0] | +| kpoff = 0.05 | S[2, -1, -1] -> K[1, 2] + S[-1, -1,  -1] | +| kpoff = 0.05 | S[2, -1, 1] -> K[1, 2] + S[-1, -1,  1] | +| kpoff = 0.05 | S[2, 1, -1] -> K[1, 2] + S[-1, 1,  -1] | +| kpoff = 0.05 | S[2, 1, 1] -> K[1, 2] + S[-1, 1,  1] | +| kpoff = 0.05 | S[2, 1, -1] -> K[2, 1] + S[2, -1,  -1] | +| kpoff = 0.05 | S[2, 1, 1] -> K[2, 1] + S[2, -1,  1] | +| kpoff = 0.05 | S[2, -1, 1] -> K[3, 1] + S[2, -1,  -1] | +| kpoff = 0.05 | S[2, 1, 1] -> K[3, 1] + S[2, 1,  -1] | +| kpoff = 0.05 | S[2, 2, 0] -> K[1, 2] + S[-1, 2,  0] | +| kpoff = 0.05 | S[2, 2, 0] -> K[2, 2] + S[2, -1,  0] | +| kpoff = 0.05 | S[2, 2, -1] -> K[1, 2] + S[-1, 2,  -1] | +| kpoff = 0.05 | S[2, 2, 1] -> K[1, 2] + S[-1, 2,  1] | +| kpoff = 0.05 | S[2, 2, -1] -> K[2, 2] + S[2, -1,  -1] | +| kpoff = 0.05 | S[2, 2, 1] -> K[2, 2] + S[2, -1,  1] | +| kpoff = 0.05 | S[2, 2, 1] -> K[3, 1] + S[2, 2,  -1] | +| kpon = 0 | K[1, 1] + S[-1, 0, 0] -> S[1, 0,  0] | +| kpon = 0 | K[1, 1] + S[-1, 0, -1] -> S[1, 0,  -1] | +| kpon = 0 | K[1, 1] + S[-1, 0, 1] -> S[1, 0,  1] | +| kpon = 0 | K[1, 1] + S[-1, -1, 0] -> S[1, -1,  0] | +| kpon = 0 | K[1, 1] + S[-1, 1, 0] -> S[1, 1,  0] | +| kpon = 0 | K[1, 1] + S[-1, -1, -1] -> S[1, -1,  -1] | +| kpon = 0 | K[1, 1] + S[-1, -1, 1] -> S[1, -1,  1] | +| kpon = 0 | K[1, 1] + S[-1, 1, -1] -> S[1, 1,  -1] | +| kpon = 0 | K[1, 1] + S[-1, 1, 1] -> S[1, 1,  1] | +| kpon = 0 | K[1, 1] + S[-1, 2, 0] -> S[1, 2,  0] | +| kpon = 0 | K[1, 1] + S[-1, 2, -1] -> S[1, 2,  -1] | +| kpon = 0 | K[1, 1] + S[-1, 2, 1] -> S[1, 2,  1] | +| kpon = 0 | K[1, 2] + S[-1, 0, 0] -> S[2, 0,  0] | +| kpon = 0 | K[1, 2] + S[-1, 0, -1] -> S[2, 0,  -1] | +| kpon = 0 | K[1, 2] + S[-1, 0, 1] -> S[2, 0,  1] | +| kpon = 0 | K[1, 2] + S[-1, -1, 0] -> S[2, -1,  0] | +| kpon = 0 | K[1, 2] + S[-1, 1, 0] -> S[2, 1,  0] | +| kpon = 0 | K[1, 2] + S[-1, -1, -1] -> S[2, -1,  -1] | +| kpon = 0 | K[1, 2] + S[-1, -1, 1] -> S[2, -1,  1] | +| kpon = 0 | K[1, 2] + S[-1, 1, -1] -> S[2, 1,  -1] | +| kpon = 0 | K[1, 2] + S[-1, 1, 1] -> S[2, 1,  1] | +| kpon = 0 | K[1, 2] + S[-1, 2, 0] -> S[2, 2,  0] | +| kpon = 0 | K[1, 2] + S[-1, 2, -1] -> S[2, 2,  -1] | +| kpon = 0 | K[1, 2] + S[-1, 2, 1] -> S[2, 2,  1] | +| kpon = 0 | K[2, 1] + S[0, -1, 0] -> S[0, 1,  0] | +| kpon = 0 | K[2, 1] + S[0, -1, -1] -> S[0, 1,  -1] | +| kpon = 0 | K[2, 1] + S[0, -1, 1] -> S[0, 1,  1] | +| kpon = 0 | K[2, 1] + S[-1, -1, 0] -> S[-1, 1,  0] | +| kpon = 0 | K[2, 1] + S[1, -1, 0] -> S[1, 1,  0] | +| kpon = 0 | K[2, 1] + S[-1, -1, -1] -> S[-1, 1,  -1] | +| kpon = 0 | K[2, 1] + S[-1, -1, 1] -> S[-1, 1,  1] | +| kpon = 0 | K[2, 1] + S[1, -1, -1] -> S[1, 1,  -1] | +| kpon = 0 | K[2, 1] + S[1, -1, 1] -> S[1, 1,  1] | +| kpon = 0 | K[2, 1] + S[2, -1, 0] -> S[2, 1,  0] | +| kpon = 0 | K[2, 1] + S[2, -1, -1] -> S[2, 1,  -1] | +| kpon = 0 | K[2, 1] + S[2, -1, 1] -> S[2, 1,  1] | +| kpon = 0 | K[2, 2] + S[0, -1, 0] -> S[0, 2,  0] | +| kpon = 0 | K[2, 2] + S[0, -1, -1] -> S[0, 2,  -1] | +| kpon = 0 | K[2, 2] + S[0, -1, 1] -> S[0, 2,  1] | +| kpon = 0 | K[2, 2] + S[-1, -1, 0] -> S[-1, 2,  0] | +| kpon = 0 | K[2, 2] + S[1, -1, 0] -> S[1, 2,  0] | +| kpon = 0 | K[2, 2] + S[-1, -1, -1] -> S[-1, 2,  -1] | +| kpon = 0 | K[2, 2] + S[-1, -1, 1] -> S[-1, 2,  1] | +| kpon = 0 | K[2, 2] + S[1, -1, -1] -> S[1, 2,  -1] | +| kpon = 0 | K[2, 2] + S[1, -1, 1] -> S[1, 2,  1] | +| kpon = 0 | K[2, 2] + S[2, -1, 0] -> S[2, 2,  0] | +| kpon = 0 | K[2, 2] + S[2, -1, -1] -> S[2, 2,  -1] | +| kpon = 0 | K[2, 2] + S[2, -1, 1] -> S[2, 2,  1] | +| kpon = 0 | K[3, 1] + S[0, 0, -1] -> S[0, 0,  1] | +| kpon = 0 | K[3, 1] + S[0, -1, -1] -> S[0, -1,  1] | +| kpon = 0 | K[3, 1] + S[0, 1, -1] -> S[0, 1,  1] | +| kpon = 0 | K[3, 1] + S[0, 2, -1] -> S[0, 2,  1] | +| kpon = 0 | K[3, 1] + S[-1, 0, -1] -> S[-1, 0,  1] | +| kpon = 0 | K[3, 1] + S[1, 0, -1] -> S[1, 0,  1] | +| kpon = 0 | K[3, 1] + S[-1, -1, -1] -> S[-1, -1,  1] | +| kpon = 0 | K[3, 1] + S[-1, 1, -1] -> S[-1, 1,  1] | +| kpon = 0 | K[3, 1] + S[1, -1, -1] -> S[1, -1,  1] | +| kpon = 0 | K[3, 1] + S[1, 1, -1] -> S[1, 1,  1] | +| kpon = 0 | K[3, 1] + S[-1, 2, -1] -> S[-1, 2,  1] | +| kpon = 0 | K[3, 1] + S[1, 2, -1] -> S[1, 2,  1] | +| kpon = 0 | K[3, 1] + S[2, 0, -1] -> S[2, 0,  1] | +| kpon = 0 | K[3, 1] + S[2, -1, -1] -> S[2, -1,  1] | +| kpon = 0 | K[3, 1] + S[2, 1, -1] -> S[2, 1,  1] | +| kpon = 0 | K[3, 1] + S[2, 2, -1] -> S[2, 2,  1] | + + +| Variable | IC   | ODE | +|:--------------------|:-------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| MAPKP | 0.3 | MAPKP'[t] == -(a8\*MAPKP[t]\*K[1, 1][t]) - a10\*MAPKP[ t]\*K[1, 2][t] + d8\*K_MAPKP[1, 1][t] + k8\*K_MAPKP[ 1, 1][t] + d10\*K_MAPKP[1, 2][t] + k10\*K_MAPKP[1,  2][t] | +| MEKP | 0.2 | MEKP'[t] == -(a4\*MEKP[t]\*K[2, 1][t]) - a6\*MEKP[t]\* K[2, 2][t] + d4\*K_MEKP[2, 1][t] + k4\*K_MEKP[2,  1][t] + d6\*K_MEKP[2, 2][t] + k6\*K_MEKP[2, 2] [t] | +| RAFK | 0.1 | RAFK'[t] == -(a1\*RAFK[t]\*K[3, 0][t]) + d1\*K_RAFK[3,  0][t] + k1\*K_RAFK[3, 0][t] - k1a\*RAFK[t]\*S[-1,  -1, 0][t] - k1a\*RAFK[t]\*S[-1, 0, 0][t] -  k1a\*RAFK[t]\*S[-1, 1, 0][t] - k1a\*RAFK[t]\*S[-1, 2,  0][t] - k1a\*RAFK[t]\*S[0, -1, 0][t] - k1a\* RAFK[t]\*S[0, 0, 0][t] - k1a\*RAFK[t]\*S[0, 1, 0][t]  - k1a\*RAFK[t]\*S[0, 2, 0][t] - k1a\*RAFK[t]\*S[1,  -1, 0][t] - k1a\*RAFK[t]\*S[1, 0, 0][t] -  k1a\*RAFK[t]\*S[1, 1, 0][t] - k1a\*RAFK[t]\*S[1, 2,  0][t] - k1a\*RAFK[t]\*S[2, -1, 0][t] - k1a\* RAFK[t]\*S[2, 0, 0][t] - k1a\*RAFK[t]\*S[2, 1, 0][t]  - k1a\*RAFK[t]\*S[2, 2, 0][t] + d1a\*S_RAFK[-1,  -1, 0][t] + k1\*S_RAFK[-1, -1, 0][t] +  d1a\*S_RAFK[-1, 0, 0][t] + k1\*S_RAFK[-1, 0,  0][t] + d1a\*S_RAFK[-1, 1, 0][t] + k1\*S_RAFK[ -1, 1, 0][t] + d1a\*S_RAFK[-1, 2, 0][t] +  k1\*S_RAFK[-1, 2, 0][t] + d1a\*S_RAFK[0, -1,  0][t] + k1\*S_RAFK[0, -1, 0][t] + d1a\*S_RAFK[ 0, 0, 0][t] + k1\*S_RAFK[0, 0, 0][t] +  d1a\*S_RAFK[0, 1, 0][t] + k1\*S_RAFK[0, 1, 0][ t] + d1a\*S_RAFK[0, 2, 0][t] + k1\*S_RAFK[0, 2,  0][t] + d1a\*S_RAFK[1, -1, 0][t] + k1\*S_RAFK[ 1, -1, 0][t] + d1a\*S_RAFK[1, 0, 0][t] +  k1\*S_RAFK[1, 0, 0][t] + d1a\*S_RAFK[1, 1, 0][ t] + k1\*S_RAFK[1, 1, 0][t] + d1a\*S_RAFK[1, 2,  0][t] + k1\*S_RAFK[1, 2, 0][t] + d1a\*S_RAFK[ 2, -1, 0][t] + k1\*S_RAFK[2, -1, 0][t] +  d1a\*S_RAFK[2, 0, 0][t] + k1\*S_RAFK[2, 0, 0][ t] + d1a\*S_RAFK[2, 1, 0][t] + k1\*S_RAFK[2, 1,  0][t] + d1a\*S_RAFK[2, 2, 0][t] + k1\*S_RAFK[ 2, 2, 0][t] | +| RAFP | 0.3 | RAFP'[t] == -(a2\*RAFP[t]\*K[3, 1][t]) + d2\*K_RAFP[3,  1][t] + k2\*K_RAFP[3, 1][t] | +| K[1, 0] | 0.4 | (K[1, 0])'[t] == -(a7\*K[1, 0][t]\*K[2, 2][t]) +  d7\*K_K[1, 0, 2, 2][t] + k8\*K_MAPKP[1, 1][t]  - kon\*K[1, 0][t]\*S[-1, -1, -1][t] - kon\*K[1,  0][t]\*S[-1, -1, 0][t] - kon\*K[1, 0][t]\*S[-1,  -1, 1][t] - kon\*K[1, 0][t]\*S[-1, 0, -1][t]  - kon\*K[1, 0][t]\*S[-1, 0, 0][t] - kon\*K[1,  0][t]\*S[-1, 0, 1][t] - kon\*K[1, 0][t]\*S[-1,  1, -1][t] - kon\*K[1, 0][t]\*S[-1, 1, 0][t]  - kon\*K[1, 0][t]\*S[-1, 1, 1][t] - kon\*K[1,  0][t]\*S[-1, 2, -1][t] - kon\*K[1, 0][t]\*S[-1,  2, 0][t] - kon\*K[1, 0][t]\*S[-1, 2, 1][t]  + koff\*S[0, -1, -1][t] + koff\*S[0, -1,  0][t] + koff\*S[0, -1, 1][t] + koff\*S[0,  0, -1][t] + koff\*S[0, 0, 0][t] + koff\* S[0, 0, 1][t] + koff\*S[0, 1, -1][t] +  koff\*S[0, 1, 0][t] + koff\*S[0, 1, 1][t]  + koff\*S[0, 2, -1][t] + koff\*S[0, 2, 0] [t] + koff\*S[0, 2, 1][t] | +| K[1, 1] | 0 | (K[1, 1])'[t] == -(a8\*MAPKP[t]\*K[1, 1][t]) -  a9\*K[1, 1][t]\*K[2, 2][t] + k7\*K_K[1, 0, 2,  2][t] + d9\*K_K[1, 1, 2, 2][t] + d8\* K_MAPKP[1, 1][t] + k10\*K_MAPKP[1, 2][t] - kpon\*K[ 1, 1][t]\*S[-1, -1, -1][t] - kpon\*K[1, 1][t]\*S[-1,  -1, 0][t] - kpon\*K[1, 1][t]\*S[-1, -1, 1][t]  - kpon\*K[1, 1][t]\*S[-1, 0, -1][t] - kpon\*K[ 1, 1][t]\*S[-1, 0, 0][t] - kpon\*K[1, 1][t]\*S[-1,  0, 1][t] - kpon\*K[1, 1][t]\*S[-1, 1, -1][t]  - kpon\*K[1, 1][t]\*S[-1, 1, 0][t] - kpon\*K[1,  1][t]\*S[-1, 1, 1][t] - kpon\*K[1, 1][t]\*S[-1,  2, -1][t] - kpon\*K[1, 1][t]\*S[-1, 2, 0][t]  - kpon\*K[1, 1][t]\*S[-1, 2, 1][t] + kpoff\*S[ 1, -1, -1][t] + kpoff\*S[1, -1, 0][t] +  kpoff\*S[1, -1, 1][t] + kpoff\*S[1, 0, -1][t]  + kpoff\*S[1, 0, 0][t] + kpoff\*S[1, 0,  1][t] + kpoff\*S[1, 1, -1][t] + kpoff\*S[1,  1, 0][t] + kpoff\*S[1, 1, 1][t] + kpoff\* S[1, 2, -1][t] + kpoff\*S[1, 2, 0][t] +  kpoff\*S[1, 2, 1][t] | +| K[1, 2] | 0 | (K[1, 2])'[t] == -(a10\*MAPKP[t]\*K[1, 2][t]) +  k9\*K_K[1, 1, 2, 2][t] + d10\*K_MAPKP[1, 2][t]  - kpon\*K[1, 2][t]\*S[-1, -1, -1][t] - kpon\*K[ 1, 2][t]\*S[-1, -1, 0][t] - kpon\*K[1, 2][t]\*S[-1,  -1, 1][t] - kpon\*K[1, 2][t]\*S[-1, 0, -1][t]  - kpon\*K[1, 2][t]\*S[-1, 0, 0][t] - kpon\*K[1,  2][t]\*S[-1, 0, 1][t] - kpon\*K[1, 2][t]\*S[-1,  1, -1][t] - kpon\*K[1, 2][t]\*S[-1, 1, 0][t]  - kpon\*K[1, 2][t]\*S[-1, 1, 1][t] - kpon\*K[1,  2][t]\*S[-1, 2, -1][t] - kpon\*K[1, 2][t]\*S[-1,  2, 0][t] - kpon\*K[1, 2][t]\*S[-1, 2, 1][t]  + kpoff\*S[2, -1, -1][t] + kpoff\*S[2, -1,  0][t] + kpoff\*S[2, -1, 1][t] + kpoff\*S[2,  0, -1][t] + kpoff\*S[2, 0, 0][t] +  kpoff\*S[2, 0, 1][t] + kpoff\*S[2, 1, -1][t]  + kpoff\*S[2, 1, 0][t] + kpoff\*S[2, 1,  1][t] + kpoff\*S[2, 2, -1][t] + kpoff\*S[2,  2, 0][t] + kpoff\*S[2, 2, 1][t] | +| K[2, 0] | 0.2 | (K[2, 0])'[t] == -(a3\*K[2, 0][t]\*K[3, 1][t]) +  d3\*K_K[2, 0, 3, 1][t] + k4\*K_MEKP[2, 1][t]  - kon\*K[2, 0][t]\*S[-1, -1, -1][t] - kon\*K[2,  0][t]\*S[-1, -1, 0][t] - kon\*K[2, 0][t]\*S[-1,  -1, 1][t] + koff\*S[-1, 0, -1][t] +  koff\*S[-1, 0, 0][t] + koff\*S[-1, 0, 1][t]  - kon\*K[2, 0][t]\*S[0, -1, -1][t] - kon\*K[2,  0][t]\*S[0, -1, 0][t] - kon\*K[2, 0][t]\*S[0, - 1, 1][t] + koff\*S[0, 0, -1][t] + koff\*S[0,  0, 0][t] + koff\*S[0, 0, 1][t] - kon\*K[ 2, 0][t]\*S[1, -1, -1][t] - kon\*K[2, 0][t]\*S[1,  -1, 0][t] - kon\*K[2, 0][t]\*S[1, -1, 1][t]  + koff\*S[1, 0, -1][t] + koff\*S[1, 0, 0] [t] + koff\*S[1, 0, 1][t] - kon\*K[2, 0][t]\*S[ 2, -1, -1][t] - kon\*K[2, 0][t]\*S[2, -1, 0][t]  - kon\*K[2, 0][t]\*S[2, -1, 1][t] + koff\*S[2,  0, -1][t] + koff\*S[2, 0, 0][t] + koff\* S[2, 0, 1][t] | +| K[2, 1] | 0 | (K[2, 1])'[t] == -(a4\*MEKP[t]\*K[2, 1][t]) -  a5\*K[2, 1][t]\*K[3, 1][t] + k3\*K_K[2, 0, 3,  1][t] + d5\*K_K[2, 1, 3, 1][t] + d4\* K_MEKP[2, 1][t] + k6\*K_MEKP[2, 2][t] - kpon\*K[2,  1][t]\*S[-1, -1, -1][t] - kpon\*K[2, 1][t]\*S[-1,  -1, 0][t] - kpon\*K[2, 1][t]\*S[-1, -1, 1][t]  + kpoff\*S[-1, 1, -1][t] + kpoff\*S[-1, 1,  0][t] + kpoff\*S[-1, 1, 1][t] - kpon\*K[2,  1][t]\*S[0, -1, -1][t] - kpon\*K[2, 1][t]\*S[0,  -1, 0][t] - kpon\*K[2, 1][t]\*S[0, -1, 1][t]  + kpoff\*S[0, 1, -1][t] + kpoff\*S[0, 1,  0][t] + kpoff\*S[0, 1, 1][t] - kpon\*K[2,  1][t]\*S[1, -1, -1][t] - kpon\*K[2, 1][t]\*S[1,  -1, 0][t] - kpon\*K[2, 1][t]\*S[1, -1, 1][t]  + kpoff\*S[1, 1, -1][t] + kpoff\*S[1, 1,  0][t] + kpoff\*S[1, 1, 1][t] - kpon\*K[2,  1][t]\*S[2, -1, -1][t] - kpon\*K[2, 1][t]\*S[2,  -1, 0][t] - kpon\*K[2, 1][t]\*S[2, -1, 1][t]  + kpoff\*S[2, 1, -1][t] + kpoff\*S[2, 1,  0][t] + kpoff\*S[2, 1, 1][t] | +| K[2, 2] | 0 | (K[2, 2])'[t] == -(a6\*MEKP[t]\*K[2, 2][t]) -  a7\*K[1, 0][t]\*K[2, 2][t] - a9\*K[1, 1][t]\*K[2,  2][t] + d7\*K_K[1, 0, 2, 2][t] + k7\*K_K[ 1, 0, 2, 2][t] + d9\*K_K[1, 1, 2, 2][t]  + k9\*K_K[1, 1, 2, 2][t] + k5\*K_K[2, 1,  3, 1][t] + d6\*K_MEKP[2, 2][t] - kpon\*K[2,  2][t]\*S[-1, -1, -1][t] - kpon\*K[2, 2][t]\*S[-1,  -1, 0][t] - kpon\*K[2, 2][t]\*S[-1, -1, 1][t]  + kpoff\*S[-1, 2, -1][t] + kpoff\*S[-1, 2,  0][t] + kpoff\*S[-1, 2, 1][t] - kpon\*K[2,  2][t]\*S[0, -1, -1][t] - kpon\*K[2, 2][t]\*S[0,  -1, 0][t] - kpon\*K[2, 2][t]\*S[0, -1, 1][t]  + kpoff\*S[0, 2, -1][t] + kpoff\*S[0, 2,  0][t] + kpoff\*S[0, 2, 1][t] - kpon\*K[2,  2][t]\*S[1, -1, -1][t] - kpon\*K[2, 2][t]\*S[1,  -1, 0][t] - kpon\*K[2, 2][t]\*S[1, -1, 1][t]  + kpoff\*S[1, 2, -1][t] + kpoff\*S[1, 2,  0][t] + kpoff\*S[1, 2, 1][t] - kpon\*K[2,  2][t]\*S[2, -1, -1][t] - kpon\*K[2, 2][t]\*S[2,  -1, 0][t] - kpon\*K[2, 2][t]\*S[2, -1, 1][t]  + kpoff\*S[2, 2, -1][t] + kpoff\*S[2, 2,  0][t] + kpoff\*S[2, 2, 1][t] | +| K[3, 0] | 0.3 | (K[3, 0])'[t] == -(a1\*RAFK[t]\*K[3, 0][t]) +  d1\*K_RAFK[3, 0][t] + k2\*K_RAFP[3, 1][t] -  kon\*K[3, 0][t]\*S[-1, -1, -1][t] + koff\*S[-1,  -1, 0][t] - kon\*K[3, 0][t]\*S[-1, 0, -1][t]  + koff\*S[-1, 0, 0][t] - kon\*K[3, 0][t]\*S[-1,  1, -1][t] + koff\*S[-1, 1, 0][t] - kon\* K[3, 0][t]\*S[-1, 2, -1][t] + koff\*S[-1, 2, 0] [t] - kon\*K[3, 0][t]\*S[0, -1, -1][t] + koff\* S[0, -1, 0][t] - kon\*K[3, 0][t]\*S[0, 0, -1][ t] + koff\*S[0, 0, 0][t] - kon\*K[3, 0][t]\*S[0,  1, -1][t] + koff\*S[0, 1, 0][t] - kon\*K[ 3, 0][t]\*S[0, 2, -1][t] + koff\*S[0, 2, 0][t]  - kon\*K[3, 0][t]\*S[1, -1, -1][t] + koff\*S[1,  -1, 0][t] - kon\*K[3, 0][t]\*S[1, 0, -1][t]  + koff\*S[1, 0, 0][t] - kon\*K[3, 0][t]\*S[1,  1, -1][t] + koff\*S[1, 1, 0][t] - kon\*K[ 3, 0][t]\*S[1, 2, -1][t] + koff\*S[1, 2, 0][t]  - kon\*K[3, 0][t]\*S[2, -1, -1][t] + koff\*S[2,  -1, 0][t] - kon\*K[3, 0][t]\*S[2, 0, -1][t]  + koff\*S[2, 0, 0][t] - kon\*K[3, 0][t]\*S[2,  1, -1][t] + koff\*S[2, 1, 0][t] - kon\*K[ 3, 0][t]\*S[2, 2, -1][t] + koff\*S[2, 2, 0][t] | +| K[3, 1] | 0 | (K[3, 1])'[t] == -(a2\*RAFP[t]\*K[3, 1][t]) -  a3\*K[2, 0][t]\*K[3, 1][t] - a5\*K[2, 1][t]\*K[3,  1][t] + d3\*K_K[2, 0, 3, 1][t] + k3\*K_K[ 2, 0, 3, 1][t] + d5\*K_K[2, 1, 3, 1][t]  + k5\*K_K[2, 1, 3, 1][t] + k1\*K_RAFK[3,  0][t] + d2\*K_RAFP[3, 1][t] - kpon\*K[3, 1][t] \*S[-1, -1, -1][t] + kpoff\*S[-1, -1, 1][t] -  kpon\*K[3, 1][t]\*S[-1, 0, -1][t] + kpoff\*S[-1,  0, 1][t] - kpon\*K[3, 1][t]\*S[-1, 1, -1][t]  + kpoff\*S[-1, 1, 1][t] - kpon\*K[3, 1][t]\*S[- 1, 2, -1][t] + kpoff\*S[-1, 2, 1][t] -  kpon\*K[3, 1][t]\*S[0, -1, -1][t] + kpoff\*S[0,  -1, 1][t] - kpon\*K[3, 1][t]\*S[0, 0, -1][t]  + kpoff\*S[0, 0, 1][t] - kpon\*K[3, 1][t]\*S[0,  1, -1][t] + kpoff\*S[0, 1, 1][t] - kpon\* K[3, 1][t]\*S[0, 2, -1][t] + kpoff\*S[0, 2, 1][ t] - kpon\*K[3, 1][t]\*S[1, -1, -1][t] + kpoff\* S[1, -1, 1][t] - kpon\*K[3, 1][t]\*S[1, 0, -1][ t] + kpoff\*S[1, 0, 1][t] - kpon\*K[3, 1][t]\*S[ 1, 1, -1][t] + kpoff\*S[1, 1, 1][t] -  kpon\*K[3, 1][t]\*S[1, 2, -1][t] + kpoff\*S[1,  2, 1][t] - kpon\*K[3, 1][t]\*S[2, -1, -1][t]  + kpoff\*S[2, -1, 1][t] - kpon\*K[3, 1][t]\*S[ 2, 0, -1][t] + kpoff\*S[2, 0, 1][t] -  kpon\*K[3, 1][t]\*S[2, 1, -1][t] + kpoff\*S[2,  1, 1][t] - kpon\*K[3, 1][t]\*S[2, 2, -1][t]  + kpoff\*S[2, 2, 1][t] | +| K_K[1, 0, 2, 2] | 0 | (K_K[1, 0, 2, 2])'[t] == a7\*K[1, 0][t]\*K[2,  2][t] - d7\*K_K[1, 0, 2, 2][t] - k7\*K_K[ 1, 0, 2, 2][t] | +| K_K[1, 1, 2, 2] | 0 | (K_K[1, 1, 2, 2])'[t] == a9\*K[1, 1][t]\*K[2,  2][t] - d9\*K_K[1, 1, 2, 2][t] - k9\*K_K[ 1, 1, 2, 2][t] | +| K_K[2, 0, 3, 1] | 0 | (K_K[2, 0, 3, 1])'[t] == a3\*K[2, 0][t]\*K[3,  1][t] - d3\*K_K[2, 0, 3, 1][t] - k3\*K_K[ 2, 0, 3, 1][t] | +| K_K[2, 1, 3, 1] | 0 | (K_K[2, 1, 3, 1])'[t] == a5\*K[2, 1][t]\*K[3,  1][t] - d5\*K_K[2, 1, 3, 1][t] - k5\*K_K[ 2, 1, 3, 1][t] | +| K_MAPKP[1, 1] | 0 | (K_MAPKP[1, 1])'[t] == a8\*MAPKP[t]\*K[1, 1][t] -  d8\*K_MAPKP[1, 1][t] - k8\*K_MAPKP[1, 1][t] | +| K_MAPKP[1, 2] | 0 | (K_MAPKP[1, 2])'[t] == a10\*MAPKP[t]\*K[1, 2][t] -  d10\*K_MAPKP[1, 2][t] - k10\*K_MAPKP[1, 2][t] | +| K_MEKP[2, 1] | 0 | (K_MEKP[2, 1])'[t] == a4\*MEKP[t]\*K[2, 1][t] -  d4\*K_MEKP[2, 1][t] - k4\*K_MEKP[2, 1][t] | +| K_MEKP[2, 2] | 0 | (K_MEKP[2, 2])'[t] == a6\*MEKP[t]\*K[2, 2][t] -  d6\*K_MEKP[2, 2][t] - k6\*K_MEKP[2, 2][t] | +| K_RAFK[3, 0] | 0 | (K_RAFK[3, 0])'[t] == a1\*RAFK[t]\*K[3, 0][t] -  d1\*K_RAFK[3, 0][t] - k1\*K_RAFK[3, 0][t] | +| K_RAFP[3, 1] | 0 | (K_RAFP[3, 1])'[t] == a2\*RAFP[t]\*K[3, 1][t] -  d2\*K_RAFP[3, 1][t] - k2\*K_RAFP[3, 1][t] | +| S[-1, -1, -1] | 0.1 | (S[-1, -1, -1])'[t] == -(kon\*K[1, 0][t]\*S[-1,  -1, -1][t]) - kpon\*K[1, 1][t]\*S[-1, -1, -1][ t] - kpon\*K[1, 2][t]\*S[-1, -1, -1][t] - kon\* K[2, 0][t]\*S[-1, -1, -1][t] - kpon\*K[2, 1][t]\*S[- 1, -1, -1][t] - kpon\*K[2, 2][t]\*S[-1, -1, -1] [t] - kon\*K[3, 0][t]\*S[-1, -1, -1][t] - kpon\* K[3, 1][t]\*S[-1, -1, -1][t] + koff\*S[-1, -1,  0][t] + kpoff\*S[-1, -1, 1][t] + koff\*S[-1,  0, -1][t] + kpoff\*S[-1, 1, -1][t] +  kpoff\*S[-1, 2, -1][t] + koff\*S[0, -1, -1][t]  + kpoff\*S[1, -1, -1][t] + kpoff\*S[2, -1,  -1][t] | +| S[-1, -1, 0] | 0 | (S[-1, -1, 0])'[t] == kon\*K[3, 0][t]\*S[-1, -1,  -1][t] - koff\*S[-1, -1, 0][t] - k1a\*RAFK[t]\* S[-1, -1, 0][t] - kon\*K[1, 0][t]\*S[-1, -1, 0] [t] - kpon\*K[1, 1][t]\*S[-1, -1, 0][t] - kpon\* K[1, 2][t]\*S[-1, -1, 0][t] - kon\*K[2, 0][t]\*S[-1,  -1, 0][t] - kpon\*K[2, 1][t]\*S[-1, -1, 0][t]  - kpon\*K[2, 2][t]\*S[-1, -1, 0][t] + koff\*S[- 1, 0, 0][t] + kpoff\*S[-1, 1, 0][t] +  kpoff\*S[-1, 2, 0][t] + koff\*S[0, -1, 0][t]  + kpoff\*S[1, -1, 0][t] + kpoff\*S[2, -1,  0][t] + d1a\*S_RAFK[-1, -1, 0][t] | +| S[-1, -1, 1] | 0 | (S[-1, -1, 1])'[t] == kpon\*K[3, 1][t]\*S[-1, - 1, -1][t] - kpoff\*S[-1, -1, 1][t] - kon\*K[1,  0][t]\*S[-1, -1, 1][t] - kpon\*K[1, 1][t]\*S[-1,  -1, 1][t] - kpon\*K[1, 2][t]\*S[-1, -1, 1][t]  - kon\*K[2, 0][t]\*S[-1, -1, 1][t] - kpon\*K[2,  1][t]\*S[-1, -1, 1][t] - kpon\*K[2, 2][t]\*S[-1,  -1, 1][t] + koff\*S[-1, 0, 1][t] +  kpoff\*S[-1, 1, 1][t] + kpoff\*S[-1, 2, 1][t]  + koff\*S[0, -1, 1][t] + kpoff\*S[1, -1,  1][t] + kpoff\*S[2, -1, 1][t] + k1\*S_RAFK[-1,  -1, 0][t] | +| S[-1, 0, -1] | 0 | (S[-1, 0, -1])'[t] == kon\*K[2, 0][t]\*S[-1, -1,  -1][t] - koff\*S[-1, 0, -1][t] - kon\*K[1,  0][t]\*S[-1, 0, -1][t] - kpon\*K[1, 1][t]\*S[-1,  0, -1][t] - kpon\*K[1, 2][t]\*S[-1, 0, -1][t]  - kon\*K[3, 0][t]\*S[-1, 0, -1][t] - kpon\*K[3,  1][t]\*S[-1, 0, -1][t] + koff\*S[-1, 0, 0][t]  + kpoff\*S[-1, 0, 1][t] + koff\*S[0, 0, - 1][t] + kpoff\*S[1, 0, -1][t] + kpoff\*S[2, 0,  -1][t] | +| S[-1, 0, 0] | 0 | (S[-1, 0, 0])'[t] == kon\*K[2, 0][t]\*S[-1, -1,  0][t] + kon\*K[3, 0][t]\*S[-1, 0, -1][t] -  2\*koff\*S[-1, 0, 0][t] - k1a\*RAFK[t]\*S[-1, 0,  0][t] - kon\*K[1, 0][t]\*S[-1, 0, 0][t] -  kpon\*K[1, 1][t]\*S[-1, 0, 0][t] - kpon\*K[1,  2][t]\*S[-1, 0, 0][t] + koff\*S[0, 0, 0][t]  + kpoff\*S[1, 0, 0][t] + kpoff\*S[2, 0,  0][t] + d1a\*S_RAFK[-1, 0, 0][t] | +| S[-1, 0, 1] | 0 | (S[-1, 0, 1])'[t] == kon\*K[2, 0][t]\*S[-1, -1,  1][t] + kpon\*K[3, 1][t]\*S[-1, 0, -1][t] -  k3\*S[-1, 0, 1][t] - koff\*S[-1, 0, 1][t]  - kpoff\*S[-1, 0, 1][t] - kon\*K[1, 0][t]\*S[- 1, 0, 1][t] - kpon\*K[1, 1][t]\*S[-1, 0, 1][t]  - kpon\*K[1, 2][t]\*S[-1, 0, 1][t] + koff\*S[0,  0, 1][t] + kpoff\*S[1, 0, 1][t] + kpoff\* S[2, 0, 1][t] + k1\*S_RAFK[-1, 0, 0][t] | +| S[-1, 1, -1] | 0 | (S[-1, 1, -1])'[t] == kpon\*K[2, 1][t]\*S[-1, - 1, -1][t] - kpoff\*S[-1, 1, -1][t] - kon\*K[1,  0][t]\*S[-1, 1, -1][t] - kpon\*K[1, 1][t]\*S[-1,  1, -1][t] - kpon\*K[1, 2][t]\*S[-1, 1, -1][t]  - kon\*K[3, 0][t]\*S[-1, 1, -1][t] - kpon\*K[3,  1][t]\*S[-1, 1, -1][t] + koff\*S[-1, 1, 0][t]  + kpoff\*S[-1, 1, 1][t] + koff\*S[0, 1, - 1][t] + kpoff\*S[1, 1, -1][t] + kpoff\*S[2, 1,  -1][t] | +| S[-1, 1, 0] | 0 | (S[-1, 1, 0])'[t] == kpon\*K[2, 1][t]\*S[-1, -1,  0][t] + kon\*K[3, 0][t]\*S[-1, 1, -1][t] -  koff\*S[-1, 1, 0][t] - kpoff\*S[-1, 1, 0][t]  - k1a\*RAFK[t]\*S[-1, 1, 0][t] - kon\*K[1, 0][ t]\*S[-1, 1, 0][t] - kpon\*K[1, 1][t]\*S[-1, 1,  0][t] - kpon\*K[1, 2][t]\*S[-1, 1, 0][t] +  koff\*S[0, 1, 0][t] + kpoff\*S[1, 1, 0][t]  + kpoff\*S[2, 1, 0][t] + d1a\*S_RAFK[-1, 1,  0][t] | +| S[-1, 1, 1] | 0 | (S[-1, 1, 1])'[t] == kpon\*K[2, 1][t]\*S[-1, -1,  1][t] + k3\*S[-1, 0, 1][t] + kpon\*K[3,  1][t]\*S[-1, 1, -1][t] - k5a\*S[-1, 1, 1][t]  - 2\*kpoff\*S[-1, 1, 1][t] - kon\*K[1, 0][t]\*S[ -1, 1, 1][t] - kpon\*K[1, 1][t]\*S[-1, 1, 1][t]  - kpon\*K[1, 2][t]\*S[-1, 1, 1][t] + koff\*S[0,  1, 1][t] + kpoff\*S[1, 1, 1][t] + kpoff\* S[2, 1, 1][t] + k1\*S_RAFK[-1, 1, 0][t] | +| S[-1, 2, -1] | 0 | (S[-1, 2, -1])'[t] == kpon\*K[2, 2][t]\*S[-1, - 1, -1][t] - kpoff\*S[-1, 2, -1][t] - kon\*K[1,  0][t]\*S[-1, 2, -1][t] - kpon\*K[1, 1][t]\*S[-1,  2, -1][t] - kpon\*K[1, 2][t]\*S[-1, 2, -1][t]  - kon\*K[3, 0][t]\*S[-1, 2, -1][t] - kpon\*K[3,  1][t]\*S[-1, 2, -1][t] + koff\*S[-1, 2, 0][t]  + kpoff\*S[-1, 2, 1][t] + koff\*S[0, 2, - 1][t] + kpoff\*S[1, 2, -1][t] + kpoff\*S[2, 2,  -1][t] | +| S[-1, 2, 0] | 0 | (S[-1, 2, 0])'[t] == kpon\*K[2, 2][t]\*S[-1, -1,  0][t] + kon\*K[3, 0][t]\*S[-1, 2, -1][t] -  koff\*S[-1, 2, 0][t] - kpoff\*S[-1, 2, 0][t]  - k1a\*RAFK[t]\*S[-1, 2, 0][t] - kon\*K[1, 0][ t]\*S[-1, 2, 0][t] - kpon\*K[1, 1][t]\*S[-1, 2,  0][t] - kpon\*K[1, 2][t]\*S[-1, 2, 0][t] +  koff\*S[0, 2, 0][t] + kpoff\*S[1, 2, 0][t]  + kpoff\*S[2, 2, 0][t] + d1a\*S_RAFK[-1, 2,  0][t] | +| S[-1, 2, 1] | 0 | (S[-1, 2, 1])'[t] == kpon\*K[2, 2][t]\*S[-1, -1,  1][t] + k5a\*S[-1, 1, 1][t] + kpon\*K[3,  1][t]\*S[-1, 2, -1][t] - 2\*kpoff\*S[-1, 2, 1][ t] - kon\*K[1, 0][t]\*S[-1, 2, 1][t] - kpon\*K[ 1, 1][t]\*S[-1, 2, 1][t] - kpon\*K[1, 2][t]\*S[-1,  2, 1][t] + koff\*S[0, 2, 1][t] + kpoff\* S[1, 2, 1][t] + kpoff\*S[2, 2, 1][t] +  k1\*S_RAFK[-1, 2, 0][t] | +| S[0, -1, -1] | 0 | (S[0, -1, -1])'[t] == kon\*K[1, 0][t]\*S[-1, -1,  -1][t] - koff\*S[0, -1, -1][t] - kon\*K[2,  0][t]\*S[0, -1, -1][t] - kpon\*K[2, 1][t]\*S[0,  -1, -1][t] - kpon\*K[2, 2][t]\*S[0, -1, -1][t]  - kon\*K[3, 0][t]\*S[0, -1, -1][t] - kpon\*K[3,  1][t]\*S[0, -1, -1][t] + koff\*S[0, -1, 0][t]  + kpoff\*S[0, -1, 1][t] + koff\*S[0, 0, - 1][t] + kpoff\*S[0, 1, -1][t] + kpoff\*S[0, 2,  -1][t] | +| S[0, -1, 0] | 0 | (S[0, -1, 0])'[t] == kon\*K[1, 0][t]\*S[-1, -1,  0][t] + kon\*K[3, 0][t]\*S[0, -1, -1][t] -  2\*koff\*S[0, -1, 0][t] - k1a\*RAFK[t]\*S[0, -1,  0][t] - kon\*K[2, 0][t]\*S[0, -1, 0][t] -  kpon\*K[2, 1][t]\*S[0, -1, 0][t] - kpon\*K[2,  2][t]\*S[0, -1, 0][t] + koff\*S[0, 0, 0][t]  + kpoff\*S[0, 1, 0][t] + kpoff\*S[0, 2,  0][t] + d1a\*S_RAFK[0, -1, 0][t] | +| S[0, -1, 1] | 0 | (S[0, -1, 1])'[t] == kon\*K[1, 0][t]\*S[-1, -1,  1][t] + kpon\*K[3, 1][t]\*S[0, -1, -1][t] -  koff\*S[0, -1, 1][t] - kpoff\*S[0, -1, 1][t]  - kon\*K[2, 0][t]\*S[0, -1, 1][t] - kpon\*K[2,  1][t]\*S[0, -1, 1][t] - kpon\*K[2, 2][t]\*S[0,  -1, 1][t] + koff\*S[0, 0, 1][t] + kpoff\* S[0, 1, 1][t] + kpoff\*S[0, 2, 1][t] +  k1\*S_RAFK[0, -1, 0][t] | +| S[0, 0, -1] | 0 | (S[0, 0, -1])'[t] == kon\*K[1, 0][t]\*S[-1, 0,  -1][t] + kon\*K[2, 0][t]\*S[0, -1, -1][t] -  2\*koff\*S[0, 0, -1][t] - kon\*K[3, 0][t]\*S[0,  0, -1][t] - kpon\*K[3, 1][t]\*S[0, 0, -1][t]  + koff\*S[0, 0, 0][t] + kpoff\*S[0, 0, 1] [t] | +| S[0, 0, 0] | 0 | (S[0, 0, 0])'[t] == kon\*K[1, 0][t]\*S[-1, 0,  0][t] + kon\*K[2, 0][t]\*S[0, -1, 0][t] +  kon\*K[3, 0][t]\*S[0, 0, -1][t] - 3\*koff\*S[0,  0, 0][t] - k1a\*RAFK[t]\*S[0, 0, 0][t] +  d1a\*S_RAFK[0, 0, 0][t] | +| S[0, 0, 1] | 0 | (S[0, 0, 1])'[t] == kon\*K[1, 0][t]\*S[-1, 0,  1][t] + kon\*K[2, 0][t]\*S[0, -1, 1][t] +  kpon\*K[3, 1][t]\*S[0, 0, -1][t] - k3\*S[0, 0,  1][t] - 2\*koff\*S[0, 0, 1][t] - kpoff\*S[0,  0, 1][t] + k1\*S_RAFK[0, 0, 0][t] | +| S[0, 1, -1] | 0 | (S[0, 1, -1])'[t] == kon\*K[1, 0][t]\*S[-1, 1,  -1][t] + kpon\*K[2, 1][t]\*S[0, -1, -1][t] -  koff\*S[0, 1, -1][t] - kpoff\*S[0, 1, -1][t]  - kon\*K[3, 0][t]\*S[0, 1, -1][t] - kpon\*K[3,  1][t]\*S[0, 1, -1][t] + koff\*S[0, 1, 0][t]  + kpoff\*S[0, 1, 1][t] | +| S[0, 1, 0] | 0 | (S[0, 1, 0])'[t] == kon\*K[1, 0][t]\*S[-1, 1,  0][t] + kpon\*K[2, 1][t]\*S[0, -1, 0][t] +  kon\*K[3, 0][t]\*S[0, 1, -1][t] - 2\*koff\*S[0,  1, 0][t] - kpoff\*S[0, 1, 0][t] - k1a\* RAFK[t]\*S[0, 1, 0][t] + d1a\*S_RAFK[0, 1, 0][t] | +| S[0, 1, 1] | 0 | (S[0, 1, 1])'[t] == kon\*K[1, 0][t]\*S[-1, 1,  1][t] + kpon\*K[2, 1][t]\*S[0, -1, 1][t] +  k3\*S[0, 0, 1][t] + kpon\*K[3, 1][t]\*S[0, 1,  -1][t] - k5a\*S[0, 1, 1][t] - koff\*S[0,  1, 1][t] - 2\*kpoff\*S[0, 1, 1][t] + k1\* S_RAFK[0, 1, 0][t] | +| S[0, 2, -1] | 0 | (S[0, 2, -1])'[t] == kon\*K[1, 0][t]\*S[-1, 2,  -1][t] + kpon\*K[2, 2][t]\*S[0, -1, -1][t] -  k7\*S[0, 2, -1][t] - koff\*S[0, 2, -1][t]  - kpoff\*S[0, 2, -1][t] - kon\*K[3, 0][t]\*S[0,  2, -1][t] - kpon\*K[3, 1][t]\*S[0, 2, -1][t]  + koff\*S[0, 2, 0][t] + kpoff\*S[0, 2, 1] [t] | +| S[0, 2, 0] | 0 | (S[0, 2, 0])'[t] == kon\*K[1, 0][t]\*S[-1, 2,  0][t] + kpon\*K[2, 2][t]\*S[0, -1, 0][t] +  kon\*K[3, 0][t]\*S[0, 2, -1][t] - k7\*S[0, 2,  0][t] - 2\*koff\*S[0, 2, 0][t] - kpoff\*S[0,  2, 0][t] - k1a\*RAFK[t]\*S[0, 2, 0][t] +  d1a\*S_RAFK[0, 2, 0][t] | +| S[0, 2, 1] | 0 | (S[0, 2, 1])'[t] == kon\*K[1, 0][t]\*S[-1, 2,  1][t] + kpon\*K[2, 2][t]\*S[0, -1, 1][t] +  k5a\*S[0, 1, 1][t] + kpon\*K[3, 1][t]\*S[0, 2,  -1][t] - k7\*S[0, 2, 1][t] - koff\*S[0,  2, 1][t] - 2\*kpoff\*S[0, 2, 1][t] + k1\* S_RAFK[0, 2, 0][t] | +| S[1, -1, -1] | 0 | (S[1, -1, -1])'[t] == kpon\*K[1, 1][t]\*S[-1, - 1, -1][t] - kpoff\*S[1, -1, -1][t] - kon\*K[2,  0][t]\*S[1, -1, -1][t] - kpon\*K[2, 1][t]\*S[1,  -1, -1][t] - kpon\*K[2, 2][t]\*S[1, -1, -1][t]  - kon\*K[3, 0][t]\*S[1, -1, -1][t] - kpon\*K[3,  1][t]\*S[1, -1, -1][t] + koff\*S[1, -1, 0][t]  + kpoff\*S[1, -1, 1][t] + koff\*S[1, 0, - 1][t] + kpoff\*S[1, 1, -1][t] + kpoff\*S[1, 2,  -1][t] | +| S[1, -1, 0] | 0 | (S[1, -1, 0])'[t] == kpon\*K[1, 1][t]\*S[-1, -1,  0][t] + kon\*K[3, 0][t]\*S[1, -1, -1][t] -  koff\*S[1, -1, 0][t] - kpoff\*S[1, -1, 0][t]  - k1a\*RAFK[t]\*S[1, -1, 0][t] - kon\*K[2, 0][ t]\*S[1, -1, 0][t] - kpon\*K[2, 1][t]\*S[1, -1,  0][t] - kpon\*K[2, 2][t]\*S[1, -1, 0][t] +  koff\*S[1, 0, 0][t] + kpoff\*S[1, 1, 0][t]  + kpoff\*S[1, 2, 0][t] + d1a\*S_RAFK[1, -1,  0][t] | +| S[1, -1, 1] | 0 | (S[1, -1, 1])'[t] == kpon\*K[1, 1][t]\*S[-1, -1,  1][t] + kpon\*K[3, 1][t]\*S[1, -1, -1][t] -  2\*kpoff\*S[1, -1, 1][t] - kon\*K[2, 0][t]\*S[1,  -1, 1][t] - kpon\*K[2, 1][t]\*S[1, -1, 1][t]  - kpon\*K[2, 2][t]\*S[1, -1, 1][t] + koff\*S[1,  0, 1][t] + kpoff\*S[1, 1, 1][t] + kpoff\* S[1, 2, 1][t] + k1\*S_RAFK[1, -1, 0][t] | +| S[1, 0, -1] | 0 | (S[1, 0, -1])'[t] == kpon\*K[1, 1][t]\*S[-1, 0,  -1][t] + kon\*K[2, 0][t]\*S[1, -1, -1][t] -  koff\*S[1, 0, -1][t] - kpoff\*S[1, 0, -1][t]  - kon\*K[3, 0][t]\*S[1, 0, -1][t] - kpon\*K[3,  1][t]\*S[1, 0, -1][t] + koff\*S[1, 0, 0][t]  + kpoff\*S[1, 0, 1][t] | +| S[1, 0, 0] | 0 | (S[1, 0, 0])'[t] == kpon\*K[1, 1][t]\*S[-1, 0,  0][t] + kon\*K[2, 0][t]\*S[1, -1, 0][t] +  kon\*K[3, 0][t]\*S[1, 0, -1][t] - 2\*koff\*S[1,  0, 0][t] - kpoff\*S[1, 0, 0][t] - k1a\* RAFK[t]\*S[1, 0, 0][t] + d1a\*S_RAFK[1, 0, 0][t] | +| S[1, 0, 1] | 0 | (S[1, 0, 1])'[t] == kpon\*K[1, 1][t]\*S[-1, 0,  1][t] + kon\*K[2, 0][t]\*S[1, -1, 1][t] +  kpon\*K[3, 1][t]\*S[1, 0, -1][t] - k3\*S[1, 0,  1][t] - koff\*S[1, 0, 1][t] - 2\*kpoff\*S[1,  0, 1][t] + k1\*S_RAFK[1, 0, 0][t] | +| S[1, 1, -1] | 0 | (S[1, 1, -1])'[t] == kpon\*K[1, 1][t]\*S[-1, 1,  -1][t] + kpon\*K[2, 1][t]\*S[1, -1, -1][t] -  2\*kpoff\*S[1, 1, -1][t] - kon\*K[3, 0][t]\*S[1,  1, -1][t] - kpon\*K[3, 1][t]\*S[1, 1, -1][t]  + koff\*S[1, 1, 0][t] + kpoff\*S[1, 1, 1] [t] | +| S[1, 1, 0] | 0 | (S[1, 1, 0])'[t] == kpon\*K[1, 1][t]\*S[-1, 1,  0][t] + kpon\*K[2, 1][t]\*S[1, -1, 0][t] +  kon\*K[3, 0][t]\*S[1, 1, -1][t] - koff\*S[1, 1,  0][t] - 2\*kpoff\*S[1, 1, 0][t] - k1a\*RAFK[t]\* S[1, 1, 0][t] + d1a\*S_RAFK[1, 1, 0][t] | +| S[1, 1, 1] | 0 | (S[1, 1, 1])'[t] == kpon\*K[1, 1][t]\*S[-1, 1,  1][t] + kpon\*K[2, 1][t]\*S[1, -1, 1][t] +  k3\*S[1, 0, 1][t] + kpon\*K[3, 1][t]\*S[1, 1,  -1][t] - k5a\*S[1, 1, 1][t] - 3\*kpoff\*S[1,  1, 1][t] + k1\*S_RAFK[1, 1, 0][t] | +| S[1, 2, -1] | 0 | (S[1, 2, -1])'[t] == kpon\*K[1, 1][t]\*S[-1, 2,  -1][t] + k7\*S[0, 2, -1][t] + kpon\*K[2,  2][t]\*S[1, -1, -1][t] - k9a\*S[1, 2, -1][t]  - 2\*kpoff\*S[1, 2, -1][t] - kon\*K[3, 0][t]\*S[ 1, 2, -1][t] - kpon\*K[3, 1][t]\*S[1, 2, -1][t]  + koff\*S[1, 2, 0][t] + kpoff\*S[1, 2, 1] [t] | +| S[1, 2, 0] | 0 | (S[1, 2, 0])'[t] == kpon\*K[1, 1][t]\*S[-1, 2,  0][t] + k7\*S[0, 2, 0][t] + kpon\*K[2, 2] [t]\*S[1, -1, 0][t] + kon\*K[3, 0][t]\*S[1, 2, - 1][t] - k9a\*S[1, 2, 0][t] - koff\*S[1, 2,  0][t] - 2\*kpoff\*S[1, 2, 0][t] - k1a\*RAFK[t]\* S[1, 2, 0][t] + d1a\*S_RAFK[1, 2, 0][t] | +| S[1, 2, 1] | 0 | (S[1, 2, 1])'[t] == kpon\*K[1, 1][t]\*S[-1, 2,  1][t] + k7\*S[0, 2, 1][t] + kpon\*K[2, 2] [t]\*S[1, -1, 1][t] + k5a\*S[1, 1, 1][t] +  kpon\*K[3, 1][t]\*S[1, 2, -1][t] - k9a\*S[1, 2,  1][t] - 3\*kpoff\*S[1, 2, 1][t] + k1\*S_RAFK[1,  2, 0][t] | +| S[2, -1, -1] | 0 | (S[2, -1, -1])'[t] == kpon\*K[1, 2][t]\*S[-1, - 1, -1][t] - kpoff\*S[2, -1, -1][t] - kon\*K[2,  0][t]\*S[2, -1, -1][t] - kpon\*K[2, 1][t]\*S[2,  -1, -1][t] - kpon\*K[2, 2][t]\*S[2, -1, -1][t]  - kon\*K[3, 0][t]\*S[2, -1, -1][t] - kpon\*K[3,  1][t]\*S[2, -1, -1][t] + koff\*S[2, -1, 0][t]  + kpoff\*S[2, -1, 1][t] + koff\*S[2, 0, - 1][t] + kpoff\*S[2, 1, -1][t] + kpoff\*S[2, 2,  -1][t] | +| S[2, -1, 0] | 0 | (S[2, -1, 0])'[t] == kpon\*K[1, 2][t]\*S[-1, -1,  0][t] + kon\*K[3, 0][t]\*S[2, -1, -1][t] -  koff\*S[2, -1, 0][t] - kpoff\*S[2, -1, 0][t]  - k1a\*RAFK[t]\*S[2, -1, 0][t] - kon\*K[2, 0][ t]\*S[2, -1, 0][t] - kpon\*K[2, 1][t]\*S[2, -1,  0][t] - kpon\*K[2, 2][t]\*S[2, -1, 0][t] +  koff\*S[2, 0, 0][t] + kpoff\*S[2, 1, 0][t]  + kpoff\*S[2, 2, 0][t] + d1a\*S_RAFK[2, -1,  0][t] | +| S[2, -1, 1] | 0 | (S[2, -1, 1])'[t] == kpon\*K[1, 2][t]\*S[-1, -1,  1][t] + kpon\*K[3, 1][t]\*S[2, -1, -1][t] -  2\*kpoff\*S[2, -1, 1][t] - kon\*K[2, 0][t]\*S[2,  -1, 1][t] - kpon\*K[2, 1][t]\*S[2, -1, 1][t]  - kpon\*K[2, 2][t]\*S[2, -1, 1][t] + koff\*S[2,  0, 1][t] + kpoff\*S[2, 1, 1][t] + kpoff\* S[2, 2, 1][t] + k1\*S_RAFK[2, -1, 0][t] | +| S[2, 0, -1] | 0 | (S[2, 0, -1])'[t] == kpon\*K[1, 2][t]\*S[-1, 0,  -1][t] + kon\*K[2, 0][t]\*S[2, -1, -1][t] -  koff\*S[2, 0, -1][t] - kpoff\*S[2, 0, -1][t]  - kon\*K[3, 0][t]\*S[2, 0, -1][t] - kpon\*K[3,  1][t]\*S[2, 0, -1][t] + koff\*S[2, 0, 0][t]  + kpoff\*S[2, 0, 1][t] | +| S[2, 0, 0] | 0 | (S[2, 0, 0])'[t] == kpon\*K[1, 2][t]\*S[-1, 0,  0][t] + kon\*K[2, 0][t]\*S[2, -1, 0][t] +  kon\*K[3, 0][t]\*S[2, 0, -1][t] - 2\*koff\*S[2,  0, 0][t] - kpoff\*S[2, 0, 0][t] - k1a\* RAFK[t]\*S[2, 0, 0][t] + d1a\*S_RAFK[2, 0, 0][t] | +| S[2, 0, 1] | 0 | (S[2, 0, 1])'[t] == kpon\*K[1, 2][t]\*S[-1, 0,  1][t] + kon\*K[2, 0][t]\*S[2, -1, 1][t] +  kpon\*K[3, 1][t]\*S[2, 0, -1][t] - k3\*S[2, 0,  1][t] - koff\*S[2, 0, 1][t] - 2\*kpoff\*S[2,  0, 1][t] + k1\*S_RAFK[2, 0, 0][t] | +| S[2, 1, -1] | 0 | (S[2, 1, -1])'[t] == kpon\*K[1, 2][t]\*S[-1, 1,  -1][t] + kpon\*K[2, 1][t]\*S[2, -1, -1][t] -  2\*kpoff\*S[2, 1, -1][t] - kon\*K[3, 0][t]\*S[2,  1, -1][t] - kpon\*K[3, 1][t]\*S[2, 1, -1][t]  + koff\*S[2, 1, 0][t] + kpoff\*S[2, 1, 1] [t] | +| S[2, 1, 0] | 0 | (S[2, 1, 0])'[t] == kpon\*K[1, 2][t]\*S[-1, 1,  0][t] + kpon\*K[2, 1][t]\*S[2, -1, 0][t] +  kon\*K[3, 0][t]\*S[2, 1, -1][t] - koff\*S[2, 1,  0][t] - 2\*kpoff\*S[2, 1, 0][t] - k1a\*RAFK[t]\* S[2, 1, 0][t] + d1a\*S_RAFK[2, 1, 0][t] | +| S[2, 1, 1] | 0 | (S[2, 1, 1])'[t] == kpon\*K[1, 2][t]\*S[-1, 1,  1][t] + kpon\*K[2, 1][t]\*S[2, -1, 1][t] +  k3\*S[2, 0, 1][t] + kpon\*K[3, 1][t]\*S[2, 1,  -1][t] - k5a\*S[2, 1, 1][t] - 3\*kpoff\*S[2,  1, 1][t] + k1\*S_RAFK[2, 1, 0][t] | +| S[2, 2, -1] | 0 | (S[2, 2, -1])'[t] == kpon\*K[1, 2][t]\*S[-1, 2,  -1][t] + k9a\*S[1, 2, -1][t] + kpon\*K[2,  2][t]\*S[2, -1, -1][t] - 2\*kpoff\*S[2, 2, -1][ t] - kon\*K[3, 0][t]\*S[2, 2, -1][t] - kpon\*K[ 3, 1][t]\*S[2, 2, -1][t] + koff\*S[2, 2, 0][t]  + kpoff\*S[2, 2, 1][t] | +| S[2, 2, 0] | 0 | (S[2, 2, 0])'[t] == kpon\*K[1, 2][t]\*S[-1, 2,  0][t] + k9a\*S[1, 2, 0][t] + kpon\*K[2,  2][t]\*S[2, -1, 0][t] + kon\*K[3, 0][t]\*S[2,  2, -1][t] - koff\*S[2, 2, 0][t] - 2\* kpoff\*S[2, 2, 0][t] - k1a\*RAFK[t]\*S[2, 2, 0][t]  + d1a\*S_RAFK[2, 2, 0][t] | +| S[2, 2, 1] | 0 | (S[2, 2, 1])'[t] == kpon\*K[1, 2][t]\*S[-1, 2,  1][t] + k9a\*S[1, 2, 1][t] + kpon\*K[2,  2][t]\*S[2, -1, 1][t] + k5a\*S[2, 1, 1][t]  + kpon\*K[3, 1][t]\*S[2, 2, -1][t] - 3\*kpoff\* S[2, 2, 1][t] + k1\*S_RAFK[2, 2, 0][t] | +| S_RAFK[-1, -1, 0] | 0 | (S_RAFK[-1, -1, 0])'[t] == k1a\*RAFK[t]\*S[-1, -1,  0][t] - d1a\*S_RAFK[-1, -1, 0][t] - k1\* S_RAFK[-1, -1, 0][t] | +| S_RAFK[-1, 0, 0] | 0 | (S_RAFK[-1, 0, 0])'[t] == k1a\*RAFK[t]\*S[-1, 0,  0][t] - d1a\*S_RAFK[-1, 0, 0][t] - k1\*S_RAFK[ -1, 0, 0][t] | +| S_RAFK[-1, 1, 0] | 0 | (S_RAFK[-1, 1, 0])'[t] == k1a\*RAFK[t]\*S[-1, 1,  0][t] - d1a\*S_RAFK[-1, 1, 0][t] - k1\*S_RAFK[ -1, 1, 0][t] | +| S_RAFK[-1, 2, 0] | 0 | (S_RAFK[-1, 2, 0])'[t] == k1a\*RAFK[t]\*S[-1, 2,  0][t] - d1a\*S_RAFK[-1, 2, 0][t] - k1\*S_RAFK[ -1, 2, 0][t] | +| S_RAFK[0, -1, 0] | 0 | (S_RAFK[0, -1, 0])'[t] == k1a\*RAFK[t]\*S[0, -1,  0][t] - d1a\*S_RAFK[0, -1, 0][t] - k1\*S_RAFK[ 0, -1, 0][t] | +| S_RAFK[0, 0, 0] | 0 | (S_RAFK[0, 0, 0])'[t] == k1a\*RAFK[t]\*S[0, 0,  0][t] - d1a\*S_RAFK[0, 0, 0][t] - k1\*S_RAFK[ 0, 0, 0][t] | +| S_RAFK[0, 1, 0] | 0 | (S_RAFK[0, 1, 0])'[t] == k1a\*RAFK[t]\*S[0, 1,  0][t] - d1a\*S_RAFK[0, 1, 0][t] - k1\*S_RAFK[ 0, 1, 0][t] | +| S_RAFK[0, 2, 0] | 0 | (S_RAFK[0, 2, 0])'[t] == k1a\*RAFK[t]\*S[0, 2,  0][t] - d1a\*S_RAFK[0, 2, 0][t] - k1\*S_RAFK[ 0, 2, 0][t] | +| S_RAFK[1, -1, 0] | 0 | (S_RAFK[1, -1, 0])'[t] == k1a\*RAFK[t]\*S[1, -1,  0][t] - d1a\*S_RAFK[1, -1, 0][t] - k1\*S_RAFK[ 1, -1, 0][t] | +| S_RAFK[1, 0, 0] | 0 | (S_RAFK[1, 0, 0])'[t] == k1a\*RAFK[t]\*S[1, 0,  0][t] - d1a\*S_RAFK[1, 0, 0][t] - k1\*S_RAFK[ 1, 0, 0][t] | +| S_RAFK[1, 1, 0] | 0 | (S_RAFK[1, 1, 0])'[t] == k1a\*RAFK[t]\*S[1, 1,  0][t] - d1a\*S_RAFK[1, 1, 0][t] - k1\*S_RAFK[ 1, 1, 0][t] | +| S_RAFK[1, 2, 0] | 0 | (S_RAFK[1, 2, 0])'[t] == k1a\*RAFK[t]\*S[1, 2,  0][t] - d1a\*S_RAFK[1, 2, 0][t] - k1\*S_RAFK[ 1, 2, 0][t] | +| S_RAFK[2, -1, 0] | 0 | (S_RAFK[2, -1, 0])'[t] == k1a\*RAFK[t]\*S[2, -1,  0][t] - d1a\*S_RAFK[2, -1, 0][t] - k1\*S_RAFK[ 2, -1, 0][t] | +| S_RAFK[2, 0, 0] | 0 | (S_RAFK[2, 0, 0])'[t] == k1a\*RAFK[t]\*S[2, 0,  0][t] - d1a\*S_RAFK[2, 0, 0][t] - k1\*S_RAFK[ 2, 0, 0][t] | +| S_RAFK[2, 1, 0] | 0 | (S_RAFK[2, 1, 0])'[t] == k1a\*RAFK[t]\*S[2, 1,  0][t] - d1a\*S_RAFK[2, 1, 0][t] - k1\*S_RAFK[ 2, 1, 0][t] | +| S_RAFK[2, 2, 0] | 0 | (S_RAFK[2, 2, 0])'[t] == k1a\*RAFK[t]\*S[2, 2,  0][t] - d1a\*S_RAFK[2, 2, 0][t] - k1\*S_RAFK[ 2, 2, 0][t] | -| | -||---------------------|--------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| :- | :- | :- | -| | -| | MAPKP | 0.3 | MAPKP'[t] == -(a8\*MAPKP[t]\*K[1, 1][t]) - a10\*MAPKP[ t]\*K[1, 2][t] + d8\*K_MAPKP[1, 1][t] + k8\*K_MAPKP[ 1, 1][t] + d10\*K_MAPKP[1, 2][t] + k10\*K_MAPKP[1,  2][t] | | -| | MEKP | 0.2 | MEKP'[t] == -(a4\*MEKP[t]\*K[2, 1][t]) - a6\*MEKP[t]\* K[2, 2][t] + d4\*K_MEKP[2, 1][t] + k4\*K_MEKP[2,  1][t] + d6\*K_MEKP[2, 2][t] + k6\*K_MEKP[2, 2] [t] | | -| | RAFK | 0.1 | RAFK'[t] == -(a1\*RAFK[t]\*K[3, 0][t]) + d1\*K_RAFK[3,  0][t] + k1\*K_RAFK[3, 0][t] - k1a\*RAFK[t]\*S[-1,  -1, 0][t] - k1a\*RAFK[t]\*S[-1, 0, 0][t] -  k1a\*RAFK[t]\*S[-1, 1, 0][t] - k1a\*RAFK[t]\*S[-1, 2,  0][t] - k1a\*RAFK[t]\*S[0, -1, 0][t] - k1a\* RAFK[t]\*S[0, 0, 0][t] - k1a\*RAFK[t]\*S[0, 1, 0][t]  - k1a\*RAFK[t]\*S[0, 2, 0][t] - k1a\*RAFK[t]\*S[1,  -1, 0][t] - k1a\*RAFK[t]\*S[1, 0, 0][t] -  k1a\*RAFK[t]\*S[1, 1, 0][t] - k1a\*RAFK[t]\*S[1, 2,  0][t] - k1a\*RAFK[t]\*S[2, -1, 0][t] - k1a\* RAFK[t]\*S[2, 0, 0][t] - k1a\*RAFK[t]\*S[2, 1, 0][t]  - k1a\*RAFK[t]\*S[2, 2, 0][t] + d1a\*S_RAFK[-1,  -1, 0][t] + k1\*S_RAFK[-1, -1, 0][t] +  d1a\*S_RAFK[-1, 0, 0][t] + k1\*S_RAFK[-1, 0,  0][t] + d1a\*S_RAFK[-1, 1, 0][t] + k1\*S_RAFK[ -1, 1, 0][t] + d1a\*S_RAFK[-1, 2, 0][t] +  k1\*S_RAFK[-1, 2, 0][t] + d1a\*S_RAFK[0, -1,  0][t] + k1\*S_RAFK[0, -1, 0][t] + d1a\*S_RAFK[ 0, 0, 0][t] + k1\*S_RAFK[0, 0, 0][t] +  d1a\*S_RAFK[0, 1, 0][t] + k1\*S_RAFK[0, 1, 0][ t] + d1a\*S_RAFK[0, 2, 0][t] + k1\*S_RAFK[0, 2,  0][t] + d1a\*S_RAFK[1, -1, 0][t] + k1\*S_RAFK[ 1, -1, 0][t] + d1a\*S_RAFK[1, 0, 0][t] +  k1\*S_RAFK[1, 0, 0][t] + d1a\*S_RAFK[1, 1, 0][ t] + k1\*S_RAFK[1, 1, 0][t] + d1a\*S_RAFK[1, 2,  0][t] + k1\*S_RAFK[1, 2, 0][t] + d1a\*S_RAFK[ 2, -1, 0][t] + k1\*S_RAFK[2, -1, 0][t] +  d1a\*S_RAFK[2, 0, 0][t] + k1\*S_RAFK[2, 0, 0][ t] + d1a\*S_RAFK[2, 1, 0][t] + k1\*S_RAFK[2, 1,  0][t] + d1a\*S_RAFK[2, 2, 0][t] + k1\*S_RAFK[ 2, 2, 0][t] | | -| | RAFP | 0.3 | RAFP'[t] == -(a2\*RAFP[t]\*K[3, 1][t]) + d2\*K_RAFP[3,  1][t] + k2\*K_RAFP[3, 1][t] | | -| | K[1, 0] | 0.4 | (K[1, 0])'[t] == -(a7\*K[1, 0][t]\*K[2, 2][t]) +  d7\*K_K[1, 0, 2, 2][t] + k8\*K_MAPKP[1, 1][t]  - kon\*K[1, 0][t]\*S[-1, -1, -1][t] - kon\*K[1,  0][t]\*S[-1, -1, 0][t] - kon\*K[1, 0][t]\*S[-1,  -1, 1][t] - kon\*K[1, 0][t]\*S[-1, 0, -1][t]  - kon\*K[1, 0][t]\*S[-1, 0, 0][t] - kon\*K[1,  0][t]\*S[-1, 0, 1][t] - kon\*K[1, 0][t]\*S[-1,  1, -1][t] - kon\*K[1, 0][t]\*S[-1, 1, 0][t]  - kon\*K[1, 0][t]\*S[-1, 1, 1][t] - kon\*K[1,  0][t]\*S[-1, 2, -1][t] - kon\*K[1, 0][t]\*S[-1,  2, 0][t] - kon\*K[1, 0][t]\*S[-1, 2, 1][t]  + koff\*S[0, -1, -1][t] + koff\*S[0, -1,  0][t] + koff\*S[0, -1, 1][t] + koff\*S[0,  0, -1][t] + koff\*S[0, 0, 0][t] + koff\* S[0, 0, 1][t] + koff\*S[0, 1, -1][t] +  koff\*S[0, 1, 0][t] + koff\*S[0, 1, 1][t]  + koff\*S[0, 2, -1][t] + koff\*S[0, 2, 0] [t] + koff\*S[0, 2, 1][t] | | -| | K[1, 1] | 0 | (K[1, 1])'[t] == -(a8\*MAPKP[t]\*K[1, 1][t]) -  a9\*K[1, 1][t]\*K[2, 2][t] + k7\*K_K[1, 0, 2,  2][t] + d9\*K_K[1, 1, 2, 2][t] + d8\* K_MAPKP[1, 1][t] + k10\*K_MAPKP[1, 2][t] - kpon\*K[ 1, 1][t]\*S[-1, -1, -1][t] - kpon\*K[1, 1][t]\*S[-1,  -1, 0][t] - kpon\*K[1, 1][t]\*S[-1, -1, 1][t]  - kpon\*K[1, 1][t]\*S[-1, 0, -1][t] - kpon\*K[ 1, 1][t]\*S[-1, 0, 0][t] - kpon\*K[1, 1][t]\*S[-1,  0, 1][t] - kpon\*K[1, 1][t]\*S[-1, 1, -1][t]  - kpon\*K[1, 1][t]\*S[-1, 1, 0][t] - kpon\*K[1,  1][t]\*S[-1, 1, 1][t] - kpon\*K[1, 1][t]\*S[-1,  2, -1][t] - kpon\*K[1, 1][t]\*S[-1, 2, 0][t]  - kpon\*K[1, 1][t]\*S[-1, 2, 1][t] + kpoff\*S[ 1, -1, -1][t] + kpoff\*S[1, -1, 0][t] +  kpoff\*S[1, -1, 1][t] + kpoff\*S[1, 0, -1][t]  + kpoff\*S[1, 0, 0][t] + kpoff\*S[1, 0,  1][t] + kpoff\*S[1, 1, -1][t] + kpoff\*S[1,  1, 0][t] + kpoff\*S[1, 1, 1][t] + kpoff\* S[1, 2, -1][t] + kpoff\*S[1, 2, 0][t] +  kpoff\*S[1, 2, 1][t] | | -| | K[1, 2] | 0 | (K[1, 2])'[t] == -(a10\*MAPKP[t]\*K[1, 2][t]) +  k9\*K_K[1, 1, 2, 2][t] + d10\*K_MAPKP[1, 2][t]  - kpon\*K[1, 2][t]\*S[-1, -1, -1][t] - kpon\*K[ 1, 2][t]\*S[-1, -1, 0][t] - kpon\*K[1, 2][t]\*S[-1,  -1, 1][t] - kpon\*K[1, 2][t]\*S[-1, 0, -1][t]  - kpon\*K[1, 2][t]\*S[-1, 0, 0][t] - kpon\*K[1,  2][t]\*S[-1, 0, 1][t] - kpon\*K[1, 2][t]\*S[-1,  1, -1][t] - kpon\*K[1, 2][t]\*S[-1, 1, 0][t]  - kpon\*K[1, 2][t]\*S[-1, 1, 1][t] - kpon\*K[1,  2][t]\*S[-1, 2, -1][t] - kpon\*K[1, 2][t]\*S[-1,  2, 0][t] - kpon\*K[1, 2][t]\*S[-1, 2, 1][t]  + kpoff\*S[2, -1, -1][t] + kpoff\*S[2, -1,  0][t] + kpoff\*S[2, -1, 1][t] + kpoff\*S[2,  0, -1][t] + kpoff\*S[2, 0, 0][t] +  kpoff\*S[2, 0, 1][t] + kpoff\*S[2, 1, -1][t]  + kpoff\*S[2, 1, 0][t] + kpoff\*S[2, 1,  1][t] + kpoff\*S[2, 2, -1][t] + kpoff\*S[2,  2, 0][t] + kpoff\*S[2, 2, 1][t] | | -| | K[2, 0] | 0.2 | (K[2, 0])'[t] == -(a3\*K[2, 0][t]\*K[3, 1][t]) +  d3\*K_K[2, 0, 3, 1][t] + k4\*K_MEKP[2, 1][t]  - kon\*K[2, 0][t]\*S[-1, -1, -1][t] - kon\*K[2,  0][t]\*S[-1, -1, 0][t] - kon\*K[2, 0][t]\*S[-1,  -1, 1][t] + koff\*S[-1, 0, -1][t] +  koff\*S[-1, 0, 0][t] + koff\*S[-1, 0, 1][t]  - kon\*K[2, 0][t]\*S[0, -1, -1][t] - kon\*K[2,  0][t]\*S[0, -1, 0][t] - kon\*K[2, 0][t]\*S[0, - 1, 1][t] + koff\*S[0, 0, -1][t] + koff\*S[0,  0, 0][t] + koff\*S[0, 0, 1][t] - kon\*K[ 2, 0][t]\*S[1, -1, -1][t] - kon\*K[2, 0][t]\*S[1,  -1, 0][t] - kon\*K[2, 0][t]\*S[1, -1, 1][t]  + koff\*S[1, 0, -1][t] + koff\*S[1, 0, 0] [t] + koff\*S[1, 0, 1][t] - kon\*K[2, 0][t]\*S[ 2, -1, -1][t] - kon\*K[2, 0][t]\*S[2, -1, 0][t]  - kon\*K[2, 0][t]\*S[2, -1, 1][t] + koff\*S[2,  0, -1][t] + koff\*S[2, 0, 0][t] + koff\* S[2, 0, 1][t] | | -| | K[2, 1] | 0 | (K[2, 1])'[t] == -(a4\*MEKP[t]\*K[2, 1][t]) -  a5\*K[2, 1][t]\*K[3, 1][t] + k3\*K_K[2, 0, 3,  1][t] + d5\*K_K[2, 1, 3, 1][t] + d4\* K_MEKP[2, 1][t] + k6\*K_MEKP[2, 2][t] - kpon\*K[2,  1][t]\*S[-1, -1, -1][t] - kpon\*K[2, 1][t]\*S[-1,  -1, 0][t] - kpon\*K[2, 1][t]\*S[-1, -1, 1][t]  + kpoff\*S[-1, 1, -1][t] + kpoff\*S[-1, 1,  0][t] + kpoff\*S[-1, 1, 1][t] - kpon\*K[2,  1][t]\*S[0, -1, -1][t] - kpon\*K[2, 1][t]\*S[0,  -1, 0][t] - kpon\*K[2, 1][t]\*S[0, -1, 1][t]  + kpoff\*S[0, 1, -1][t] + kpoff\*S[0, 1,  0][t] + kpoff\*S[0, 1, 1][t] - kpon\*K[2,  1][t]\*S[1, -1, -1][t] - kpon\*K[2, 1][t]\*S[1,  -1, 0][t] - kpon\*K[2, 1][t]\*S[1, -1, 1][t]  + kpoff\*S[1, 1, -1][t] + kpoff\*S[1, 1,  0][t] + kpoff\*S[1, 1, 1][t] - kpon\*K[2,  1][t]\*S[2, -1, -1][t] - kpon\*K[2, 1][t]\*S[2,  -1, 0][t] - kpon\*K[2, 1][t]\*S[2, -1, 1][t]  + kpoff\*S[2, 1, -1][t] + kpoff\*S[2, 1,  0][t] + kpoff\*S[2, 1, 1][t] | | -| | K[2, 2] | 0 | (K[2, 2])'[t] == -(a6\*MEKP[t]\*K[2, 2][t]) -  a7\*K[1, 0][t]\*K[2, 2][t] - a9\*K[1, 1][t]\*K[2,  2][t] + d7\*K_K[1, 0, 2, 2][t] + k7\*K_K[ 1, 0, 2, 2][t] + d9\*K_K[1, 1, 2, 2][t]  + k9\*K_K[1, 1, 2, 2][t] + k5\*K_K[2, 1,  3, 1][t] + d6\*K_MEKP[2, 2][t] - kpon\*K[2,  2][t]\*S[-1, -1, -1][t] - kpon\*K[2, 2][t]\*S[-1,  -1, 0][t] - kpon\*K[2, 2][t]\*S[-1, -1, 1][t]  + kpoff\*S[-1, 2, -1][t] + kpoff\*S[-1, 2,  0][t] + kpoff\*S[-1, 2, 1][t] - kpon\*K[2,  2][t]\*S[0, -1, -1][t] - kpon\*K[2, 2][t]\*S[0,  -1, 0][t] - kpon\*K[2, 2][t]\*S[0, -1, 1][t]  + kpoff\*S[0, 2, -1][t] + kpoff\*S[0, 2,  0][t] + kpoff\*S[0, 2, 1][t] - kpon\*K[2,  2][t]\*S[1, -1, -1][t] - kpon\*K[2, 2][t]\*S[1,  -1, 0][t] - kpon\*K[2, 2][t]\*S[1, -1, 1][t]  + kpoff\*S[1, 2, -1][t] + kpoff\*S[1, 2,  0][t] + kpoff\*S[1, 2, 1][t] - kpon\*K[2,  2][t]\*S[2, -1, -1][t] - kpon\*K[2, 2][t]\*S[2,  -1, 0][t] - kpon\*K[2, 2][t]\*S[2, -1, 1][t]  + kpoff\*S[2, 2, -1][t] + kpoff\*S[2, 2,  0][t] + kpoff\*S[2, 2, 1][t] | | -| | K[3, 0] | 0.3 | (K[3, 0])'[t] == -(a1\*RAFK[t]\*K[3, 0][t]) +  d1\*K_RAFK[3, 0][t] + k2\*K_RAFP[3, 1][t] -  kon\*K[3, 0][t]\*S[-1, -1, -1][t] + koff\*S[-1,  -1, 0][t] - kon\*K[3, 0][t]\*S[-1, 0, -1][t]  + koff\*S[-1, 0, 0][t] - kon\*K[3, 0][t]\*S[-1,  1, -1][t] + koff\*S[-1, 1, 0][t] - kon\* K[3, 0][t]\*S[-1, 2, -1][t] + koff\*S[-1, 2, 0] [t] - kon\*K[3, 0][t]\*S[0, -1, -1][t] + koff\* S[0, -1, 0][t] - kon\*K[3, 0][t]\*S[0, 0, -1][ t] + koff\*S[0, 0, 0][t] - kon\*K[3, 0][t]\*S[0,  1, -1][t] + koff\*S[0, 1, 0][t] - kon\*K[ 3, 0][t]\*S[0, 2, -1][t] + koff\*S[0, 2, 0][t]  - kon\*K[3, 0][t]\*S[1, -1, -1][t] + koff\*S[1,  -1, 0][t] - kon\*K[3, 0][t]\*S[1, 0, -1][t]  + koff\*S[1, 0, 0][t] - kon\*K[3, 0][t]\*S[1,  1, -1][t] + koff\*S[1, 1, 0][t] - kon\*K[ 3, 0][t]\*S[1, 2, -1][t] + koff\*S[1, 2, 0][t]  - kon\*K[3, 0][t]\*S[2, -1, -1][t] + koff\*S[2,  -1, 0][t] - kon\*K[3, 0][t]\*S[2, 0, -1][t]  + koff\*S[2, 0, 0][t] - kon\*K[3, 0][t]\*S[2,  1, -1][t] + koff\*S[2, 1, 0][t] - kon\*K[ 3, 0][t]\*S[2, 2, -1][t] + koff\*S[2, 2, 0][t] | | -| | K[3, 1] | 0 | (K[3, 1])'[t] == -(a2\*RAFP[t]\*K[3, 1][t]) -  a3\*K[2, 0][t]\*K[3, 1][t] - a5\*K[2, 1][t]\*K[3,  1][t] + d3\*K_K[2, 0, 3, 1][t] + k3\*K_K[ 2, 0, 3, 1][t] + d5\*K_K[2, 1, 3, 1][t]  + k5\*K_K[2, 1, 3, 1][t] + k1\*K_RAFK[3,  0][t] + d2\*K_RAFP[3, 1][t] - kpon\*K[3, 1][t] \*S[-1, -1, -1][t] + kpoff\*S[-1, -1, 1][t] -  kpon\*K[3, 1][t]\*S[-1, 0, -1][t] + kpoff\*S[-1,  0, 1][t] - kpon\*K[3, 1][t]\*S[-1, 1, -1][t]  + kpoff\*S[-1, 1, 1][t] - kpon\*K[3, 1][t]\*S[- 1, 2, -1][t] + kpoff\*S[-1, 2, 1][t] -  kpon\*K[3, 1][t]\*S[0, -1, -1][t] + kpoff\*S[0,  -1, 1][t] - kpon\*K[3, 1][t]\*S[0, 0, -1][t]  + kpoff\*S[0, 0, 1][t] - kpon\*K[3, 1][t]\*S[0,  1, -1][t] + kpoff\*S[0, 1, 1][t] - kpon\* K[3, 1][t]\*S[0, 2, -1][t] + kpoff\*S[0, 2, 1][ t] - kpon\*K[3, 1][t]\*S[1, -1, -1][t] + kpoff\* S[1, -1, 1][t] - kpon\*K[3, 1][t]\*S[1, 0, -1][ t] + kpoff\*S[1, 0, 1][t] - kpon\*K[3, 1][t]\*S[ 1, 1, -1][t] + kpoff\*S[1, 1, 1][t] -  kpon\*K[3, 1][t]\*S[1, 2, -1][t] + kpoff\*S[1,  2, 1][t] - kpon\*K[3, 1][t]\*S[2, -1, -1][t]  + kpoff\*S[2, -1, 1][t] - kpon\*K[3, 1][t]\*S[ 2, 0, -1][t] + kpoff\*S[2, 0, 1][t] -  kpon\*K[3, 1][t]\*S[2, 1, -1][t] + kpoff\*S[2,  1, 1][t] - kpon\*K[3, 1][t]\*S[2, 2, -1][t]  + kpoff\*S[2, 2, 1][t] | | -| | K_K[1, 0, 2, 2] | 0 | (K_K[1, 0, 2, 2])'[t] == a7\*K[1, 0][t]\*K[2,  2][t] - d7\*K_K[1, 0, 2, 2][t] - k7\*K_K[ 1, 0, 2, 2][t] | | -| | K_K[1, 1, 2, 2] | 0 | (K_K[1, 1, 2, 2])'[t] == a9\*K[1, 1][t]\*K[2,  2][t] - d9\*K_K[1, 1, 2, 2][t] - k9\*K_K[ 1, 1, 2, 2][t] | | -| | K_K[2, 0, 3, 1] | 0 | (K_K[2, 0, 3, 1])'[t] == a3\*K[2, 0][t]\*K[3,  1][t] - d3\*K_K[2, 0, 3, 1][t] - k3\*K_K[ 2, 0, 3, 1][t] | | -| | K_K[2, 1, 3, 1] | 0 | (K_K[2, 1, 3, 1])'[t] == a5\*K[2, 1][t]\*K[3,  1][t] - d5\*K_K[2, 1, 3, 1][t] - k5\*K_K[ 2, 1, 3, 1][t] | | -| | K_MAPKP[1, 1] | 0 | (K_MAPKP[1, 1])'[t] == a8\*MAPKP[t]\*K[1, 1][t] -  d8\*K_MAPKP[1, 1][t] - k8\*K_MAPKP[1, 1][t] | | -| | K_MAPKP[1, 2] | 0 | (K_MAPKP[1, 2])'[t] == a10\*MAPKP[t]\*K[1, 2][t] -  d10\*K_MAPKP[1, 2][t] - k10\*K_MAPKP[1, 2][t] | | -| | K_MEKP[2, 1] | 0 | (K_MEKP[2, 1])'[t] == a4\*MEKP[t]\*K[2, 1][t] -  d4\*K_MEKP[2, 1][t] - k4\*K_MEKP[2, 1][t] | | -| | K_MEKP[2, 2] | 0 | (K_MEKP[2, 2])'[t] == a6\*MEKP[t]\*K[2, 2][t] -  d6\*K_MEKP[2, 2][t] - k6\*K_MEKP[2, 2][t] | | -| | K_RAFK[3, 0] | 0 | (K_RAFK[3, 0])'[t] == a1\*RAFK[t]\*K[3, 0][t] -  d1\*K_RAFK[3, 0][t] - k1\*K_RAFK[3, 0][t] | | -| | K_RAFP[3, 1] | 0 | (K_RAFP[3, 1])'[t] == a2\*RAFP[t]\*K[3, 1][t] -  d2\*K_RAFP[3, 1][t] - k2\*K_RAFP[3, 1][t] | | -| | S[-1, -1, -1] | 0.1 | (S[-1, -1, -1])'[t] == -(kon\*K[1, 0][t]\*S[-1,  -1, -1][t]) - kpon\*K[1, 1][t]\*S[-1, -1, -1][ t] - kpon\*K[1, 2][t]\*S[-1, -1, -1][t] - kon\* K[2, 0][t]\*S[-1, -1, -1][t] - kpon\*K[2, 1][t]\*S[- 1, -1, -1][t] - kpon\*K[2, 2][t]\*S[-1, -1, -1] [t] - kon\*K[3, 0][t]\*S[-1, -1, -1][t] - kpon\* K[3, 1][t]\*S[-1, -1, -1][t] + koff\*S[-1, -1,  0][t] + kpoff\*S[-1, -1, 1][t] + koff\*S[-1,  0, -1][t] + kpoff\*S[-1, 1, -1][t] +  kpoff\*S[-1, 2, -1][t] + koff\*S[0, -1, -1][t]  + kpoff\*S[1, -1, -1][t] + kpoff\*S[2, -1,  -1][t] | | -| | S[-1, -1, 0] | 0 | (S[-1, -1, 0])'[t] == kon\*K[3, 0][t]\*S[-1, -1,  -1][t] - koff\*S[-1, -1, 0][t] - k1a\*RAFK[t]\* S[-1, -1, 0][t] - kon\*K[1, 0][t]\*S[-1, -1, 0] [t] - kpon\*K[1, 1][t]\*S[-1, -1, 0][t] - kpon\* K[1, 2][t]\*S[-1, -1, 0][t] - kon\*K[2, 0][t]\*S[-1,  -1, 0][t] - kpon\*K[2, 1][t]\*S[-1, -1, 0][t]  - kpon\*K[2, 2][t]\*S[-1, -1, 0][t] + koff\*S[- 1, 0, 0][t] + kpoff\*S[-1, 1, 0][t] +  kpoff\*S[-1, 2, 0][t] + koff\*S[0, -1, 0][t]  + kpoff\*S[1, -1, 0][t] + kpoff\*S[2, -1,  0][t] + d1a\*S_RAFK[-1, -1, 0][t] | | -| | S[-1, -1, 1] | 0 | (S[-1, -1, 1])'[t] == kpon\*K[3, 1][t]\*S[-1, - 1, -1][t] - kpoff\*S[-1, -1, 1][t] - kon\*K[1,  0][t]\*S[-1, -1, 1][t] - kpon\*K[1, 1][t]\*S[-1,  -1, 1][t] - kpon\*K[1, 2][t]\*S[-1, -1, 1][t]  - kon\*K[2, 0][t]\*S[-1, -1, 1][t] - kpon\*K[2,  1][t]\*S[-1, -1, 1][t] - kpon\*K[2, 2][t]\*S[-1,  -1, 1][t] + koff\*S[-1, 0, 1][t] +  kpoff\*S[-1, 1, 1][t] + kpoff\*S[-1, 2, 1][t]  + koff\*S[0, -1, 1][t] + kpoff\*S[1, -1,  1][t] + kpoff\*S[2, -1, 1][t] + k1\*S_RAFK[-1,  -1, 0][t] | | -| | S[-1, 0, -1] | 0 | (S[-1, 0, -1])'[t] == kon\*K[2, 0][t]\*S[-1, -1,  -1][t] - koff\*S[-1, 0, -1][t] - kon\*K[1,  0][t]\*S[-1, 0, -1][t] - kpon\*K[1, 1][t]\*S[-1,  0, -1][t] - kpon\*K[1, 2][t]\*S[-1, 0, -1][t]  - kon\*K[3, 0][t]\*S[-1, 0, -1][t] - kpon\*K[3,  1][t]\*S[-1, 0, -1][t] + koff\*S[-1, 0, 0][t]  + kpoff\*S[-1, 0, 1][t] + koff\*S[0, 0, - 1][t] + kpoff\*S[1, 0, -1][t] + kpoff\*S[2, 0,  -1][t] | | -| | S[-1, 0, 0] | 0 | (S[-1, 0, 0])'[t] == kon\*K[2, 0][t]\*S[-1, -1,  0][t] + kon\*K[3, 0][t]\*S[-1, 0, -1][t] -  2\*koff\*S[-1, 0, 0][t] - k1a\*RAFK[t]\*S[-1, 0,  0][t] - kon\*K[1, 0][t]\*S[-1, 0, 0][t] -  kpon\*K[1, 1][t]\*S[-1, 0, 0][t] - kpon\*K[1,  2][t]\*S[-1, 0, 0][t] + koff\*S[0, 0, 0][t]  + kpoff\*S[1, 0, 0][t] + kpoff\*S[2, 0,  0][t] + d1a\*S_RAFK[-1, 0, 0][t] | | -| | S[-1, 0, 1] | 0 | (S[-1, 0, 1])'[t] == kon\*K[2, 0][t]\*S[-1, -1,  1][t] + kpon\*K[3, 1][t]\*S[-1, 0, -1][t] -  k3\*S[-1, 0, 1][t] - koff\*S[-1, 0, 1][t]  - kpoff\*S[-1, 0, 1][t] - kon\*K[1, 0][t]\*S[- 1, 0, 1][t] - kpon\*K[1, 1][t]\*S[-1, 0, 1][t]  - kpon\*K[1, 2][t]\*S[-1, 0, 1][t] + koff\*S[0,  0, 1][t] + kpoff\*S[1, 0, 1][t] + kpoff\* S[2, 0, 1][t] + k1\*S_RAFK[-1, 0, 0][t] | | -| | S[-1, 1, -1] | 0 | (S[-1, 1, -1])'[t] == kpon\*K[2, 1][t]\*S[-1, - 1, -1][t] - kpoff\*S[-1, 1, -1][t] - kon\*K[1,  0][t]\*S[-1, 1, -1][t] - kpon\*K[1, 1][t]\*S[-1,  1, -1][t] - kpon\*K[1, 2][t]\*S[-1, 1, -1][t]  - kon\*K[3, 0][t]\*S[-1, 1, -1][t] - kpon\*K[3,  1][t]\*S[-1, 1, -1][t] + koff\*S[-1, 1, 0][t]  + kpoff\*S[-1, 1, 1][t] + koff\*S[0, 1, - 1][t] + kpoff\*S[1, 1, -1][t] + kpoff\*S[2, 1,  -1][t] | | -| | S[-1, 1, 0] | 0 | (S[-1, 1, 0])'[t] == kpon\*K[2, 1][t]\*S[-1, -1,  0][t] + kon\*K[3, 0][t]\*S[-1, 1, -1][t] -  koff\*S[-1, 1, 0][t] - kpoff\*S[-1, 1, 0][t]  - k1a\*RAFK[t]\*S[-1, 1, 0][t] - kon\*K[1, 0][ t]\*S[-1, 1, 0][t] - kpon\*K[1, 1][t]\*S[-1, 1,  0][t] - kpon\*K[1, 2][t]\*S[-1, 1, 0][t] +  koff\*S[0, 1, 0][t] + kpoff\*S[1, 1, 0][t]  + kpoff\*S[2, 1, 0][t] + d1a\*S_RAFK[-1, 1,  0][t] | | -| | S[-1, 1, 1] | 0 | (S[-1, 1, 1])'[t] == kpon\*K[2, 1][t]\*S[-1, -1,  1][t] + k3\*S[-1, 0, 1][t] + kpon\*K[3,  1][t]\*S[-1, 1, -1][t] - k5a\*S[-1, 1, 1][t]  - 2\*kpoff\*S[-1, 1, 1][t] - kon\*K[1, 0][t]\*S[ -1, 1, 1][t] - kpon\*K[1, 1][t]\*S[-1, 1, 1][t]  - kpon\*K[1, 2][t]\*S[-1, 1, 1][t] + koff\*S[0,  1, 1][t] + kpoff\*S[1, 1, 1][t] + kpoff\* S[2, 1, 1][t] + k1\*S_RAFK[-1, 1, 0][t] | | -| | S[-1, 2, -1] | 0 | (S[-1, 2, -1])'[t] == kpon\*K[2, 2][t]\*S[-1, - 1, -1][t] - kpoff\*S[-1, 2, -1][t] - kon\*K[1,  0][t]\*S[-1, 2, -1][t] - kpon\*K[1, 1][t]\*S[-1,  2, -1][t] - kpon\*K[1, 2][t]\*S[-1, 2, -1][t]  - kon\*K[3, 0][t]\*S[-1, 2, -1][t] - kpon\*K[3,  1][t]\*S[-1, 2, -1][t] + koff\*S[-1, 2, 0][t]  + kpoff\*S[-1, 2, 1][t] + koff\*S[0, 2, - 1][t] + kpoff\*S[1, 2, -1][t] + kpoff\*S[2, 2,  -1][t] | | -| | S[-1, 2, 0] | 0 | (S[-1, 2, 0])'[t] == kpon\*K[2, 2][t]\*S[-1, -1,  0][t] + kon\*K[3, 0][t]\*S[-1, 2, -1][t] -  koff\*S[-1, 2, 0][t] - kpoff\*S[-1, 2, 0][t]  - k1a\*RAFK[t]\*S[-1, 2, 0][t] - kon\*K[1, 0][ t]\*S[-1, 2, 0][t] - kpon\*K[1, 1][t]\*S[-1, 2,  0][t] - kpon\*K[1, 2][t]\*S[-1, 2, 0][t] +  koff\*S[0, 2, 0][t] + kpoff\*S[1, 2, 0][t]  + kpoff\*S[2, 2, 0][t] + d1a\*S_RAFK[-1, 2,  0][t] | | -| | S[-1, 2, 1] | 0 | (S[-1, 2, 1])'[t] == kpon\*K[2, 2][t]\*S[-1, -1,  1][t] + k5a\*S[-1, 1, 1][t] + kpon\*K[3,  1][t]\*S[-1, 2, -1][t] - 2\*kpoff\*S[-1, 2, 1][ t] - kon\*K[1, 0][t]\*S[-1, 2, 1][t] - kpon\*K[ 1, 1][t]\*S[-1, 2, 1][t] - kpon\*K[1, 2][t]\*S[-1,  2, 1][t] + koff\*S[0, 2, 1][t] + kpoff\* S[1, 2, 1][t] + kpoff\*S[2, 2, 1][t] +  k1\*S_RAFK[-1, 2, 0][t] | | -| | S[0, -1, -1] | 0 | (S[0, -1, -1])'[t] == kon\*K[1, 0][t]\*S[-1, -1,  -1][t] - koff\*S[0, -1, -1][t] - kon\*K[2,  0][t]\*S[0, -1, -1][t] - kpon\*K[2, 1][t]\*S[0,  -1, -1][t] - kpon\*K[2, 2][t]\*S[0, -1, -1][t]  - kon\*K[3, 0][t]\*S[0, -1, -1][t] - kpon\*K[3,  1][t]\*S[0, -1, -1][t] + koff\*S[0, -1, 0][t]  + kpoff\*S[0, -1, 1][t] + koff\*S[0, 0, - 1][t] + kpoff\*S[0, 1, -1][t] + kpoff\*S[0, 2,  -1][t] | | -| | S[0, -1, 0] | 0 | (S[0, -1, 0])'[t] == kon\*K[1, 0][t]\*S[-1, -1,  0][t] + kon\*K[3, 0][t]\*S[0, -1, -1][t] -  2\*koff\*S[0, -1, 0][t] - k1a\*RAFK[t]\*S[0, -1,  0][t] - kon\*K[2, 0][t]\*S[0, -1, 0][t] -  kpon\*K[2, 1][t]\*S[0, -1, 0][t] - kpon\*K[2,  2][t]\*S[0, -1, 0][t] + koff\*S[0, 0, 0][t]  + kpoff\*S[0, 1, 0][t] + kpoff\*S[0, 2,  0][t] + d1a\*S_RAFK[0, -1, 0][t] | | -| | S[0, -1, 1] | 0 | (S[0, -1, 1])'[t] == kon\*K[1, 0][t]\*S[-1, -1,  1][t] + kpon\*K[3, 1][t]\*S[0, -1, -1][t] -  koff\*S[0, -1, 1][t] - kpoff\*S[0, -1, 1][t]  - kon\*K[2, 0][t]\*S[0, -1, 1][t] - kpon\*K[2,  1][t]\*S[0, -1, 1][t] - kpon\*K[2, 2][t]\*S[0,  -1, 1][t] + koff\*S[0, 0, 1][t] + kpoff\* S[0, 1, 1][t] + kpoff\*S[0, 2, 1][t] +  k1\*S_RAFK[0, -1, 0][t] | | -| | S[0, 0, -1] | 0 | (S[0, 0, -1])'[t] == kon\*K[1, 0][t]\*S[-1, 0,  -1][t] + kon\*K[2, 0][t]\*S[0, -1, -1][t] -  2\*koff\*S[0, 0, -1][t] - kon\*K[3, 0][t]\*S[0,  0, -1][t] - kpon\*K[3, 1][t]\*S[0, 0, -1][t]  + koff\*S[0, 0, 0][t] + kpoff\*S[0, 0, 1] [t] | | -| | S[0, 0, 0] | 0 | (S[0, 0, 0])'[t] == kon\*K[1, 0][t]\*S[-1, 0,  0][t] + kon\*K[2, 0][t]\*S[0, -1, 0][t] +  kon\*K[3, 0][t]\*S[0, 0, -1][t] - 3\*koff\*S[0,  0, 0][t] - k1a\*RAFK[t]\*S[0, 0, 0][t] +  d1a\*S_RAFK[0, 0, 0][t] | | -| | S[0, 0, 1] | 0 | (S[0, 0, 1])'[t] == kon\*K[1, 0][t]\*S[-1, 0,  1][t] + kon\*K[2, 0][t]\*S[0, -1, 1][t] +  kpon\*K[3, 1][t]\*S[0, 0, -1][t] - k3\*S[0, 0,  1][t] - 2\*koff\*S[0, 0, 1][t] - kpoff\*S[0,  0, 1][t] + k1\*S_RAFK[0, 0, 0][t] | | -| | S[0, 1, -1] | 0 | (S[0, 1, -1])'[t] == kon\*K[1, 0][t]\*S[-1, 1,  -1][t] + kpon\*K[2, 1][t]\*S[0, -1, -1][t] -  koff\*S[0, 1, -1][t] - kpoff\*S[0, 1, -1][t]  - kon\*K[3, 0][t]\*S[0, 1, -1][t] - kpon\*K[3,  1][t]\*S[0, 1, -1][t] + koff\*S[0, 1, 0][t]  + kpoff\*S[0, 1, 1][t] | | -| | S[0, 1, 0] | 0 | (S[0, 1, 0])'[t] == kon\*K[1, 0][t]\*S[-1, 1,  0][t] + kpon\*K[2, 1][t]\*S[0, -1, 0][t] +  kon\*K[3, 0][t]\*S[0, 1, -1][t] - 2\*koff\*S[0,  1, 0][t] - kpoff\*S[0, 1, 0][t] - k1a\* RAFK[t]\*S[0, 1, 0][t] + d1a\*S_RAFK[0, 1, 0][t] | | -| | S[0, 1, 1] | 0 | (S[0, 1, 1])'[t] == kon\*K[1, 0][t]\*S[-1, 1,  1][t] + kpon\*K[2, 1][t]\*S[0, -1, 1][t] +  k3\*S[0, 0, 1][t] + kpon\*K[3, 1][t]\*S[0, 1,  -1][t] - k5a\*S[0, 1, 1][t] - koff\*S[0,  1, 1][t] - 2\*kpoff\*S[0, 1, 1][t] + k1\* S_RAFK[0, 1, 0][t] | | -| | S[0, 2, -1] | 0 | (S[0, 2, -1])'[t] == kon\*K[1, 0][t]\*S[-1, 2,  -1][t] + kpon\*K[2, 2][t]\*S[0, -1, -1][t] -  k7\*S[0, 2, -1][t] - koff\*S[0, 2, -1][t]  - kpoff\*S[0, 2, -1][t] - kon\*K[3, 0][t]\*S[0,  2, -1][t] - kpon\*K[3, 1][t]\*S[0, 2, -1][t]  + koff\*S[0, 2, 0][t] + kpoff\*S[0, 2, 1] [t] | | -| | S[0, 2, 0] | 0 | (S[0, 2, 0])'[t] == kon\*K[1, 0][t]\*S[-1, 2,  0][t] + kpon\*K[2, 2][t]\*S[0, -1, 0][t] +  kon\*K[3, 0][t]\*S[0, 2, -1][t] - k7\*S[0, 2,  0][t] - 2\*koff\*S[0, 2, 0][t] - kpoff\*S[0,  2, 0][t] - k1a\*RAFK[t]\*S[0, 2, 0][t] +  d1a\*S_RAFK[0, 2, 0][t] | | -| | S[0, 2, 1] | 0 | (S[0, 2, 1])'[t] == kon\*K[1, 0][t]\*S[-1, 2,  1][t] + kpon\*K[2, 2][t]\*S[0, -1, 1][t] +  k5a\*S[0, 1, 1][t] + kpon\*K[3, 1][t]\*S[0, 2,  -1][t] - k7\*S[0, 2, 1][t] - koff\*S[0,  2, 1][t] - 2\*kpoff\*S[0, 2, 1][t] + k1\* S_RAFK[0, 2, 0][t] | | -| | S[1, -1, -1] | 0 | (S[1, -1, -1])'[t] == kpon\*K[1, 1][t]\*S[-1, - 1, -1][t] - kpoff\*S[1, -1, -1][t] - kon\*K[2,  0][t]\*S[1, -1, -1][t] - kpon\*K[2, 1][t]\*S[1,  -1, -1][t] - kpon\*K[2, 2][t]\*S[1, -1, -1][t]  - kon\*K[3, 0][t]\*S[1, -1, -1][t] - kpon\*K[3,  1][t]\*S[1, -1, -1][t] + koff\*S[1, -1, 0][t]  + kpoff\*S[1, -1, 1][t] + koff\*S[1, 0, - 1][t] + kpoff\*S[1, 1, -1][t] + kpoff\*S[1, 2,  -1][t] | | -| | S[1, -1, 0] | 0 | (S[1, -1, 0])'[t] == kpon\*K[1, 1][t]\*S[-1, -1,  0][t] + kon\*K[3, 0][t]\*S[1, -1, -1][t] -  koff\*S[1, -1, 0][t] - kpoff\*S[1, -1, 0][t]  - k1a\*RAFK[t]\*S[1, -1, 0][t] - kon\*K[2, 0][ t]\*S[1, -1, 0][t] - kpon\*K[2, 1][t]\*S[1, -1,  0][t] - kpon\*K[2, 2][t]\*S[1, -1, 0][t] +  koff\*S[1, 0, 0][t] + kpoff\*S[1, 1, 0][t]  + kpoff\*S[1, 2, 0][t] + d1a\*S_RAFK[1, -1,  0][t] | | -| | S[1, -1, 1] | 0 | (S[1, -1, 1])'[t] == kpon\*K[1, 1][t]\*S[-1, -1,  1][t] + kpon\*K[3, 1][t]\*S[1, -1, -1][t] -  2\*kpoff\*S[1, -1, 1][t] - kon\*K[2, 0][t]\*S[1,  -1, 1][t] - kpon\*K[2, 1][t]\*S[1, -1, 1][t]  - kpon\*K[2, 2][t]\*S[1, -1, 1][t] + koff\*S[1,  0, 1][t] + kpoff\*S[1, 1, 1][t] + kpoff\* S[1, 2, 1][t] + k1\*S_RAFK[1, -1, 0][t] | | -| | S[1, 0, -1] | 0 | (S[1, 0, -1])'[t] == kpon\*K[1, 1][t]\*S[-1, 0,  -1][t] + kon\*K[2, 0][t]\*S[1, -1, -1][t] -  koff\*S[1, 0, -1][t] - kpoff\*S[1, 0, -1][t]  - kon\*K[3, 0][t]\*S[1, 0, -1][t] - kpon\*K[3,  1][t]\*S[1, 0, -1][t] + koff\*S[1, 0, 0][t]  + kpoff\*S[1, 0, 1][t] | | -| | S[1, 0, 0] | 0 | (S[1, 0, 0])'[t] == kpon\*K[1, 1][t]\*S[-1, 0,  0][t] + kon\*K[2, 0][t]\*S[1, -1, 0][t] +  kon\*K[3, 0][t]\*S[1, 0, -1][t] - 2\*koff\*S[1,  0, 0][t] - kpoff\*S[1, 0, 0][t] - k1a\* RAFK[t]\*S[1, 0, 0][t] + d1a\*S_RAFK[1, 0, 0][t] | | -| | S[1, 0, 1] | 0 | (S[1, 0, 1])'[t] == kpon\*K[1, 1][t]\*S[-1, 0,  1][t] + kon\*K[2, 0][t]\*S[1, -1, 1][t] +  kpon\*K[3, 1][t]\*S[1, 0, -1][t] - k3\*S[1, 0,  1][t] - koff\*S[1, 0, 1][t] - 2\*kpoff\*S[1,  0, 1][t] + k1\*S_RAFK[1, 0, 0][t] | | -| | S[1, 1, -1] | 0 | (S[1, 1, -1])'[t] == kpon\*K[1, 1][t]\*S[-1, 1,  -1][t] + kpon\*K[2, 1][t]\*S[1, -1, -1][t] -  2\*kpoff\*S[1, 1, -1][t] - kon\*K[3, 0][t]\*S[1,  1, -1][t] - kpon\*K[3, 1][t]\*S[1, 1, -1][t]  + koff\*S[1, 1, 0][t] + kpoff\*S[1, 1, 1] [t] | | -| | S[1, 1, 0] | 0 | (S[1, 1, 0])'[t] == kpon\*K[1, 1][t]\*S[-1, 1,  0][t] + kpon\*K[2, 1][t]\*S[1, -1, 0][t] +  kon\*K[3, 0][t]\*S[1, 1, -1][t] - koff\*S[1, 1,  0][t] - 2\*kpoff\*S[1, 1, 0][t] - k1a\*RAFK[t]\* S[1, 1, 0][t] + d1a\*S_RAFK[1, 1, 0][t] | | -| | S[1, 1, 1] | 0 | (S[1, 1, 1])'[t] == kpon\*K[1, 1][t]\*S[-1, 1,  1][t] + kpon\*K[2, 1][t]\*S[1, -1, 1][t] +  k3\*S[1, 0, 1][t] + kpon\*K[3, 1][t]\*S[1, 1,  -1][t] - k5a\*S[1, 1, 1][t] - 3\*kpoff\*S[1,  1, 1][t] + k1\*S_RAFK[1, 1, 0][t] | | -| | S[1, 2, -1] | 0 | (S[1, 2, -1])'[t] == kpon\*K[1, 1][t]\*S[-1, 2,  -1][t] + k7\*S[0, 2, -1][t] + kpon\*K[2,  2][t]\*S[1, -1, -1][t] - k9a\*S[1, 2, -1][t]  - 2\*kpoff\*S[1, 2, -1][t] - kon\*K[3, 0][t]\*S[ 1, 2, -1][t] - kpon\*K[3, 1][t]\*S[1, 2, -1][t]  + koff\*S[1, 2, 0][t] + kpoff\*S[1, 2, 1] [t] | | -| | S[1, 2, 0] | 0 | (S[1, 2, 0])'[t] == kpon\*K[1, 1][t]\*S[-1, 2,  0][t] + k7\*S[0, 2, 0][t] + kpon\*K[2, 2] [t]\*S[1, -1, 0][t] + kon\*K[3, 0][t]\*S[1, 2, - 1][t] - k9a\*S[1, 2, 0][t] - koff\*S[1, 2,  0][t] - 2\*kpoff\*S[1, 2, 0][t] - k1a\*RAFK[t]\* S[1, 2, 0][t] + d1a\*S_RAFK[1, 2, 0][t] | | -| | S[1, 2, 1] | 0 | (S[1, 2, 1])'[t] == kpon\*K[1, 1][t]\*S[-1, 2,  1][t] + k7\*S[0, 2, 1][t] + kpon\*K[2, 2] [t]\*S[1, -1, 1][t] + k5a\*S[1, 1, 1][t] +  kpon\*K[3, 1][t]\*S[1, 2, -1][t] - k9a\*S[1, 2,  1][t] - 3\*kpoff\*S[1, 2, 1][t] + k1\*S_RAFK[1,  2, 0][t] | | -| | S[2, -1, -1] | 0 | (S[2, -1, -1])'[t] == kpon\*K[1, 2][t]\*S[-1, - 1, -1][t] - kpoff\*S[2, -1, -1][t] - kon\*K[2,  0][t]\*S[2, -1, -1][t] - kpon\*K[2, 1][t]\*S[2,  -1, -1][t] - kpon\*K[2, 2][t]\*S[2, -1, -1][t]  - kon\*K[3, 0][t]\*S[2, -1, -1][t] - kpon\*K[3,  1][t]\*S[2, -1, -1][t] + koff\*S[2, -1, 0][t]  + kpoff\*S[2, -1, 1][t] + koff\*S[2, 0, - 1][t] + kpoff\*S[2, 1, -1][t] + kpoff\*S[2, 2,  -1][t] | | -| | S[2, -1, 0] | 0 | (S[2, -1, 0])'[t] == kpon\*K[1, 2][t]\*S[-1, -1,  0][t] + kon\*K[3, 0][t]\*S[2, -1, -1][t] -  koff\*S[2, -1, 0][t] - kpoff\*S[2, -1, 0][t]  - k1a\*RAFK[t]\*S[2, -1, 0][t] - kon\*K[2, 0][ t]\*S[2, -1, 0][t] - kpon\*K[2, 1][t]\*S[2, -1,  0][t] - kpon\*K[2, 2][t]\*S[2, -1, 0][t] +  koff\*S[2, 0, 0][t] + kpoff\*S[2, 1, 0][t]  + kpoff\*S[2, 2, 0][t] + d1a\*S_RAFK[2, -1,  0][t] | | -| | S[2, -1, 1] | 0 | (S[2, -1, 1])'[t] == kpon\*K[1, 2][t]\*S[-1, -1,  1][t] + kpon\*K[3, 1][t]\*S[2, -1, -1][t] -  2\*kpoff\*S[2, -1, 1][t] - kon\*K[2, 0][t]\*S[2,  -1, 1][t] - kpon\*K[2, 1][t]\*S[2, -1, 1][t]  - kpon\*K[2, 2][t]\*S[2, -1, 1][t] + koff\*S[2,  0, 1][t] + kpoff\*S[2, 1, 1][t] + kpoff\* S[2, 2, 1][t] + k1\*S_RAFK[2, -1, 0][t] | | -| | S[2, 0, -1] | 0 | (S[2, 0, -1])'[t] == kpon\*K[1, 2][t]\*S[-1, 0,  -1][t] + kon\*K[2, 0][t]\*S[2, -1, -1][t] -  koff\*S[2, 0, -1][t] - kpoff\*S[2, 0, -1][t]  - kon\*K[3, 0][t]\*S[2, 0, -1][t] - kpon\*K[3,  1][t]\*S[2, 0, -1][t] + koff\*S[2, 0, 0][t]  + kpoff\*S[2, 0, 1][t] | | -| | S[2, 0, 0] | 0 | (S[2, 0, 0])'[t] == kpon\*K[1, 2][t]\*S[-1, 0,  0][t] + kon\*K[2, 0][t]\*S[2, -1, 0][t] +  kon\*K[3, 0][t]\*S[2, 0, -1][t] - 2\*koff\*S[2,  0, 0][t] - kpoff\*S[2, 0, 0][t] - k1a\* RAFK[t]\*S[2, 0, 0][t] + d1a\*S_RAFK[2, 0, 0][t] | | -| | S[2, 0, 1] | 0 | (S[2, 0, 1])'[t] == kpon\*K[1, 2][t]\*S[-1, 0,  1][t] + kon\*K[2, 0][t]\*S[2, -1, 1][t] +  kpon\*K[3, 1][t]\*S[2, 0, -1][t] - k3\*S[2, 0,  1][t] - koff\*S[2, 0, 1][t] - 2\*kpoff\*S[2,  0, 1][t] + k1\*S_RAFK[2, 0, 0][t] | | -| | S[2, 1, -1] | 0 | (S[2, 1, -1])'[t] == kpon\*K[1, 2][t]\*S[-1, 1,  -1][t] + kpon\*K[2, 1][t]\*S[2, -1, -1][t] -  2\*kpoff\*S[2, 1, -1][t] - kon\*K[3, 0][t]\*S[2,  1, -1][t] - kpon\*K[3, 1][t]\*S[2, 1, -1][t]  + koff\*S[2, 1, 0][t] + kpoff\*S[2, 1, 1] [t] | | -| | S[2, 1, 0] | 0 | (S[2, 1, 0])'[t] == kpon\*K[1, 2][t]\*S[-1, 1,  0][t] + kpon\*K[2, 1][t]\*S[2, -1, 0][t] +  kon\*K[3, 0][t]\*S[2, 1, -1][t] - koff\*S[2, 1,  0][t] - 2\*kpoff\*S[2, 1, 0][t] - k1a\*RAFK[t]\* S[2, 1, 0][t] + d1a\*S_RAFK[2, 1, 0][t] | | -| | S[2, 1, 1] | 0 | (S[2, 1, 1])'[t] == kpon\*K[1, 2][t]\*S[-1, 1,  1][t] + kpon\*K[2, 1][t]\*S[2, -1, 1][t] +  k3\*S[2, 0, 1][t] + kpon\*K[3, 1][t]\*S[2, 1,  -1][t] - k5a\*S[2, 1, 1][t] - 3\*kpoff\*S[2,  1, 1][t] + k1\*S_RAFK[2, 1, 0][t] | | -| | S[2, 2, -1] | 0 | (S[2, 2, -1])'[t] == kpon\*K[1, 2][t]\*S[-1, 2,  -1][t] + k9a\*S[1, 2, -1][t] + kpon\*K[2,  2][t]\*S[2, -1, -1][t] - 2\*kpoff\*S[2, 2, -1][ t] - kon\*K[3, 0][t]\*S[2, 2, -1][t] - kpon\*K[ 3, 1][t]\*S[2, 2, -1][t] + koff\*S[2, 2, 0][t]  + kpoff\*S[2, 2, 1][t] | | -| | S[2, 2, 0] | 0 | (S[2, 2, 0])'[t] == kpon\*K[1, 2][t]\*S[-1, 2,  0][t] + k9a\*S[1, 2, 0][t] + kpon\*K[2,  2][t]\*S[2, -1, 0][t] + kon\*K[3, 0][t]\*S[2,  2, -1][t] - koff\*S[2, 2, 0][t] - 2\* kpoff\*S[2, 2, 0][t] - k1a\*RAFK[t]\*S[2, 2, 0][t]  + d1a\*S_RAFK[2, 2, 0][t] | | -| | S[2, 2, 1] | 0 | (S[2, 2, 1])'[t] == kpon\*K[1, 2][t]\*S[-1, 2,  1][t] + k9a\*S[1, 2, 1][t] + kpon\*K[2,  2][t]\*S[2, -1, 1][t] + k5a\*S[2, 1, 1][t]  + kpon\*K[3, 1][t]\*S[2, 2, -1][t] - 3\*kpoff\* S[2, 2, 1][t] + k1\*S_RAFK[2, 2, 0][t] | | -| | S_RAFK[-1, -1, 0] | 0 | (S_RAFK[-1, -1, 0])'[t] == k1a\*RAFK[t]\*S[-1, -1,  0][t] - d1a\*S_RAFK[-1, -1, 0][t] - k1\* S_RAFK[-1, -1, 0][t] | | -| | S_RAFK[-1, 0, 0] | 0 | (S_RAFK[-1, 0, 0])'[t] == k1a\*RAFK[t]\*S[-1, 0,  0][t] - d1a\*S_RAFK[-1, 0, 0][t] - k1\*S_RAFK[ -1, 0, 0][t] | | -| | S_RAFK[-1, 1, 0] | 0 | (S_RAFK[-1, 1, 0])'[t] == k1a\*RAFK[t]\*S[-1, 1,  0][t] - d1a\*S_RAFK[-1, 1, 0][t] - k1\*S_RAFK[ -1, 1, 0][t] | | -| | S_RAFK[-1, 2, 0] | 0 | (S_RAFK[-1, 2, 0])'[t] == k1a\*RAFK[t]\*S[-1, 2,  0][t] - d1a\*S_RAFK[-1, 2, 0][t] - k1\*S_RAFK[ -1, 2, 0][t] | | -| | S_RAFK[0, -1, 0] | 0 | (S_RAFK[0, -1, 0])'[t] == k1a\*RAFK[t]\*S[0, -1,  0][t] - d1a\*S_RAFK[0, -1, 0][t] - k1\*S_RAFK[ 0, -1, 0][t] | | -| | S_RAFK[0, 0, 0] | 0 | (S_RAFK[0, 0, 0])'[t] == k1a\*RAFK[t]\*S[0, 0,  0][t] - d1a\*S_RAFK[0, 0, 0][t] - k1\*S_RAFK[ 0, 0, 0][t] | | -| | S_RAFK[0, 1, 0] | 0 | (S_RAFK[0, 1, 0])'[t] == k1a\*RAFK[t]\*S[0, 1,  0][t] - d1a\*S_RAFK[0, 1, 0][t] - k1\*S_RAFK[ 0, 1, 0][t] | | -| | S_RAFK[0, 2, 0] | 0 | (S_RAFK[0, 2, 0])'[t] == k1a\*RAFK[t]\*S[0, 2,  0][t] - d1a\*S_RAFK[0, 2, 0][t] - k1\*S_RAFK[ 0, 2, 0][t] | | -| | S_RAFK[1, -1, 0] | 0 | (S_RAFK[1, -1, 0])'[t] == k1a\*RAFK[t]\*S[1, -1,  0][t] - d1a\*S_RAFK[1, -1, 0][t] - k1\*S_RAFK[ 1, -1, 0][t] | | -| | S_RAFK[1, 0, 0] | 0 | (S_RAFK[1, 0, 0])'[t] == k1a\*RAFK[t]\*S[1, 0,  0][t] - d1a\*S_RAFK[1, 0, 0][t] - k1\*S_RAFK[ 1, 0, 0][t] | | -| | S_RAFK[1, 1, 0] | 0 | (S_RAFK[1, 1, 0])'[t] == k1a\*RAFK[t]\*S[1, 1,  0][t] - d1a\*S_RAFK[1, 1, 0][t] - k1\*S_RAFK[ 1, 1, 0][t] | | -| | S_RAFK[1, 2, 0] | 0 | (S_RAFK[1, 2, 0])'[t] == k1a\*RAFK[t]\*S[1, 2,  0][t] - d1a\*S_RAFK[1, 2, 0][t] - k1\*S_RAFK[ 1, 2, 0][t] | | -| | S_RAFK[2, -1, 0] | 0 | (S_RAFK[2, -1, 0])'[t] == k1a\*RAFK[t]\*S[2, -1,  0][t] - d1a\*S_RAFK[2, -1, 0][t] - k1\*S_RAFK[ 2, -1, 0][t] | | -| | S_RAFK[2, 0, 0] | 0 | (S_RAFK[2, 0, 0])'[t] == k1a\*RAFK[t]\*S[2, 0,  0][t] - d1a\*S_RAFK[2, 0, 0][t] - k1\*S_RAFK[ 2, 0, 0][t] | | -| | S_RAFK[2, 1, 0] | 0 | (S_RAFK[2, 1, 0])'[t] == k1a\*RAFK[t]\*S[2, 1,  0][t] - d1a\*S_RAFK[2, 1, 0][t] - k1\*S_RAFK[ 2, 1, 0][t] | | -| | S_RAFK[2, 2, 0] | 0 | (S_RAFK[2, 2, 0])'[t] == k1a\*RAFK[t]\*S[2, 2,  0][t] - d1a\*S_RAFK[2, 2, 0][t] - k1\*S_RAFK[ 2, 2, 0][t] | | Generated by Cellerator Version 1.0 update 2.1203 using Mathematica 4.2 for Mac OS X (June 4, 2002), December 4, 2002 15:06:10, using (PowerMac,PowerPC,Mac OS diff --git a/doc/examples/biomodels/BIOMD0000000015_url.txt b/doc/examples/biomodels/BIOMD0000000015/BIOMD0000000015_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000015_url.txt rename to doc/examples/biomodels/BIOMD0000000015/BIOMD0000000015_url.txt index d4159dd7a..c6acc1359 100644 --- a/doc/examples/biomodels/BIOMD0000000015_url.txt +++ b/doc/examples/biomodels/BIOMD0000000015/BIOMD0000000015_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000015() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000016_url.txt b/doc/examples/biomodels/BIOMD0000000016/BIOMD0000000016_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000016_url.txt rename to doc/examples/biomodels/BIOMD0000000016/BIOMD0000000016_url.txt index d78ccaf80..f6de03da3 100644 --- a/doc/examples/biomodels/BIOMD0000000016_url.txt +++ b/doc/examples/biomodels/BIOMD0000000016/BIOMD0000000016_url.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Goldbeter1995() // Compartments and Species: compartment default, CYTOPLASM, compartment_0000004; species $EmptySet in default, M in CYTOPLASM, P0 in CYTOPLASM, P1 in CYTOPLASM; - species P2 in CYTOPLASM, Pn in compartment_0000004, $Pt in CYTOPLASM; + species P2 in CYTOPLASM, Pn in compartment_0000004, Pt in CYTOPLASM; // Assignment Rules: Pt := P0 + P1 + P2 + Pn; diff --git a/doc/examples/biomodels/BIOMD0000000017_url.txt b/doc/examples/biomodels/BIOMD0000000017/BIOMD0000000017_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000017_url.txt rename to doc/examples/biomodels/BIOMD0000000017/BIOMD0000000017_url.txt index 4ed605f42..a34bdcab8 100644 --- a/doc/examples/biomodels/BIOMD0000000017_url.txt +++ b/doc/examples/biomodels/BIOMD0000000017/BIOMD0000000017_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hoefnagel2002_PyruvateBranches() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000018_url.txt b/doc/examples/biomodels/BIOMD0000000018/BIOMD0000000018_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000018_url.txt rename to doc/examples/biomodels/BIOMD0000000018/BIOMD0000000018_url.txt index f1de8fed7..d33381010 100644 --- a/doc/examples/biomodels/BIOMD0000000018_url.txt +++ b/doc/examples/biomodels/BIOMD0000000018/BIOMD0000000018_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MorrisonAllegra() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000019_url.txt b/doc/examples/biomodels/BIOMD0000000019/BIOMD0000000019_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000019_url.txt rename to doc/examples/biomodels/BIOMD0000000019/BIOMD0000000019_url.txt index 6ed2486ca..08a3a2be3 100644 --- a/doc/examples/biomodels/BIOMD0000000019_url.txt +++ b/doc/examples/biomodels/BIOMD0000000019/BIOMD0000000019_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000019() // Compartments and Species: @@ -719,16 +719,15 @@ k(r)39 by k(r)37, k(r)46 by k(r)44, k51 by k49, k(r)54 by k(r)52 and k62 by k62. In particular the parameter values described in the column "remark" of supplementary table 1 override the values explicitely written in the numerical columns: -| | -||------|----------------------|---------------------|---------| -| - | - | - | - | -| | -| | kr16 | 0.055 | 0.275 | | | -| | k30 | 7.9e6 | 2.1e6 | as k20 | | -| | kr30 | 0.3 | 0.4 | as kr24 | | -| | k38 | 3e7 | 1e7 | as k20 | | -| | kr38 | 0.055 | 0.55 | as kr24 | | -| | k52 | 1.1e5 | 5.34e7 | | | +| name | in suppl. value used | in model value used | remarks | +|------|----------------------|---------------------|---------| +| kr16 | 0.055 | 0.275 | | +| k30 | 7.9e6 | 2.1e6 | as k20 | +| kr30 | 0.3 | 0.4 | as kr24 | +| k38 | 3e7 | 1e7 | as k20 | +| kr38 | 0.055 | 0.55 | as kr24 | +| k52 | 1.1e5 | 5.34e7 | | + k5 was used for v116, v119, v122 and v125 in addition of v107, v110 and v113 as listed in the legend of supplementary figure 2. k5 is calculated using th eformula from @@ -744,13 +743,12 @@ an endosomal volume of 4.3 al (= 4.3\*10 -18 litre). The extracellular EGF concentration was converted to molecules per picolitre with a MW of 6045 Da. -| | -||---------|-----------| -| - | - | -| | -| | 50 | 4962 | | -| | 0.5 | 49.6 | | -| | 0.125 | 12.4 | | +| [ng/ml] | [numb/pl] | +|---------|-----------| +| 50 | 4962 | +| 0.5 | 49.6 | +| 0.125 | 12.4 | + With the initial conditions given in the paper, the results could not be reproduced at all. Therefore the initial conditions used in the MATLAB file were adopted for diff --git a/doc/examples/biomodels/BIOMD0000000020_url.txt b/doc/examples/biomodels/BIOMD0000000020/BIOMD0000000020_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000020_url.txt rename to doc/examples/biomodels/BIOMD0000000020/BIOMD0000000020_url.txt index 82839c71d..d7e2d90f8 100644 --- a/doc/examples/biomodels/BIOMD0000000020_url.txt +++ b/doc/examples/biomodels/BIOMD0000000020/BIOMD0000000020_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *hhsa_1952() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000021_url.txt b/doc/examples/biomodels/BIOMD0000000021/BIOMD0000000021_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000021_url.txt rename to doc/examples/biomodels/BIOMD0000000021/BIOMD0000000021_url.txt index e1d5a8924..be3ab319e 100644 --- a/doc/examples/biomodels/BIOMD0000000021_url.txt +++ b/doc/examples/biomodels/BIOMD0000000021/BIOMD0000000021_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Leloup1999_CircClock_periodic() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000022_url.txt b/doc/examples/biomodels/BIOMD0000000022/BIOMD0000000022_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000022_url.txt rename to doc/examples/biomodels/BIOMD0000000022/BIOMD0000000022_url.txt index 425a3430c..2b2531eab 100644 --- a/doc/examples/biomodels/BIOMD0000000022_url.txt +++ b/doc/examples/biomodels/BIOMD0000000022/BIOMD0000000022_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ueda2001_CircClock() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000023_url.txt b/doc/examples/biomodels/BIOMD0000000023/BIOMD0000000023_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000023_url.txt rename to doc/examples/biomodels/BIOMD0000000023/BIOMD0000000023_url.txt index 4b1cdfee4..ca5896655 100644 --- a/doc/examples/biomodels/BIOMD0000000023_url.txt +++ b/doc/examples/biomodels/BIOMD0000000023/BIOMD0000000023_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Rohwer2001_Sucrose() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000024_url.txt b/doc/examples/biomodels/BIOMD0000000024/BIOMD0000000024_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000024_url.txt rename to doc/examples/biomodels/BIOMD0000000024/BIOMD0000000024_url.txt index c768fc6dd..843022f4f 100644 --- a/doc/examples/biomodels/BIOMD0000000024_url.txt +++ b/doc/examples/biomodels/BIOMD0000000024/BIOMD0000000024_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Scheper1999() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000025_url.txt b/doc/examples/biomodels/BIOMD0000000025/BIOMD0000000025_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000025_url.txt rename to doc/examples/biomodels/BIOMD0000000025/BIOMD0000000025_url.txt index c9291aa05..54309d2ae 100644 --- a/doc/examples/biomodels/BIOMD0000000025_url.txt +++ b/doc/examples/biomodels/BIOMD0000000025/BIOMD0000000025_url.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Smolen2002() // Compartments and Species: compartment CELL; - species $EmptySet in CELL, Per in CELL, dClk in CELL, $dClkF in CELL; + species $EmptySet in CELL, Per in CELL, dClk in CELL, dClkF in CELL; // Assignment Rules: dClkF := piecewise(0, (dClk - Per) < 0, dClk - Per); diff --git a/doc/examples/biomodels/BIOMD0000000026_url.txt b/doc/examples/biomodels/BIOMD0000000026/BIOMD0000000026_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000026_url.txt rename to doc/examples/biomodels/BIOMD0000000026/BIOMD0000000026_url.txt index f21e6be91..aab5f2c7e 100644 --- a/doc/examples/biomodels/BIOMD0000000026_url.txt +++ b/doc/examples/biomodels/BIOMD0000000026/BIOMD0000000026_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Markevich2004_MAPK_orderedelementary() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000027_url.txt b/doc/examples/biomodels/BIOMD0000000027/BIOMD0000000027_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000027_url.txt rename to doc/examples/biomodels/BIOMD0000000027/BIOMD0000000027_url.txt index 8361d80fe..6eeb22332 100644 --- a/doc/examples/biomodels/BIOMD0000000027_url.txt +++ b/doc/examples/biomodels/BIOMD0000000027/BIOMD0000000027_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Markevich2004_MAPK_orderedMM() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000028_url.txt b/doc/examples/biomodels/BIOMD0000000028/BIOMD0000000028_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000028_url.txt rename to doc/examples/biomodels/BIOMD0000000028/BIOMD0000000028_url.txt index 922dfa8dc..20d0e7d7c 100644 --- a/doc/examples/biomodels/BIOMD0000000028_url.txt +++ b/doc/examples/biomodels/BIOMD0000000028/BIOMD0000000028_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000029_url.txt b/doc/examples/biomodels/BIOMD0000000029/BIOMD0000000029_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000029_url.txt rename to doc/examples/biomodels/BIOMD0000000029/BIOMD0000000029_url.txt index 06ad9a10d..52af87265 100644 --- a/doc/examples/biomodels/BIOMD0000000029_url.txt +++ b/doc/examples/biomodels/BIOMD0000000029/BIOMD0000000029_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000030_url.txt b/doc/examples/biomodels/BIOMD0000000030/BIOMD0000000030_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000030_url.txt rename to doc/examples/biomodels/BIOMD0000000030/BIOMD0000000030_url.txt index 55a1554b4..058706aa7 100644 --- a/doc/examples/biomodels/BIOMD0000000030_url.txt +++ b/doc/examples/biomodels/BIOMD0000000030/BIOMD0000000030_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000031_url.txt b/doc/examples/biomodels/BIOMD0000000031/BIOMD0000000031_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000031_url.txt rename to doc/examples/biomodels/BIOMD0000000031/BIOMD0000000031_url.txt index 57050e72d..e2a729deb 100644 --- a/doc/examples/biomodels/BIOMD0000000031_url.txt +++ b/doc/examples/biomodels/BIOMD0000000031/BIOMD0000000031_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Markevich2004_MAPK_orderedMM2kinases() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000032_url.txt b/doc/examples/biomodels/BIOMD0000000032/BIOMD0000000032_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000032_url.txt rename to doc/examples/biomodels/BIOMD0000000032/BIOMD0000000032_url.txt index 13e1e825b..3e862c057 100644 --- a/doc/examples/biomodels/BIOMD0000000032_url.txt +++ b/doc/examples/biomodels/BIOMD0000000032/BIOMD0000000032_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kofahl2004_PheromonePathway() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000033_url.txt b/doc/examples/biomodels/BIOMD0000000033/BIOMD0000000033_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000033_url.txt rename to doc/examples/biomodels/BIOMD0000000033/BIOMD0000000033_url.txt index 1c63fa265..061ee1df3 100644 --- a/doc/examples/biomodels/BIOMD0000000033_url.txt +++ b/doc/examples/biomodels/BIOMD0000000033/BIOMD0000000033_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Brown2004_NGF_EGF_signaling() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000034_url.txt b/doc/examples/biomodels/BIOMD0000000034/BIOMD0000000034_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000034_url.txt rename to doc/examples/biomodels/BIOMD0000000034/BIOMD0000000034_url.txt index fc19cad0d..08f1539fd 100644 --- a/doc/examples/biomodels/BIOMD0000000034_url.txt +++ b/doc/examples/biomodels/BIOMD0000000034/BIOMD0000000034_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000035_url.txt b/doc/examples/biomodels/BIOMD0000000035/BIOMD0000000035_url.txt similarity index 69% rename from doc/examples/biomodels/BIOMD0000000035_url.txt rename to doc/examples/biomodels/BIOMD0000000035/BIOMD0000000035_url.txt index 317130b76..d7598a76a 100644 --- a/doc/examples/biomodels/BIOMD0000000035_url.txt +++ b/doc/examples/biomodels/BIOMD0000000035/BIOMD0000000035_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *vilarOscillator() // Compartments and Species: @@ -114,52 +114,48 @@ model *vilarOscillator() # # Minimal Model for Circadian Oscillations -| | -||---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| - | -| | -| | Vilar JMG, Kueh HY, Barkai N, Leibler S, (2002) . Mechanisms of noise resistance in genetic oscillators, PNAS, 99(9):5988-5992. [http://www.pnas.org/cgi/content/abstract/ 99/9/5988](http://www.pnas.org/%20%20%20%20%20%20%20%20cgi/content/abstract/99/9/5988) | | - -| | -||-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| - | -| | -| | A minimal model of genomically based oscillation, based on two mutually interacting genes, an activator and a repressor. Postive feedback is provided by the activator protein, which binds to the promotors of both the activator and the repressor genes. Negative feedback is provided by the repressor protein which binds to the activator protein. | | - -| | -||----------------------------|------------------------| -| - | - | -| | -| | alphaA = 50 | DA -> DA + MA | | -| | alphaAp = 500 | DAp -> DAp + MA | | -| | alphaR = 0.01 | DR -> DR + MR | | -| | alphaRp = 50 | DRp -> DRp + MR | | -| | betaA = 50 | MA -> A + MA | | -| | betaR = 5 | MR -> MR + R | | -| | gammaA = 1 | A + DA -> DAp | | -| | gammaC = 2 | A + R -> C | | -| | gammaR = 1 | A + DR -> DRp | | -| | deltaA = 1 | A -> EmptySet | | -| | deltaA = 1 | C -> R | | -| | deltaMA = 10 | MA -> EmptySet | | -| | deltaMR = 0.5 | MR -> EmptySet | | -| | deltaR = 0.2 | R -> EmptySet | | -| | thetaA = 50 | DAp -> A + DA | | -| | thetaR = 100 | DRp -> A + DR | | - -| | -||----------|--------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| - | - | - | -| | -| | A | 0 | A'[t] == -(deltaA\*A[t]) - gammaA\*A[t]\*DA[t] + thetaA\*DAp[ t] - gammaR\*A[t]\*DR[t] + thetaR\*DRp[t] + betaA\*MA[t] -  gammaC\*A[t]\*R[t] | | -| | C | 0 | C'[t] == -(deltaA\*C[t]) + gammaC\*A[t]\*R[t] | | -| | DA | 1 | DA'[t] == -(gammaA\*A[t]\*DA[t]) + thetaA\*DAp[t] | | -| | DAp | 0 | DAp'[t] == gammaA\*A[t]\*DA[t] - thetaA\*DAp[t] | | -| | DR | 1 | DR'[t] == -(gammaR\*A[t]\*DR[t]) + thetaR\*DRp[t] | | -| | DRp | 0 | DRp'[t] == gammaR\*A[t]\*DR[t] - thetaR\*DRp[t] | | -| | MA | 0 | MA'[t] == alphaA\*DA[t] + alphaAp\*DAp[t] - deltaMA\*MA[t] | | -| | MR | 0 | MR'[t] == alphaR\*DR[t] + alphaRp\*DRp[t] - deltaMR\*MR[t] | | -| | R | 0 | R'[t] == deltaA\*C[t] + betaR\*MR[t] - deltaR\*R[t] -  gammaC\*A[t]\*R[t] | | +| Citation | +|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| Vilar JMG, Kueh HY, Barkai N, Leibler S, (2002) . Mechanisms of noise resistance in genetic oscillators, PNAS, 99(9):5988-5992. [http://www.pnas.org/cgi/content/abstract/ 99/9/5988](http://www.pnas.org/%20%20%20%20%20%20%20%20cgi/content/abstract/99/9/5988) | + + +| Description | +|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| A minimal model of genomically based oscillation, based on two mutually interacting genes, an activator and a repressor. Postive feedback is provided by the activator protein, which binds to the promotors of both the activator and the repressor genes. Negative feedback is provided by the repressor protein which binds to the activator protein. | + + +| Rate constant       | Reaction | +|----------------------------|------------------------| +| alphaA = 50 | DA -> DA + MA | +| alphaAp = 500 | DAp -> DAp + MA | +| alphaR = 0.01 | DR -> DR + MR | +| alphaRp = 50 | DRp -> DRp + MR | +| betaA = 50 | MA -> A + MA | +| betaR = 5 | MR -> MR + R | +| gammaA = 1 | A + DA -> DAp | +| gammaC = 2 | A + R -> C | +| gammaR = 1 | A + DR -> DRp | +| deltaA = 1 | A -> EmptySet | +| deltaA = 1 | C -> R | +| deltaMA = 10 | MA -> EmptySet | +| deltaMR = 0.5 | MR -> EmptySet | +| deltaR = 0.2 | R -> EmptySet | +| thetaA = 50 | DAp -> A + DA | +| thetaR = 100 | DRp -> A + DR | + + +| Variable | IC   | ODE | +|----------|--------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| A | 0 | A'[t] == -(deltaA\*A[t]) - gammaA\*A[t]\*DA[t] + thetaA\*DAp[ t] - gammaR\*A[t]\*DR[t] + thetaR\*DRp[t] + betaA\*MA[t] -  gammaC\*A[t]\*R[t] | +| C | 0 | C'[t] == -(deltaA\*C[t]) + gammaC\*A[t]\*R[t] | +| DA | 1 | DA'[t] == -(gammaA\*A[t]\*DA[t]) + thetaA\*DAp[t] | +| DAp | 0 | DAp'[t] == gammaA\*A[t]\*DA[t] - thetaA\*DAp[t] | +| DR | 1 | DR'[t] == -(gammaR\*A[t]\*DR[t]) + thetaR\*DRp[t] | +| DRp | 0 | DRp'[t] == gammaR\*A[t]\*DR[t] - thetaR\*DRp[t] | +| MA | 0 | MA'[t] == alphaA\*DA[t] + alphaAp\*DAp[t] - deltaMA\*MA[t] | +| MR | 0 | MR'[t] == alphaR\*DR[t] + alphaRp\*DRp[t] - deltaMR\*MR[t] | +| R | 0 | R'[t] == deltaA\*C[t] + betaR\*MR[t] - deltaR\*R[t] -  gammaC\*A[t]\*R[t] | + Generated by Cellerator Version 1.0 update 2.1127 using Mathematica 4.2 for Mac OS X (June 4, 2002), November 27, 2002 12:17:46, using (PowerMac,PowerPC, Mac diff --git a/doc/examples/biomodels/BIOMD0000000036_url.txt b/doc/examples/biomodels/BIOMD0000000036/BIOMD0000000036_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000036_url.txt rename to doc/examples/biomodels/BIOMD0000000036/BIOMD0000000036_url.txt index 52dafb70e..cc83d9c39 100644 --- a/doc/examples/biomodels/BIOMD0000000036_url.txt +++ b/doc/examples/biomodels/BIOMD0000000036/BIOMD0000000036_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Tyson1999() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000037_url.txt b/doc/examples/biomodels/BIOMD0000000037/BIOMD0000000037_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000037_url.txt rename to doc/examples/biomodels/BIOMD0000000037/BIOMD0000000037_url.txt index 6ef5b792c..91391b43c 100644 --- a/doc/examples/biomodels/BIOMD0000000037_url.txt +++ b/doc/examples/biomodels/BIOMD0000000037/BIOMD0000000037_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000037() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000038_url.txt b/doc/examples/biomodels/BIOMD0000000038/BIOMD0000000038_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000038_url.txt rename to doc/examples/biomodels/BIOMD0000000038/BIOMD0000000038_url.txt index 528254832..99fc5a8f8 100644 --- a/doc/examples/biomodels/BIOMD0000000038_url.txt +++ b/doc/examples/biomodels/BIOMD0000000038/BIOMD0000000038_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Rohwer2000_Phosphotransferase_System() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000039_url.txt b/doc/examples/biomodels/BIOMD0000000039/BIOMD0000000039_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000039_url.txt rename to doc/examples/biomodels/BIOMD0000000039/BIOMD0000000039_url.txt index 360ca4969..08b25e994 100644 --- a/doc/examples/biomodels/BIOMD0000000039_url.txt +++ b/doc/examples/biomodels/BIOMD0000000039/BIOMD0000000039_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Marhl_Calcium_Oscillations_role_of_mitochondria_and_cytosolic_proteins() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000040_url.txt b/doc/examples/biomodels/BIOMD0000000040/BIOMD0000000040_url.txt similarity index 85% rename from doc/examples/biomodels/BIOMD0000000040_url.txt rename to doc/examples/biomodels/BIOMD0000000040/BIOMD0000000040_url.txt index 075232612..66cde17b5 100644 --- a/doc/examples/biomodels/BIOMD0000000040_url.txt +++ b/doc/examples/biomodels/BIOMD0000000040/BIOMD0000000040_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Field1974_Oregonator() // Compartments and Species: @@ -6,14 +6,14 @@ model *Field1974_Oregonator() species Br in BZ, $BrO3 in BZ, Ce in BZ, HBrO2 in BZ, $HOBr in BZ; // Assignment Rules: - Ce_Br_stoichiometry := f; + Reaction5_Br_stoichiometry0 := f; // Reactions: Reaction1: Br + $BrO3 => HBrO2 + $HOBr; Br*BrO3*Reaction1_k1*BZ; Reaction2: Br + HBrO2 => 2 $HOBr; Br*HBrO2*Reaction2_k2*BZ; Reaction3: $BrO3 + HBrO2 => Ce + 2 HBrO2; BrO3*HBrO2*Reaction3_k3*BZ; Reaction4: 2 HBrO2 => $BrO3 + $HOBr; HBrO2^2*Reaction4_k4*BZ; - Reaction5: Ce => Ce_Br_stoichiometry Br; Ce*Reaction5_k5*BZ; + Reaction5: Ce => Reaction5_Br_stoichiometry0 Br; Ce*Reaction5_k5*BZ; // Species initializations: Br = 1e-07; @@ -70,17 +70,15 @@ model *Field1974_Oregonator() model notes ``` # Field-Noyes Model of BZ Reaction -| | -||----------------------------------------------------| -| :- | -| | -| | R.J.Field and R.M.Noyes,J.Chem.Phys.60,1877 (1974) | | - -| | -||-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| :- | -| | -| | Field Noyes Version of Belousov-Zhabotinsky Reaction. BrO3 is held constant; HOBr is typically ignored, and can be replaced by an empty-set. The stoichiometry f is typically taken as 1/2 or 1. . | | +| Citation | +|:---------------------------------------------------| +| R.J.Field and R.M.Noyes,J.Chem.Phys.60,1877 (1974) | + + +| Description | +|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| Field Noyes Version of Belousov-Zhabotinsky Reaction. BrO3 is held constant; HOBr is typically ignored, and can be replaced by an empty-set. The stoichiometry f is typically taken as 1/2 or 1. . | + Initially Generated by Cellerator Version 1.0 update 2.1220 using Mathematica 4.2 for Mac OS X (June 4, 2002), December 26, 2002 10:43:53, using (PowerMac,PowerPC, Mac diff --git a/doc/examples/biomodels/BIOMD0000000041_url.txt b/doc/examples/biomodels/BIOMD0000000041/BIOMD0000000041_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000041_url.txt rename to doc/examples/biomodels/BIOMD0000000041/BIOMD0000000041_url.txt index 6bfdb81fd..792049aba 100644 --- a/doc/examples/biomodels/BIOMD0000000041_url.txt +++ b/doc/examples/biomodels/BIOMD0000000041/BIOMD0000000041_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kongas___Van_Beek() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000042_url.txt b/doc/examples/biomodels/BIOMD0000000042/BIOMD0000000042_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000042_url.txt rename to doc/examples/biomodels/BIOMD0000000042/BIOMD0000000042_url.txt index 174ca8583..974aa3569 100644 --- a/doc/examples/biomodels/BIOMD0000000042_url.txt +++ b/doc/examples/biomodels/BIOMD0000000042/BIOMD0000000042_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Glycolysis_Nielsen() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000043_url.txt b/doc/examples/biomodels/BIOMD0000000043/BIOMD0000000043_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000043_url.txt rename to doc/examples/biomodels/BIOMD0000000043/BIOMD0000000043_url.txt index 39042351f..05e9935ac 100644 --- a/doc/examples/biomodels/BIOMD0000000043_url.txt +++ b/doc/examples/biomodels/BIOMD0000000043/BIOMD0000000043_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_channel_inhibition() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000044_url.txt b/doc/examples/biomodels/BIOMD0000000044/BIOMD0000000044_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000044_url.txt rename to doc/examples/biomodels/BIOMD0000000044/BIOMD0000000044_url.txt index 7a803c193..72893187d 100644 --- a/doc/examples/biomodels/BIOMD0000000044_url.txt +++ b/doc/examples/biomodels/BIOMD0000000044/BIOMD0000000044_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_Activated_degradation_of_IP3() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000045_url.txt b/doc/examples/biomodels/BIOMD0000000045/BIOMD0000000045_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000045_url.txt rename to doc/examples/biomodels/BIOMD0000000045/BIOMD0000000045_url.txt index 0382a3278..b99918357 100644 --- a/doc/examples/biomodels/BIOMD0000000045_url.txt +++ b/doc/examples/biomodels/BIOMD0000000045/BIOMD0000000045_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Goldbeter_Calcium_Oscillation_based_onCICR_AND_two_pool_model() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000046_url.txt b/doc/examples/biomodels/BIOMD0000000046/BIOMD0000000046_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000046_url.txt rename to doc/examples/biomodels/BIOMD0000000046/BIOMD0000000046_url.txt index 26333608d..555779bfa 100644 --- a/doc/examples/biomodels/BIOMD0000000046_url.txt +++ b/doc/examples/biomodels/BIOMD0000000046/BIOMD0000000046_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Olsen2003_peroxidase() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000047_url.txt b/doc/examples/biomodels/BIOMD0000000047/BIOMD0000000047_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000047_url.txt rename to doc/examples/biomodels/BIOMD0000000047/BIOMD0000000047_url.txt index 4069ff042..1a39760ae 100644 --- a/doc/examples/biomodels/BIOMD0000000047_url.txt +++ b/doc/examples/biomodels/BIOMD0000000047/BIOMD0000000047_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Oxhamre_Bacteria_induced_Ca_oscillations() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000048_url.txt b/doc/examples/biomodels/BIOMD0000000048/BIOMD0000000048_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000048_url.txt rename to doc/examples/biomodels/BIOMD0000000048/BIOMD0000000048_url.txt index f0295690c..42902c5a4 100644 --- a/doc/examples/biomodels/BIOMD0000000048_url.txt +++ b/doc/examples/biomodels/BIOMD0000000048/BIOMD0000000048_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kholodenko1999___EGFR_signaling() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000049_url.txt b/doc/examples/biomodels/BIOMD0000000049/BIOMD0000000049_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000049_url.txt rename to doc/examples/biomodels/BIOMD0000000049/BIOMD0000000049_url.txt index 97caccfb4..0b73230e9 100644 --- a/doc/examples/biomodels/BIOMD0000000049_url.txt +++ b/doc/examples/biomodels/BIOMD0000000049/BIOMD0000000049_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Sasagawa2005_MAPK() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000050_url.txt b/doc/examples/biomodels/BIOMD0000000050/BIOMD0000000050_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000050_url.txt rename to doc/examples/biomodels/BIOMD0000000050/BIOMD0000000050_url.txt index 2d54fa75f..647f583e5 100644 --- a/doc/examples/biomodels/BIOMD0000000050_url.txt +++ b/doc/examples/biomodels/BIOMD0000000050/BIOMD0000000050_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kinetic_modelling_of_Amadori_degradation() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000051_url.txt b/doc/examples/biomodels/BIOMD0000000051/BIOMD0000000051_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000051_url.txt rename to doc/examples/biomodels/BIOMD0000000051/BIOMD0000000051_url.txt index 34a2ea5bd..24dade142 100644 --- a/doc/examples/biomodels/BIOMD0000000051_url.txt +++ b/doc/examples/biomodels/BIOMD0000000051/BIOMD0000000051_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Chassagnole2002_Carbon_Metabolism() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000052_url.txt b/doc/examples/biomodels/BIOMD0000000052/BIOMD0000000052_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000052_url.txt rename to doc/examples/biomodels/BIOMD0000000052/BIOMD0000000052_url.txt index 1ce35d3de..985916e7e 100644 --- a/doc/examples/biomodels/BIOMD0000000052_url.txt +++ b/doc/examples/biomodels/BIOMD0000000052/BIOMD0000000052_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL8177704759() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000053_url.txt b/doc/examples/biomodels/BIOMD0000000053/BIOMD0000000053_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000053_url.txt rename to doc/examples/biomodels/BIOMD0000000053/BIOMD0000000053_url.txt index 07f341c3a..c00d5de01 100644 --- a/doc/examples/biomodels/BIOMD0000000053_url.txt +++ b/doc/examples/biomodels/BIOMD0000000053/BIOMD0000000053_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ferreira_CML_generation() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000054_url.txt b/doc/examples/biomodels/BIOMD0000000054/BIOMD0000000054_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000054_url.txt rename to doc/examples/biomodels/BIOMD0000000054/BIOMD0000000054_url.txt index 1caf596c8..4456525ec 100644 --- a/doc/examples/biomodels/BIOMD0000000054_url.txt +++ b/doc/examples/biomodels/BIOMD0000000054/BIOMD0000000054_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ataullahkhanov1996_Adenylate() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000055_url.txt b/doc/examples/biomodels/BIOMD0000000055/BIOMD0000000055_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000055_url.txt rename to doc/examples/biomodels/BIOMD0000000055/BIOMD0000000055_url.txt index 38fd08b53..24b96d0df 100644 --- a/doc/examples/biomodels/BIOMD0000000055_url.txt +++ b/doc/examples/biomodels/BIOMD0000000055/BIOMD0000000055_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Locke2005_CircadianClock() // Compartments and Species: @@ -42,6 +42,20 @@ model *Locke2005_CircadianClock() two23: cPn => ; compartment_*(m15*cPn/(k13 + cPn)); three23: cPn => ; compartment_*q3*ceil(sin(pi*time/dayLength + 0.001)/2)*cPn; + // Interactions: + _I0: cPn -( one11; ; + _I1: cXn -( two11; ; + _I2: cLm -( one12; ; + _I3: cYn -( one14; ; + _I4: cLn -( one14; ; + _I5: cTm -( one15; ; + _I6: cTn -( one17; ; + _I7: cXm -( one18; ; + _I8: cPn -( one20; ; + _I9: cTn -( one20; ; + _I10: cLn -( one20; ; + _I11: cYm -( one21; ; + // Species initializations: cLm = 0.539; cLc = 0.015; diff --git a/doc/examples/biomodels/BIOMD0000000056_url.txt b/doc/examples/biomodels/BIOMD0000000056/BIOMD0000000056_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000056_url.txt rename to doc/examples/biomodels/BIOMD0000000056/BIOMD0000000056_url.txt index 6d31126f4..657c1acc6 100644 --- a/doc/examples/biomodels/BIOMD0000000056_url.txt +++ b/doc/examples/biomodels/BIOMD0000000056/BIOMD0000000056_url.txt @@ -1,20 +1,20 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000056() // Compartments and Species: compartment cell; - substanceOnly species $BCK2 in cell, MASS in cell, BUB2 in cell, BUD in cell; + substanceOnly species BCK2 in cell, MASS in cell, BUB2 in cell, BUD in cell; substanceOnly species C2 in cell, C2P in cell, C5 in cell, C5P in cell; - substanceOnly species CDC14 in cell, $CDC14T in cell, RENT in cell, RENTP in cell; + substanceOnly species CDC14 in cell, CDC14T in cell, RENT in cell, RENTP in cell; substanceOnly species CDC15 in cell, $CDC15i in cell, CDC20 in cell, CDC20i in cell; - substanceOnly species CDC6 in cell, CDC6P in cell, $CDC6T in cell, F2 in cell; + substanceOnly species CDC6 in cell, CDC6P in cell, CDC6T in cell, F2 in cell; substanceOnly species F5 in cell, F2P in cell, F5P in cell, CDH1 in cell; - substanceOnly species CDH1i in cell, $CKIT in cell, $SIC1T in cell, CLB2 in cell; - substanceOnly species $CLB2T in cell, CLB5 in cell, $CLB5T in cell, CLN2 in cell; - substanceOnly species $CLN3 in cell, ESP1 in cell, $IE in cell, IEP in cell; - substanceOnly species LTE1 in cell, MAD2 in cell, $MCM1 in cell, NET1 in cell; - substanceOnly species NET1P in cell, $NET1T in cell, ORI in cell, PDS1 in cell; - substanceOnly species $PE in cell, PPX in cell, $SBF in cell, SIC1 in cell; + substanceOnly species CDH1i in cell, CKIT in cell, SIC1T in cell, CLB2 in cell; + substanceOnly species CLB2T in cell, CLB5 in cell, CLB5T in cell, CLN2 in cell; + substanceOnly species CLN3 in cell, ESP1 in cell, $IE in cell, IEP in cell; + substanceOnly species LTE1 in cell, MAD2 in cell, MCM1 in cell, NET1 in cell; + substanceOnly species NET1P in cell, NET1T in cell, ORI in cell, PDS1 in cell; + substanceOnly species $PE in cell, PPX in cell, SBF in cell, SIC1 in cell; substanceOnly species SIC1P in cell, SPN in cell, SWI5 in cell, SWI5P in cell; substanceOnly species $TEM1GDP in cell, TEM1GTP in cell; @@ -153,9 +153,9 @@ model *BIOMD0000000056() // Events: reset_ORI: at (CLB2 + CLB5 - KEZ2) < 0: ORI = 0; - start_S: at (ORI - 1) > 0: BUB2 = bub2h, MAD2 = mad2h; - spindle_checkpoint: at (SPN - 1) > 0: BUB2 = bub2l, LTE1 = lte1h, MAD2 = mad2l; - cell_division: at (CLB2 - KEZ) < 0: SPN = 0, BUD = 0, LTE1 = lte1l, MASS = F*MASS; + start_S: at (ORI - 1) > 0: MAD2 = mad2h, BUB2 = bub2h; + spindle_checkpoint: at (SPN - 1) > 0: MAD2 = mad2l, LTE1 = lte1h, BUB2 = bub2l; + cell_division: at (CLB2 - KEZ) < 0: MASS = F*MASS, LTE1 = lte1l, BUD = 0, SPN = 0; // Species initializations: MASS = 1.206019; diff --git a/doc/examples/biomodels/BIOMD0000000057_url.txt b/doc/examples/biomodels/BIOMD0000000057/BIOMD0000000057_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000057_url.txt rename to doc/examples/biomodels/BIOMD0000000057/BIOMD0000000057_url.txt index c970d41ff..422652f09 100644 --- a/doc/examples/biomodels/BIOMD0000000057_url.txt +++ b/doc/examples/biomodels/BIOMD0000000057/BIOMD0000000057_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Sneyd2002_dynamic_model_of_IP3_Receptor() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000058_url.txt b/doc/examples/biomodels/BIOMD0000000058/BIOMD0000000058_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000058_url.txt rename to doc/examples/biomodels/BIOMD0000000058/BIOMD0000000058_url.txt index dca124e42..1178ee5fd 100644 --- a/doc/examples/biomodels/BIOMD0000000058_url.txt +++ b/doc/examples/biomodels/BIOMD0000000058/BIOMD0000000058_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bindschadler_Ca_Oscillator() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000059_url.txt b/doc/examples/biomodels/BIOMD0000000059/BIOMD0000000059_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000059_url.txt rename to doc/examples/biomodels/BIOMD0000000059/BIOMD0000000059_url.txt index 6292eaea4..61b23a0ea 100644 --- a/doc/examples/biomodels/BIOMD0000000059_url.txt +++ b/doc/examples/biomodels/BIOMD0000000059/BIOMD0000000059_url.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Fridlyand2003_Ca_flux_pancreatic_cells() // Compartments and Species: compartment Cytoplasm, ER; species Ca_cyt in Cytoplasm, Ca_er in ER, IP3_cyt in Cytoplasm, Na_cyt in Cytoplasm; - species ATP_cyt in Cytoplasm, $ADP_cyt in Cytoplasm; + species ATP_cyt in Cytoplasm, ADP_cyt in Cytoplasm; // Assignment Rules: ADP_cyt := 4000 - ATP_cyt; diff --git a/doc/examples/biomodels/BIOMD0000000060_url.txt b/doc/examples/biomodels/BIOMD0000000060/BIOMD0000000060_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000060_url.txt rename to doc/examples/biomodels/BIOMD0000000060/BIOMD0000000060_url.txt index e4bf48656..f968662f4 100644 --- a/doc/examples/biomodels/BIOMD0000000060_url.txt +++ b/doc/examples/biomodels/BIOMD0000000060/BIOMD0000000060_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Keizer1996_Ryanodine_receptor_adaptation() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000061_url.txt b/doc/examples/biomodels/BIOMD0000000061/BIOMD0000000061_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000061_url.txt rename to doc/examples/biomodels/BIOMD0000000061/BIOMD0000000061_url.txt index dd47d285e..51bfa1825 100644 --- a/doc/examples/biomodels/BIOMD0000000061_url.txt +++ b/doc/examples/biomodels/BIOMD0000000061/BIOMD0000000061_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hynne2001_Glycolysis() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000062_url.txt b/doc/examples/biomodels/BIOMD0000000062/BIOMD0000000062_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000062_url.txt rename to doc/examples/biomodels/BIOMD0000000062/BIOMD0000000062_url.txt index 9d955879a..a6bed1140 100644 --- a/doc/examples/biomodels/BIOMD0000000062_url.txt +++ b/doc/examples/biomodels/BIOMD0000000062/BIOMD0000000062_url.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bhartiya2003_Tryptophan_operon() // Compartments and Species: compartment compartment_; - species Enz in compartment_, Ts in compartment_, $Tt in compartment_, $To in compartment_; + species Enz in compartment_, Ts in compartment_, Tt in compartment_, $To in compartment_; // Assignment Rules: Tt := To + Ts; diff --git a/doc/examples/biomodels/BIOMD0000000063_url.txt b/doc/examples/biomodels/BIOMD0000000063/BIOMD0000000063_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000063_url.txt rename to doc/examples/biomodels/BIOMD0000000063/BIOMD0000000063_url.txt index 4b39decf9..15ef2e829 100644 --- a/doc/examples/biomodels/BIOMD0000000063_url.txt +++ b/doc/examples/biomodels/BIOMD0000000063/BIOMD0000000063_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Galazzo1990_FermentationPathwayKinetics() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000064_url.txt b/doc/examples/biomodels/BIOMD0000000064/BIOMD0000000064_url.txt similarity index 94% rename from doc/examples/biomodels/BIOMD0000000064_url.txt rename to doc/examples/biomodels/BIOMD0000000064/BIOMD0000000064_url.txt index f5ee00285..e80117e84 100644 --- a/doc/examples/biomodels/BIOMD0000000064_url.txt +++ b/doc/examples/biomodels/BIOMD0000000064/BIOMD0000000064_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Teusink2000_Glycolysis() // Compartments and Species: @@ -8,7 +8,7 @@ model *Teusink2000_Glycolysis() species PEP in cytosol, PYR in cytosol, ACE in cytosol, P in cytosol, NAD in cytosol; species NADH in cytosol, $Glyc in cytosol, $Trh in cytosol, $CO2 in cytosol; species $SUCC in cytosol, $GLCo in extracellular, $ETOH in cytosol, $GLY in cytosol; - species $ATP in cytosol, $ADP in cytosol, $SUM_P in cytosol, $AMP in cytosol; + species ATP in cytosol, ADP in cytosol, $SUM_P in cytosol, AMP in cytosol; species $F26BP in cytosol; // Assignment Rules: @@ -441,49 +441,48 @@ The equilibrium constant for the ADH reaction in the paper is given for the reve reaction (Keq = 1.45\*10 4 ). The value used in this model is for the forward reaction: 1/Keq = 6.9\*10 -5 . Vmax parameters values used (in [mM/min] except VmGLT): -| | -||---------------|---------|----------|| -| | **VmGLK** | 226.45 | | | -| | **VmPGI** | 339.667 | | | -| | **VmPFK** | 182.903 | | | -| | **VmALD** | 322.258 | | | -| | **VmGAPDH_f** | 1184.52 | | | -| | **VmGAPDH_r** | 6549.68 | | | -| | **VmPGK** | 1306.45 | | | -| | **VmPGM** | 2525.81 | | | -| | **VmENO** | 365.806 | | | -| | **VmPYK** | 1088.71 | | | -| | **VmPDC** | 174.194 | | | -| | **VmG3PDH** | 70.15 | | | +| **VmGLT** | 97.264 | mmol/min | +| **VmGLK** | 226.45 | | +| **VmPGI** | 339.667 | | +| **VmPFK** | 182.903 | | +| **VmALD** | 322.258 | | +| **VmGAPDH_f** | 1184.52 | | +| **VmGAPDH_r** | 6549.68 | | +| **VmPGK** | 1306.45 | | +| **VmPGM** | 2525.81 | | +| **VmENO** | 365.806 | | +| **VmPYK** | 1088.71 | | +| **VmPDC** | 174.194 | | +| **VmG3PDH** | 70.15 | | + The result of the G6P steady state concentration (marked in red) differs slightly from the one given in table 4. of the publication Results for steady state: -| | -|||---------------|------------| -| :- | :- | :-: | -| | -| | **Fluxes[mM/min]**   | | | | -| | Glucose  | 88  | 88  | | -| | Ethanol  | 129  | 129  | | -| | Glycogen  | 6  | 6  | | -| | Trehalose  | 4.8  | 4.8  | (G6P flux through trehalose branch) | | -| | Glycerol  | 18.2  | 18.2  | | -| | Succinate  | 3.6  | 3.6  | | -| | **Conc.[mM]**   | | | | -| | G6P  | 1.07  | 1.03  | | -| | F6P  | 0.11  | 0.11  | | -| | F1,6P  | 0.6  | 0.6  | | -| | DHAP  | 0.74  | 0.74  | | -| | 3PGA  | 0.36  | 0.36  | | -| | 2PGA  | 0.04  | 0.04  | | -| | PEP  | 0.07  | 0.07  | | -| | PYR  | 8.52  | 8.52  | | -| | AcAld  | 0.17  | 0.17  | | -| | ATP  | 2.51  | 2.51  | | -| | ADP  | 1.29  | 1.29  | | -| | AMP  | 0.3  | 0.3  | | -| | NAD  | 1.55  | 1.55  | | -| | NADH  | 0.04  | 0.04  | | +| | orig. article | this model | +|:---------------------------------------|:--------------|:----------:| +| **Fluxes[mM/min]**   | | +| Glucose  | 88  | 88  | +| Ethanol  | 129  | 129  | +| Glycogen  | 6  | 6  | +| Trehalose  | 4.8  | 4.8  | (G6P flux through trehalose branch) | +| Glycerol  | 18.2  | 18.2  | +| Succinate  | 3.6  | 3.6  | +| **Conc.[mM]**   | | +| G6P  | 1.07  | 1.03  | +| F6P  | 0.11  | 0.11  | +| F1,6P  | 0.6  | 0.6  | +| DHAP  | 0.74  | 0.74  | +| 3PGA  | 0.36  | 0.36  | +| 2PGA  | 0.04  | 0.04  | +| PEP  | 0.07  | 0.07  | +| PYR  | 8.52  | 8.52  | +| AcAld  | 0.17  | 0.17  | +| ATP  | 2.51  | 2.51  | +| ADP  | 1.29  | 1.29  | +| AMP  | 0.3  | 0.3  | +| NAD  | 1.55  | 1.55  | +| NADH  | 0.04  | 0.04  | + Authors of the publication also mentioned a few misprints in the original article: in the kinetic law for *ADH* : diff --git a/doc/examples/biomodels/BIOMD0000000065_url.txt b/doc/examples/biomodels/BIOMD0000000065/BIOMD0000000065_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000065_url.txt rename to doc/examples/biomodels/BIOMD0000000065/BIOMD0000000065_url.txt index 554f3807b..2aafd991d 100644 --- a/doc/examples/biomodels/BIOMD0000000065_url.txt +++ b/doc/examples/biomodels/BIOMD0000000065/BIOMD0000000065_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Yildirim2003_Lac_operon() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000066_url.txt b/doc/examples/biomodels/BIOMD0000000066/BIOMD0000000066_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000066_url.txt rename to doc/examples/biomodels/BIOMD0000000066/BIOMD0000000066_url.txt index fa98c827d..a1eee970f 100644 --- a/doc/examples/biomodels/BIOMD0000000066_url.txt +++ b/doc/examples/biomodels/BIOMD0000000066/BIOMD0000000066_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Chassagnole2001_Threonine_Synthesis() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000067_url.txt b/doc/examples/biomodels/BIOMD0000000067/BIOMD0000000067_url.txt similarity index 88% rename from doc/examples/biomodels/BIOMD0000000067_url.txt rename to doc/examples/biomodels/BIOMD0000000067/BIOMD0000000067_url.txt index a88536f5e..e3c529e07 100644 --- a/doc/examples/biomodels/BIOMD0000000067_url.txt +++ b/doc/examples/biomodels/BIOMD0000000067/BIOMD0000000067_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Fung2005_Metabolator() // Compartments and Species: @@ -138,23 +138,22 @@ model *Fung2005_Metabolator() # A Synthetic Gene-Metabolic Oscillator **Reference:** [ *Fung et al; Nature (2005) 435:118-122* ](http://www.nature.com/nature/journal/v435/n7038/abs/nature03508.html) -| | -||---------------------------------------------------|----------------------------| -| :- | :- | -| | -| | Glycolytic flux, V_gly: | nil -> AcCoA; | | -| | Flux to TCA cycle/ETOH, V_TCA: | AcCoA -> TCA/EtOH; | | -| | HOAc ex/import,reversible, V_out: | HOAc -> HOAc_E | | -| | V_Pta: | AcCoA + Pi -> AcP + CoA | | -| | reversible, V_Ack: | AcP + ADP -> OAc + ATP | | -| | V_Acs: | OAC + ATP -> AcCoA +PPi | | -| | Acetic acid-base equillibrium, reversible, V_Ace: | OAC + H -> HOAc | | -| | Expression of LacI, R_LacI: | nil -> LacI | | -| | Expression of Acs, R_Acs: | nil -> Acs | | -| | Expression of Pta, R_Pta: | nil -> Pta | | -| | LacI degradation, R_dLacI: | LacI -> nil | | -| | Acs degradation, R_dAcs: | Acs -> nil | | -| | Pta degradation, R_dPta: | Pta -> nil | | +| Name of kinetic law | Reaction | +|:--------------------------------------------------|:---------------------------| +| Glycolytic flux, V_gly: | nil -> AcCoA; | +| Flux to TCA cycle/ETOH, V_TCA: | AcCoA -> TCA/EtOH; | +| HOAc ex/import,reversible, V_out: | HOAc -> HOAc_E | +| V_Pta: | AcCoA + Pi -> AcP + CoA | +| reversible, V_Ack: | AcP + ADP -> OAc + ATP | +| V_Acs: | OAC + ATP -> AcCoA +PPi | +| Acetic acid-base equillibrium, reversible, V_Ace: | OAC + H -> HOAc | +| Expression of LacI, R_LacI: | nil -> LacI | +| Expression of Acs, R_Acs: | nil -> Acs | +| Expression of Pta, R_Pta: | nil -> Pta | +| LacI degradation, R_dLacI: | LacI -> nil | +| Acs degradation, R_dAcs: | Acs -> nil | +| Pta degradation, R_dPta: | Pta -> nil | + For this model the differential equation for V_Ace was changed from: C\*(AcP\*H-K_eq\*OAC) with C = 100 in the supplemental material diff --git a/doc/examples/biomodels/BIOMD0000000068_url.txt b/doc/examples/biomodels/BIOMD0000000068/BIOMD0000000068_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000068_url.txt rename to doc/examples/biomodels/BIOMD0000000068/BIOMD0000000068_url.txt index 3d6d1f5e2..007ef38b0 100644 --- a/doc/examples/biomodels/BIOMD0000000068_url.txt +++ b/doc/examples/biomodels/BIOMD0000000068/BIOMD0000000068_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Curien2003_MetThr_synthesis() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000069_url.txt b/doc/examples/biomodels/BIOMD0000000069/BIOMD0000000069_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000069_url.txt rename to doc/examples/biomodels/BIOMD0000000069/BIOMD0000000069_url.txt index 2f823505c..049e8b050 100644 --- a/doc/examples/biomodels/BIOMD0000000069_url.txt +++ b/doc/examples/biomodels/BIOMD0000000069/BIOMD0000000069_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Src_MitoticActivation() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000070_url.txt b/doc/examples/biomodels/BIOMD0000000070/BIOMD0000000070_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000070_url.txt rename to doc/examples/biomodels/BIOMD0000000070/BIOMD0000000070_url.txt index 8de76392f..b0275b7ea 100644 --- a/doc/examples/biomodels/BIOMD0000000070_url.txt +++ b/doc/examples/biomodels/BIOMD0000000070/BIOMD0000000070_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Holzhutter2004_Erythrocyte_Metabolism() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000071_url.txt b/doc/examples/biomodels/BIOMD0000000071/BIOMD0000000071_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000071_url.txt rename to doc/examples/biomodels/BIOMD0000000071/BIOMD0000000071_url.txt index 4b7b943af..17c7edd00 100644 --- a/doc/examples/biomodels/BIOMD0000000071_url.txt +++ b/doc/examples/biomodels/BIOMD0000000071/BIOMD0000000071_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bakker2001_Glycolysis() // Compartments and Species: @@ -7,9 +7,9 @@ model *Bakker2001_Glycolysis() species Fru16BP in glycosome, DHAP in tot_cell, GAP in glycosome, NAD in glycosome; species BPGA13 in glycosome, NADH in glycosome, Pyr in cytosol, Nb in tot_cell; species Pc in cytosol, $PyrE in extracellular, $Gly in glycosome, $GlcE in extracellular; - species $Gly3P in tot_cell, $Gly3Pc in cytosol, $Gly3Pg in glycosome, $ATPc in cytosol; - species $ADPc in cytosol, $ATPg in glycosome, $ADPg in glycosome, $DHAPg in glycosome; - species $DHAPc in cytosol, $PGAg in glycosome, $PEPc in cytosol; + species $Gly3P in tot_cell, Gly3Pc in cytosol, Gly3Pg in glycosome, ATPc in cytosol; + species ADPc in cytosol, ATPg in glycosome, ADPg in glycosome, DHAPg in glycosome; + species DHAPc in cytosol, PGAg in glycosome, PEPc in cytosol; // Assignment Rules: Gly3P := (Gly3Pc*cytosol + Gly3Pg*glycosome)/tot_cell; diff --git a/doc/examples/biomodels/BIOMD0000000072_url.txt b/doc/examples/biomodels/BIOMD0000000072/BIOMD0000000072_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000072_url.txt rename to doc/examples/biomodels/BIOMD0000000072/BIOMD0000000072_url.txt index 99fd1fd08..e05ee8d2b 100644 --- a/doc/examples/biomodels/BIOMD0000000072_url.txt +++ b/doc/examples/biomodels/BIOMD0000000072/BIOMD0000000072_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000073_url.txt b/doc/examples/biomodels/BIOMD0000000073/BIOMD0000000073_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000073_url.txt rename to doc/examples/biomodels/BIOMD0000000073/BIOMD0000000073_url.txt index be37945ba..2bf01c6b4 100644 --- a/doc/examples/biomodels/BIOMD0000000073_url.txt +++ b/doc/examples/biomodels/BIOMD0000000073/BIOMD0000000073_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000074_url.txt b/doc/examples/biomodels/BIOMD0000000074/BIOMD0000000074_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000074_url.txt rename to doc/examples/biomodels/BIOMD0000000074/BIOMD0000000074_url.txt index b2d89b42c..643a4e0fa 100644 --- a/doc/examples/biomodels/BIOMD0000000074_url.txt +++ b/doc/examples/biomodels/BIOMD0000000074/BIOMD0000000074_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000075_url.txt b/doc/examples/biomodels/BIOMD0000000075/BIOMD0000000075_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000075_url.txt rename to doc/examples/biomodels/BIOMD0000000075/BIOMD0000000075_url.txt index f21494369..430830dc3 100644 --- a/doc/examples/biomodels/BIOMD0000000075_url.txt +++ b/doc/examples/biomodels/BIOMD0000000075/BIOMD0000000075_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Xu2003_Phosphoinositide_turnover() // Compartments and Species: @@ -129,7 +129,7 @@ model *Xu2003_Phosphoinositide_turnover() unit length = metre; unit area = (1e-6 metre)^2; unit volume = litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = item; unit unit_0 = 1e-18 avogadro; unit unit_1 = item / (1e6 metre)^2; diff --git a/doc/examples/biomodels/BIOMD0000000076_url.txt b/doc/examples/biomodels/BIOMD0000000076/BIOMD0000000076_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000076_url.txt rename to doc/examples/biomodels/BIOMD0000000076/BIOMD0000000076_url.txt index 47f26aa5d..ab2155859 100644 --- a/doc/examples/biomodels/BIOMD0000000076_url.txt +++ b/doc/examples/biomodels/BIOMD0000000076/BIOMD0000000076_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Cronwright2002_Glycerol_Synthesis() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000077_url.txt b/doc/examples/biomodels/BIOMD0000000077/BIOMD0000000077_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000077_url.txt rename to doc/examples/biomodels/BIOMD0000000077/BIOMD0000000077_url.txt index 64c22e1eb..c30f66a01 100644 --- a/doc/examples/biomodels/BIOMD0000000077_url.txt +++ b/doc/examples/biomodels/BIOMD0000000077/BIOMD0000000077_url.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: compartment cell; species H in cell, HR in cell, R in cell, HRRH in cell, E in cell, GQ in cell; - species IP3 in cell, $CHO in cell; + species IP3 in cell, CHO in cell; // Assignment Rules: CHO := 0.001*alpha*IP3*(0.3 + 0.3*beta*time*exp(1 - beta*time))/(1 + 0.001*alpha*IP3); diff --git a/doc/examples/biomodels/BIOMD0000000078_url.txt b/doc/examples/biomodels/BIOMD0000000078/BIOMD0000000078_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000078_url.txt rename to doc/examples/biomodels/BIOMD0000000078/BIOMD0000000078_url.txt index 50a6d2727..bb2d2163c 100644 --- a/doc/examples/biomodels/BIOMD0000000078_url.txt +++ b/doc/examples/biomodels/BIOMD0000000078/BIOMD0000000078_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000079_url.txt b/doc/examples/biomodels/BIOMD0000000079/BIOMD0000000079_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000079_url.txt rename to doc/examples/biomodels/BIOMD0000000079/BIOMD0000000079_url.txt index 22c1d993e..f60e509c3 100644 --- a/doc/examples/biomodels/BIOMD0000000079_url.txt +++ b/doc/examples/biomodels/BIOMD0000000079/BIOMD0000000079_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_0() // Compartments and Species: @@ -14,9 +14,9 @@ model *Model_0() reaction_5: R => ; reaction_5_V*R/(reaction_5_Km + R); // Species initializations: - P = 0.43/body; - Q = 0.8/body; - R = 0.55/body; + P = 0.43*body; + Q = 0.8*body; + R = 0.55*body; // Compartment initializations: body = 1; diff --git a/doc/examples/biomodels/BIOMD0000000080_url.txt b/doc/examples/biomodels/BIOMD0000000080/BIOMD0000000080_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000080_url.txt rename to doc/examples/biomodels/BIOMD0000000080/BIOMD0000000080_url.txt index f0ec71fa8..cfad6eed5 100644 --- a/doc/examples/biomodels/BIOMD0000000080_url.txt +++ b/doc/examples/biomodels/BIOMD0000000080/BIOMD0000000080_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000081_url.txt b/doc/examples/biomodels/BIOMD0000000081/BIOMD0000000081_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000081_url.txt rename to doc/examples/biomodels/BIOMD0000000081/BIOMD0000000081_url.txt index c5cc7830f..85d40e7e1 100644 --- a/doc/examples/biomodels/BIOMD0000000081_url.txt +++ b/doc/examples/biomodels/BIOMD0000000081/BIOMD0000000081_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Suh2004_KCNQ_regulation() // Compartments and Species: @@ -146,7 +146,7 @@ model *Suh2004_KCNQ_regulation() unit length = metre; unit area = (1e-6 metre)^2; unit volume = litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = item; unit unit_0 = 1 / dimensionless^-0; unit unit_1 = item / (1e6 metre)^2; diff --git a/doc/examples/biomodels/BIOMD0000000082_url.txt b/doc/examples/biomodels/BIOMD0000000082/BIOMD0000000082_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000082_url.txt rename to doc/examples/biomodels/BIOMD0000000082/BIOMD0000000082_url.txt index aa2407e8d..79af7aa99 100644 --- a/doc/examples/biomodels/BIOMD0000000082_url.txt +++ b/doc/examples/biomodels/BIOMD0000000082/BIOMD0000000082_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000083_url.txt b/doc/examples/biomodels/BIOMD0000000083/BIOMD0000000083_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000083_url.txt rename to doc/examples/biomodels/BIOMD0000000083/BIOMD0000000083_url.txt index 5a7e530f9..7ba033e76 100644 --- a/doc/examples/biomodels/BIOMD0000000083_url.txt +++ b/doc/examples/biomodels/BIOMD0000000083/BIOMD0000000083_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Leloup2003_CircClock_LD_REV_ERBalpha() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000084_url.txt b/doc/examples/biomodels/BIOMD0000000084/BIOMD0000000084_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000084_url.txt rename to doc/examples/biomodels/BIOMD0000000084/BIOMD0000000084_url.txt index 5bc38ec82..c04f19a79 100644 --- a/doc/examples/biomodels/BIOMD0000000084_url.txt +++ b/doc/examples/biomodels/BIOMD0000000084/BIOMD0000000084_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hornberg2005_ERKcascade() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000085_url.txt b/doc/examples/biomodels/BIOMD0000000085/BIOMD0000000085_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000085_url.txt rename to doc/examples/biomodels/BIOMD0000000085/BIOMD0000000085_url.txt index 0552cfbfc..289d4d244 100644 --- a/doc/examples/biomodels/BIOMD0000000085_url.txt +++ b/doc/examples/biomodels/BIOMD0000000085/BIOMD0000000085_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Maurya2005() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000086_url.txt b/doc/examples/biomodels/BIOMD0000000086/BIOMD0000000086_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000086_url.txt rename to doc/examples/biomodels/BIOMD0000000086/BIOMD0000000086_url.txt index afa585efa..84ba5ea10 100644 --- a/doc/examples/biomodels/BIOMD0000000086_url.txt +++ b/doc/examples/biomodels/BIOMD0000000086/BIOMD0000000086_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_0() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000087_url.txt b/doc/examples/biomodels/BIOMD0000000087/BIOMD0000000087_url.txt similarity index 96% rename from doc/examples/biomodels/BIOMD0000000087_url.txt rename to doc/examples/biomodels/BIOMD0000000087/BIOMD0000000087_url.txt index 1ae3704ed..77c473d76 100644 --- a/doc/examples/biomodels/BIOMD0000000087_url.txt +++ b/doc/examples/biomodels/BIOMD0000000087/BIOMD0000000087_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *YeastWTmodel2() // Compartments and Species: @@ -69,13 +69,13 @@ model *YeastWTmodel2() // Events: Rad9KinaseActivation: at Mec1RPAssDNA >= 800: Rad9Kin = 1; - ssDNAremoval: at (Mec1RPAssDNA + RPAssDNA + ssDNA) <= 1: ssDNA = 0, RPAssDNA = 0, Mec1RPAssDNA = 0, recovery = 1; - G2MRecoveryCompleted: at (G2 == 1) && (Rad17Utelo == 0): Rad53A = 0, Rad53I = 6900, ExoXI = 70, ExoXA = 0, Exo1I = 670, Exo1A = 0, Dun1I = 3000, Dun1A = 0, Chk1I = 60, Chk1A = 0, Rad9I = 20, Rad9A = 0, recovery = 0, G2Moff = 0, G2Mon = 1; + ssDNAremoval: at (Mec1RPAssDNA + RPAssDNA + ssDNA) <= 1: recovery = 1, Mec1RPAssDNA = 0, RPAssDNA = 0, ssDNA = 0; + G2MRecoveryCompleted: at (G2 == 1) && (Rad17Utelo == 0): G2Mon = 1, G2Moff = 0, recovery = 0, Rad9A = 0, Rad9I = 20, Chk1A = 0, Chk1I = 60, Dun1A = 0, Dun1I = 3000, Exo1A = 0, Exo1I = 670, ExoXA = 0, ExoXI = 70, Rad53I = 6900, Rad53A = 0; SphaseRecoveryCompleted: at Rad17Utelo == 0: recovery = 0; - G1CdkActivation: at G1cyclin > 100: G1CdkI = 0, G1CdkA = 1; - SCdkActivation: at Scyclin > 100: SCdkI = 0, SCdkA = 1; - G2CdkActivation: at G2cyclin > 100: G2CdkI = 0, G2CdkA = 1; - MCdkActivation: at Mcyclin > 100: MCdkI = 0, MCdkA = 1; + G1CdkActivation: at G1cyclin > 100: G1CdkA = 1, G1CdkI = 0; + SCdkActivation: at Scyclin > 100: SCdkA = 1, SCdkI = 0; + G2CdkActivation: at G2cyclin > 100: G2CdkA = 1, G2CdkI = 0; + MCdkActivation: at Mcyclin > 100: MCdkA = 1, MCdkI = 0; CellDeath: at (Mec1RPAssDNA + RPAssDNA + ssDNA) >= 2000: kalive = 0; // Species initializations: diff --git a/doc/examples/biomodels/BIOMD0000000088_url.txt b/doc/examples/biomodels/BIOMD0000000088/BIOMD0000000088_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000088_url.txt rename to doc/examples/biomodels/BIOMD0000000088/BIOMD0000000088_url.txt index 3b710bde9..d7c2fe722 100644 --- a/doc/examples/biomodels/BIOMD0000000088_url.txt +++ b/doc/examples/biomodels/BIOMD0000000088/BIOMD0000000088_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Maeda2006_MyosinPhosphorylation() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000089_url.txt b/doc/examples/biomodels/BIOMD0000000089/BIOMD0000000089_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000089_url.txt rename to doc/examples/biomodels/BIOMD0000000089/BIOMD0000000089_url.txt index 68d9448ea..d9c75e0fa 100644 --- a/doc/examples/biomodels/BIOMD0000000089_url.txt +++ b/doc/examples/biomodels/BIOMD0000000089/BIOMD0000000089_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Locke2006_CircClock_LL() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000090_url.txt b/doc/examples/biomodels/BIOMD0000000090/BIOMD0000000090_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000090_url.txt rename to doc/examples/biomodels/BIOMD0000000090/BIOMD0000000090_url.txt index 2e1c21f76..be128dfa7 100644 --- a/doc/examples/biomodels/BIOMD0000000090_url.txt +++ b/doc/examples/biomodels/BIOMD0000000090/BIOMD0000000090_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wolf2001_Respiratory_Oscillations() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000091_url.txt b/doc/examples/biomodels/BIOMD0000000091/BIOMD0000000091_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000091_url.txt rename to doc/examples/biomodels/BIOMD0000000091/BIOMD0000000091_url.txt index 298f7361a..166957877 100644 --- a/doc/examples/biomodels/BIOMD0000000091_url.txt +++ b/doc/examples/biomodels/BIOMD0000000091/BIOMD0000000091_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Proctor2005_Hsp90() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000092_url.txt b/doc/examples/biomodels/BIOMD0000000092/BIOMD0000000092_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000092_url.txt rename to doc/examples/biomodels/BIOMD0000000092/BIOMD0000000092_url.txt index ecd0adcca..a350eb140 100644 --- a/doc/examples/biomodels/BIOMD0000000092_url.txt +++ b/doc/examples/biomodels/BIOMD0000000092/BIOMD0000000092_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Fuentes2005_ZymogenActivation() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000093_url.txt b/doc/examples/biomodels/BIOMD0000000093/BIOMD0000000093_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000093_url.txt rename to doc/examples/biomodels/BIOMD0000000093/BIOMD0000000093_url.txt index 8c62d7a3b..d21606088 100644 --- a/doc/examples/biomodels/BIOMD0000000093_url.txt +++ b/doc/examples/biomodels/BIOMD0000000093/BIOMD0000000093_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Yamada2003_JAK_STAT_Pathway() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000094_url.txt b/doc/examples/biomodels/BIOMD0000000094/BIOMD0000000094_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000094_url.txt rename to doc/examples/biomodels/BIOMD0000000094/BIOMD0000000094_url.txt index 3b07defcc..f513b27d7 100644 --- a/doc/examples/biomodels/BIOMD0000000094_url.txt +++ b/doc/examples/biomodels/BIOMD0000000094/BIOMD0000000094_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Yamada2003_JAK_STAT_SOCS1_knockout() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000095_url.txt b/doc/examples/biomodels/BIOMD0000000095/BIOMD0000000095_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000095_url.txt rename to doc/examples/biomodels/BIOMD0000000095/BIOMD0000000095_url.txt index ffa65aa91..b2e3a63c2 100644 --- a/doc/examples/biomodels/BIOMD0000000095_url.txt +++ b/doc/examples/biomodels/BIOMD0000000095/BIOMD0000000095_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zeilinger2006_PRR7_PRR9_Y() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000096_url.txt b/doc/examples/biomodels/BIOMD0000000096/BIOMD0000000096_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000096_url.txt rename to doc/examples/biomodels/BIOMD0000000096/BIOMD0000000096_url.txt index 9de69d90e..ba674d220 100644 --- a/doc/examples/biomodels/BIOMD0000000096_url.txt +++ b/doc/examples/biomodels/BIOMD0000000096/BIOMD0000000096_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zeilinger2006_PRR7_PRR9light_Y() // Compartments and Species: @@ -58,7 +58,7 @@ model *Zeilinger2006_PRR7_PRR9light_Y() R45: cP9n => ; nucleus*m21*cP9n/(k19 + cP9n); // Events: - event_0000001: at (Day_in_hours - time) <= 0: ld = 1, Day_in_hours = Day_in_hours + 24; + event_0000001: at (Day_in_hours - time) <= 0: Day_in_hours = Day_in_hours + 24, ld = 1; event_0000002: at ((Day_in_hours - time) <= 12) && ((Day_in_hours - time) > 0): ld = 0; // Species initializations: diff --git a/doc/examples/biomodels/BIOMD0000000097_url.txt b/doc/examples/biomodels/BIOMD0000000097/BIOMD0000000097_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000097_url.txt rename to doc/examples/biomodels/BIOMD0000000097/BIOMD0000000097_url.txt index a3fc038ef..8f9eb45d8 100644 --- a/doc/examples/biomodels/BIOMD0000000097_url.txt +++ b/doc/examples/biomodels/BIOMD0000000097/BIOMD0000000097_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zeilinger2006_PRR7_PRR9light_Yprime() // Compartments and Species: @@ -58,7 +58,7 @@ model *Zeilinger2006_PRR7_PRR9light_Yprime() R45: cP9n => ; nucleus*m21*cP9n/(k19 + cP9n); // Events: - event_0000001: at (Day_in_hours - time) <= 0: ld = 1, Day_in_hours = Day_in_hours + 24; + event_0000001: at (Day_in_hours - time) <= 0: Day_in_hours = Day_in_hours + 24, ld = 1; event_0000002: at ((Day_in_hours - time) <= 16) && ((Day_in_hours - time) > 0): ld = 0; // Species initializations: diff --git a/doc/examples/biomodels/BIOMD0000000098_url.txt b/doc/examples/biomodels/BIOMD0000000098/BIOMD0000000098_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000098_url.txt rename to doc/examples/biomodels/BIOMD0000000098/BIOMD0000000098_url.txt index 866dde44d..f371699f0 100644 --- a/doc/examples/biomodels/BIOMD0000000098_url.txt +++ b/doc/examples/biomodels/BIOMD0000000098/BIOMD0000000098_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Goldbeter1990_CalciumSpike_CICR() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000099_url.txt b/doc/examples/biomodels/BIOMD0000000099/BIOMD0000000099_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000099_url.txt rename to doc/examples/biomodels/BIOMD0000000099/BIOMD0000000099_url.txt index c64f0d07a..c669ea420 100644 --- a/doc/examples/biomodels/BIOMD0000000099_url.txt +++ b/doc/examples/biomodels/BIOMD0000000099/BIOMD0000000099_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000100_url.txt b/doc/examples/biomodels/BIOMD0000000100/BIOMD0000000100_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000100_url.txt rename to doc/examples/biomodels/BIOMD0000000100/BIOMD0000000100_url.txt index ace3f7a44..2a9d9392f 100644 --- a/doc/examples/biomodels/BIOMD0000000100_url.txt +++ b/doc/examples/biomodels/BIOMD0000000100/BIOMD0000000100_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Rozi2003_Glycogen_Phosphorylase_Activation() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000101_url.txt b/doc/examples/biomodels/BIOMD0000000101/BIOMD0000000101_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000101_url.txt rename to doc/examples/biomodels/BIOMD0000000101/BIOMD0000000101_url.txt index 06269f499..076dc4e5c 100644 --- a/doc/examples/biomodels/BIOMD0000000101_url.txt +++ b/doc/examples/biomodels/BIOMD0000000101/BIOMD0000000101_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Vilar2006_TGFbeta() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000102_url.txt b/doc/examples/biomodels/BIOMD0000000102/BIOMD0000000102_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000102_url.txt rename to doc/examples/biomodels/BIOMD0000000102/BIOMD0000000102_url.txt index ee1d753bb..a4aacef48 100644 --- a/doc/examples/biomodels/BIOMD0000000102_url.txt +++ b/doc/examples/biomodels/BIOMD0000000102/BIOMD0000000102_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Legewie2006_apoptosis_WT() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000103_url.txt b/doc/examples/biomodels/BIOMD0000000103/BIOMD0000000103_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000103_url.txt rename to doc/examples/biomodels/BIOMD0000000103/BIOMD0000000103_url.txt index 4252dae1f..b875b71b3 100644 --- a/doc/examples/biomodels/BIOMD0000000103_url.txt +++ b/doc/examples/biomodels/BIOMD0000000103/BIOMD0000000103_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Legewie2006_apoptosis_NC() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000104_url.txt b/doc/examples/biomodels/BIOMD0000000104/BIOMD0000000104_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000104_url.txt rename to doc/examples/biomodels/BIOMD0000000104/BIOMD0000000104_url.txt index 89c3ece81..e050238de 100644 --- a/doc/examples/biomodels/BIOMD0000000104_url.txt +++ b/doc/examples/biomodels/BIOMD0000000104/BIOMD0000000104_url.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_0() // Compartments and Species: compartment compartment_0; species species_0 in compartment_0, species_1 in compartment_0, species_2 in compartment_0; - species $species_3 in compartment_0, $species_5 in compartment_0, species_4 in compartment_0; + species species_3 in compartment_0, $species_5 in compartment_0, species_4 in compartment_0; // Assignment Rules: species_3 := species_5 - species_2; diff --git a/doc/examples/biomodels/BIOMD0000000105_url.txt b/doc/examples/biomodels/BIOMD0000000105/BIOMD0000000105_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000105_url.txt rename to doc/examples/biomodels/BIOMD0000000105/BIOMD0000000105_url.txt index 5fd2bc3b0..59ba954a3 100644 --- a/doc/examples/biomodels/BIOMD0000000105_url.txt +++ b/doc/examples/biomodels/BIOMD0000000105/BIOMD0000000105_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000105() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000106_url.txt b/doc/examples/biomodels/BIOMD0000000106/BIOMD0000000106_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000106_url.txt rename to doc/examples/biomodels/BIOMD0000000106/BIOMD0000000106_url.txt index c9cb32b7d..90fc74696 100644 --- a/doc/examples/biomodels/BIOMD0000000106_url.txt +++ b/doc/examples/biomodels/BIOMD0000000106/BIOMD0000000106_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Yang2007_ArachidonicAcid() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000107_url.txt b/doc/examples/biomodels/BIOMD0000000107/BIOMD0000000107_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000107_url.txt rename to doc/examples/biomodels/BIOMD0000000107/BIOMD0000000107_url.txt index a27f9b571..86876e54f 100644 --- a/doc/examples/biomodels/BIOMD0000000107_url.txt +++ b/doc/examples/biomodels/BIOMD0000000107/BIOMD0000000107_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Novak1993_M_phase_control() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000108_url.txt b/doc/examples/biomodels/BIOMD0000000108/BIOMD0000000108_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000108_url.txt rename to doc/examples/biomodels/BIOMD0000000108/BIOMD0000000108_url.txt index 9e6da36ab..95276d613 100644 --- a/doc/examples/biomodels/BIOMD0000000108_url.txt +++ b/doc/examples/biomodels/BIOMD0000000108/BIOMD0000000108_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000109_url.txt b/doc/examples/biomodels/BIOMD0000000109/BIOMD0000000109_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000109_url.txt rename to doc/examples/biomodels/BIOMD0000000109/BIOMD0000000109_url.txt index 6724c4f1c..3da8507dd 100644 --- a/doc/examples/biomodels/BIOMD0000000109_url.txt +++ b/doc/examples/biomodels/BIOMD0000000109/BIOMD0000000109_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Haberichter2007_cellcycle() // Compartments and Species: @@ -16,9 +16,9 @@ model *Haberichter2007_cellcycle() species Cdk4Y01YpRbY01YpRbY11YInt in X, Cdk4Y10 in X, Cdk4Y11 in X, CyclinA in X; species CyclinD in X, CyclinE in X, E2F in X, Emi1 in X, p27 in X, pRbY00 in X; species pRbY01 in X, pRbY10 in X, pRbY11 in X, pRbY20 in X, pRbY21 in X; - species $totalYCyclinYD in X, $totalYCyclinYE in X, $totalYCyclinYA in X; - species $totalYp27 in X, $hypophosphorylatedYpRb in X, $hyperphosphorylatedYpRb in X; - species $totalYEmi1 in X, $activeYCdk2 in X; + species totalYCyclinYD in X, totalYCyclinYE in X, totalYCyclinYA in X, totalYp27 in X; + species hypophosphorylatedYpRb in X, hyperphosphorylatedYpRb in X, totalYEmi1 in X; + species activeYCdk2 in X; // Assignment Rules: totalYCyclinYD := CyclinD + Cdk4Y01 + Cdk4Y11; diff --git a/doc/examples/biomodels/BIOMD0000000110_url.txt b/doc/examples/biomodels/BIOMD0000000110/BIOMD0000000110_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000110_url.txt rename to doc/examples/biomodels/BIOMD0000000110/BIOMD0000000110_url.txt index adecc9406..ed0774518 100644 --- a/doc/examples/biomodels/BIOMD0000000110_url.txt +++ b/doc/examples/biomodels/BIOMD0000000110/BIOMD0000000110_url.txt @@ -1,11 +1,11 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Qu2003_CellCycle() // Compartments and Species: compartment cell; - species x1 in cell, x in cell, c0 in cell, $c in cell, ix in cell, ixp in cell; + species x1 in cell, x in cell, c0 in cell, c in cell, ix in cell, ixp in cell; species z0 in cell, z1 in cell, z2 in cell, w0 in cell, w1 in cell, u in cell; - species i in cell, y in cell, $totalCyclin in cell; + species i in cell, y in cell, totalCyclin in cell; // Assignment Rules: c := (c0 - (x + x1 + ix + ixp))/(c0*cell); diff --git a/doc/examples/biomodels/BIOMD0000000111_url.txt b/doc/examples/biomodels/BIOMD0000000111/BIOMD0000000111_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000111_url.txt rename to doc/examples/biomodels/BIOMD0000000111/BIOMD0000000111_url.txt index 07a5513bc..ea01d780c 100644 --- a/doc/examples/biomodels/BIOMD0000000111_url.txt +++ b/doc/examples/biomodels/BIOMD0000000111/BIOMD0000000111_url.txt @@ -1,11 +1,11 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Novak2001_FissionYeast_CellCycle() // Compartments and Species: compartment cell; substanceOnly species cdc13T in cell, preMPF in cell, ste9 in cell, slp1T in cell; substanceOnly species slp1 in cell, IEP in cell, rum1T in cell, SK in cell; - substanceOnly species M in cell, $MPF in cell; + substanceOnly species M in cell, MPF in cell; // Assignment Rules: MPF := (cdc13T - preMPF)*(cdc13T - Trimer)/cdc13T; @@ -37,7 +37,7 @@ model *Novak2001_FissionYeast_CellCycle() R19: => M; mu*M; // Events: - event_0000001: at (MPF <= 0.1) && (flag_MPF == 1): flag_MPF = 0, M = M/2; + event_0000001: at (MPF <= 0.1) && (flag_MPF == 1): M = M/2, flag_MPF = 0; event_0000002: at MPF > 0.1: flag_MPF = 1; // Species initializations: diff --git a/doc/examples/biomodels/BIOMD0000000112_url.txt b/doc/examples/biomodels/BIOMD0000000112/BIOMD0000000112_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000112_url.txt rename to doc/examples/biomodels/BIOMD0000000112/BIOMD0000000112_url.txt index 3af7b4ca0..6261e4963 100644 --- a/doc/examples/biomodels/BIOMD0000000112_url.txt +++ b/doc/examples/biomodels/BIOMD0000000112/BIOMD0000000112_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Clarke2006_Smad_signalling() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000113_url.txt b/doc/examples/biomodels/BIOMD0000000113/BIOMD0000000113_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000113_url.txt rename to doc/examples/biomodels/BIOMD0000000113/BIOMD0000000113_url.txt index b78000b6d..33b7a6cf4 100644 --- a/doc/examples/biomodels/BIOMD0000000113_url.txt +++ b/doc/examples/biomodels/BIOMD0000000113/BIOMD0000000113_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Dupont1992_Ca_dpt_protein_phospho() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000114_url.txt b/doc/examples/biomodels/BIOMD0000000114/BIOMD0000000114_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000114_url.txt rename to doc/examples/biomodels/BIOMD0000000114/BIOMD0000000114_url.txt index 29d7cbfad..423737277 100644 --- a/doc/examples/biomodels/BIOMD0000000114_url.txt +++ b/doc/examples/biomodels/BIOMD0000000114/BIOMD0000000114_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000115_url.txt b/doc/examples/biomodels/BIOMD0000000115/BIOMD0000000115_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000115_url.txt rename to doc/examples/biomodels/BIOMD0000000115/BIOMD0000000115_url.txt index 9c84581b6..2fd5258f4 100644 --- a/doc/examples/biomodels/BIOMD0000000115_url.txt +++ b/doc/examples/biomodels/BIOMD0000000115/BIOMD0000000115_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000116_url.txt b/doc/examples/biomodels/BIOMD0000000116/BIOMD0000000116_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000116_url.txt rename to doc/examples/biomodels/BIOMD0000000116/BIOMD0000000116_url.txt index f8c43f46a..58887b042 100644 --- a/doc/examples/biomodels/BIOMD0000000116_url.txt +++ b/doc/examples/biomodels/BIOMD0000000116/BIOMD0000000116_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_0() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000117_url.txt b/doc/examples/biomodels/BIOMD0000000117/BIOMD0000000117_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000117_url.txt rename to doc/examples/biomodels/BIOMD0000000117/BIOMD0000000117_url.txt index a8bde6393..e0b18cabb 100644 --- a/doc/examples/biomodels/BIOMD0000000117_url.txt +++ b/doc/examples/biomodels/BIOMD0000000117/BIOMD0000000117_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000118_url.txt b/doc/examples/biomodels/BIOMD0000000118/BIOMD0000000118_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000118_url.txt rename to doc/examples/biomodels/BIOMD0000000118/BIOMD0000000118_url.txt index 00ae4b168..66ff2c18f 100644 --- a/doc/examples/biomodels/BIOMD0000000118_url.txt +++ b/doc/examples/biomodels/BIOMD0000000118/BIOMD0000000118_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000119_url.txt b/doc/examples/biomodels/BIOMD0000000119/BIOMD0000000119_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000119_url.txt rename to doc/examples/biomodels/BIOMD0000000119/BIOMD0000000119_url.txt index 735551d3c..d894152dc 100644 --- a/doc/examples/biomodels/BIOMD0000000119_url.txt +++ b/doc/examples/biomodels/BIOMD0000000119/BIOMD0000000119_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000120_url.txt b/doc/examples/biomodels/BIOMD0000000120/BIOMD0000000120_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000120_url.txt rename to doc/examples/biomodels/BIOMD0000000120/BIOMD0000000120_url.txt index 2d589f502..e689c01b4 100644 --- a/doc/examples/biomodels/BIOMD0000000120_url.txt +++ b/doc/examples/biomodels/BIOMD0000000120/BIOMD0000000120_url.txt @@ -1,11 +1,11 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Chan2004_TCell_receptor_activation() // Compartments and Species: compartment compartment_; substanceOnly species lck_inactive in compartment_, lck_active in compartment_; substanceOnly species phosphatase_inactive in compartment_, phosphatase_active in compartment_; - substanceOnly species $lck_total in compartment_; + substanceOnly species lck_total in compartment_; // Assignment Rules: lck_total := lck_inactive + lck_active; diff --git a/doc/examples/biomodels/BIOMD0000000121_url.txt b/doc/examples/biomodels/BIOMD0000000121/BIOMD0000000121_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000121_url.txt rename to doc/examples/biomodels/BIOMD0000000121/BIOMD0000000121_url.txt index 063cd493e..f9565d094 100644 --- a/doc/examples/biomodels/BIOMD0000000121_url.txt +++ b/doc/examples/biomodels/BIOMD0000000121/BIOMD0000000121_url.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: compartment cell; - species c3 in cell, c2 in cell, c1 in cell, o in cell, i in cell, $ik in cell; + species c3 in cell, c2 in cell, c1 in cell, o in cell, i in cell, ik in cell; // Assignment Rules: ik := Gk*o*(v - vk); diff --git a/doc/examples/biomodels/BIOMD0000000122_url.txt b/doc/examples/biomodels/BIOMD0000000122/BIOMD0000000122_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000122_url.txt rename to doc/examples/biomodels/BIOMD0000000122/BIOMD0000000122_url.txt index 6cd2ae3c6..b0504b5cd 100644 --- a/doc/examples/biomodels/BIOMD0000000122_url.txt +++ b/doc/examples/biomodels/BIOMD0000000122/BIOMD0000000122_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Fisher2006_Ca_Oscillation_dpdnt_NFAT_dynamics() // Compartments and Species: @@ -29,9 +29,9 @@ model *Fisher2006_Ca_Oscillation_dpdnt_NFAT_dynamics() R16: $Ca_Cyt -> $Ca_Nuc; cytosol*k21*Ca_Cyt - nucleus*k22*Ca_Nuc; // Events: - event_0000001: at ((Time_in_Seconds - time) <= 0) && (time < 1500): Ca_Nuc = 1, Ca_Cyt = 1, Time_in_Seconds = Time_in_Seconds + 100; - event_0000002: at ((Time_in_Seconds - time) <= 90) && (time < 1500): Ca_Nuc = 0.1, Ca_Cyt = 0.1; - event_0000003: at time >= 1500: Ca_Nuc = 0.1, Ca_Cyt = 0.1; + event_0000001: at ((Time_in_Seconds - time) <= 0) && (time < 1500): Time_in_Seconds = Time_in_Seconds + 100, Ca_Cyt = 1, Ca_Nuc = 1; + event_0000002: at ((Time_in_Seconds - time) <= 90) && (time < 1500): Ca_Cyt = 0.1, Ca_Nuc = 0.1; + event_0000003: at time >= 1500: Ca_Cyt = 0.1, Ca_Nuc = 0.1; // Species initializations: Ca_Nuc = 1; diff --git a/doc/examples/biomodels/BIOMD0000000123_url.txt b/doc/examples/biomodels/BIOMD0000000123/BIOMD0000000123_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000123_url.txt rename to doc/examples/biomodels/BIOMD0000000123/BIOMD0000000123_url.txt index 402018710..9cf16b34b 100644 --- a/doc/examples/biomodels/BIOMD0000000123_url.txt +++ b/doc/examples/biomodels/BIOMD0000000123/BIOMD0000000123_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Fisher2006_NFAT_Activation() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000124_url.txt b/doc/examples/biomodels/BIOMD0000000124/BIOMD0000000124_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000124_url.txt rename to doc/examples/biomodels/BIOMD0000000124/BIOMD0000000124_url.txt index c55db3a6e..e70204b20 100644 --- a/doc/examples/biomodels/BIOMD0000000124_url.txt +++ b/doc/examples/biomodels/BIOMD0000000124/BIOMD0000000124_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000125_url.txt b/doc/examples/biomodels/BIOMD0000000125/BIOMD0000000125_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000125_url.txt rename to doc/examples/biomodels/BIOMD0000000125/BIOMD0000000125_url.txt index 289bbdd66..52f0064a4 100644 --- a/doc/examples/biomodels/BIOMD0000000125_url.txt +++ b/doc/examples/biomodels/BIOMD0000000125/BIOMD0000000125_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000126_url.txt b/doc/examples/biomodels/BIOMD0000000126/BIOMD0000000126_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000126_url.txt rename to doc/examples/biomodels/BIOMD0000000126/BIOMD0000000126_url.txt index b4491257d..e763a8b3d 100644 --- a/doc/examples/biomodels/BIOMD0000000126_url.txt +++ b/doc/examples/biomodels/BIOMD0000000126/BIOMD0000000126_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000127_url.txt b/doc/examples/biomodels/BIOMD0000000127/BIOMD0000000127_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000127_url.txt rename to doc/examples/biomodels/BIOMD0000000127/BIOMD0000000127_url.txt index 9b657cb44..89e2c79ab 100644 --- a/doc/examples/biomodels/BIOMD0000000127_url.txt +++ b/doc/examples/biomodels/BIOMD0000000127/BIOMD0000000127_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: @@ -9,7 +9,7 @@ model *model_0000001() U' = a*(b*v - U); // Events: - event_0000001: at v > Vthresh: U = U + d, v = c; + event_0000001: at v > Vthresh: v = c, U = U + d; event_0000002: at time > 10: i = 10; // Compartment initializations: diff --git a/doc/examples/biomodels/BIOMD0000000128_url.txt b/doc/examples/biomodels/BIOMD0000000128/BIOMD0000000128_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000128_url.txt rename to doc/examples/biomodels/BIOMD0000000128/BIOMD0000000128_url.txt index b6b2ca373..a4c7ed7e9 100644 --- a/doc/examples/biomodels/BIOMD0000000128_url.txt +++ b/doc/examples/biomodels/BIOMD0000000128/BIOMD0000000128_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: @@ -35,7 +35,7 @@ model *model_0000001() reaction_000003: => cAMP; cell*ETswitch*((cAMPlow - cAMP)/taudir); // Events: - event_0000001: at time > 60000: ETswitch = 1, girk = 3000, IP3 = 0.3; + event_0000001: at time > 60000: IP3 = 0.3, girk = 3000, ETswitch = 1; // Species initializations: c = 0.3; diff --git a/doc/examples/biomodels/BIOMD0000000129_url.txt b/doc/examples/biomodels/BIOMD0000000129/BIOMD0000000129_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000129_url.txt rename to doc/examples/biomodels/BIOMD0000000129/BIOMD0000000129_url.txt index 934275a00..6ab247699 100644 --- a/doc/examples/biomodels/BIOMD0000000129_url.txt +++ b/doc/examples/biomodels/BIOMD0000000129/BIOMD0000000129_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Izhikevich2004_SpikingNeurons_inhibitionInducedSpiking() // Compartments and Species: @@ -9,7 +9,7 @@ model *Izhikevich2004_SpikingNeurons_inhibitionInducedSpiking() u' = a*(b*v - u); // Events: - event_0000001: at v > Vthresh: u = u + d, v = c; + event_0000001: at v > Vthresh: v = c, u = u + d; event_0000002: at (time >= 50) && (time <= 250): i = 75; event_0000003: at time >= 250: i = 80; diff --git a/doc/examples/biomodels/BIOMD0000000130_url.txt b/doc/examples/biomodels/BIOMD0000000130/BIOMD0000000130_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000130_url.txt rename to doc/examples/biomodels/BIOMD0000000130/BIOMD0000000130_url.txt index a570fe8f8..10761ec27 100644 --- a/doc/examples/biomodels/BIOMD0000000130_url.txt +++ b/doc/examples/biomodels/BIOMD0000000130/BIOMD0000000130_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Izhikevich2004_SpikingNeurons_integrator() // Compartments and Species: @@ -9,7 +9,7 @@ model *Izhikevich2004_SpikingNeurons_integrator() u' = a*(b*v - u); // Events: - event_0000001: at v > Vthresh: u = u + d, v = c; + event_0000001: at v > Vthresh: v = c, u = u + d; event_0000002: at ((time > 9) && (time < 11)) || ((time > 14) && (time < 16)): i = 9; event_0000003: at ((time > 70) && (time < 72)) || ((time > 80) && (time < 82)): i = 9; event_0000004: at ((time >= 11) && (time <= 14)) || ((time >= 14) && (time < 16)): i = 0; diff --git a/doc/examples/biomodels/BIOMD0000000131_url.txt b/doc/examples/biomodels/BIOMD0000000131/BIOMD0000000131_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000131_url.txt rename to doc/examples/biomodels/BIOMD0000000131/BIOMD0000000131_url.txt index 67e885dff..2fe83da8e 100644 --- a/doc/examples/biomodels/BIOMD0000000131_url.txt +++ b/doc/examples/biomodels/BIOMD0000000131/BIOMD0000000131_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Izhikevich2004_SpikingNeurons_reboundBurst() // Compartments and Species: @@ -9,7 +9,7 @@ model *Izhikevich2004_SpikingNeurons_reboundBurst() u' = a*(b*v - u); // Events: - event_0000001: at v > Vthresh: u = u + d, v = c; + event_0000001: at v > Vthresh: v = c, u = u + d; event_0000003: at (time > 20) && (time < 25): i = -15; event_0000004: at time >= 25: i = 0; diff --git a/doc/examples/biomodels/BIOMD0000000132_url.txt b/doc/examples/biomodels/BIOMD0000000132/BIOMD0000000132_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000132_url.txt rename to doc/examples/biomodels/BIOMD0000000132/BIOMD0000000132_url.txt index 4f694b3c2..e0b9cb691 100644 --- a/doc/examples/biomodels/BIOMD0000000132_url.txt +++ b/doc/examples/biomodels/BIOMD0000000132/BIOMD0000000132_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Izhikevich2004_SpikingNeurons_reboundSpike() // Compartments and Species: @@ -9,7 +9,7 @@ model *Izhikevich2004_SpikingNeurons_reboundSpike() u' = a*(b*v - u); // Events: - event_0000001: at v > Vthresh: u = u + d, v = c; + event_0000001: at v > Vthresh: v = c, u = u + d; event_0000003: at (time > 20) && (time < 25): i = -15; event_0000004: at time >= 25: i = 0; diff --git a/doc/examples/biomodels/BIOMD0000000133_url.txt b/doc/examples/biomodels/BIOMD0000000133/BIOMD0000000133_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000133_url.txt rename to doc/examples/biomodels/BIOMD0000000133/BIOMD0000000133_url.txt index f5f0c3a5a..452de62d2 100644 --- a/doc/examples/biomodels/BIOMD0000000133_url.txt +++ b/doc/examples/biomodels/BIOMD0000000133/BIOMD0000000133_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Izhikevich2004_SpikingNeurons_resonator() // Compartments and Species: @@ -9,7 +9,7 @@ model *Izhikevich2004_SpikingNeurons_resonator() u' = a*(b*v - u); // Events: - event_0000001: at v > Vthresh: u = u + d, v = c; + event_0000001: at v > Vthresh: v = c, u = u + d; event_0000003: at ((time > 280) && (time < 284)) || ((time > 320) && (time < 324)) || ((time > 40) && (time < 44)) || ((time > 60) && (time < 64)): i = 0.65; event_0000004: at ((time >= 44) && (time <= 60)) || ((time >= 64) && (time <= 280)): i = 0; event_0000005: at ((time >= 284) && (time <= 320)) || (time >= 324): i = 0; diff --git a/doc/examples/biomodels/BIOMD0000000134_url.txt b/doc/examples/biomodels/BIOMD0000000134/BIOMD0000000134_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000134_url.txt rename to doc/examples/biomodels/BIOMD0000000134/BIOMD0000000134_url.txt index f4953ff3c..236659fcb 100644 --- a/doc/examples/biomodels/BIOMD0000000134_url.txt +++ b/doc/examples/biomodels/BIOMD0000000134/BIOMD0000000134_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: @@ -9,7 +9,7 @@ model *model_0000001() u' = a*(b*v - u); // Events: - event_0000001: at v > Vthresh: u = u + d, v = c; + event_0000001: at v > Vthresh: v = c, u = u + d; event_0000002: at (time > 10) && (time < 13): i = 7.04; event_0000003: at time >= 13: i = 0; diff --git a/doc/examples/biomodels/BIOMD0000000135_url.txt b/doc/examples/biomodels/BIOMD0000000135/BIOMD0000000135_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000135_url.txt rename to doc/examples/biomodels/BIOMD0000000135/BIOMD0000000135_url.txt index f4a343de5..d3ec90fe5 100644 --- a/doc/examples/biomodels/BIOMD0000000135_url.txt +++ b/doc/examples/biomodels/BIOMD0000000135/BIOMD0000000135_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: @@ -9,7 +9,7 @@ model *model_0000001() u' = a*(b*v - u); // Events: - event_0000001: at v > Vthresh: u = u + d, v = c; + event_0000001: at v > Vthresh: v = c, u = u + d; event_0000002: at (time > 20) && (time < 25): i = 2; event_0000003: at time >= 25: i = 0; diff --git a/doc/examples/biomodels/BIOMD0000000136_url.txt b/doc/examples/biomodels/BIOMD0000000136/BIOMD0000000136_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000136_url.txt rename to doc/examples/biomodels/BIOMD0000000136/BIOMD0000000136_url.txt index aa30edeed..14cbce9c0 100644 --- a/doc/examples/biomodels/BIOMD0000000136_url.txt +++ b/doc/examples/biomodels/BIOMD0000000136/BIOMD0000000136_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: @@ -9,7 +9,7 @@ model *model_0000001() u' = a*(b*v - u); // Events: - event_0000001: at v > Vthresh: u = u + d, v = c; + event_0000001: at v > Vthresh: v = c, u = u + d; event_0000002: at ((time > 10) && (time < 15)) || ((time > 80) && (time < 85)): i = 1; event_0000003: at (time > 70) && (time < 75): i = -6; event_0000004: at ((time >= 15) && (time <= 70)) || ((time >= 75) && (time <= 80)) || (time >= 85): i = 0; diff --git a/doc/examples/biomodels/BIOMD0000000137_url.txt b/doc/examples/biomodels/BIOMD0000000137/BIOMD0000000137_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000137_url.txt rename to doc/examples/biomodels/BIOMD0000000137/BIOMD0000000137_url.txt index 21ac29a30..225a3195e 100644 --- a/doc/examples/biomodels/BIOMD0000000137_url.txt +++ b/doc/examples/biomodels/BIOMD0000000137/BIOMD0000000137_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Sedaghat2002_InsulinSignalling_noFeedback() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000138_url.txt b/doc/examples/biomodels/BIOMD0000000138/BIOMD0000000138_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000138_url.txt rename to doc/examples/biomodels/BIOMD0000000138/BIOMD0000000138_url.txt index d00dffc3e..66ace81be 100644 --- a/doc/examples/biomodels/BIOMD0000000138_url.txt +++ b/doc/examples/biomodels/BIOMD0000000138/BIOMD0000000138_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000139_url.txt b/doc/examples/biomodels/BIOMD0000000139/BIOMD0000000139_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000139_url.txt rename to doc/examples/biomodels/BIOMD0000000139/BIOMD0000000139_url.txt index 39844d6e9..01eb57440 100644 --- a/doc/examples/biomodels/BIOMD0000000139_url.txt +++ b/doc/examples/biomodels/BIOMD0000000139/BIOMD0000000139_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hoffmann2002_KnockOut_IkBNFkB_Signaling() // Compartments and Species: @@ -69,7 +69,7 @@ model *Hoffmann2002_KnockOut_IkBNFkB_Signaling() v45: IKK => ; cytoplasm*k02*IKK; // Events: - event_0000001: at (time >= 2000) && (trigger_value == 0): flag_for_after_trigger = 0, trigger_value = 1, IKK = 0.1; + event_0000001: at (time >= 2000) && (trigger_value == 0): IKK = 0.1, trigger_value = 1, flag_for_after_trigger = 0; // Species initializations: IkBalpha = 0.1; diff --git a/doc/examples/biomodels/BIOMD0000000140_url.txt b/doc/examples/biomodels/BIOMD0000000140/BIOMD0000000140_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000140_url.txt rename to doc/examples/biomodels/BIOMD0000000140/BIOMD0000000140_url.txt index 948d76a4d..cdbd2d255 100644 --- a/doc/examples/biomodels/BIOMD0000000140_url.txt +++ b/doc/examples/biomodels/BIOMD0000000140/BIOMD0000000140_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hoffmann2002_WT_IkBNFkB_Signaling() // Compartments and Species: @@ -69,7 +69,7 @@ model *Hoffmann2002_WT_IkBNFkB_Signaling() v45: IKK => ; cytoplasm*k02*IKK; // Events: - event_0000001: at (time >= 2000) && (trigger_value == 0): flag_for_after_trigger = 0, trigger_value = 1, IKK = 0.1; + event_0000001: at (time >= 2000) && (trigger_value == 0): IKK = 0.1, trigger_value = 1, flag_for_after_trigger = 0; // Species initializations: IkBalpha = 0.1; diff --git a/doc/examples/biomodels/BIOMD0000000141_url.txt b/doc/examples/biomodels/BIOMD0000000141/BIOMD0000000141_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000141_url.txt rename to doc/examples/biomodels/BIOMD0000000141/BIOMD0000000141_url.txt index 82f61eca9..9f2cc140d 100644 --- a/doc/examples/biomodels/BIOMD0000000141_url.txt +++ b/doc/examples/biomodels/BIOMD0000000141/BIOMD0000000141_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: @@ -12,7 +12,7 @@ model *model_0000001() u' = a*(b*v - u); // Events: - event_0000001: at v > Vthresh: u = u + d, v = c; + event_0000001: at v > Vthresh: v = c, u = u + d; // Compartment initializations: cell = 1; diff --git a/doc/examples/biomodels/BIOMD0000000142_url.txt b/doc/examples/biomodels/BIOMD0000000142/BIOMD0000000142_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000142_url.txt rename to doc/examples/biomodels/BIOMD0000000142/BIOMD0000000142_url.txt index 305522d52..8efb6cee6 100644 --- a/doc/examples/biomodels/BIOMD0000000142_url.txt +++ b/doc/examples/biomodels/BIOMD0000000142/BIOMD0000000142_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: @@ -12,7 +12,7 @@ model *model_0000001() u' = a*(b*v - u); // Events: - event_0000001: at v > Vthresh: u = u + d, v = c; + event_0000001: at v > Vthresh: v = c, u = u + d; // Compartment initializations: cell = 1; diff --git a/doc/examples/biomodels/BIOMD0000000143_url.txt b/doc/examples/biomodels/BIOMD0000000143/BIOMD0000000143_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000143_url.txt rename to doc/examples/biomodels/BIOMD0000000143/BIOMD0000000143_url.txt index a5d73caa2..2433f9655 100644 --- a/doc/examples/biomodels/BIOMD0000000143_url.txt +++ b/doc/examples/biomodels/BIOMD0000000143/BIOMD0000000143_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Olsen2003_neutrophil_oscillatory_metabolism() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000144_url.txt b/doc/examples/biomodels/BIOMD0000000144/BIOMD0000000144_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000144_url.txt rename to doc/examples/biomodels/BIOMD0000000144/BIOMD0000000144_url.txt index 9e516013b..53b2cb75b 100644 --- a/doc/examples/biomodels/BIOMD0000000144_url.txt +++ b/doc/examples/biomodels/BIOMD0000000144/BIOMD0000000144_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_generated_by_BIOCHAM() // Compartments and Species: @@ -71,7 +71,7 @@ model *Model_generated_by_BIOCHAM() _51: => Xp; cytoplasm*ksxp_1*Xm; // Events: - _E0: at FZYa >= kez_1: MPFc = MPFc*((1 - N*E_1)/(1 - 1.95*N*E_1)), StgPn = StgPn/1.95, Stgc = Stgc*((1 - N*E_1)/(1 - 1.95*N*E_1)), StgPc = StgPc*((1 - N*E_1)/(1 - 1.95*N*E_1)), Stgn = Stgn/1.95, Wee1c = Wee1c*((1 - N*E_1)/(1 - 1.95*N*E_1)), Wee1Pn = Wee1Pn/1.95, Wee1n = Wee1n/1.95, preMPFn = preMPFn/1.95, MPFn = MPFn/1.95, N = factor_1*N; + _E0: at FZYa >= kez_1: N = factor_1*N, MPFn = MPFn/1.95, preMPFn = preMPFn/1.95, Wee1n = Wee1n/1.95, Wee1Pn = Wee1Pn/1.95, Wee1c = Wee1c*((1 - N*E_1)/(1 - 1.95*N*E_1)), Stgn = Stgn/1.95, StgPc = StgPc*((1 - N*E_1)/(1 - 1.95*N*E_1)), Stgc = Stgc*((1 - N*E_1)/(1 - 1.95*N*E_1)), StgPn = StgPn/1.95, MPFc = MPFc*((1 - N*E_1)/(1 - 1.95*N*E_1)); // Species initializations: MPFc = 1; diff --git a/doc/examples/biomodels/BIOMD0000000145_url.txt b/doc/examples/biomodels/BIOMD0000000145/BIOMD0000000145_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000145_url.txt rename to doc/examples/biomodels/BIOMD0000000145/BIOMD0000000145_url.txt index 9d0a5946a..a4940a076 100644 --- a/doc/examples/biomodels/BIOMD0000000145_url.txt +++ b/doc/examples/biomodels/BIOMD0000000145/BIOMD0000000145_url.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000145() // Compartments and Species: compartment Cytosol, ER; species Galpha_GTP in Cytosol, APLC in Cytosol, IP3 in Cytosol, Ca_ER in ER; - species Ca_Cyt in Cytosol, $PLC in Cytosol, $DG in Cytosol; + species Ca_Cyt in Cytosol, PLC in Cytosol, DG in Cytosol; // Assignment Rules: PLC := Cplc_total - APLC; diff --git a/doc/examples/biomodels/BIOMD0000000146_url.txt b/doc/examples/biomodels/BIOMD0000000146/BIOMD0000000146_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000146_url.txt rename to doc/examples/biomodels/BIOMD0000000146/BIOMD0000000146_url.txt index 41ffd8fe2..967987ff9 100644 --- a/doc/examples/biomodels/BIOMD0000000146_url.txt +++ b/doc/examples/biomodels/BIOMD0000000146/BIOMD0000000146_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000147_url.txt b/doc/examples/biomodels/BIOMD0000000147/BIOMD0000000147_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000147_url.txt rename to doc/examples/biomodels/BIOMD0000000147/BIOMD0000000147_url.txt index 452d3a906..b74869b22 100644 --- a/doc/examples/biomodels/BIOMD0000000147_url.txt +++ b/doc/examples/biomodels/BIOMD0000000147/BIOMD0000000147_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *ODea2007_IkappaB() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000148_url.txt b/doc/examples/biomodels/BIOMD0000000148/BIOMD0000000148_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000148_url.txt rename to doc/examples/biomodels/BIOMD0000000148/BIOMD0000000148_url.txt index 897e405be..821bf7891 100644 --- a/doc/examples/biomodels/BIOMD0000000148_url.txt +++ b/doc/examples/biomodels/BIOMD0000000148/BIOMD0000000148_url.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Komarova2003_BoneRemodeling() // Compartments and Species: compartment compartment_; - substanceOnly species x1 in compartment_, x2 in compartment_, $x1_bar in compartment_; - substanceOnly species $x2_bar in compartment_, z in compartment_, y1 in compartment_; + substanceOnly species x1 in compartment_, x2 in compartment_, x1_bar in compartment_; + substanceOnly species x2_bar in compartment_, z in compartment_, y1 in compartment_; substanceOnly species y2 in compartment_; // Assignment Rules: diff --git a/doc/examples/biomodels/BIOMD0000000149_url.txt b/doc/examples/biomodels/BIOMD0000000149/BIOMD0000000149_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000149_url.txt rename to doc/examples/biomodels/BIOMD0000000149/BIOMD0000000149_url.txt index f5e7a6a2b..050f0a49a 100644 --- a/doc/examples/biomodels/BIOMD0000000149_url.txt +++ b/doc/examples/biomodels/BIOMD0000000149/BIOMD0000000149_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000149() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000150_url.txt b/doc/examples/biomodels/BIOMD0000000150/BIOMD0000000150_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000150_url.txt rename to doc/examples/biomodels/BIOMD0000000150/BIOMD0000000150_url.txt index 55c2376ff..9a7ed8e5e 100644 --- a/doc/examples/biomodels/BIOMD0000000150_url.txt +++ b/doc/examples/biomodels/BIOMD0000000150/BIOMD0000000150_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Morris2002_CellCycle_CDK2Cyclin() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000151_url.txt b/doc/examples/biomodels/BIOMD0000000151/BIOMD0000000151_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000151_url.txt rename to doc/examples/biomodels/BIOMD0000000151/BIOMD0000000151_url.txt index 3af5309ea..14d93777a 100644 --- a/doc/examples/biomodels/BIOMD0000000151_url.txt +++ b/doc/examples/biomodels/BIOMD0000000151/BIOMD0000000151_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Singh2006_IL6_Signal_Transduction() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000152_url.txt b/doc/examples/biomodels/BIOMD0000000152/BIOMD0000000152_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000152_url.txt rename to doc/examples/biomodels/BIOMD0000000152/BIOMD0000000152_url.txt index ee79a48e4..0390b94e0 100644 --- a/doc/examples/biomodels/BIOMD0000000152_url.txt +++ b/doc/examples/biomodels/BIOMD0000000152/BIOMD0000000152_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000153_url.txt b/doc/examples/biomodels/BIOMD0000000153/BIOMD0000000153_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000153_url.txt rename to doc/examples/biomodels/BIOMD0000000153/BIOMD0000000153_url.txt index d8681144a..b2b2d84b7 100644 --- a/doc/examples/biomodels/BIOMD0000000153_url.txt +++ b/doc/examples/biomodels/BIOMD0000000153/BIOMD0000000153_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000154_url.txt b/doc/examples/biomodels/BIOMD0000000154/BIOMD0000000154_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000154_url.txt rename to doc/examples/biomodels/BIOMD0000000154/BIOMD0000000154_url.txt index 386a263ef..d867aee74 100644 --- a/doc/examples/biomodels/BIOMD0000000154_url.txt +++ b/doc/examples/biomodels/BIOMD0000000154/BIOMD0000000154_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zatorsky2006_p53_Model3() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000155_url.txt b/doc/examples/biomodels/BIOMD0000000155/BIOMD0000000155_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000155_url.txt rename to doc/examples/biomodels/BIOMD0000000155/BIOMD0000000155_url.txt index f145124ee..9fa546f44 100644 --- a/doc/examples/biomodels/BIOMD0000000155_url.txt +++ b/doc/examples/biomodels/BIOMD0000000155/BIOMD0000000155_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zatorsky2006_p53_Model6() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000156_url.txt b/doc/examples/biomodels/BIOMD0000000156/BIOMD0000000156_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000156_url.txt rename to doc/examples/biomodels/BIOMD0000000156/BIOMD0000000156_url.txt index 5299e1162..41fe83196 100644 --- a/doc/examples/biomodels/BIOMD0000000156_url.txt +++ b/doc/examples/biomodels/BIOMD0000000156/BIOMD0000000156_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zatorsky2006_p53_Model5() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000157_url.txt b/doc/examples/biomodels/BIOMD0000000157/BIOMD0000000157_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000157_url.txt rename to doc/examples/biomodels/BIOMD0000000157/BIOMD0000000157_url.txt index 634482a5e..9d9ac0cc6 100644 --- a/doc/examples/biomodels/BIOMD0000000157_url.txt +++ b/doc/examples/biomodels/BIOMD0000000157/BIOMD0000000157_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zatorsky2006_p53_Model4() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000158_url.txt b/doc/examples/biomodels/BIOMD0000000158/BIOMD0000000158_url.txt similarity index 96% rename from doc/examples/biomodels/BIOMD0000000158_url.txt rename to doc/examples/biomodels/BIOMD0000000158/BIOMD0000000158_url.txt index 8679ef630..aebfd41b6 100644 --- a/doc/examples/biomodels/BIOMD0000000158_url.txt +++ b/doc/examples/biomodels/BIOMD0000000158/BIOMD0000000158_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zatorsky2006_p53_Model2() // Compartments and Species: @@ -17,8 +17,8 @@ model *Zatorsky2006_p53_Model2() R6: y -> ; compartment_*alpha_y*y; // Events: - event_0000001: at x >= xmax: flag3 = 0, flag2 = 0, flag1 = 1; - event_0000002: at x < xmax: flag3 = 1, flag2 = 0, flag1 = 0; + event_0000001: at x >= xmax: flag1 = 1, flag2 = 0, flag3 = 0; + event_0000002: at x < xmax: flag1 = 0, flag2 = 0, flag3 = 1; // Species initializations: x = 0.28; diff --git a/doc/examples/biomodels/BIOMD0000000159_url.txt b/doc/examples/biomodels/BIOMD0000000159/BIOMD0000000159_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000159_url.txt rename to doc/examples/biomodels/BIOMD0000000159/BIOMD0000000159_url.txt index c0833d4fc..39d7c6ccf 100644 --- a/doc/examples/biomodels/BIOMD0000000159_url.txt +++ b/doc/examples/biomodels/BIOMD0000000159/BIOMD0000000159_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zatorsky2006_p53_Model1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000160_url.txt b/doc/examples/biomodels/BIOMD0000000160/BIOMD0000000160_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000160_url.txt rename to doc/examples/biomodels/BIOMD0000000160/BIOMD0000000160_url.txt index dd68f7864..e212da56d 100644 --- a/doc/examples/biomodels/BIOMD0000000160_url.txt +++ b/doc/examples/biomodels/BIOMD0000000160/BIOMD0000000160_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Xie2007_CircClock() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000161_url.txt b/doc/examples/biomodels/BIOMD0000000161/BIOMD0000000161_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000161_url.txt rename to doc/examples/biomodels/BIOMD0000000161/BIOMD0000000161_url.txt index ba6894fa2..dd550740f 100644 --- a/doc/examples/biomodels/BIOMD0000000161_url.txt +++ b/doc/examples/biomodels/BIOMD0000000161/BIOMD0000000161_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Eungdamrong2007_Ras_Activation() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000162_url.txt b/doc/examples/biomodels/BIOMD0000000162/BIOMD0000000162_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000162_url.txt rename to doc/examples/biomodels/BIOMD0000000162/BIOMD0000000162_url.txt index 2a256428b..92c655f7b 100644 --- a/doc/examples/biomodels/BIOMD0000000162_url.txt +++ b/doc/examples/biomodels/BIOMD0000000162/BIOMD0000000162_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hernjak2005_Calcium_Signaling() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000163_url.txt b/doc/examples/biomodels/BIOMD0000000163/BIOMD0000000163_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000163_url.txt rename to doc/examples/biomodels/BIOMD0000000163/BIOMD0000000163_url.txt index 1053faebd..6355ad80f 100644 --- a/doc/examples/biomodels/BIOMD0000000163_url.txt +++ b/doc/examples/biomodels/BIOMD0000000163/BIOMD0000000163_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zi2007_TGFbeta_signaling() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000164_url.txt b/doc/examples/biomodels/BIOMD0000000164/BIOMD0000000164_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000164_url.txt rename to doc/examples/biomodels/BIOMD0000000164/BIOMD0000000164_url.txt index 013f26105..0d09358ce 100644 --- a/doc/examples/biomodels/BIOMD0000000164_url.txt +++ b/doc/examples/biomodels/BIOMD0000000164/BIOMD0000000164_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *SmithAE2002_RanTransport() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000165_url.txt b/doc/examples/biomodels/BIOMD0000000165/BIOMD0000000165_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000165_url.txt rename to doc/examples/biomodels/BIOMD0000000165/BIOMD0000000165_url.txt index 83569f25a..af6047980 100644 --- a/doc/examples/biomodels/BIOMD0000000165_url.txt +++ b/doc/examples/biomodels/BIOMD0000000165/BIOMD0000000165_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Saucerman2006_PKA() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000166_url.txt b/doc/examples/biomodels/BIOMD0000000166/BIOMD0000000166_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000166_url.txt rename to doc/examples/biomodels/BIOMD0000000166/BIOMD0000000166_url.txt index 3b876c3a1..89fb17525 100644 --- a/doc/examples/biomodels/BIOMD0000000166_url.txt +++ b/doc/examples/biomodels/BIOMD0000000166/BIOMD0000000166_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zhu2007_TF_syn_modulated_by_Ca() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000167_url.txt b/doc/examples/biomodels/BIOMD0000000167/BIOMD0000000167_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000167_url.txt rename to doc/examples/biomodels/BIOMD0000000167/BIOMD0000000167_url.txt index ed39fccee..e77e046a9 100644 --- a/doc/examples/biomodels/BIOMD0000000167_url.txt +++ b/doc/examples/biomodels/BIOMD0000000167/BIOMD0000000167_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Mayya2005_STATmodule() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000168_url.txt b/doc/examples/biomodels/BIOMD0000000168/BIOMD0000000168_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000168_url.txt rename to doc/examples/biomodels/BIOMD0000000168/BIOMD0000000168_url.txt index 55da41d12..edc367a56 100644 --- a/doc/examples/biomodels/BIOMD0000000168_url.txt +++ b/doc/examples/biomodels/BIOMD0000000168/BIOMD0000000168_url.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Obeyesekere1999_CellCycle() // Compartments and Species: compartment cell_1; species D_1 in cell_1, E_1 in cell_1, RS_1 in cell_1, R_1 in cell_1, X_1 in cell_1; - species $E2F_1 in cell_1, $RP_1 in cell_1; + species E2F_1 in cell_1, RP_1 in cell_1; // Assignment Rules: E2F_1 := theta_1 - RS_1; diff --git a/doc/examples/biomodels/BIOMD0000000169_url.txt b/doc/examples/biomodels/BIOMD0000000169/BIOMD0000000169_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000169_url.txt rename to doc/examples/biomodels/BIOMD0000000169/BIOMD0000000169_url.txt index 065b58336..4fa8cfb44 100644 --- a/doc/examples/biomodels/BIOMD0000000169_url.txt +++ b/doc/examples/biomodels/BIOMD0000000169/BIOMD0000000169_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Aguda1999_CellCycle() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000170_url.txt b/doc/examples/biomodels/BIOMD0000000170/BIOMD0000000170_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000170_url.txt rename to doc/examples/biomodels/BIOMD0000000170/BIOMD0000000170_url.txt index 9840a832e..7fc2f8606 100644 --- a/doc/examples/biomodels/BIOMD0000000170_url.txt +++ b/doc/examples/biomodels/BIOMD0000000170/BIOMD0000000170_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Weimann2004_CircadianOscillator() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000171_url.txt b/doc/examples/biomodels/BIOMD0000000171/BIOMD0000000171_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000171_url.txt rename to doc/examples/biomodels/BIOMD0000000171/BIOMD0000000171_url.txt index fc9e840ac..5e3b8c8ea 100644 --- a/doc/examples/biomodels/BIOMD0000000171_url.txt +++ b/doc/examples/biomodels/BIOMD0000000171/BIOMD0000000171_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000172_url.txt b/doc/examples/biomodels/BIOMD0000000172/BIOMD0000000172_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000172_url.txt rename to doc/examples/biomodels/BIOMD0000000172/BIOMD0000000172_url.txt index 960b4a909..c989d7ffe 100644 --- a/doc/examples/biomodels/BIOMD0000000172_url.txt +++ b/doc/examples/biomodels/BIOMD0000000172/BIOMD0000000172_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Pritchard2002_glycolysis() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000173_url.txt b/doc/examples/biomodels/BIOMD0000000173/BIOMD0000000173_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000173_url.txt rename to doc/examples/biomodels/BIOMD0000000173/BIOMD0000000173_url.txt index 0bb896021..a5c2aa8c7 100644 --- a/doc/examples/biomodels/BIOMD0000000173_url.txt +++ b/doc/examples/biomodels/BIOMD0000000173/BIOMD0000000173_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Schmierer_2008_Smad_Tgfb() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000174_url.txt b/doc/examples/biomodels/BIOMD0000000174/BIOMD0000000174_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000174_url.txt rename to doc/examples/biomodels/BIOMD0000000174/BIOMD0000000174_url.txt index 87b405ed4..5e6ad5919 100644 --- a/doc/examples/biomodels/BIOMD0000000174_url.txt +++ b/doc/examples/biomodels/BIOMD0000000174/BIOMD0000000174_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000175_url.txt b/doc/examples/biomodels/BIOMD0000000175/BIOMD0000000175_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000175_url.txt rename to doc/examples/biomodels/BIOMD0000000175/BIOMD0000000175_url.txt index 45d6c6f1b..deb81b7b7 100644 --- a/doc/examples/biomodels/BIOMD0000000175_url.txt +++ b/doc/examples/biomodels/BIOMD0000000175/BIOMD0000000175_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *ErbB() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000176_url.txt b/doc/examples/biomodels/BIOMD0000000176/BIOMD0000000176_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000176_url.txt rename to doc/examples/biomodels/BIOMD0000000176/BIOMD0000000176_url.txt index 344524a9b..69f2848f2 100644 --- a/doc/examples/biomodels/BIOMD0000000176_url.txt +++ b/doc/examples/biomodels/BIOMD0000000176/BIOMD0000000176_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Conant2007_WGD_glycolysis_2A3AB() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000177_url.txt b/doc/examples/biomodels/BIOMD0000000177/BIOMD0000000177_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000177_url.txt rename to doc/examples/biomodels/BIOMD0000000177/BIOMD0000000177_url.txt index 5c065c3ab..8c0a786c0 100644 --- a/doc/examples/biomodels/BIOMD0000000177_url.txt +++ b/doc/examples/biomodels/BIOMD0000000177/BIOMD0000000177_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Conant2007_glycolysis_2C() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000178_url.txt b/doc/examples/biomodels/BIOMD0000000178/BIOMD0000000178_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000178_url.txt rename to doc/examples/biomodels/BIOMD0000000178/BIOMD0000000178_url.txt index 4e66248a2..5a55a31ec 100644 --- a/doc/examples/biomodels/BIOMD0000000178_url.txt +++ b/doc/examples/biomodels/BIOMD0000000178/BIOMD0000000178_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Lebeda2008_BoTN_Paralysis_4stepModel() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000179_url.txt b/doc/examples/biomodels/BIOMD0000000179/BIOMD0000000179_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000179_url.txt rename to doc/examples/biomodels/BIOMD0000000179/BIOMD0000000179_url.txt index cee660baa..fe9c6e0e8 100644 --- a/doc/examples/biomodels/BIOMD0000000179_url.txt +++ b/doc/examples/biomodels/BIOMD0000000179/BIOMD0000000179_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kim2007_CellularMemory_AsymmetricModel() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000180_url.txt b/doc/examples/biomodels/BIOMD0000000180/BIOMD0000000180_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000180_url.txt rename to doc/examples/biomodels/BIOMD0000000180/BIOMD0000000180_url.txt index fc52ff349..c851f8683 100644 --- a/doc/examples/biomodels/BIOMD0000000180_url.txt +++ b/doc/examples/biomodels/BIOMD0000000180/BIOMD0000000180_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kim2007_CellularMemory_SymmetricModel() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000181_url.txt b/doc/examples/biomodels/BIOMD0000000181/BIOMD0000000181_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000181_url.txt rename to doc/examples/biomodels/BIOMD0000000181/BIOMD0000000181_url.txt index ebe5d616e..2c5a0e8b9 100644 --- a/doc/examples/biomodels/BIOMD0000000181_url.txt +++ b/doc/examples/biomodels/BIOMD0000000181/BIOMD0000000181_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Sriram2007_CellCycle() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000182_url.txt b/doc/examples/biomodels/BIOMD0000000182/BIOMD0000000182_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000182_url.txt rename to doc/examples/biomodels/BIOMD0000000182/BIOMD0000000182_url.txt index fdbd5ad7a..01b7f2540 100644 --- a/doc/examples/biomodels/BIOMD0000000182_url.txt +++ b/doc/examples/biomodels/BIOMD0000000182/BIOMD0000000182_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL8609366518() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000183_url.txt b/doc/examples/biomodels/BIOMD0000000183/BIOMD0000000183_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000183_url.txt rename to doc/examples/biomodels/BIOMD0000000183/BIOMD0000000183_url.txt index ece569680..163c3be22 100644 --- a/doc/examples/biomodels/BIOMD0000000183_url.txt +++ b/doc/examples/biomodels/BIOMD0000000183/BIOMD0000000183_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000183() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000184_url.txt b/doc/examples/biomodels/BIOMD0000000184/BIOMD0000000184_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000184_url.txt rename to doc/examples/biomodels/BIOMD0000000184/BIOMD0000000184_url.txt index 1aefca796..d3722b2c6 100644 --- a/doc/examples/biomodels/BIOMD0000000184_url.txt +++ b/doc/examples/biomodels/BIOMD0000000184/BIOMD0000000184_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Lavrentovich2008_Ca_Oscillations() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000185_url.txt b/doc/examples/biomodels/BIOMD0000000185/BIOMD0000000185_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000185_url.txt rename to doc/examples/biomodels/BIOMD0000000185/BIOMD0000000185_url.txt index af47bbeeb..d56d100b7 100644 --- a/doc/examples/biomodels/BIOMD0000000185_url.txt +++ b/doc/examples/biomodels/BIOMD0000000185/BIOMD0000000185_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Locke2008_Circadian_Clock() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000186_url.txt b/doc/examples/biomodels/BIOMD0000000186/BIOMD0000000186_url.txt similarity index 96% rename from doc/examples/biomodels/BIOMD0000000186_url.txt rename to doc/examples/biomodels/BIOMD0000000186/BIOMD0000000186_url.txt index 24b98f087..1d76e5bfd 100644 --- a/doc/examples/biomodels/BIOMD0000000186_url.txt +++ b/doc/examples/biomodels/BIOMD0000000186/BIOMD0000000186_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL6655615431() // Compartments and Species: @@ -20,7 +20,7 @@ model *MODEL6655615431() R8: APC + Cdc20 -> APC_Cdc20; Cytoplasm*(k8f*APC*Cdc20 - k8r*APC_Cdc20); // Events: - mt_attachment: at time > 2000: u_prime = const_val_1, u = const_val_0; + mt_attachment: at time > 2000: u = const_val_0, u_prime = const_val_1; // Species initializations: Mad1_CMad2 = 5e-08; @@ -284,14 +284,12 @@ rules for u and u_prime and comment out the list of events. In accordance with the authors due to typos in the original publication some initial conditions and parameters were slightly changed in the model: -| | -|||-----------------------------------------------------------|-----------------------------------------------------------| -| - | - | - | -| | -| | *[O-Mad2]* | 1.5e-7 M | 1.3e-7 M | | -| | *[BubR1:Bub3]* | 1.30e-7 M | 1.27e-7 M | | -| | *k -4* | 0.01 M -1 s -1 | 0.02 M -1 s -1 | | -| | *k -5* | 0.1 M -1 s -1 | 0.2 M -1 s -1 | | +| | article | model | +|-----------------------|-----------------------------------------------------------|-----------------------------------------------------------| +| *[O-Mad2]* | 1.5e-7 M | 1.3e-7 M | +| *[BubR1:Bub3]* | 1.30e-7 M | 1.27e-7 M | +| *k -4* | 0.01 M -1 s -1 | 0.02 M -1 s -1 | +| *k -5* | 0.1 M -1 s -1 | 0.2 M -1 s -1 | This model is hosted on [BioModels Database](http://www.ebi.ac.uk/biomodels/) and identified by: [MODEL6655615431](http://identifiers.org/biomodels.db/MODEL6655615431) . diff --git a/doc/examples/biomodels/BIOMD0000000187_url.txt b/doc/examples/biomodels/BIOMD0000000187/BIOMD0000000187_url.txt similarity index 96% rename from doc/examples/biomodels/BIOMD0000000187_url.txt rename to doc/examples/biomodels/BIOMD0000000187/BIOMD0000000187_url.txt index 3e3f38af6..29f70132f 100644 --- a/doc/examples/biomodels/BIOMD0000000187_url.txt +++ b/doc/examples/biomodels/BIOMD0000000187/BIOMD0000000187_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL6655578762() // Compartments and Species: @@ -20,7 +20,7 @@ model *MODEL6655578762() R8: APC + Cdc20 -> APC_Cdc20; Cytoplasm*(k8f*APC*Cdc20 - k8r*APC_Cdc20); // Events: - mt_attachment: at time > 2000: u_prime = const_val_1, u = const_val_0; + mt_attachment: at time > 2000: u = const_val_0, u_prime = const_val_1; // Species initializations: Mad1_CMad2 = 5e-08; @@ -285,14 +285,12 @@ rules for u and u_prime and comment out the list of events. In accordance with the authors due to typos in the original publication some initial conditions and parameters were slightly changed in the model: -| | -|||-----------------------------------------------------------|-----------------------------------------------------------| -| - | - | - | -| | -| | *[O-Mad2]* | 1.5e-7 M | 1.3e-7 M | | -| | *[BubR1:Bub3]* | 1.30e-7 M | 1.27e-7 M | | -| | *k -4* | 0.01 M -1 s -1 | 0.02 M -1 s -1 | | -| | *k -5* | 0.1 M -1 s -1 | 0.2 M -1 s -1 | | +| | article | model | +|-----------------------|-----------------------------------------------------------|-----------------------------------------------------------| +| *[O-Mad2]* | 1.5e-7 M | 1.3e-7 M | +| *[BubR1:Bub3]* | 1.30e-7 M | 1.27e-7 M | +| *k -4* | 0.01 M -1 s -1 | 0.02 M -1 s -1 | +| *k -5* | 0.1 M -1 s -1 | 0.2 M -1 s -1 | This model is hosted on [BioModels Database](http://www.ebi.ac.uk/biomodels/) and identified by: [MODEL6655578762](http://identifiers.org/biomodels.db/MODEL6655578762) . diff --git a/doc/examples/biomodels/BIOMD0000000188_url.txt b/doc/examples/biomodels/BIOMD0000000188/BIOMD0000000188_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000188_url.txt rename to doc/examples/biomodels/BIOMD0000000188/BIOMD0000000188_url.txt index ac05a4a6a..8d3d89c4f 100644 --- a/doc/examples/biomodels/BIOMD0000000188_url.txt +++ b/doc/examples/biomodels/BIOMD0000000188/BIOMD0000000188_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000188() // Compartments and Species: @@ -7,8 +7,8 @@ model *BIOMD0000000188() substanceOnly species p53_mRNA in cell, ATMA in cell, ATMI in cell, p53_P in cell; substanceOnly species Mdm2_P in cell, damDNA in cell, $Sink in cell, $Source in cell; substanceOnly species p53deg in cell, p53syn in cell, mdm2deg in cell, mdm2syn in cell; - substanceOnly species Mdm2mRNAdeg in cell, Mdm2mRNAsyn in cell, $totp53 in cell; - substanceOnly species $totMdm2 in cell; + substanceOnly species Mdm2mRNAdeg in cell, Mdm2mRNAsyn in cell, totp53 in cell; + substanceOnly species totMdm2 in cell; // Assignment Rules: totp53 := p53 + Mdm2_p53 + p53_P; diff --git a/doc/examples/biomodels/BIOMD0000000189_url.txt b/doc/examples/biomodels/BIOMD0000000189/BIOMD0000000189_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000189_url.txt rename to doc/examples/biomodels/BIOMD0000000189/BIOMD0000000189_url.txt index 9b2a9a967..ecf34670a 100644 --- a/doc/examples/biomodels/BIOMD0000000189_url.txt +++ b/doc/examples/biomodels/BIOMD0000000189/BIOMD0000000189_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000189() // Compartments and Species: @@ -7,7 +7,7 @@ model *BIOMD0000000189() substanceOnly species ARF in cell, ARF_Mdm2 in cell, damDNA in cell, $Sink in cell; substanceOnly species $Source in cell, p53deg in cell, p53syn in cell, mdm2deg in cell; substanceOnly species mdm2syn in cell, Mdm2mRNAdeg in cell, Mdm2mRNAsyn in cell; - substanceOnly species totdamDNA in cell, $totp53 in cell, $totMdm2 in cell; + substanceOnly species totdamDNA in cell, totp53 in cell, totMdm2 in cell; // Assignment Rules: totp53 := p53 + Mdm2_p53; diff --git a/doc/examples/biomodels/BIOMD0000000190_url.txt b/doc/examples/biomodels/BIOMD0000000190/BIOMD0000000190_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000190_url.txt rename to doc/examples/biomodels/BIOMD0000000190/BIOMD0000000190_url.txt index ef99c6c23..81b9d5b08 100644 --- a/doc/examples/biomodels/BIOMD0000000190_url.txt +++ b/doc/examples/biomodels/BIOMD0000000190/BIOMD0000000190_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: @@ -221,6 +221,15 @@ model *Model_1() P_efflux is "Putrescine efflux"; aD_efflux is "aD efflux"; + // SBO terms: + PAO_for_aD.kineticLaw.sboTerm = 270 + PAO_for_aS.kineticLaw.sboTerm = 270 + MAT.kineticLaw.sboTerm = 260 + VCoA.kineticLaw.sboTerm = 49 + VacCoA.kineticLaw.sboTerm = 49 + P_efflux.kineticLaw.sboTerm = 49 + aD_efflux.kineticLaw.sboTerm = 49 + // CV terms: cytosol identity "http://identifiers.org/go/GO:0005829" SAM identity "http://identifiers.org/chebi/CHEBI:15414", diff --git a/doc/examples/biomodels/BIOMD0000000191_url.txt b/doc/examples/biomodels/BIOMD0000000191/BIOMD0000000191_url.txt similarity index 96% rename from doc/examples/biomodels/BIOMD0000000191_url.txt rename to doc/examples/biomodels/BIOMD0000000191/BIOMD0000000191_url.txt index ffe3b4c5f..d6157a393 100644 --- a/doc/examples/biomodels/BIOMD0000000191_url.txt +++ b/doc/examples/biomodels/BIOMD0000000191/BIOMD0000000191_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: @@ -12,6 +12,11 @@ model *Model_1() NOS: ARGin => ; cytosol*(NOS_Vmaxnos1*ARGin/(NOS_Kmnos1 + ARGin)); ODC: ORN => ; cytosol*(ODC_Vmaxodc*ORN/(ODC_Kmodc + ORN)); + // Interactions: + _I0: ORN -| Arginine_transport; ; + _I1: $ARGex -| Ornithine_efflux; ; + _I2: ARGin -| Ornithine_efflux; ; + // Species initializations: ARGex = 330; ORN = 1; @@ -84,10 +89,12 @@ model *Model_1() ORN.sboTerm = 247 ARGin.sboTerm = 247 Arginase.sboTerm = 211 + Arginase.kineticLaw.sboTerm = 260 Arginase_Vmaxarg.sboTerm = 324 Arginase_Kmarg.sboTerm = 322 Arginase_Kioarg.sboTerm = 261 Arginine_transport.sboTerm = 185 + Arginine_transport.kineticLaw.sboTerm = 277 Arginine_transport_Kmhat.sboTerm = 322 Arginine_transport_Vmaxhat.sboTerm = 324 Arginine_transport_Kmlat.sboTerm = 322 @@ -101,8 +108,10 @@ model *Model_1() Ornithine_efflux_Kmeffllat.sboTerm = 322 Ornithine_efflux_Kiornhat.sboTerm = 261 NOS.sboTerm = 211 + NOS.kineticLaw.sboTerm = 28 NOS_Vmaxnos1.sboTerm = 324 ODC.sboTerm = 211 + ODC.kineticLaw.sboTerm = 28 ODC_Vmaxodc.sboTerm = 324 ODC_Kmodc.sboTerm = 322 diff --git a/doc/examples/biomodels/BIOMD0000000192_url.txt b/doc/examples/biomodels/BIOMD0000000192/BIOMD0000000192_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000192_url.txt rename to doc/examples/biomodels/BIOMD0000000192/BIOMD0000000192_url.txt index ac6798a5b..efc981dea 100644 --- a/doc/examples/biomodels/BIOMD0000000192_url.txt +++ b/doc/examples/biomodels/BIOMD0000000192/BIOMD0000000192_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *RanGTP_gradient() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000193_url.txt b/doc/examples/biomodels/BIOMD0000000193/BIOMD0000000193_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000193_url.txt rename to doc/examples/biomodels/BIOMD0000000193/BIOMD0000000193_url.txt index bb9040d0b..f2635e743 100644 --- a/doc/examples/biomodels/BIOMD0000000193_url.txt +++ b/doc/examples/biomodels/BIOMD0000000193/BIOMD0000000193_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *KDM() // Compartments and Species: @@ -103,11 +103,17 @@ model *KDM() k4f.sboTerm = 339 k4r.sboTerm = 338 R1.sboTerm = 177 + R1.kineticLaw.sboTerm = 101 R2.sboTerm = 176 + R2.kineticLaw.sboTerm = 54 R3.sboTerm = 180 + R3.kineticLaw.sboTerm = 49 R4.sboTerm = 177 + R4.kineticLaw.sboTerm = 103 R5.sboTerm = 177 + R5.kineticLaw.sboTerm = 103 R6.sboTerm = 177 + R6.kineticLaw.sboTerm = 54 // CV terms: Cytoplasm identity "http://identifiers.org/go/GO:0005737" diff --git a/doc/examples/biomodels/BIOMD0000000194_url.txt b/doc/examples/biomodels/BIOMD0000000194/BIOMD0000000194_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000194_url.txt rename to doc/examples/biomodels/BIOMD0000000194/BIOMD0000000194_url.txt index 1c873c92b..bd6c8756d 100644 --- a/doc/examples/biomodels/BIOMD0000000194_url.txt +++ b/doc/examples/biomodels/BIOMD0000000194/BIOMD0000000194_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *TM() // Compartments and Species: @@ -71,6 +71,9 @@ model *TM() gamma_T.sboTerm = 36 alpha_T.sboTerm = 339 beta_T.sboTerm = 338 + R6.kineticLaw.sboTerm = 101 + R7.kineticLaw.sboTerm = 54 + R8.kineticLaw.sboTerm = 49 // CV terms: Cytoplasm identity "http://identifiers.org/go/GO:0005737" diff --git a/doc/examples/biomodels/BIOMD0000000195_url.txt b/doc/examples/biomodels/BIOMD0000000195/BIOMD0000000195_url.txt similarity index 93% rename from doc/examples/biomodels/BIOMD0000000195_url.txt rename to doc/examples/biomodels/BIOMD0000000195/BIOMD0000000195_url.txt index af55afc65..432fa73f1 100644 --- a/doc/examples/biomodels/BIOMD0000000195_url.txt +++ b/doc/examples/biomodels/BIOMD0000000195/BIOMD0000000195_url.txt @@ -1,11 +1,11 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Tyson2001_Cell_Cycle_Regulation() // Compartments and Species: compartment cell; - substanceOnly species CycBt in cell, $CycB in cell, CKIt in cell, Cdc20a in cell; - substanceOnly species $Trimer in cell, Cdh1 in cell, m in cell, Cdc20t in cell; - substanceOnly species IEP in cell, $Mad in cell, SK in cell; + substanceOnly species CycBt in cell, CycB in cell, CKIt in cell, Cdc20a in cell; + substanceOnly species Trimer in cell, Cdh1 in cell, m in cell, Cdc20t in cell; + substanceOnly species IEP in cell, Mad in cell, SK in cell; // Assignment Rules: CycB := CycBt - 2*CycBt*CKIt/(CycBt + CKIt + 1/Keq + ((CycBt + CKIt + 1/Keq)^2 - 4*CycBt*CKIt)^(1/2)); @@ -123,6 +123,16 @@ model *Tyson2001_Cell_Cycle_Regulation() SKsynthesis is "SK synthesis"; SKdegradation is "SK degradation"; + // SBO terms: + CycBt_synthesis.kineticLaw.sboTerm = 47 + CycBdegradation.kineticLaw.sboTerm = 49 + Cdc20t_deg.kineticLaw.sboTerm = 49 + Cdc20adegradation.kineticLaw.sboTerm = 49 + IEPdegradation.kineticLaw.sboTerm = 49 + CKItsynthesis.kineticLaw.sboTerm = 47 + CKIdegradation.kineticLaw.sboTerm = 49 + SKdegradation.kineticLaw.sboTerm = 49 + // CV terms: cell identity "http://identifiers.org/go/GO:0005623" CycBt hasPart "http://identifiers.org/uniprot/P00546", diff --git a/doc/examples/biomodels/BIOMD0000000196_url.txt b/doc/examples/biomodels/BIOMD0000000196/BIOMD0000000196_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000196_url.txt rename to doc/examples/biomodels/BIOMD0000000196/BIOMD0000000196_url.txt index fea20c864..a695e4035 100644 --- a/doc/examples/biomodels/BIOMD0000000196_url.txt +++ b/doc/examples/biomodels/BIOMD0000000196/BIOMD0000000196_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Srividhya2006_CellCycle() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000197_url.txt b/doc/examples/biomodels/BIOMD0000000197/BIOMD0000000197_url.txt similarity index 93% rename from doc/examples/biomodels/BIOMD0000000197_url.txt rename to doc/examples/biomodels/BIOMD0000000197/BIOMD0000000197_url.txt index 66d0053b7..91875cb8e 100644 --- a/doc/examples/biomodels/BIOMD0000000197_url.txt +++ b/doc/examples/biomodels/BIOMD0000000197/BIOMD0000000197_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MDCKII_Transport() // Compartments and Species: @@ -170,22 +170,23 @@ SBML model exported from PottersWheel on 2007-09-19 15:35:47. The values for parameters and the inital concentrations of this model where directly provided by the main author: -| Parameter values | -||-----------|----------|----------------| -| - | - | - | -| | -| | p1 | 0.0025 | 1/min | | -| | p2 | 0.0784 | 1/min | | -| | p3 | 0.0013 | 1/min | | -| | p4 | 0.0827 | 1/min | | -| | p5 | 0.0091 | 1/min | | -| | p6 | 0.000064 | 1/(nmole\*min) | | -| | p7 | 0.0397 | 1/min | | -| | p8 | 1000 | nmole | | -| | p9 | 0.0098 | 1/(nmole\*min) | | -| | p10 | 1.6 | 1/min | | -| | p11 | 1000 | nmole | | -| | p12 | 0.0003 | ml/min | | +**Parameter values** + +| parameter | value | unit | +|-----------|----------|----------------| +| p1 | 0.0025 | 1/min | +| p2 | 0.0784 | 1/min | +| p3 | 0.0013 | 1/min | +| p4 | 0.0827 | 1/min | +| p5 | 0.0091 | 1/min | +| p6 | 0.000064 | 1/(nmole\*min) | +| p7 | 0.0397 | 1/min | +| p8 | 1000 | nmole | +| p9 | 0.0098 | 1/(nmole\*min) | +| p10 | 1.6 | 1/min | +| p11 | 1000 | nmole | +| p12 | 0.0003 | ml/min | + The basal chamber volume was taken as 1 ml, the apical as 1.5. As starting values x1 was set to 88 nmole, all other species to 0. diff --git a/doc/examples/biomodels/BIOMD0000000198_url.txt b/doc/examples/biomodels/BIOMD0000000198/BIOMD0000000198_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000198_url.txt rename to doc/examples/biomodels/BIOMD0000000198/BIOMD0000000198_url.txt index f26497840..e67f22cc8 100644 --- a/doc/examples/biomodels/BIOMD0000000198_url.txt +++ b/doc/examples/biomodels/BIOMD0000000198/BIOMD0000000198_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *testid() // Compartments and Species: @@ -6,7 +6,7 @@ model *testid() species $NO in cytosol, sGCfast in cytosol, NO_sGCfast in cytosol, NO_sGCfast_6coord in cytosol; species NO_sGCfast_5coord in cytosol, sGCslow in cytosol, NO_sGCslow in cytosol; species NO_sGCslow_6coord in cytosol, NO_sGCslow_6coord_NO_int in cytosol; - species NO_sGCslow_5coord in cytosol, $NO_sGC_5coord_tot in cytosol, $sGC_inact_tot in cytosol; + species NO_sGCslow_5coord in cytosol, NO_sGC_5coord_tot in cytosol, sGC_inact_tot in cytosol; // Assignment Rules: NO_sGC_5coord_tot := NO_sGCfast_5coord + NO_sGCslow_5coord; diff --git a/doc/examples/biomodels/BIOMD0000000199_url.txt b/doc/examples/biomodels/BIOMD0000000199/BIOMD0000000199_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000199_url.txt rename to doc/examples/biomodels/BIOMD0000000199/BIOMD0000000199_url.txt index dc8a3bc15..f00e8015b 100644 --- a/doc/examples/biomodels/BIOMD0000000199_url.txt +++ b/doc/examples/biomodels/BIOMD0000000199/BIOMD0000000199_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *testid() // Compartments and Species: @@ -6,7 +6,7 @@ model *testid() species FeIII in cytosol, FeII in cytosol, FeII_O2 in cytosol, FeIII_star in cytosol; species FeII_star in cytosol, FeII_star_O2 in cytosol, FeIII_NO in cytosol; species FeII_NO in cytosol, $NADPH in cytosol, $O2 in cytosol, $citrulline in cytosol; - species $NO3 in cytosol, $NO in cytosol, $NADPplus in cytosol, $FeIII_t in cytosol; + species $NO3 in cytosol, $NO in cytosol, $NADPplus in cytosol, FeIII_t in cytosol; // Assignment Rules: FeIII_t := FeIII + FeIII_star; diff --git a/doc/examples/biomodels/BIOMD0000000200_url.txt b/doc/examples/biomodels/BIOMD0000000200/BIOMD0000000200_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000200_url.txt rename to doc/examples/biomodels/BIOMD0000000200/BIOMD0000000200_url.txt index a59b7a9c4..cc9a7c3d1 100644 --- a/doc/examples/biomodels/BIOMD0000000200_url.txt +++ b/doc/examples/biomodels/BIOMD0000000200/BIOMD0000000200_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bray1995_chemotaxis_receptorlinkedcomplex() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000201_url.txt b/doc/examples/biomodels/BIOMD0000000201/BIOMD0000000201_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000201_url.txt rename to doc/examples/biomodels/BIOMD0000000201/BIOMD0000000201_url.txt index 0705950b6..14922b513 100644 --- a/doc/examples/biomodels/BIOMD0000000201_url.txt +++ b/doc/examples/biomodels/BIOMD0000000201/BIOMD0000000201_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Goldbeter2008_Somite_Segmentation_Clock_Notch_Wnt_FGF() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000202_url.txt b/doc/examples/biomodels/BIOMD0000000202/BIOMD0000000202_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000202_url.txt rename to doc/examples/biomodels/BIOMD0000000202/BIOMD0000000202_url.txt index 70e8aaa58..669a7b720 100644 --- a/doc/examples/biomodels/BIOMD0000000202_url.txt +++ b/doc/examples/biomodels/BIOMD0000000202/BIOMD0000000202_url.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *ChenXF2008_CICR() // Compartments and Species: compartment Cytoplasm, ER, PM; - species Ca_Cyt in Cytoplasm, IP3_Cyt in Cytoplasm, Ca_ER in ER, $S2 in ER; - species S2a in ER, S4 in ER, Oc in PM, O_o in PM, $Orai1 in PM; + species Ca_Cyt in Cytoplasm, IP3_Cyt in Cytoplasm, Ca_ER in ER, S2 in ER; + species S2a in ER, S4 in ER, Oc in PM, O_o in PM, Orai1 in PM; // Assignment Rules: S2 := (K1^2/(Ca_ER^2 + K1^2))*(St - S2a); diff --git a/doc/examples/biomodels/BIOMD0000000203_url.txt b/doc/examples/biomodels/BIOMD0000000203/BIOMD0000000203_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000203_url.txt rename to doc/examples/biomodels/BIOMD0000000203/BIOMD0000000203_url.txt index e2bd8c0ab..1df84ccd3 100644 --- a/doc/examples/biomodels/BIOMD0000000203_url.txt +++ b/doc/examples/biomodels/BIOMD0000000203/BIOMD0000000203_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL7957907314() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000204_url.txt b/doc/examples/biomodels/BIOMD0000000204/BIOMD0000000204_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000204_url.txt rename to doc/examples/biomodels/BIOMD0000000204/BIOMD0000000204_url.txt index a944e6e38..7bb701597 100644 --- a/doc/examples/biomodels/BIOMD0000000204_url.txt +++ b/doc/examples/biomodels/BIOMD0000000204/BIOMD0000000204_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL7957942740() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000205_url.txt b/doc/examples/biomodels/BIOMD0000000205/BIOMD0000000205_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000205_url.txt rename to doc/examples/biomodels/BIOMD0000000205/BIOMD0000000205_url.txt index 76e9a764a..8112816fb 100644 --- a/doc/examples/biomodels/BIOMD0000000205_url.txt +++ b/doc/examples/biomodels/BIOMD0000000205/BIOMD0000000205_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ung2008_EGFR_Endocytosis() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000206_url.txt b/doc/examples/biomodels/BIOMD0000000206/BIOMD0000000206_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000206_url.txt rename to doc/examples/biomodels/BIOMD0000000206/BIOMD0000000206_url.txt index 7585ba624..3dfa04eca 100644 --- a/doc/examples/biomodels/BIOMD0000000206_url.txt +++ b/doc/examples/biomodels/BIOMD0000000206/BIOMD0000000206_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wolf2000_Glycolytic_Oscillations() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000207_url.txt b/doc/examples/biomodels/BIOMD0000000207/BIOMD0000000207_url.txt similarity index 93% rename from doc/examples/biomodels/BIOMD0000000207_url.txt rename to doc/examples/biomodels/BIOMD0000000207/BIOMD0000000207_url.txt index 1404cb5c1..be89aa4f1 100644 --- a/doc/examples/biomodels/BIOMD0000000207_url.txt +++ b/doc/examples/biomodels/BIOMD0000000207/BIOMD0000000207_url.txt @@ -1,11 +1,11 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Romond1999_CellCycle() // Compartments and Species: compartment compartment_; species C1 in compartment_, C2 in compartment_; - substanceOnly species $M1 in compartment_, $X1 in compartment_, $M2 in compartment_; - substanceOnly species $X2 in compartment_; + substanceOnly species M1 in compartment_, X1 in compartment_, M2 in compartment_; + substanceOnly species X2 in compartment_; // Assignment Rules: V1 := (C1/(Kc1 + C1))*V_M1; @@ -31,15 +31,15 @@ model *Romond1999_CellCycle() C1 = 2; C1 has uM; M1 = 1; - M1 has dimensionless_per_volume; + M1 has dimensionless; X1 = 0; - X1 has dimensionless_per_volume; + X1 has dimensionless; C2 = 0; C2 has uM; M2 = 0; - M2 has dimensionless_per_volume; + M2 has dimensionless; X2 = 0; - X2 has dimensionless_per_volume; + X2 has dimensionless; // Compartment initializations: compartment_ = 1; @@ -118,7 +118,6 @@ model *Romond1999_CellCycle() unit micromole = 1e-6 mole; unit min_1 = 1 / 60 second; unit uM_min_1 = 1e-6 mole / (litre * 60 second); - unit dimensionless_per_volume = dimensionless / litre; // Display Names: time_unit is "minute"; diff --git a/doc/examples/biomodels/BIOMD0000000208_url.txt b/doc/examples/biomodels/BIOMD0000000208/BIOMD0000000208_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000208_url.txt rename to doc/examples/biomodels/BIOMD0000000208/BIOMD0000000208_url.txt index 9469fd3d3..04d107d04 100644 --- a/doc/examples/biomodels/BIOMD0000000208_url.txt +++ b/doc/examples/biomodels/BIOMD0000000208/BIOMD0000000208_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Deineko2003_CellCycle() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000209_url.txt b/doc/examples/biomodels/BIOMD0000000209/BIOMD0000000209_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000209_url.txt rename to doc/examples/biomodels/BIOMD0000000209/BIOMD0000000209_url.txt index cd94ef4f8..71e202455 100644 --- a/doc/examples/biomodels/BIOMD0000000209_url.txt +++ b/doc/examples/biomodels/BIOMD0000000209/BIOMD0000000209_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL8390025091() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000210_url.txt b/doc/examples/biomodels/BIOMD0000000210/BIOMD0000000210_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000210_url.txt rename to doc/examples/biomodels/BIOMD0000000210/BIOMD0000000210_url.txt index 55f6d7b82..5c5214150 100644 --- a/doc/examples/biomodels/BIOMD0000000210_url.txt +++ b/doc/examples/biomodels/BIOMD0000000210/BIOMD0000000210_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL8389825246() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000211_url.txt b/doc/examples/biomodels/BIOMD0000000211/BIOMD0000000211_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000211_url.txt rename to doc/examples/biomodels/BIOMD0000000211/BIOMD0000000211_url.txt index e1fcb9d5d..c72a0c044 100644 --- a/doc/examples/biomodels/BIOMD0000000211_url.txt +++ b/doc/examples/biomodels/BIOMD0000000211/BIOMD0000000211_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000212_url.txt b/doc/examples/biomodels/BIOMD0000000212/BIOMD0000000212_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000212_url.txt rename to doc/examples/biomodels/BIOMD0000000212/BIOMD0000000212_url.txt index 14ae45e4a..15b668e50 100644 --- a/doc/examples/biomodels/BIOMD0000000212_url.txt +++ b/doc/examples/biomodels/BIOMD0000000212/BIOMD0000000212_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Curien2009_Aspartate_Metabolism() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000213_url.txt b/doc/examples/biomodels/BIOMD0000000213/BIOMD0000000213_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000213_url.txt rename to doc/examples/biomodels/BIOMD0000000213/BIOMD0000000213_url.txt index 42459c045..2ce5e0064 100644 --- a/doc/examples/biomodels/BIOMD0000000213_url.txt +++ b/doc/examples/biomodels/BIOMD0000000213/BIOMD0000000213_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Folate2004() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000214_url.txt b/doc/examples/biomodels/BIOMD0000000214/BIOMD0000000214_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000214_url.txt rename to doc/examples/biomodels/BIOMD0000000214/BIOMD0000000214_url.txt index 0ce99a018..f182cbe35 100644 --- a/doc/examples/biomodels/BIOMD0000000214_url.txt +++ b/doc/examples/biomodels/BIOMD0000000214/BIOMD0000000214_url.txt @@ -1,12 +1,12 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Akman2008_Circadian_Clock_Model2() // Compartments and Species: compartment cytosol, nucleus; species E1F in cytosol, E1Fp in cytosol, E1W in cytosol, E2F in cytosol; species E2Fp in cytosol, E2W in cytosol, MF in nucleus, MW in nucleus, PF in nucleus; - species PFp in nucleus, PW in nucleus, PWL in nucleus, $sFrq_tot in nucleus; - species $lFrq_tot in nucleus, $Frq_tot in nucleus, $WC1_tot in nucleus; + species PFp in nucleus, PW in nucleus, PWL in nucleus, sFrq_tot in nucleus; + species lFrq_tot in nucleus, Frq_tot in nucleus, WC1_tot in nucleus; // Assignment Rules: sFrq_tot := PF + E2F + E1F; diff --git a/doc/examples/biomodels/BIOMD0000000215_url.txt b/doc/examples/biomodels/BIOMD0000000215/BIOMD0000000215_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000215_url.txt rename to doc/examples/biomodels/BIOMD0000000215/BIOMD0000000215_url.txt index 2787a8fac..5d55c96ae 100644 --- a/doc/examples/biomodels/BIOMD0000000215_url.txt +++ b/doc/examples/biomodels/BIOMD0000000215/BIOMD0000000215_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Schulz2009_Th1_differentiation() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000216_url.txt b/doc/examples/biomodels/BIOMD0000000216/BIOMD0000000216_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000216_url.txt rename to doc/examples/biomodels/BIOMD0000000216/BIOMD0000000216_url.txt index cec0cbb16..75a6d882c 100644 --- a/doc/examples/biomodels/BIOMD0000000216_url.txt +++ b/doc/examples/biomodels/BIOMD0000000216/BIOMD0000000216_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hong2009_CircadianClock() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000217_url.txt b/doc/examples/biomodels/BIOMD0000000217/BIOMD0000000217_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000217_url.txt rename to doc/examples/biomodels/BIOMD0000000217/BIOMD0000000217_url.txt index 901569fc5..5afd433c1 100644 --- a/doc/examples/biomodels/BIOMD0000000217_url.txt +++ b/doc/examples/biomodels/BIOMD0000000217/BIOMD0000000217_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bruggeman2005_AmmoniumAssimilation() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000218_url.txt b/doc/examples/biomodels/BIOMD0000000218/BIOMD0000000218_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000218_url.txt rename to doc/examples/biomodels/BIOMD0000000218/BIOMD0000000218_url.txt index d172628bb..7864b943e 100644 --- a/doc/examples/biomodels/BIOMD0000000218_url.txt +++ b/doc/examples/biomodels/BIOMD0000000218/BIOMD0000000218_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Singh2006_TCA_mtu_model2() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000219_url.txt b/doc/examples/biomodels/BIOMD0000000219/BIOMD0000000219_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000219_url.txt rename to doc/examples/biomodels/BIOMD0000000219/BIOMD0000000219_url.txt index 9eca4f56f..d207499ee 100644 --- a/doc/examples/biomodels/BIOMD0000000219_url.txt +++ b/doc/examples/biomodels/BIOMD0000000219/BIOMD0000000219_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Singh2006_TCA_mtu_model1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000220_url.txt b/doc/examples/biomodels/BIOMD0000000220/BIOMD0000000220_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000220_url.txt rename to doc/examples/biomodels/BIOMD0000000220/BIOMD0000000220_url.txt index 657c9a899..d531cdc20 100644 --- a/doc/examples/biomodels/BIOMD0000000220_url.txt +++ b/doc/examples/biomodels/BIOMD0000000220/BIOMD0000000220_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *untitled() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000221_url.txt b/doc/examples/biomodels/BIOMD0000000221/BIOMD0000000221_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000221_url.txt rename to doc/examples/biomodels/BIOMD0000000221/BIOMD0000000221_url.txt index 28fe4b169..ef2a54d6c 100644 --- a/doc/examples/biomodels/BIOMD0000000221_url.txt +++ b/doc/examples/biomodels/BIOMD0000000221/BIOMD0000000221_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Singh2006_TCA_Ecoli_acetate() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000222_url.txt b/doc/examples/biomodels/BIOMD0000000222/BIOMD0000000222_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000222_url.txt rename to doc/examples/biomodels/BIOMD0000000222/BIOMD0000000222_url.txt index e8c8f0f7d..f63fb3406 100644 --- a/doc/examples/biomodels/BIOMD0000000222_url.txt +++ b/doc/examples/biomodels/BIOMD0000000222/BIOMD0000000222_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Singh2006_TCA_Ecoli_glucose() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000223_url.txt b/doc/examples/biomodels/BIOMD0000000223/BIOMD0000000223_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000223_url.txt rename to doc/examples/biomodels/BIOMD0000000223/BIOMD0000000223_url.txt index ce017077f..3d065f77d 100644 --- a/doc/examples/biomodels/BIOMD0000000223_url.txt +++ b/doc/examples/biomodels/BIOMD0000000223/BIOMD0000000223_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *InsEGFdiam_2008_10_03_debugged() // Compartments and Species: @@ -21,7 +21,7 @@ model *InsEGFdiam_2008_10_03_debugged() species aPX in cell, aPX_GS in cell, IRSp_PI3K in cell, IRSp_GS in cell; species IRSp_SHP2 in cell, GABp in cell, GABp_PI3K in cell, GABp_GS in cell; species GABp_RasGAP in cell, GABp_SHP2 in cell, GABp_pSHP2 in cell, GABp_pSHP2_GS in cell; - species imGABp in cell, bRasGAP in cell, $phosphorylated_Akt in cell; + species imGABp in cell, bRasGAP in cell, phosphorylated_Akt in cell; // Assignment Rules: phosphorylated_Akt := pAkt + ppAkt; diff --git a/doc/examples/biomodels/BIOMD0000000224_url.txt b/doc/examples/biomodels/BIOMD0000000224/BIOMD0000000224_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000224_url.txt rename to doc/examples/biomodels/BIOMD0000000224/BIOMD0000000224_url.txt index 5a3bb55a7..943c28ff0 100644 --- a/doc/examples/biomodels/BIOMD0000000224_url.txt +++ b/doc/examples/biomodels/BIOMD0000000224/BIOMD0000000224_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Meyer1991_CalciumSpike_ICC() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000225_url.txt b/doc/examples/biomodels/BIOMD0000000225/BIOMD0000000225_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000225_url.txt rename to doc/examples/biomodels/BIOMD0000000225/BIOMD0000000225_url.txt index 39ff90a9d..73c3cdfdf 100644 --- a/doc/examples/biomodels/BIOMD0000000225_url.txt +++ b/doc/examples/biomodels/BIOMD0000000225/BIOMD0000000225_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Westermark2003_Pancreatic_GlycOsc_basic() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000226_url.txt b/doc/examples/biomodels/BIOMD0000000226/BIOMD0000000226_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000226_url.txt rename to doc/examples/biomodels/BIOMD0000000226/BIOMD0000000226_url.txt index ddde6f098..4288665f9 100644 --- a/doc/examples/biomodels/BIOMD0000000226_url.txt +++ b/doc/examples/biomodels/BIOMD0000000226/BIOMD0000000226_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Radulescu2008_NFkB_hierarchy_M_14_25_28_Lipniacky() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000227_url.txt b/doc/examples/biomodels/BIOMD0000000227/BIOMD0000000227_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000227_url.txt rename to doc/examples/biomodels/BIOMD0000000227/BIOMD0000000227_url.txt index 1153f480f..99c6aeca4 100644 --- a/doc/examples/biomodels/BIOMD0000000227_url.txt +++ b/doc/examples/biomodels/BIOMD0000000227/BIOMD0000000227_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Radulescu2008_NFkB_hierarchy_M_39_65_90() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000228_url.txt b/doc/examples/biomodels/BIOMD0000000228/BIOMD0000000228_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000228_url.txt rename to doc/examples/biomodels/BIOMD0000000228/BIOMD0000000228_url.txt index 5bcb370b4..1d601f017 100644 --- a/doc/examples/biomodels/BIOMD0000000228_url.txt +++ b/doc/examples/biomodels/BIOMD0000000228/BIOMD0000000228_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Swat2004_Mammalian_G1_S_Transition() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000229_url.txt b/doc/examples/biomodels/BIOMD0000000229/BIOMD0000000229_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000229_url.txt rename to doc/examples/biomodels/BIOMD0000000229/BIOMD0000000229_url.txt index 07e49477e..df255e294 100644 --- a/doc/examples/biomodels/BIOMD0000000229_url.txt +++ b/doc/examples/biomodels/BIOMD0000000229/BIOMD0000000229_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ma2002_cAMP_oscillations() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000230_url.txt b/doc/examples/biomodels/BIOMD0000000230/BIOMD0000000230_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000230_url.txt rename to doc/examples/biomodels/BIOMD0000000230/BIOMD0000000230_url.txt index 6a1202198..bf2e6c982 100644 --- a/doc/examples/biomodels/BIOMD0000000230_url.txt +++ b/doc/examples/biomodels/BIOMD0000000230/BIOMD0000000230_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ihekwaba2004_NFkB_Sensitivity() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000231_url.txt b/doc/examples/biomodels/BIOMD0000000231/BIOMD0000000231_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000231_url.txt rename to doc/examples/biomodels/BIOMD0000000231/BIOMD0000000231_url.txt index a3e2461a3..ff5088e55 100644 --- a/doc/examples/biomodels/BIOMD0000000231_url.txt +++ b/doc/examples/biomodels/BIOMD0000000231/BIOMD0000000231_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Valero2006_Adenine_TernaryCycle() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000232_url.txt b/doc/examples/biomodels/BIOMD0000000232/BIOMD0000000232_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000232_url.txt rename to doc/examples/biomodels/BIOMD0000000232/BIOMD0000000232_url.txt index ecdf23f3c..60dad273b 100644 --- a/doc/examples/biomodels/BIOMD0000000232_url.txt +++ b/doc/examples/biomodels/BIOMD0000000232/BIOMD0000000232_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Nazaret2009_TCA_RC_ATP() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000233_url.txt b/doc/examples/biomodels/BIOMD0000000233/BIOMD0000000233_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000233_url.txt rename to doc/examples/biomodels/BIOMD0000000233/BIOMD0000000233_url.txt index 8f5dc9cc9..6fb30f727 100644 --- a/doc/examples/biomodels/BIOMD0000000233_url.txt +++ b/doc/examples/biomodels/BIOMD0000000233/BIOMD0000000233_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wilhelm2009_BistableReaction() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000234_url.txt b/doc/examples/biomodels/BIOMD0000000234/BIOMD0000000234_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000234_url.txt rename to doc/examples/biomodels/BIOMD0000000234/BIOMD0000000234_url.txt index c563c6e5c..e1358e9cc 100644 --- a/doc/examples/biomodels/BIOMD0000000234_url.txt +++ b/doc/examples/biomodels/BIOMD0000000234/BIOMD0000000234_url.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Tham2008_PDmodel_TumourShrinkage() // Compartments and Species: compartment COMpartment; - species $Ce in COMpartment; + species Ce in COMpartment; // Assignment Rules: Exposure := piecewise(Dose, (time < (Cycle_Int*N_Cycle)) && (Dose_Int1 < rem_time) && (rem_time < Dose_Length), Dose, (time < (Cycle_Int*N_Cycle)) && (Dose_Int2 < rem_time) && (rem_time < (Dose_Int2 + Dose_Length)), 0); diff --git a/doc/examples/biomodels/GemcitabineCorrected.txt b/doc/examples/biomodels/BIOMD0000000234/GemcitabineCorrected.txt similarity index 99% rename from doc/examples/biomodels/GemcitabineCorrected.txt rename to doc/examples/biomodels/BIOMD0000000234/GemcitabineCorrected.txt index 09bcba001..17b5c1770 100644 --- a/doc/examples/biomodels/GemcitabineCorrected.txt +++ b/doc/examples/biomodels/BIOMD0000000234/GemcitabineCorrected.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Tham2008___PDmodel__Tumour_shrinkage_by_gemcitabine_and_carboplatin() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000235_url.txt b/doc/examples/biomodels/BIOMD0000000235/BIOMD0000000235_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000235_url.txt rename to doc/examples/biomodels/BIOMD0000000235/BIOMD0000000235_url.txt index 02dfc70f6..67df33bd5 100644 --- a/doc/examples/biomodels/BIOMD0000000235_url.txt +++ b/doc/examples/biomodels/BIOMD0000000235/BIOMD0000000235_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kuhn2009_EndoMesodermNetwork() // Compartments and Species: @@ -1096,20 +1096,20 @@ model *Kuhn2009_EndoMesodermNetwork() mRNA_P_z13_translation_0: $none => PROTEIN_P_z13; mRNA_P_z13_translation_0_P_k_translation*mRNA_P_z13; // Events: - e24: at 0 after time >= 24: M_UMANrl_S1 = 1, M_UMANrl_S2 = 0, E_SuH_S1 = 1, E_SuH_S2 = 0, E_VEGF_S1 = 1, E_VEGF_S2 = 0; - e21: at 0 after time >= 21: P_L1_S2 = 0, P_L1_S1 = 1, E_Notch_S2 = 0, E_Notch_S1 = 1; - e19: at 0 after time >= 19: M_UMADelta_S2 = 0, M_UMADelta_S1 = 1; - e18: at 0 after time >= 18: E_UVAOtx_S2 = 0, E_UVAOtx_S1 = 1; - e15: at 0 after time >= 15: P_Otx_S2 = 0, P_Otx_S1 = 1, M_UMR_S2 = 0, M_UMR_S1 = 1, E_UMR_S2 = 0, E_UMR_S1 = 1; - e12: at 0 after time >= 12: M_SuH_S2 = 0, M_SuH_S1 = 1; - e30: at 0 after time >= 30: M_UMR_S1 = 0, M_UMR_S2 = 1, E_UMR_S1 = 0, E_UMR_S2 = 1, M_SuH_S1 = 0, M_SuH_S2 = 1, P_UbiqEts1_S2 = 1, P_UbiqEts1_S1 = 0, P_UbiqAlx1_S2 = 1, P_UbiqAlx1_S1 = 0, M_Notch_S2 = 1, M_Notch_S1 = 0, E_UVAOtx_S1 = 0, E_UVAOtx_S2 = 1, M_UMADelta_S1 = 0, M_UMADelta_S2 = 1, P_L1_S1 = 0, P_L1_S2 = 1, E_Notch_S1 = 0, E_Notch_S2 = 1, M_UMANrl_S1 = 0, M_UMANrl_S2 = 1, E_SuH_S1 = 0, E_SuH_S2 = 1, E_VEGF_S1 = 0, E_VEGF_S2 = 1; - e23: at 0 after time >= 23: P_UbiqHnf6_S2 = 1, P_UbiqHnf6_S1 = 0; - e29: at 0 after time >= 29: P_UbiqTel_S1 = 0, P_UbiqTel_S2 = 1; - e20: at 0 after time >= 20: P_UbiqES_S2 = 1, P_UbiqES_S1 = 0, P_Gcad_S2 = 1, P_Gcad_S1 = 0, M_Gcad_S2 = 1, M_Gcad_S1 = 0; - e17: at 0 after time >= 17: E_UbiqSoxC_S1 = 0, E_UbiqSoxC_S2 = 1, P_UbiqSoxC_S1 = 0, P_UbiqSoxC_S2 = 1; - e14: at 0 after time >= 14: M_UbiqSoxB1_S2 = 1, M_UbiqSoxB1_S1 = 0, P_cB_S2 = 1, P_cB_S1 = 0, M_SoxB1_S2 = 1, M_SoxB1_S1 = 0, E_SoxB1_S2 = 1, E_SoxB1_S1 = 0; - e8: at 0 after time >= 8: P_UbiqHesC_S1 = 0, P_UbiqHesC_S2 = 1; - e11: at 0 after time >= 11: M_Otx_S2 = 1, M_Otx_S1 = 0, E_Otx_S2 = 1, E_Otx_S1 = 0, E_Gcad_S2 = 1, E_Gcad_S1 = 0, M_cB_S2 = 1, M_cB_S1 = 0, E_cB_S2 = 1, E_cB_S1 = 0, P_Ets1_S2 = 1, P_Ets1_S1 = 0; + e24: at 0 after time >= 24: E_VEGF_S2 = 0, E_VEGF_S1 = 1, E_SuH_S2 = 0, E_SuH_S1 = 1, M_UMANrl_S2 = 0, M_UMANrl_S1 = 1; + e21: at 0 after time >= 21: E_Notch_S1 = 1, E_Notch_S2 = 0, P_L1_S1 = 1, P_L1_S2 = 0; + e19: at 0 after time >= 19: M_UMADelta_S1 = 1, M_UMADelta_S2 = 0; + e18: at 0 after time >= 18: E_UVAOtx_S1 = 1, E_UVAOtx_S2 = 0; + e15: at 0 after time >= 15: E_UMR_S1 = 1, E_UMR_S2 = 0, M_UMR_S1 = 1, M_UMR_S2 = 0, P_Otx_S1 = 1, P_Otx_S2 = 0; + e12: at 0 after time >= 12: M_SuH_S1 = 1, M_SuH_S2 = 0; + e30: at 0 after time >= 30: E_VEGF_S2 = 1, E_VEGF_S1 = 0, E_SuH_S2 = 1, E_SuH_S1 = 0, M_UMANrl_S2 = 1, M_UMANrl_S1 = 0, E_Notch_S2 = 1, E_Notch_S1 = 0, P_L1_S2 = 1, P_L1_S1 = 0, M_UMADelta_S2 = 1, M_UMADelta_S1 = 0, E_UVAOtx_S2 = 1, E_UVAOtx_S1 = 0, M_Notch_S1 = 0, M_Notch_S2 = 1, P_UbiqAlx1_S1 = 0, P_UbiqAlx1_S2 = 1, P_UbiqEts1_S1 = 0, P_UbiqEts1_S2 = 1, M_SuH_S2 = 1, M_SuH_S1 = 0, E_UMR_S2 = 1, E_UMR_S1 = 0, M_UMR_S2 = 1, M_UMR_S1 = 0; + e23: at 0 after time >= 23: P_UbiqHnf6_S1 = 0, P_UbiqHnf6_S2 = 1; + e29: at 0 after time >= 29: P_UbiqTel_S2 = 1, P_UbiqTel_S1 = 0; + e20: at 0 after time >= 20: M_Gcad_S1 = 0, M_Gcad_S2 = 1, P_Gcad_S1 = 0, P_Gcad_S2 = 1, P_UbiqES_S1 = 0, P_UbiqES_S2 = 1; + e17: at 0 after time >= 17: P_UbiqSoxC_S2 = 1, P_UbiqSoxC_S1 = 0, E_UbiqSoxC_S2 = 1, E_UbiqSoxC_S1 = 0; + e14: at 0 after time >= 14: E_SoxB1_S1 = 0, E_SoxB1_S2 = 1, M_SoxB1_S1 = 0, M_SoxB1_S2 = 1, P_cB_S1 = 0, P_cB_S2 = 1, M_UbiqSoxB1_S1 = 0, M_UbiqSoxB1_S2 = 1; + e8: at 0 after time >= 8: P_UbiqHesC_S2 = 1, P_UbiqHesC_S1 = 0; + e11: at 0 after time >= 11: P_Ets1_S1 = 0, P_Ets1_S2 = 1, E_cB_S1 = 0, E_cB_S2 = 1, M_cB_S1 = 0, M_cB_S2 = 1, E_Gcad_S1 = 0, E_Gcad_S2 = 1, E_Otx_S1 = 0, E_Otx_S2 = 1, M_Otx_S1 = 0, M_Otx_S2 = 1; // Species initializations: GENE_E_Alx1 = 0; diff --git a/doc/examples/biomodels/BIOMD0000000236_url.txt b/doc/examples/biomodels/BIOMD0000000236/BIOMD0000000236_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000236_url.txt rename to doc/examples/biomodels/BIOMD0000000236/BIOMD0000000236_url.txt index f57620301..1ec6f9090 100644 --- a/doc/examples/biomodels/BIOMD0000000236_url.txt +++ b/doc/examples/biomodels/BIOMD0000000236/BIOMD0000000236_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Westermark2003_Pancreatic_GlycOsc_extended() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000237_url.txt b/doc/examples/biomodels/BIOMD0000000237/BIOMD0000000237_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000237_url.txt rename to doc/examples/biomodels/BIOMD0000000237/BIOMD0000000237_url.txt index 66ae35298..9eb1ecc6a 100644 --- a/doc/examples/biomodels/BIOMD0000000237_url.txt +++ b/doc/examples/biomodels/BIOMD0000000237/BIOMD0000000237_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Schaber2006_Pheromone_Starvation_Crosstalk() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000238_url.txt b/doc/examples/biomodels/BIOMD0000000238/BIOMD0000000238_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000238_url.txt rename to doc/examples/biomodels/BIOMD0000000238/BIOMD0000000238_url.txt index b5063db0a..e347517de 100644 --- a/doc/examples/biomodels/BIOMD0000000238_url.txt +++ b/doc/examples/biomodels/BIOMD0000000238/BIOMD0000000238_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Overgaard2007_PDmodel_IL21() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000239_url.txt b/doc/examples/biomodels/BIOMD0000000239/BIOMD0000000239_url.txt similarity index 87% rename from doc/examples/biomodels/BIOMD0000000239_url.txt rename to doc/examples/biomodels/BIOMD0000000239/BIOMD0000000239_url.txt index b7807e6b3..f62d5e6dd 100644 --- a/doc/examples/biomodels/BIOMD0000000239_url.txt +++ b/doc/examples/biomodels/BIOMD0000000239/BIOMD0000000239_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000239() // Compartments and Species: @@ -43,17 +43,17 @@ model *BIOMD0000000239() v18: Mal + NAD_p -> NADH + OXA; MATRIX*((v18_KcF*Mal*NAD_p/v18_KiS1/v18_KmS2 - v18_KcR*OXA*NADH/v18_KmP1/v18_KiP2)*v18_v18_MDH/(1 + Mal/v18_KiS1 + v18_KmS1*NAD_p/v18_KiS1/v18_KmS2 + v18_KmP2*OXA/v18_KmP1/v18_KiP2 + NADH/v18_KiP2 + Mal*NAD_p/v18_KiS1/v18_KmS2 + v18_KmP2*Mal*OXA/v18_KiS1/v18_KmP1/v18_KiP2 + v18_KmS1*NAD_p*NADH/v18_KiS1/v18_KmS2/v18_KiP2 + (OXA*NADH/v18_KmP1)*v18_KiP2 + Mal*NAD_p*OXA/v18_KiS1/v18_KmS2/v18_KiP1 + NAD_p*OXA*NADH/v18_KiS2/v18_KmP1/v18_KiP2)); v20: Ala + OG -> Glu + Pyr; MATRIX*(v20_KcF*v20_KcR*v20_v20_AlaTA*(Ala*OG - Glu*Pyr/v20_Keq)/(v20_KcR*v20_KmS2*Ala + v20_KcR*v20_KmS1*OG + v20_KcF*v20_KmP2*Glu/v20_Keq + v20_KcF*v20_KmP1*Pyr/v20_Keq + v20_KcR*Ala*OG + v20_KcF*v20_KmP2*Ala*Glu/(v20_Keq*v20_KiS1) + v20_KcF*Glu*Pyr/v20_Keq + v20_KcR*v20_KmS1*OG*Pyr/v20_KiP2)); v21: OXA + Glu -> Asp + OG; MATRIX*(v21_KcF*v21_KcR*v21_v21_AspTA*(OXA*Glu - Asp*OG/v21_Keq)/(v21_KcR*v21_KmS2*OXA + v21_KcR*v21_KmS1*Glu + v21_KcF*v21_KmP2*Asp/v21_Keq + v21_KcF*v21_KmP1*OG/v21_Keq + v21_KcR*OXA*Glu + v21_KcF*v21_KmP2*OXA*Asp/(v21_Keq*v21_KiS1) + v21_KcF*Asp*OG/v21_Keq + v21_KcR*v21_KmS1*Glu*OG/v21_KiP2)); - v22: Glu_cyt + Asp -> Asp_cyt + Glu; MATRIX*(((Asp*Glu_cyt/v22_alpha/v22_KiS1/v22_KiS2)*v22_KcF - (Glu*Asp_cyt/v22_beta/v22_KiP1/v22_KiP2)*v22_KcR)*v22_v22_AGC/(1 + Asp/v22_KiS1 + Glu_cyt/v22_KiS2 + Glu/v22_KiP1 + Asp_cyt/v22_KiP2 + Asp*Glu_cyt/v22_alpha/v22_KiS1/v22_KiS2 + Glu*Asp_cyt/v22_beta/v22_KiP1/v22_KiP2 + Glu_cyt*Asp_cyt/v22_gamma/v22_KiS2/v22_KiP2 + Asp*Glu/v22_delta/v22_KiS1/v22_KiP1)); + v22: Glu_cyt + Asp -> Asp_cyt + Glu; MATRIX*(((Asp*Glu_cyt/v22_alpha/v22_KiS1/v22_KiS2)*v22_KcF - (Glu*Asp_cyt/v22_beta/v22_KiP1/v22_KiP2)*v22_KcR)*v22_v22_AGC/(1 + Asp/v22_KiS1 + Glu_cyt/v22_KiS2 + Glu/v22_KiP1 + Asp_cyt/v22_KiP2 + Asp*Glu_cyt/v22_alpha/v22_KiS1/v22_KiS2 + Glu*Asp_cyt/v22_beta/v22_KiP1/v22_KiP2 + Glu_cyt*Asp_cyt/v22_gamma_/v22_KiS2/v22_KiP2 + Asp*Glu/v22_delta/v22_KiS1/v22_KiP1)); v24: NADH + Q -> NAD_p + QH2; MATRIX*(v24_KcF*v24_KcR*v24_v24_Complex_I*(NADH*Q - NAD_p*QH2/v24_Keq)/(v24_KcR*v24_KmS2*NADH + v24_KcR*v24_KmS1*Q + v24_KcF*v24_KmP2*NAD_p/v24_Keq + v24_KcF*v24_KmP1*QH2/v24_Keq + v24_KcR*NADH*Q + v24_KcF*v24_KmP2*NADH*NAD_p/(v24_Keq*v24_KiS1) + v24_KcF*NAD_p*QH2/v24_Keq + v24_KcR*v24_KmS1*Q*QH2/v24_KiP2)); v25: QH2 + 2 Cytc3p => Q + 2 Cytc2p; MT_IMS*(v25_KcF*v25_v25_Complex_III*QH2*Cytc3p/((v25_KmA*v25_Kq2*v25_Kb2 + v25_KmA*v25_Kq2*Cytc3p + (v25_KcF/v25_k8)*v25_Kq1*QH2*v25_Kb1 + (v25_KcF/v25_k8)*v25_Kq1*QH2*Cytc3p)*Cytc2p + v25_KmA*Cytc3p + v25_KmB*QH2 + QH2*Cytc3p)); v26: Cytc2p => Cytc3p; MT_IMS*(v26_KcF*v26_v26_Complex_IV*Cytc2p/(v26_Ks + Cytc2p)); v27: Cit_cyt + CoA_cyt -> OXA_cyt + Acetyl_CoA_cyt; CYTOPLASM*v27_Kid*v27_Kc*(v27_V*Acetyl_CoA_cyt*OXA_cyt*v27_v10_CS/(Acetyl_CoA_cyt*OXA_cyt + v27_Ka*OXA_cyt + v27_Kb*Acetyl_CoA_cyt + v27_Kia*v27_Kib))/(v27_Keq*v27_Kia*v27_Kb); v28: ADP + Pi -> ATP + H2O; MATRIX*v28_v28_Complex_V*v28_V*ADP/(v28_Km + ADP + ADP*ADP/v28_Ki); v29: Cit_cyt -> IsoCitcyt; CYTOPLASM*((v29_KcF*v29_Kp*Cit_cyt - v29_KcR*v29_Ks*IsoCitcyt)*v29_v29_ACO/(v29_Ks*IsoCitcyt + v29_Kp*Cit_cyt + v29_Ks*v29_Kp)); - v30: Mal_cyt + OG -> OG_cyt + Mal; MATRIX*(((OG*Mal_cyt/v30_alpha/v30_KiS1/v30_KiS2)*v30_KcF - (Mal*OG_cyt/v30_beta/v30_KiP1/v30_KiP2)*v30_KcR)*v30_v30_OGC/(1 + OG/v30_KiS1 + Mal_cyt/v30_KiS2 + Mal/v30_KiP1 + OG_cyt/v30_KiP2 + OG*Mal_cyt/v30_alpha/v30_KiS1/v30_KiS2 + Mal*OG_cyt/v30_beta/v30_KiP1/v30_KiP2 + Mal_cyt*OG_cyt/v30_gamma/v30_KiS2/v30_KiP2 + OG*Mal/v30_delta/v30_KiS1/v30_KiP1)); + v30: Mal_cyt + OG -> OG_cyt + Mal; MATRIX*(((OG*Mal_cyt/v30_alpha/v30_KiS1/v30_KiS2)*v30_KcF - (Mal*OG_cyt/v30_beta/v30_KiP1/v30_KiP2)*v30_KcR)*v30_v30_OGC/(1 + OG/v30_KiS1 + Mal_cyt/v30_KiS2 + Mal/v30_KiP1 + OG_cyt/v30_KiP2 + OG*Mal_cyt/v30_alpha/v30_KiS1/v30_KiS2 + Mal*OG_cyt/v30_beta/v30_KiP1/v30_KiP2 + Mal_cyt*OG_cyt/v30_gamma_/v30_KiS2/v30_KiP2 + OG*Mal/v30_delta/v30_KiS1/v30_KiP1)); v31: NADH_cyt + OXA_cyt => Mal_cyt + NAD; CYTOPLASM*(v31_v31_MDH*(v31_k1*v31_k2*v31_k3*v31_k4*NADH_cyt*OXA_cyt - v31_kminus1*v31_kminus2*v31_kminus3*v31_kminus4*Mal_cyt*NAD)/(v31_kminus1*(v31_kminus2 + v31_k3)*v31_k4 + v31_k1*(v31_kminus2 + v31_k3)*v31_k4*NADH_cyt + v31_kminus1*(v31_kminus2 + v31_k3)*v31_kminus4*NAD + v31_k2*v31_k3*v31_k4*OXA_cyt + v31_kminus1*v31_kminus2*v31_kminus3*Mal_cyt + v31_k1*v31_k2*(v31_k3 + v31_k4)*NADH_cyt*OXA_cyt + (v31_kminus1 + v31_kminus2)*v31_kminus3*v31_kminus4*Mal_cyt*NAD + v31_k1 + v31_kminus2 + v31_kminus3*NADH_cyt*Mal_cyt + v31_k1*v31_k2*v31_kminus3*NADH_cyt*OXA_cyt*Mal_cyt + v31_k2*v31_k3*v31_kminus4*OXA_cyt*NAD + v31_k2*v31_kminus3*v31_kminus4*OXA_cyt*Mal_cyt*NAD)); v32: Asp_cyt + OG_cyt -> OXA_cyt + Glu_cyt; CYTOPLASM*(v32_KcF*v32_KcR*v32_v32_AspTA*(Asp_cyt*OG_cyt - OXA_cyt*Glu_cyt/v32_Keq)/(v32_KcR*v32_KmS2*Asp_cyt + v32_KcR*v32_KmS1*OG_cyt + v32_KcF*v32_KmP2*OXA_cyt/v32_Keq + v32_KcF*v32_KmP1*Glu_cyt/v32_Keq + v32_KcR*Asp_cyt*OG_cyt + v32_KcF*v32_KmP2*Asp_cyt*OXA_cyt/(v32_Keq*v32_KiS1) + v32_KcF*OXA_cyt*Glu_cyt/v32_Keq + v32_KcR*v32_KmS1*OG_cyt*Glu_cyt/v32_KiP2)); - v33: Cit_cyt + Mal -> Mal_cyt + Cit; MATRIX*(((Cit_cyt*Mal/v33_alpha/v33_KiS1/v33_KiS2)*v33_KcF - (Mal_cyt*Cit/v33_beta/v33_KiP1/v33_KiP2)*v33_KcR)*v33_v33_CIC/(1 + Cit_cyt/v33_KiS1 + Mal/v33_KiS2 + Mal_cyt/v33_KiP1 + Cit/v33_KiP2 + Cit_cyt*Mal/v33_alpha/v33_KiS1/v33_KiS2 + Mal_cyt*Cit/v33_beta/v33_KiP1/v33_KiP2 + Mal*Cit/v33_gamma/v33_KiS2/v33_KiP2 + Cit_cyt*Mal_cyt/v33_delta/v33_KiS1/v33_KiP1)); + v33: Cit_cyt + Mal -> Mal_cyt + Cit; MATRIX*(((Cit_cyt*Mal/v33_alpha/v33_KiS1/v33_KiS2)*v33_KcF - (Mal_cyt*Cit/v33_beta/v33_KiP1/v33_KiP2)*v33_KcR)*v33_v33_CIC/(1 + Cit_cyt/v33_KiS1 + Mal/v33_KiS2 + Mal_cyt/v33_KiP1 + Cit/v33_KiP2 + Cit_cyt*Mal/v33_alpha/v33_KiS1/v33_KiS2 + Mal_cyt*Cit/v33_beta/v33_KiP1/v33_KiP2 + Mal*Cit/v33_gamma_/v33_KiS2/v33_KiP2 + Cit_cyt*Mal_cyt/v33_delta/v33_KiS1/v33_KiP1)); v34: ETFred + Q -> ETFox + QH2; MATRIX*(v34_KcF*v34_KcR*v34_v34_ETF_QO*(ETFred*Q - ETFox*QH2/v34_Keq)/(v34_KcR*v34_KmS2*ETFred + v34_KcR*v34_KmS1*Q + v34_KcF*v34_KmP2*ETFox/v34_Keq + v34_KcF*v34_KmP1*QH2/v34_Keq + v34_KcR*ETFred*Q + v34_KcF*v34_KmP2*ETFred*ETFox/(v34_Keq*v34_KiS1) + v34_KcF*ETFox*QH2/v34_Keq + v34_KcR*v34_KmS1*Q*QH2/v34_KiP2)); v35: FADH2 + ETFox -> ETFred + FAD; MATRIX*(v35_KcF*v35_KcR*v35_v35_ACD*(FADH2*ETFox - ETFred*FAD/v35_Keq)/(v35_KcR*v35_KiS1*v35_KmS2 + v35_KcR*v35_KmS2*FADH2 + v35_KcR*v35_KmS1*ETFox + v35_KcF*v35_KmP2*ETFred/v35_Keq + v35_KcF*v35_KmP1*FAD/v35_Keq + v35_KcR*FADH2*ETFox + v35_KcF*v35_KmP2*FADH2*ETFred/(v35_Keq*v35_KiS1) + v35_KcF*ETFred*FAD/v35_Keq + v35_KcR*v35_KmS1*ETFox*FAD/v35_KiP2 + v35_KcR*FADH2*ETFox*ETFred/v35_KiP1 + v35_KcF*ETFox*ETFred*FAD/(v35_KiS2*v35_Keq))); v36: ATP + CO2 + Pyr -> Pi + ADP + OXA; MATRIX*(v36_KcF*v36_KcR*v36_v36_PC*(ATP*CO2*Pyr - pi*ADP*OXA/v36_Keq)/(v36_Kia*v36_KmB*v36_KcR*Pyr + v36_KmC*v36_KcR*ATP*CO2 + v36_KmA*v36_KcR*CO2*Pyr + v36_KmB*v36_KcR*ATP*Pyr + v36_KcR*ATP*CO2*Pyr + v36_Kip*v36_KmQ*v36_KcF*OXA/v36_Keq + v36_KmQ*v36_KcF*pi*OXA/v36_Keq + v36_KmP*v36_KcF*ADP*OXA/v36_Keq + v36_KmR*v36_KcF*pi*ADP/v36_Keq + v36_KcF*pi*ADP*OXA/v36_Keq + v36_Kia*v36_KmB*v36_KcR*Pyr*pi/v36_Kip + v36_Kia*v36_KmB*v36_KcR*Pyr*ADP/v36_Kia + v36_Kiq*v36_KmP*v36_KcF*CO2*OXA/v36_Kib/v36_Keq + v36_Kia*v36_KmP*v36_KcF*ATP*OXA/v36_Kia/v36_Keq + v36_KmA*v36_KcR*ATP*CO2*OXA/v36_Kir + v36_KmR*v36_KcF*Pyr*pi*ADP/v36_Kic/v36_Keq + v36_KmA*v36_KcR*CO2*Pyr*ADP/v36_Kiq + v36_KmA*v36_KcR*CO2*Pyr*pi/v36_Kip + v36_KmP*v36_KcF*CO2*ADP*OXA/v36_Kib/v36_Keq + v36_KmQ*v36_KcF*CO2*pi*OXA/v36_Kib/v36_Keq)); @@ -61,7 +61,7 @@ model *BIOMD0000000239() v38: NADH_cyt + DHAP => G3P + NAD; CYTOPLASM*(v38_V*v38_v38_GUT2P*NADH_cyt/(v38_K + NADH_cyt)); v40: ADP_cyt => ADP; MATRIX*(v40_V*v40_v40_AAC*ADP_cyt/(v40_K + ADP_cyt)); v41: IsoCitcyt + NADP_cyt -> OG_cyt + NADPH_cyt; CYTOPLASM*v41_v41_IDHc*(IsoCitcyt*NADP_cyt/(v41_phi0*IsoCitcyt*NADP_cyt + v41_phi1*NADP_cyt + v41_phi2*IsoCitcyt + v41_phi12) - OG_cyt*NADPH_cyt*CO2/(v41_phir0*OG_cyt*NADPH_cyt*CO2 + v41_phir1*NADPH_cyt*CO2 + v41_phir2*OG_cyt*CO2 + v41_phir3*OG_cyt*NADPH_cyt + v41_phir12*CO2 + v41_phir13*NADPH_cyt + v41_phir23*OG_cyt + v41_phir123)); - v42: IsoCitcyt + Mal -> Mal_cyt + IsoCit; MATRIX*(((IsoCitcyt*Mal/v42_alpha/v42_KiS1/v42_KiS2)*v42_KcF - (Mal_cyt*IsoCit/v42_beta/v42_KiP1/v42_KiP2)*v42_KcR)*v42_v42_CIC/(1 + IsoCitcyt/v42_KiS1 + Mal/v42_KiS2 + Mal_cyt/v42_KiP1 + IsoCit/v42_KiP2 + IsoCitcyt*Mal/v42_alpha/v42_KiS1/v42_KiS2 + Mal_cyt*IsoCit/v42_beta/v42_KiP1/v42_KiP2 + Mal*IsoCit/v42_gamma/v42_KiS2/v42_KiP2 + IsoCitcyt*Mal_cyt/v42_delta/v42_KiS1/v42_KiP1)); + v42: IsoCitcyt + Mal -> Mal_cyt + IsoCit; MATRIX*(((IsoCitcyt*Mal/v42_alpha/v42_KiS1/v42_KiS2)*v42_KcF - (Mal_cyt*IsoCit/v42_beta/v42_KiP1/v42_KiP2)*v42_KcR)*v42_v42_CIC/(1 + IsoCitcyt/v42_KiS1 + Mal/v42_KiS2 + Mal_cyt/v42_KiP1 + IsoCit/v42_KiP2 + IsoCitcyt*Mal/v42_alpha/v42_KiS1/v42_KiS2 + Mal_cyt*IsoCit/v42_beta/v42_KiP1/v42_KiP2 + Mal*IsoCit/v42_gamma_/v42_KiS2/v42_KiP2 + IsoCitcyt*Mal_cyt/v42_delta/v42_KiS1/v42_KiP1)); v43: ATP => ATP_cyt; MATRIX*(v43_V*v43_v43_AAC*ATP/(v43_K + ATP)); v39: Mal_cyt + NADP_cyt -> NADPH_cyt + PYR_cyt; CYTOPLASM*(v39_v39_MDH*v39_Kcat*Mal_cyt*NADP_cyt/((v39_Kmal + Mal_cyt)*(v39_Knadp + NADP_cyt))); v44: Mal + NADP_p -> NADPH + Pyr; MATRIX*(v44_v44_MDH*v44_Kcat*Mal/(v44_Km + Mal)); @@ -275,7 +275,7 @@ model *BIOMD0000000239() v22_KcR = 10; v22_alpha = 1; v22_beta = 1; - v22_gamma = 1; + v22_gamma_ = 1; v22_delta = 1; v22_v22_AGC = 0.00033211; v24_KmS1 = 9.2e-06; @@ -326,7 +326,7 @@ model *BIOMD0000000239() v30_KcR = 4.83; v30_alpha = 1; v30_beta = 1; - v30_gamma = 1; + v30_gamma_ = 1; v30_delta = 1; v30_v30_OGC = 0.00033211; v31_k1 = 34000000; @@ -356,7 +356,7 @@ model *BIOMD0000000239() v33_KcR = 3.5; v33_alpha = 1; v33_beta = 1; - v33_gamma = 1; + v33_gamma_ = 1; v33_delta = 1; v33_v33_CIC = 0.00033211; v34_KmS1 = 3.1e-07; @@ -427,7 +427,7 @@ model *BIOMD0000000239() v42_KcR = 3.5; v42_alpha = 1; v42_beta = 1; - v42_gamma = 1; + v42_gamma_ = 1; v42_delta = 1; v42_v42_CIC = 0.00033211; v43_V = 1.11667; @@ -663,50 +663,118 @@ model *BIOMD0000000239() Cytc2p identity "http://identifiers.org/chebi/CHEBI:15991", "http://identifiers.org/kegg.compound/C00125" v1 identity "http://identifiers.org/ec-code/2.7.1.2" + v1.kineticLaw publication "http://identifiers.org/pubmed/17029704" v2 identity "http://identifiers.org/ec-code/2.7.1.11" + v2.kineticLaw publication "http://identifiers.org/pubmed/17029704" v3 identity "http://identifiers.org/ec-code/4.1.2.13" + v3.kineticLaw publication "http://identifiers.org/pubmed/17029704" v4 identity "http://identifiers.org/ec-code/1.2.1.12" + v4.kineticLaw publication "http://identifiers.org/pubmed/17029704" v5 identity "http://identifiers.org/ec-code/5.4.2.4", "http://identifiers.org/ec-code/5.4.2.1" + v5.kineticLaw publication "http://identifiers.org/pubmed/17029704" v6 identity "http://identifiers.org/ec-code/2.7.1.40" + v6.kineticLaw publication "http://identifiers.org/pubmed/17029704" v7 identity "http://identifiers.org/ec-code/1.1.1.27" + v7.kineticLaw publication "http://identifiers.org/pubmed/17029704" hidden_1 isVersionOf "http://identifiers.org/go/GO:0004017" v8 isVersionOf "http://identifiers.org/go/GO:0005477" + v8.kineticLaw publication "http://identifiers.org/pubmed/1156402" v9 identity "http://identifiers.org/ec-code/1.2.4.1" + v9.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/169232" v10 identity "http://identifiers.org/ec-code/2.3.3.3", "http://identifiers.org/ec-code/2.3.3.1" + v10.kineticLaw publication "http://identifiers.org/pubmed/4201777" v11 identity "http://identifiers.org/ec-code/4.2.1.3" + v11.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/755796" v12 identity "http://identifiers.org/ec-code/1.1.1.41" + v12.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/4361827" v14 identity "http://identifiers.org/ec-code/1.2.4.2" + v14.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/169232" v15 identity "http://identifiers.org/ec-code/6.2.1.4" + v15.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/14213385" v16 identity "http://identifiers.org/ec-code/1.3.5.1" + v16.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/8417779" v17 identity "http://identifiers.org/ec-code/4.2.1.2" + v17.kineticLaw publication "http://identifiers.org/pubmed/14962921" v18 identity "http://identifiers.org/ec-code/1.1.1.37" + v18.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/6625603" v20 identity "http://identifiers.org/ec-code/2.6.1.2" + v20.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/454616" v21 identity "http://identifiers.org/ec-code/2.6.1.1" + v21.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/13925259", + "http://identifiers.org/pubmed/14155095" + v22.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/2065061" v24 identity "http://identifiers.org/ec-code/2.7.4.6" + v24.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/8611577" v25 identity "http://identifiers.org/ec-code/1.10.2.2" + v25.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/1318882" v26 identity "http://identifiers.org/ec-code/1.9.3.1" + v26.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/2991462" v27 identity "http://identifiers.org/ec-code/2.3.3.3", "http://identifiers.org/ec-code/2.3.3.1" + v27.kineticLaw publication "http://identifiers.org/pubmed/4201777" v28 identity "http://identifiers.org/ec-code/3.6.1.3", "http://identifiers.org/ec-code/3.6.1.5" + v28.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/8394322" v29 identity "http://identifiers.org/ec-code/4.2.1.3" + v29.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/755796" v30 isVersionOf "http://identifiers.org/go/GO:0015367" + v30.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/2040299" v31 identity "http://identifiers.org/ec-code/1.1.1.37" + v31.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/6625603" v32 identity "http://identifiers.org/ec-code/2.6.1.1" + v32.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/13925259", + "http://identifiers.org/pubmed/14155095" v33 isVersionOf "http://identifiers.org/go/GO:0015137" + v33.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/8457581" v34 identity "http://identifiers.org/ec-code/1.5.5.1" + v34.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/2996585" v35 identity "http://identifiers.org/ec-code/1.8.1.7" + v35.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/429316" v36 identity "http://identifiers.org/ec-code/6.4.1.1" + v36.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/5010071" v37 identity "http://identifiers.org/ec-code/1.1.99.5" + v37.kineticLaw publication "http://identifiers.org/pubmed/12032156" v38 identity "http://identifiers.org/ec-code/1.1.1.8" + v38.kineticLaw publication "http://identifiers.org/pubmed/12032156" v40 isVersionOf "http://identifiers.org/go/GO:0015217" + v40.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/6280754" v41 identity "http://identifiers.org/ec-code/1.1.1.42" + v41.kineticLaw publication "http://identifiers.org/pubmed/14962921" v42 isVersionOf "http://identifiers.org/go/GO:0006843" + v42.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/8457581" v43 isVersionOf "http://identifiers.org/go/GO:0005347" + v43.kineticLaw publication "http://identifiers.org/pubmed/14962921", + "http://identifiers.org/pubmed/6280754" v39 identity "http://identifiers.org/ec-code/1.1.1.40" + v39.kineticLaw publication "http://identifiers.org/pubmed/7437446" v44 identity "http://identifiers.org/ec-code/1.1.1.40" + v44.kineticLaw publication "http://identifiers.org/pubmed/7437446" model model_source "http://identifiers.org/biomodels.db/MODEL1469251725" model model_source "http://identifiers.org/biomodels.db/BIOMD0000000239" diff --git a/doc/examples/biomodels/BIOMD0000000240_url.txt b/doc/examples/biomodels/BIOMD0000000240/BIOMD0000000240_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000240_url.txt rename to doc/examples/biomodels/BIOMD0000000240/BIOMD0000000240_url.txt index faba9a1d1..5fdda64ad 100644 --- a/doc/examples/biomodels/BIOMD0000000240_url.txt +++ b/doc/examples/biomodels/BIOMD0000000240/BIOMD0000000240_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Veening2008_DegU_Regulation() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000241_url.txt b/doc/examples/biomodels/BIOMD0000000241/BIOMD0000000241_url.txt similarity index 95% rename from doc/examples/biomodels/BIOMD0000000241_url.txt rename to doc/examples/biomodels/BIOMD0000000241/BIOMD0000000241_url.txt index 3a9d421ce..a78b02d0a 100644 --- a/doc/examples/biomodels/BIOMD0000000241_url.txt +++ b/doc/examples/biomodels/BIOMD0000000241/BIOMD0000000241_url.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Shi1993_Caffeine_pressor_tolerance() // Compartments and Species: compartment Gut, C, P, Tol, Eff; - species $C_p in C, $C_per in P, $C_e in Eff, $C_t in Tol; - substanceOnly species $X_gut in Gut; + species C_p in C, C_per in P, C_e in Eff, C_t in Tol; + substanceOnly species X_gut in Gut; // Assignment Rules: E := E_0 + S*C_e/(1 + C_t/T_50); @@ -17,11 +17,11 @@ model *Shi1993_Caffeine_pressor_tolerance() C_t' = k_tol*(C_p - C_t); // Events: - coffecup: at time >= (t_int*cups + t_lag): X_gut = X_gut + cupsize/bodyweight, cups = cups + 1; + coffecup: at time >= (t_int*cups + t_lag): cups = cups + 1, X_gut = X_gut + cupsize/bodyweight; // Species initializations: X_gut = 0; - X_gut has mg_per_kg_per_volume; + X_gut has mg_per_kg; C_p = 0; C_per = 0; C_e = 0; @@ -85,7 +85,6 @@ model *Shi1993_Caffeine_pressor_tolerance() unit mm_Hg_l_per_mg = 1e-3 metre * litre / 1e-6 kilogram; unit mg_per_l = 1e-6 kilogram / litre; unit mg_per_kg = dimensionless; - unit mg_per_kg_per_volume = dimensionless / litre; // Display Names: substance is "mg"; diff --git a/doc/examples/biomodels/BIOMD0000000242_url.txt b/doc/examples/biomodels/BIOMD0000000242/BIOMD0000000242_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000242_url.txt rename to doc/examples/biomodels/BIOMD0000000242/BIOMD0000000242_url.txt index 860c975fa..3a63b5ed5 100644 --- a/doc/examples/biomodels/BIOMD0000000242_url.txt +++ b/doc/examples/biomodels/BIOMD0000000242/BIOMD0000000242_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bai2003_G1phaseRegulation() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000243_url.txt b/doc/examples/biomodels/BIOMD0000000243/BIOMD0000000243_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000243_url.txt rename to doc/examples/biomodels/BIOMD0000000243/BIOMD0000000243_url.txt index dd10f8757..0bd25e47c 100644 --- a/doc/examples/biomodels/BIOMD0000000243_url.txt +++ b/doc/examples/biomodels/BIOMD0000000243/BIOMD0000000243_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Neumann2010_CD95Stimulation_NFkB_Apoptosis() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000244_url.txt b/doc/examples/biomodels/BIOMD0000000244/BIOMD0000000244_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000244_url.txt rename to doc/examples/biomodels/BIOMD0000000244/BIOMD0000000244_url.txt index 2c1807cff..e81ac9020 100644 --- a/doc/examples/biomodels/BIOMD0000000244_url.txt +++ b/doc/examples/biomodels/BIOMD0000000244/BIOMD0000000244_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kotte2010_Ecoli_Metabolic_Adaption() // Compartments and Species: @@ -143,12 +143,12 @@ model *Kotte2010_Ecoli_Metabolic_Adaption() env_ACTex: => ACT; (env_uc*env_M_ACT*BM*Acoa2act*e_Acoa2act_kcat*ACoA/e_Acoa2act_Kacoa)*(1 + ACoA/e_Acoa2act_Kacoa)^(e_Acoa2act_n - 1)/((1 + ACoA/e_Acoa2act_Kacoa)^e_Acoa2act_n + e_Acoa2act_L/(1 + PYR/e_Acoa2act_Kpyr)^e_Acoa2act_n); // Events: - first_shift: at time >= (3600*shift1): BM = BM_1, ACT = ACT_1, GLC = GLC_1; - second_shift: at time >= (3600*shift2): BM = BM_2, ACT = ACT_2, GLC = GLC_2; + first_shift: at time >= (3600*shift1): GLC = GLC_1, ACT = ACT_1, BM = BM_1; + second_shift: at time >= (3600*shift2): GLC = GLC_2, ACT = ACT_2, BM = BM_2; // Species initializations: BM = 0.03; - BM has od_per_volume; + BM has od; ACT = 0; ACT has gram_per_litre; GLC = 4.8/Environment; @@ -460,7 +460,6 @@ model *Kotte2010_Ecoli_Metabolic_Adaption() unit time_unit = second; unit hour = 3600 second; unit gram_per_litre = gram / litre; - unit od_per_volume = dimensionless / litre; // Display Names: od is "OD"; diff --git a/doc/examples/biomodels/BIOMD0000000245_url.txt b/doc/examples/biomodels/BIOMD0000000245/BIOMD0000000245_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000245_url.txt rename to doc/examples/biomodels/BIOMD0000000245/BIOMD0000000245_url.txt index 18dfa2965..1dc84e0dd 100644 --- a/doc/examples/biomodels/BIOMD0000000245_url.txt +++ b/doc/examples/biomodels/BIOMD0000000245/BIOMD0000000245_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *lei2001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000246_url.txt b/doc/examples/biomodels/BIOMD0000000246/BIOMD0000000246_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000246_url.txt rename to doc/examples/biomodels/BIOMD0000000246/BIOMD0000000246_url.txt index c981a6e31..f23685be7 100644 --- a/doc/examples/biomodels/BIOMD0000000246_url.txt +++ b/doc/examples/biomodels/BIOMD0000000246/BIOMD0000000246_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *vasalou2010() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000247_url.txt b/doc/examples/biomodels/BIOMD0000000247/BIOMD0000000247_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000247_url.txt rename to doc/examples/biomodels/BIOMD0000000247/BIOMD0000000247_url.txt index 9e136d719..353b5a93c 100644 --- a/doc/examples/biomodels/BIOMD0000000247_url.txt +++ b/doc/examples/biomodels/BIOMD0000000247/BIOMD0000000247_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *ralser() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000248_url.txt b/doc/examples/biomodels/BIOMD0000000248/BIOMD0000000248_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000248_url.txt rename to doc/examples/biomodels/BIOMD0000000248/BIOMD0000000248_url.txt index b05598a77..5bbf36063 100644 --- a/doc/examples/biomodels/BIOMD0000000248_url.txt +++ b/doc/examples/biomodels/BIOMD0000000248/BIOMD0000000248_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Lai2007_O2_Transport_Metabolism() // Compartments and Species: @@ -172,8 +172,10 @@ model *Lai2007_O2_Transport_Metabolism() CFcap.sboTerm = 247 CFtis.sboTerm = 247 ATPase.sboTerm = 376 + ATPase.kineticLaw.sboTerm = 49 CreatineKinase.sboTerm = 216 OxidativePhosphorylation.sboTerm = 216 + OxidativePhosphorylation.kineticLaw.sboTerm = 432 ConvectionTransport.sboTerm = 185 DiffusionTransport.sboTerm = 185 diff --git a/doc/examples/biomodels/BIOMD0000000249_url.txt b/doc/examples/biomodels/BIOMD0000000249/BIOMD0000000249_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000249_url.txt rename to doc/examples/biomodels/BIOMD0000000249/BIOMD0000000249_url.txt index 17162fbfc..95ed545c7 100644 --- a/doc/examples/biomodels/BIOMD0000000249_url.txt +++ b/doc/examples/biomodels/BIOMD0000000249/BIOMD0000000249_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *restif06() // Compartments and Species: @@ -45,11 +45,11 @@ model *restif06() r20: R_p => S; sigma*R_p; // Species initializations: - N = 1/env; - S = 0.0588912/env; - I_1 = 0.003775/env; - I_2 = 1e-06/env; - R_1 = 0.93733/env; + N = 1*env; + S = 0.0588912*env; + I_1 = 0.003775*env; + I_2 = 1e-06*env; + R_1 = 0.93733*env; R_2 = 0; I_1p = 0; I_2p = 0; diff --git a/doc/examples/biomodels/BIOMD0000000250_url.txt b/doc/examples/biomodels/BIOMD0000000250/BIOMD0000000250_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000250_url.txt rename to doc/examples/biomodels/BIOMD0000000250/BIOMD0000000250_url.txt index b87bfe986..c0d86ebb8 100644 --- a/doc/examples/biomodels/BIOMD0000000250_url.txt +++ b/doc/examples/biomodels/BIOMD0000000250/BIOMD0000000250_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000251_url.txt b/doc/examples/biomodels/BIOMD0000000251/BIOMD0000000251_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000251_url.txt rename to doc/examples/biomodels/BIOMD0000000251/BIOMD0000000251_url.txt index d2800923f..1c54519d4 100644 --- a/doc/examples/biomodels/BIOMD0000000251_url.txt +++ b/doc/examples/biomodels/BIOMD0000000251/BIOMD0000000251_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Nakakuki2010_CellFateDecision_Core() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000252_url.txt b/doc/examples/biomodels/BIOMD0000000252/BIOMD0000000252_url.txt similarity index 94% rename from doc/examples/biomodels/BIOMD0000000252_url.txt rename to doc/examples/biomodels/BIOMD0000000252/BIOMD0000000252_url.txt index 06338d518..4808d132c 100644 --- a/doc/examples/biomodels/BIOMD0000000252_url.txt +++ b/doc/examples/biomodels/BIOMD0000000252/BIOMD0000000252_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hunziker2010_p53_StressSpecificResponse() // Compartments and Species: @@ -120,12 +120,12 @@ changed. The parameter values corresponding to different stress conditions are s in the following table. -| | -||----------------------------|--------|---------|--------------|--------------|| -| | Nutlin | 11hr-1 | 0.2hr-1 | 0.03nM-1hr-1 | 500nM-1hr-1 | | -| | Oncogene | 2hr-1 | 0.2hr-1 | 0.03nM-1hr-1 | 5000nM-1hr-1 | | -| | DNA damage | 2hr-1 | 0.5hr-1 | 0.03nM-1hr-1 | 2500nM-1hr-1 | | -| | Hypoxia | 2hr-1 | 0.2hr-1 | 0.01nM-1hr-1 | 5000nM-1hr-1 | | +| Stress Condition/Parameter | delta | gamma | kt | kf | +| Nutlin | 11hr-1 | 0.2hr-1 | 0.03nM-1hr-1 | 500nM-1hr-1 | +| Oncogene | 2hr-1 | 0.2hr-1 | 0.03nM-1hr-1 | 5000nM-1hr-1 | +| DNA damage | 2hr-1 | 0.5hr-1 | 0.03nM-1hr-1 | 2500nM-1hr-1 | +| Hypoxia | 2hr-1 | 0.2hr-1 | 0.01nM-1hr-1 | 5000nM-1hr-1 | + This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2011 The BioModels.net Team. diff --git a/doc/examples/biomodels/BIOMD0000000253_url.txt b/doc/examples/biomodels/BIOMD0000000253/BIOMD0000000253_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000253_url.txt rename to doc/examples/biomodels/BIOMD0000000253/BIOMD0000000253_url.txt index 5e87bc32c..7e64d3cc1 100644 --- a/doc/examples/biomodels/BIOMD0000000253_url.txt +++ b/doc/examples/biomodels/BIOMD0000000253/BIOMD0000000253_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Teusink1998_Glycolysis_TurboDesign() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000254_url.txt b/doc/examples/biomodels/BIOMD0000000254/BIOMD0000000254_url.txt similarity index 96% rename from doc/examples/biomodels/BIOMD0000000254_url.txt rename to doc/examples/biomodels/BIOMD0000000254/BIOMD0000000254_url.txt index 04003a31c..3a0175762 100644 --- a/doc/examples/biomodels/BIOMD0000000254_url.txt +++ b/doc/examples/biomodels/BIOMD0000000254/BIOMD0000000254_url.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bier2000_GlycolyticOscillation() // Compartments and Species: compartment compartment_; - species $G1 in compartment_, $T1 in compartment_, $T2 in compartment_, $G2 in compartment_; + species G1 in compartment_, T1 in compartment_, T2 in compartment_, G2 in compartment_; // Assignment Rules: Tsum := T2 + T1; diff --git a/doc/examples/biomodels/BIOMD0000000255_url.txt b/doc/examples/biomodels/BIOMD0000000255/BIOMD0000000255_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000255_url.txt rename to doc/examples/biomodels/BIOMD0000000255/BIOMD0000000255_url.txt index 113e84b32..f0ccd7155 100644 --- a/doc/examples/biomodels/BIOMD0000000255_url.txt +++ b/doc/examples/biomodels/BIOMD0000000255/BIOMD0000000255_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *A431_ErbB() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000256_url.txt b/doc/examples/biomodels/BIOMD0000000256/BIOMD0000000256_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000256_url.txt rename to doc/examples/biomodels/BIOMD0000000256/BIOMD0000000256_url.txt index c8df895a9..4233a8470 100644 --- a/doc/examples/biomodels/BIOMD0000000256_url.txt +++ b/doc/examples/biomodels/BIOMD0000000256/BIOMD0000000256_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Rehm2006_Caspase() // Compartments and Species: @@ -90,7 +90,7 @@ model *Rehm2006_Caspase() CytC_release: CytC_mit -> CytC_cell; cell*CytC_mit*ln(2)/th_CytC; // Events: - Production_Breakdown: at Substrate < S_breakdown: k1 = 0, k1r = 0, k2 = 0, k2r = 0, k38 = 0.0058, k39 = 0.0058, k40 = 0.0058, k43 = 0.0058, k44 = 0.0058, k46 = 0.0058, k48 = 0.0058, k50 = 0.0058, k51 = 0.0058; + Production_Breakdown: at Substrate < S_breakdown: k51 = 0.0058, k50 = 0.0058, k48 = 0.0058, k46 = 0.0058, k44 = 0.0058, k43 = 0.0058, k40 = 0.0058, k39 = 0.0058, k38 = 0.0058, k2r = 0, k2 = 0, k1r = 0, k1 = 0; // Species initializations: PC3 = 0.12; diff --git a/doc/examples/biomodels/BIOMD0000000257_url.txt b/doc/examples/biomodels/BIOMD0000000257/BIOMD0000000257_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000257_url.txt rename to doc/examples/biomodels/BIOMD0000000257/BIOMD0000000257_url.txt index e6ca7370d..2f81c934b 100644 --- a/doc/examples/biomodels/BIOMD0000000257_url.txt +++ b/doc/examples/biomodels/BIOMD0000000257/BIOMD0000000257_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Piedrafita2010_MR_System() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000258_url.txt b/doc/examples/biomodels/BIOMD0000000258/BIOMD0000000258_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000258_url.txt rename to doc/examples/biomodels/BIOMD0000000258/BIOMD0000000258_url.txt index a96c60e0c..5c4c5b338 100644 --- a/doc/examples/biomodels/BIOMD0000000258_url.txt +++ b/doc/examples/biomodels/BIOMD0000000258/BIOMD0000000258_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ortega2006_bistability_doublePhosphorylation() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000259_url.txt b/doc/examples/biomodels/BIOMD0000000259/BIOMD0000000259_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000259_url.txt rename to doc/examples/biomodels/BIOMD0000000259/BIOMD0000000259_url.txt index 8402ae6e2..02336c0cc 100644 --- a/doc/examples/biomodels/BIOMD0000000259_url.txt +++ b/doc/examples/biomodels/BIOMD0000000259/BIOMD0000000259_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Tiago2010_FeMetabolism_FeDeficient() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000260_url.txt b/doc/examples/biomodels/BIOMD0000000260/BIOMD0000000260_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000260_url.txt rename to doc/examples/biomodels/BIOMD0000000260/BIOMD0000000260_url.txt index d70c477a7..c4b391503 100644 --- a/doc/examples/biomodels/BIOMD0000000260_url.txt +++ b/doc/examples/biomodels/BIOMD0000000260/BIOMD0000000260_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Tiago2010_FeMetabolism_FeAdequate() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000261_url.txt b/doc/examples/biomodels/BIOMD0000000261/BIOMD0000000261_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000261_url.txt rename to doc/examples/biomodels/BIOMD0000000261/BIOMD0000000261_url.txt index 4f26ac0af..8b0dbdb55 100644 --- a/doc/examples/biomodels/BIOMD0000000261_url.txt +++ b/doc/examples/biomodels/BIOMD0000000261/BIOMD0000000261_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Tiago2010_FeMetabolism_FeLoaded() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000262_url.txt b/doc/examples/biomodels/BIOMD0000000262/BIOMD0000000262_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000262_url.txt rename to doc/examples/biomodels/BIOMD0000000262/BIOMD0000000262_url.txt index afc82b890..08d0affa7 100644 --- a/doc/examples/biomodels/BIOMD0000000262_url.txt +++ b/doc/examples/biomodels/BIOMD0000000262/BIOMD0000000262_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000263_url.txt b/doc/examples/biomodels/BIOMD0000000263/BIOMD0000000263_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000263_url.txt rename to doc/examples/biomodels/BIOMD0000000263/BIOMD0000000263_url.txt index 33ad3d172..bafba109b 100644 --- a/doc/examples/biomodels/BIOMD0000000263_url.txt +++ b/doc/examples/biomodels/BIOMD0000000263/BIOMD0000000263_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000264_url.txt b/doc/examples/biomodels/BIOMD0000000264/BIOMD0000000264_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000264_url.txt rename to doc/examples/biomodels/BIOMD0000000264/BIOMD0000000264_url.txt index d95cebfe0..1d958a7f8 100644 --- a/doc/examples/biomodels/BIOMD0000000264_url.txt +++ b/doc/examples/biomodels/BIOMD0000000264/BIOMD0000000264_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000265_url.txt b/doc/examples/biomodels/BIOMD0000000265/BIOMD0000000265_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000265_url.txt rename to doc/examples/biomodels/BIOMD0000000265/BIOMD0000000265_url.txt index e31ce20cd..b98f8a1af 100644 --- a/doc/examples/biomodels/BIOMD0000000265_url.txt +++ b/doc/examples/biomodels/BIOMD0000000265/BIOMD0000000265_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Conradie2010_RPControl_CellCycle() // Compartments and Species: @@ -77,7 +77,7 @@ model *Conradie2010_RPControl_CellCycle() // Events: r31Ifpart1: at ((var4 + var5 + var6)*(var1 + var4 + var5 + var6)^-1) > 0.8: r31switch = 0; r31Ifpart2: at ((var4 + var5 + var6)*(var1 + var4 + var5 + var6)^-1) < 0.8: r31switch = 1; - divisionEvent: at (CDh1 > 0.2) && (Flag == 1): Flag = 2, MASS = 0.5*MASS, GM = 0.5*GM; + divisionEvent: at (CDh1 > 0.2) && (Flag == 1): GM = 0.5*GM, MASS = 0.5*MASS, Flag = 2; checkEvent: at (CDh1 < 0.2) && (Flag == 2): Flag = 1; // Species initializations: diff --git a/doc/examples/biomodels/BIOMD0000000266_url.txt b/doc/examples/biomodels/BIOMD0000000266/BIOMD0000000266_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000266_url.txt rename to doc/examples/biomodels/BIOMD0000000266/BIOMD0000000266_url.txt index 3de908393..fc618a181 100644 --- a/doc/examples/biomodels/BIOMD0000000266_url.txt +++ b/doc/examples/biomodels/BIOMD0000000266/BIOMD0000000266_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *voit03() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000267_url.txt b/doc/examples/biomodels/BIOMD0000000267/BIOMD0000000267_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000267_url.txt rename to doc/examples/biomodels/BIOMD0000000267/BIOMD0000000267_url.txt index 004a5a479..1bccf1976 100644 --- a/doc/examples/biomodels/BIOMD0000000267_url.txt +++ b/doc/examples/biomodels/BIOMD0000000267/BIOMD0000000267_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Lebeda2008_BoNT_Paralysis_3stepModel() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000268_url.txt b/doc/examples/biomodels/BIOMD0000000268/BIOMD0000000268_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000268_url.txt rename to doc/examples/biomodels/BIOMD0000000268/BIOMD0000000268_url.txt index 491f18fcb..57b9607ba 100644 --- a/doc/examples/biomodels/BIOMD0000000268_url.txt +++ b/doc/examples/biomodels/BIOMD0000000268/BIOMD0000000268_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Reed2008() // Compartments and Species: @@ -724,17 +724,16 @@ of autism when oxidative stress is substantially increased and the adenosine con is raised. Finally, we discuss how individual variation arises and its consequences for one-carbon and glutathione metabolism. -| | -||--------------|---------------|------------| -| :- | :- | :-: | -| | -| | Vm_CBS | 700000 | 420000 | | -| | Vm_GNMT | 245 | 260 | | -| | K_sam_GNMT | 32 | 63 | | -| | Vr_MTD(mito) | 600000 | 595000 | | -| | V_CBS | kinetic law | rearranged | | -| | V_bmetc | 913 | 913.4 | | -| | Vm_GR | 8925 | 892.5 | | +| parameter | orig. article | this model | +|:-------------|:--------------|:----------:| +| Vm_CBS | 700000 | 420000 | +| Vm_GNMT | 245 | 260 | +| K_sam_GNMT | 32 | 63 | +| Vr_MTD(mito) | 600000 | 595000 | +| V_CBS | kinetic law | rearranged | +| V_bmetc | 913 | 913.4 | +| Vm_GR | 8925 | 892.5 | + This version of the model contains a feeding rhythm as used in figure 5 of the original article. Four parameters, *breakfast*, *lunch* *dinner* and *fasting*, describe diff --git a/doc/examples/biomodels/BIOMD0000000269_url.txt b/doc/examples/biomodels/BIOMD0000000269/BIOMD0000000269_url.txt similarity index 96% rename from doc/examples/biomodels/BIOMD0000000269_url.txt rename to doc/examples/biomodels/BIOMD0000000269/BIOMD0000000269_url.txt index 07c2d0bfb..2f205f481 100644 --- a/doc/examples/biomodels/BIOMD0000000269_url.txt +++ b/doc/examples/biomodels/BIOMD0000000269/BIOMD0000000269_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: @@ -39,6 +39,24 @@ model *Model_1() v_Auxin: $IAA => Auxin; compartment_1*k_auxin*IAA; v_Cytokinin: $CK_ex => CK; compartment_1*k_cytokinin*CK_ex; + // Interactions: + _I0: X -| reaction_1; ; + _I1: ET -o reaction_2; ; + _I2: CK -| reaction_2; ; + _I3: PLSp -o reaction_2; ; + _I4: X -o reaction_3; ; + _I5: Auxin -o reaction_4; ; + _I6: Ra_star -o reaction_6; ; + _I7: ET -| reaction_6; ; + _I8: PLSm -o reaction_8; ; + _I9: PLSp -o reaction_10; ; + _I10: ET -o reaction_11; ; + _I11: Auxin -o reaction_12; ; + _I12: CK -o reaction_12; ; + _I13: Re_star -o reaction_14; ; + _I14: CTR1_star -| reaction_16; ; + _I15: Auxin -| reaction_18; ; + // Species initializations: Auxin = 0.1; X = 0.1; diff --git a/doc/examples/biomodels/BIOMD0000000270_url.txt b/doc/examples/biomodels/BIOMD0000000270/BIOMD0000000270_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000270_url.txt rename to doc/examples/biomodels/BIOMD0000000270/BIOMD0000000270_url.txt index dd5614967..d20c1c010 100644 --- a/doc/examples/biomodels/BIOMD0000000270_url.txt +++ b/doc/examples/biomodels/BIOMD0000000270/BIOMD0000000270_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Schilling2009_ERK_distributive() // Compartments and Species: @@ -67,6 +67,29 @@ model *Schilling2009_ERK_distributive() reaction_41: mSOS => pSOS; ppERK_neg_feedback_on_mSOS*mSOS*ppERK2*cell; reaction_42: pSOS => SOS; pSOS_dephosphorylation*pSOS*cell; + // Interactions: + _I0: Epo -o reaction_1; ; + _I1: pJAK2 -o reaction_2; ; + _I2: pEpoR -( reaction_3; ; + _I3: actSHP1 -o reaction_14; ; + _I4: actSHP1 -o reaction_15; ; + _I5: pEpoR -o reaction_16; ; + _I6: mSOS -o reaction_18; ; + _I7: pRaf -o reaction_20; ; + _I8: pRaf -o reaction_21; ; + _I9: pRaf -o reaction_22; ; + _I10: pRaf -o reaction_23; ; + _I11: ppMEK2 -o reaction_28; ; + _I12: ppMEK2 -o reaction_29; ; + _I13: ppMEK1 -o reaction_30; ; + _I14: ppMEK1 -o reaction_31; ; + _I15: ppMEK2 -o reaction_32; ; + _I16: ppMEK2 -o reaction_33; ; + _I17: ppMEK1 -o reaction_34; ; + _I18: ppMEK1 -o reaction_35; ; + _I19: ppERK1 -o reaction_40; ; + _I20: ppERK2 -o reaction_41; ; + // Species initializations: JAK2 = 2; EpoR = 1; diff --git a/doc/examples/biomodels/BIOMD0000000271_url.txt b/doc/examples/biomodels/BIOMD0000000271/BIOMD0000000271_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000271_url.txt rename to doc/examples/biomodels/BIOMD0000000271/BIOMD0000000271_url.txt index 3622e6370..af53f1c95 100644 --- a/doc/examples/biomodels/BIOMD0000000271_url.txt +++ b/doc/examples/biomodels/BIOMD0000000271/BIOMD0000000271_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BeckerSchilling2010_EpoR_CoreModel() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000272_url.txt b/doc/examples/biomodels/BIOMD0000000272/BIOMD0000000272_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000272_url.txt rename to doc/examples/biomodels/BIOMD0000000272/BIOMD0000000272_url.txt index e43445809..db6113caa 100644 --- a/doc/examples/biomodels/BIOMD0000000272_url.txt +++ b/doc/examples/biomodels/BIOMD0000000272/BIOMD0000000272_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BeckerSchilling2010_EpoR_AuxiliaryMode() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000273_url.txt b/doc/examples/biomodels/BIOMD0000000273/BIOMD0000000273_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000273_url.txt rename to doc/examples/biomodels/BIOMD0000000273/BIOMD0000000273_url.txt index ae2785e39..b7a0e344e 100644 --- a/doc/examples/biomodels/BIOMD0000000273_url.txt +++ b/doc/examples/biomodels/BIOMD0000000273/BIOMD0000000273_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Pokhilko2010_CircClock() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000274_url.txt b/doc/examples/biomodels/BIOMD0000000274/BIOMD0000000274_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000274_url.txt rename to doc/examples/biomodels/BIOMD0000000274/BIOMD0000000274_url.txt index d651c5079..aa83317f7 100644 --- a/doc/examples/biomodels/BIOMD0000000274_url.txt +++ b/doc/examples/biomodels/BIOMD0000000274/BIOMD0000000274_url.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Rattanakul2003_BoneFormationModel() // Compartments and Species: compartment Compartment; - species $x in Compartment, $y in Compartment, $z in Compartment; + species x in Compartment, y in Compartment, z in Compartment; // Rate Rules: x' = a1/(k1 + y) - b1*x; diff --git a/doc/examples/biomodels/BIOMD0000000275_url.txt b/doc/examples/biomodels/BIOMD0000000275/BIOMD0000000275_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000275_url.txt rename to doc/examples/biomodels/BIOMD0000000275/BIOMD0000000275_url.txt index a4d781825..4fe14c46d 100644 --- a/doc/examples/biomodels/BIOMD0000000275_url.txt +++ b/doc/examples/biomodels/BIOMD0000000275/BIOMD0000000275_url.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *goldbeter2007() // Compartments and Species: compartment PSM; - species RA in PSM, M_C in PSM, C in PSM, F in PSM, $M_F in PSM; + species RA in PSM, M_C in PSM, C in PSM, F in PSM, M_F in PSM; // Assignment Rules: M_F := M_0*(x/L); diff --git a/doc/examples/biomodels/BIOMD0000000276_url.txt b/doc/examples/biomodels/BIOMD0000000276/BIOMD0000000276_url.txt similarity index 90% rename from doc/examples/biomodels/BIOMD0000000276_url.txt rename to doc/examples/biomodels/BIOMD0000000276/BIOMD0000000276_url.txt index 84cd6192e..deae111ae 100644 --- a/doc/examples/biomodels/BIOMD0000000276_url.txt +++ b/doc/examples/biomodels/BIOMD0000000276/BIOMD0000000276_url.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Shrestha2010_HypoCalcemia_PTHresponse() // Compartments and Species: compartment PTG_pool, Plasma_pool; - species $x1 in PTG_pool, $x2 in Plasma_pool, $Ca in Plasma_pool; + species x1 in PTG_pool, x2 in Plasma_pool, Ca in Plasma_pool; // Assignment Rules: k := lambda_2*x2_n + lambda_1*x1_n; @@ -123,24 +123,23 @@ plots corresponding to "subject 2" and "subject 3" the following parameters to be changed: lambda_1, lambda_2, m1, m2, R, beta, x1_n, x2_n, x2_min, x2_max, Ca0, Ca1, t0 and alpha. -| | -||-----------|-----------|-----------|-----------| -| :- | -: | -: | -: | -| | -| | lambda_1 | 0.0125 | 0.0122 | 0.0269 | | -| | lambda_2 | 0.5595 | 0.4642 | 0.4935 | | -| | m1 | 112.5200 | 150.0000 | 90.8570 | | -| | m2 | 15.0000 | 15.0000 | 15.0000 | | -| | R | 1.2162 | 1.1627 | 1.1889 | | -| | beta | 10e+06 | 10e+06 | 10e+06 | | -| | x1_n | 490.7800 | 452.8200 | 298.8200 | | -| | x2_n | 6.6290 | 9.5894 | 5.4600 | | -| | x2_min | 0.6697 | 1.4813 | 0.8287 | | -| | x2_max | 14.0430 | 17.8710 | 15.1990 | | -| | Ca0 | 1.2550 | 1.2369 | 1.2475 | | -| | Ca1 | 0.1817 | 0.2211 | 0.1985 | | -| | t0 | 575 | 577 | 575 | | -| | alpha | 0.0442 | 0.0488 | 0.0472 | | +| parameter | Subject 1 | Subject 2 | Subject 3 | +|:----------|----------:|----------:|----------:| +| lambda_1 | 0.0125 | 0.0122 | 0.0269 | +| lambda_2 | 0.5595 | 0.4642 | 0.4935 | +| m1 | 112.5200 | 150.0000 | 90.8570 | +| m2 | 15.0000 | 15.0000 | 15.0000 | +| R | 1.2162 | 1.1627 | 1.1889 | +| beta | 10e+06 | 10e+06 | 10e+06 | +| x1_n | 490.7800 | 452.8200 | 298.8200 | +| x2_n | 6.6290 | 9.5894 | 5.4600 | +| x2_min | 0.6697 | 1.4813 | 0.8287 | +| x2_max | 14.0430 | 17.8710 | 15.1990 | +| Ca0 | 1.2550 | 1.2369 | 1.2475 | +| Ca1 | 0.1817 | 0.2211 | 0.1985 | +| t0 | 575 | 577 | 575 | +| alpha | 0.0442 | 0.0488 | 0.0472 | + This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2010 The BioModels.net diff --git a/doc/examples/biomodels/BIOMD0000000277_url.txt b/doc/examples/biomodels/BIOMD0000000277/BIOMD0000000277_url.txt similarity index 90% rename from doc/examples/biomodels/BIOMD0000000277_url.txt rename to doc/examples/biomodels/BIOMD0000000277/BIOMD0000000277_url.txt index 0afd56bd4..8d3ffd64c 100644 --- a/doc/examples/biomodels/BIOMD0000000277_url.txt +++ b/doc/examples/biomodels/BIOMD0000000277/BIOMD0000000277_url.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Shrestha2010_HyperCalcemia_PTHresponse() // Compartments and Species: compartment PTG_pool, Plasma_pool; - species $x1 in PTG_pool, $x2 in Plasma_pool, $Ca in Plasma_pool; + species x1 in PTG_pool, x2 in Plasma_pool, Ca in Plasma_pool; // Assignment Rules: k := lambda_2*x2_n + lambda_1*x1_n; @@ -123,24 +123,23 @@ plots corresponding to "subject 2" and "subject 3" the following parameters to be changed: lambda_1, lambda_2, m1, m2, R, beta, x1_n, x2_n, x2_min, x2_max, t0, Ca0, Ca1 and alpha. -| | -||-----------|-----------|-----------|-----------| -| :- | -: | -: | -: | -| | -| | lambda_1 | 0.0125 | 0.0122 | 0.0269 | | -| | lambda_2 | 0.5595 | 0.4642 | 0.4935 | | -| | m1 | 112.5200 | 150.0000 | 90.8570 | | -| | m2 | 15.0000 | 15.0000 | 15.0000 | | -| | R | 1.2162 | 1.1627 | 1.1889 | | -| | beta | 10e+06 | 10e+06 | 10e+06 | | -| | x1_n | 490.7800 | 452.8200 | 298.8200 | | -| | x2_n | 6.6290 | 9.5894 | 5.4600 | | -| | x2_min | 0.6697 | 1.4813 | 0.8287 | | -| | x2_max | 14.0430 | 17.8710 | 15.1990 | | -| | Ca0 | 1.2200 | 1.2513 | 1.2480 | | -| | Ca1 | 0.2624 | 0.2267 | 0.2132 | | -| | t0 | 575 | 575 | 575 | | -| | alpha | 0.0569 | 0.0563 | 0.0421 | | +| parameter | Subject 1 | Subject 2 | Subject 3 | +|:----------|----------:|----------:|----------:| +| lambda_1 | 0.0125 | 0.0122 | 0.0269 | +| lambda_2 | 0.5595 | 0.4642 | 0.4935 | +| m1 | 112.5200 | 150.0000 | 90.8570 | +| m2 | 15.0000 | 15.0000 | 15.0000 | +| R | 1.2162 | 1.1627 | 1.1889 | +| beta | 10e+06 | 10e+06 | 10e+06 | +| x1_n | 490.7800 | 452.8200 | 298.8200 | +| x2_n | 6.6290 | 9.5894 | 5.4600 | +| x2_min | 0.6697 | 1.4813 | 0.8287 | +| x2_max | 14.0430 | 17.8710 | 15.1990 | +| Ca0 | 1.2200 | 1.2513 | 1.2480 | +| Ca1 | 0.2624 | 0.2267 | 0.2132 | +| t0 | 575 | 575 | 575 | +| alpha | 0.0569 | 0.0563 | 0.0421 | + This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2010 The BioModels.net diff --git a/doc/examples/biomodels/BIOMD0000000278_url.txt b/doc/examples/biomodels/BIOMD0000000278/BIOMD0000000278_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000278_url.txt rename to doc/examples/biomodels/BIOMD0000000278/BIOMD0000000278_url.txt index 848b71c85..e2629b83a 100644 --- a/doc/examples/biomodels/BIOMD0000000278_url.txt +++ b/doc/examples/biomodels/BIOMD0000000278/BIOMD0000000278_url.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000278() // Compartments and Species: compartment Compartment; - species $R in Compartment, $B in Compartment, $C in Compartment; + species R in Compartment, B in Compartment, C in Compartment; // Assignment Rules: Phi_C := (C + f0*C_s)/(C + C_s); diff --git a/doc/examples/biomodels/lemaire04_addB.txt b/doc/examples/biomodels/BIOMD0000000278/lemaire04_addB.txt similarity index 97% rename from doc/examples/biomodels/lemaire04_addB.txt rename to doc/examples/biomodels/BIOMD0000000278/lemaire04_addB.txt index 508ce2998..c4a5e57d0 100644 --- a/doc/examples/biomodels/lemaire04_addB.txt +++ b/doc/examples/biomodels/BIOMD0000000278/lemaire04_addB.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Lemaire2004_BoneRemodeling_addOsteoblast() // Compartments and Species: compartment Compartment; - species $R in Compartment, $B in Compartment, $C in Compartment; + species R in Compartment, B in Compartment, C in Compartment; // Assignment Rules: Phi_C := (C + f0*C_s)/(C + C_s); diff --git a/doc/examples/biomodels/lemaire04_addC.txt b/doc/examples/biomodels/BIOMD0000000278/lemaire04_addC.txt similarity index 97% rename from doc/examples/biomodels/lemaire04_addC.txt rename to doc/examples/biomodels/BIOMD0000000278/lemaire04_addC.txt index c33bdd5b0..22ef38edc 100644 --- a/doc/examples/biomodels/lemaire04_addC.txt +++ b/doc/examples/biomodels/BIOMD0000000278/lemaire04_addC.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Lemaire2004_BoneRemodeling_addOsteoclast() // Compartments and Species: compartment Compartment; - species $R in Compartment, $B in Compartment, $C in Compartment; + species R in Compartment, B in Compartment, C in Compartment; // Assignment Rules: Phi_C := (C + f0*C_s)/(C + C_s); diff --git a/doc/examples/biomodels/lemaire04_addOPG.txt b/doc/examples/biomodels/BIOMD0000000278/lemaire04_addOPG.txt similarity index 97% rename from doc/examples/biomodels/lemaire04_addOPG.txt rename to doc/examples/biomodels/BIOMD0000000278/lemaire04_addOPG.txt index 216f958a8..2a1dc3ca1 100644 --- a/doc/examples/biomodels/lemaire04_addOPG.txt +++ b/doc/examples/biomodels/BIOMD0000000278/lemaire04_addOPG.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Lemaire2004_BoneRemodeling_addOPG() // Compartments and Species: compartment Compartment; - species $R in Compartment, $B in Compartment, $C in Compartment; + species R in Compartment, B in Compartment, C in Compartment; // Assignment Rules: Phi_C := (C + f0*C_s)/(C + C_s); diff --git a/doc/examples/biomodels/lemaire04_addOPG_addRANKL.txt b/doc/examples/biomodels/BIOMD0000000278/lemaire04_addOPG_addRANKL.txt similarity index 97% rename from doc/examples/biomodels/lemaire04_addOPG_addRANKL.txt rename to doc/examples/biomodels/BIOMD0000000278/lemaire04_addOPG_addRANKL.txt index 74ae4905a..235151fdc 100644 --- a/doc/examples/biomodels/lemaire04_addOPG_addRANKL.txt +++ b/doc/examples/biomodels/BIOMD0000000278/lemaire04_addOPG_addRANKL.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Lemaire2004_BoneRemodeling_addRANKLandOPG() // Compartments and Species: compartment Compartment; - species $R in Compartment, $B in Compartment, $C in Compartment; + species R in Compartment, B in Compartment, C in Compartment; // Assignment Rules: Phi_C := (C + f0*C_s)/(C + C_s); diff --git a/doc/examples/biomodels/lemaire04_addPTH.txt b/doc/examples/biomodels/BIOMD0000000278/lemaire04_addPTH.txt similarity index 97% rename from doc/examples/biomodels/lemaire04_addPTH.txt rename to doc/examples/biomodels/BIOMD0000000278/lemaire04_addPTH.txt index 5a5a579b3..d72a1c846 100644 --- a/doc/examples/biomodels/lemaire04_addPTH.txt +++ b/doc/examples/biomodels/BIOMD0000000278/lemaire04_addPTH.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Lemaire2004_BoneRemodeling_addPTH() // Compartments and Species: compartment Compartment; - species $R in Compartment, $B in Compartment, $C in Compartment; + species R in Compartment, B in Compartment, C in Compartment; // Assignment Rules: Phi_C := (C + f0*C_s)/(C + C_s); diff --git a/doc/examples/biomodels/lemaire04_addR.txt b/doc/examples/biomodels/BIOMD0000000278/lemaire04_addR.txt similarity index 97% rename from doc/examples/biomodels/lemaire04_addR.txt rename to doc/examples/biomodels/BIOMD0000000278/lemaire04_addR.txt index 447a8b6ff..4955c49a5 100644 --- a/doc/examples/biomodels/lemaire04_addR.txt +++ b/doc/examples/biomodels/BIOMD0000000278/lemaire04_addR.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Lemaire2004_BoneRemodeling_addRespondingOsteoblast() // Compartments and Species: compartment Compartment; - species $R in Compartment, $B in Compartment, $C in Compartment; + species R in Compartment, B in Compartment, C in Compartment; // Assignment Rules: Phi_C := (C + f0*C_s)/(C + C_s); diff --git a/doc/examples/biomodels/lemaire04_removeB.txt b/doc/examples/biomodels/BIOMD0000000278/lemaire04_removeB.txt similarity index 97% rename from doc/examples/biomodels/lemaire04_removeB.txt rename to doc/examples/biomodels/BIOMD0000000278/lemaire04_removeB.txt index 7e9950846..efcfdd5ac 100644 --- a/doc/examples/biomodels/lemaire04_removeB.txt +++ b/doc/examples/biomodels/BIOMD0000000278/lemaire04_removeB.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Lemaire2004_BoneRemodeling_removeOsteoblast() // Compartments and Species: compartment Compartment; - species $R in Compartment, $B in Compartment, $C in Compartment; + species R in Compartment, B in Compartment, C in Compartment; // Assignment Rules: Phi_C := (C + f0*C_s)/(C + C_s); diff --git a/doc/examples/biomodels/lemaire04_removeC.txt b/doc/examples/biomodels/BIOMD0000000278/lemaire04_removeC.txt similarity index 97% rename from doc/examples/biomodels/lemaire04_removeC.txt rename to doc/examples/biomodels/BIOMD0000000278/lemaire04_removeC.txt index 1f334d143..8472576ce 100644 --- a/doc/examples/biomodels/lemaire04_removeC.txt +++ b/doc/examples/biomodels/BIOMD0000000278/lemaire04_removeC.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Lemaire2004_BoneRemodeling_OsteoblastOsteoclast() // Compartments and Species: compartment Compartment; - species $R in Compartment, $B in Compartment, $C in Compartment; + species R in Compartment, B in Compartment, C in Compartment; // Assignment Rules: Phi_C := (C + f0*C_s)/(C + C_s); diff --git a/doc/examples/biomodels/lemaire04_removeR.txt b/doc/examples/biomodels/BIOMD0000000278/lemaire04_removeR.txt similarity index 97% rename from doc/examples/biomodels/lemaire04_removeR.txt rename to doc/examples/biomodels/BIOMD0000000278/lemaire04_removeR.txt index 46e108bdb..816c2efce 100644 --- a/doc/examples/biomodels/lemaire04_removeR.txt +++ b/doc/examples/biomodels/BIOMD0000000278/lemaire04_removeR.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Lemaire2004_BoneRemodeling_OsteoblastOsteoclast() // Compartments and Species: compartment Compartment; - species $R in Compartment, $B in Compartment, $C in Compartment; + species R in Compartment, B in Compartment, C in Compartment; // Assignment Rules: Phi_C := (C + f0*C_s)/(C + C_s); diff --git a/doc/examples/biomodels/BIOMD0000000279_url.txt b/doc/examples/biomodels/BIOMD0000000279/BIOMD0000000279_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000279_url.txt rename to doc/examples/biomodels/BIOMD0000000279/BIOMD0000000279_url.txt index adf6d01ad..0bac06234 100644 --- a/doc/examples/biomodels/BIOMD0000000279_url.txt +++ b/doc/examples/biomodels/BIOMD0000000279/BIOMD0000000279_url.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Komarova2005_PTHaction_OsteoclastOsteoblastCoupling() // Compartments and Species: compartment Compartment; - species $x1 in Compartment, $x2 in Compartment, $z in Compartment; + species x1 in Compartment, x2 in Compartment, z in Compartment; // Assignment Rules: y2 := piecewise(x2 - x2_bar, x2 > x2_bar, 0); diff --git a/doc/examples/biomodels/BIOMD0000000280_url.txt b/doc/examples/biomodels/BIOMD0000000280/BIOMD0000000280_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000280_url.txt rename to doc/examples/biomodels/BIOMD0000000280/BIOMD0000000280_url.txt index 566031641..63e16d25a 100644 --- a/doc/examples/biomodels/BIOMD0000000280_url.txt +++ b/doc/examples/biomodels/BIOMD0000000280/BIOMD0000000280_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Morris1981_MuscleFibre_Voltage_reduced() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000281_url.txt b/doc/examples/biomodels/BIOMD0000000281/BIOMD0000000281_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000281_url.txt rename to doc/examples/biomodels/BIOMD0000000281/BIOMD0000000281_url.txt index 9afaafd03..33b7d5d75 100644 --- a/doc/examples/biomodels/BIOMD0000000281_url.txt +++ b/doc/examples/biomodels/BIOMD0000000281/BIOMD0000000281_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *chance() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000282_url.txt b/doc/examples/biomodels/BIOMD0000000282/BIOMD0000000282_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000282_url.txt rename to doc/examples/biomodels/BIOMD0000000282/BIOMD0000000282_url.txt index 94be0250b..843936a74 100644 --- a/doc/examples/biomodels/BIOMD0000000282_url.txt +++ b/doc/examples/biomodels/BIOMD0000000282/BIOMD0000000282_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *chance() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000283_url.txt b/doc/examples/biomodels/BIOMD0000000283/BIOMD0000000283_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000283_url.txt rename to doc/examples/biomodels/BIOMD0000000283/BIOMD0000000283_url.txt index 7bb8e79ab..4ca34cdec 100644 --- a/doc/examples/biomodels/BIOMD0000000283_url.txt +++ b/doc/examples/biomodels/BIOMD0000000283/BIOMD0000000283_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *chance() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000284_url.txt b/doc/examples/biomodels/BIOMD0000000284/BIOMD0000000284_url.txt similarity index 92% rename from doc/examples/biomodels/BIOMD0000000284_url.txt rename to doc/examples/biomodels/BIOMD0000000284/BIOMD0000000284_url.txt index bac458770..50e8b2355 100644 --- a/doc/examples/biomodels/BIOMD0000000284_url.txt +++ b/doc/examples/biomodels/BIOMD0000000284/BIOMD0000000284_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *hofmeyer() // Compartments and Species: @@ -16,6 +16,11 @@ model *hofmeyer() R7: E -> F; cell*((5*E - F)/(1 + E + F)); R8: F -> $Z; cell*((10*F - Z)/(1 + F + Z)); + // Interactions: + _I0: B -| R1; ; + _I1: D -| R3; ; + _I2: F -| R6; ; + // Species initializations: A = 0; B = 0; @@ -49,13 +54,21 @@ model *hofmeyer() Y.sboTerm = 247 Z.sboTerm = 247 R1.sboTerm = 176 + R1.kineticLaw.sboTerm = 430 R2.sboTerm = 176 + R2.kineticLaw.sboTerm = 326 R3.sboTerm = 176 + R3.kineticLaw.sboTerm = 430 R4.sboTerm = 176 + R4.kineticLaw.sboTerm = 326 R5.sboTerm = 176 + R5.kineticLaw.sboTerm = 326 R6.sboTerm = 176 + R6.kineticLaw.sboTerm = 430 R7.sboTerm = 176 + R7.kineticLaw.sboTerm = 326 R8.sboTerm = 176 + R8.kineticLaw.sboTerm = 326 // CV terms: cell identity "http://identifiers.org/go/GO:0005623" diff --git a/doc/examples/biomodels/BIOMD0000000285_url.txt b/doc/examples/biomodels/BIOMD0000000285/BIOMD0000000285_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000285_url.txt rename to doc/examples/biomodels/BIOMD0000000285/BIOMD0000000285_url.txt index 884749145..96f33410e 100644 --- a/doc/examples/biomodels/BIOMD0000000285_url.txt +++ b/doc/examples/biomodels/BIOMD0000000285/BIOMD0000000285_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Tang2010_PolyGlutamate() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000286_url.txt b/doc/examples/biomodels/BIOMD0000000286/BIOMD0000000286_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000286_url.txt rename to doc/examples/biomodels/BIOMD0000000286/BIOMD0000000286_url.txt index c03402c12..d7b24979d 100644 --- a/doc/examples/biomodels/BIOMD0000000286_url.txt +++ b/doc/examples/biomodels/BIOMD0000000286/BIOMD0000000286_url.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000462() // Compartments and Species: compartment cell; - species $IR in cell; + species IR in cell; substanceOnly species Mdm2 in cell, p53 in cell, Mdm2_p53 in cell, Mdm2_mRNA in cell; substanceOnly species p53_mRNA in cell, ATMA in cell, ATMI in cell, p53_P in cell; substanceOnly species Mdm2_P in cell, ROS in cell, basalROS in cell, damDNA in cell; diff --git a/doc/examples/biomodels/BIOMD0000000287_url.txt b/doc/examples/biomodels/BIOMD0000000287/BIOMD0000000287_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000287_url.txt rename to doc/examples/biomodels/BIOMD0000000287/BIOMD0000000287_url.txt index 8e22a3029..a55dc68bb 100644 --- a/doc/examples/biomodels/BIOMD0000000287_url.txt +++ b/doc/examples/biomodels/BIOMD0000000287/BIOMD0000000287_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Passos2010_DNAdamage_CellularSenescence() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000288_url.txt b/doc/examples/biomodels/BIOMD0000000288/BIOMD0000000288_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000288_url.txt rename to doc/examples/biomodels/BIOMD0000000288/BIOMD0000000288_url.txt index 38cf17a27..b783e16d9 100644 --- a/doc/examples/biomodels/BIOMD0000000288_url.txt +++ b/doc/examples/biomodels/BIOMD0000000288/BIOMD0000000288_url.txt @@ -1,11 +1,11 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000288() // Compartments and Species: compartment cell; - species sumrc1 in cell, $r in cell, $c1 in cell, c2 in cell, $ePI3K in cell; - species m3PI in cell, $eGEF in cell, fGEF in cell, mRas in cell, x1 in cell; - species x2 in cell, y in cell, $yp in cell, ypp in cell, z in cell, $zp in cell; + species sumrc1 in cell, r in cell, c1 in cell, c2 in cell, ePI3K in cell; + species m3PI in cell, eGEF in cell, fGEF in cell, mRas in cell, x1 in cell; + species x2 in cell, y in cell, yp in cell, ypp in cell, z in cell, zp in cell; species zpp in cell, w in cell, eph in cell; // Assignment Rules: diff --git a/doc/examples/biomodels/BIOMD0000000289_url.txt b/doc/examples/biomodels/BIOMD0000000289/BIOMD0000000289_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000289_url.txt rename to doc/examples/biomodels/BIOMD0000000289/BIOMD0000000289_url.txt index a031f9867..58ff3f2e4 100644 --- a/doc/examples/biomodels/BIOMD0000000289_url.txt +++ b/doc/examples/biomodels/BIOMD0000000289/BIOMD0000000289_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Alexander2010_Tcell_Regulation_Sys1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000290_url.txt b/doc/examples/biomodels/BIOMD0000000290/BIOMD0000000290_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000290_url.txt rename to doc/examples/biomodels/BIOMD0000000290/BIOMD0000000290_url.txt index 80d7ec81f..5820e65d1 100644 --- a/doc/examples/biomodels/BIOMD0000000290_url.txt +++ b/doc/examples/biomodels/BIOMD0000000290/BIOMD0000000290_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Alexander2010_Tcell_Regulation_Sys2() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000291_url.txt b/doc/examples/biomodels/BIOMD0000000291/BIOMD0000000291_url.txt similarity index 95% rename from doc/examples/biomodels/BIOMD0000000291_url.txt rename to doc/examples/biomodels/BIOMD0000000291/BIOMD0000000291_url.txt index 0a9196aa9..ce869cbcf 100644 --- a/doc/examples/biomodels/BIOMD0000000291_url.txt +++ b/doc/examples/biomodels/BIOMD0000000291/BIOMD0000000291_url.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Nikolaev2005_AlbuminBilirubinAdsorption() // Compartments and Species: compartment compartment_; - species $x1 in compartment_, $x5 in compartment_, $x6 in compartment_, $x7 in compartment_; - species $x4 in compartment_, $x2 in compartment_, $x3 in compartment_, $A0 in compartment_; + species x1 in compartment_, x5 in compartment_, x6 in compartment_, x7 in compartment_; + species x4 in compartment_, x2 in compartment_, x3 in compartment_, $A0 in compartment_; species $B0 in compartment_, $C0 in compartment_; // Assignment Rules: diff --git a/doc/examples/biomodels/BIOMD0000000292_url.txt b/doc/examples/biomodels/BIOMD0000000292/BIOMD0000000292_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000292_url.txt rename to doc/examples/biomodels/BIOMD0000000292/BIOMD0000000292_url.txt index f7b71686e..53a0a90a7 100644 --- a/doc/examples/biomodels/BIOMD0000000292_url.txt +++ b/doc/examples/biomodels/BIOMD0000000292/BIOMD0000000292_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Rovers1995_Photsynthetic_Oscillations() // Compartments and Species: @@ -15,6 +15,9 @@ model *Rovers1995_Photsynthetic_Oscillations() v2: $Y + NADPH + ATP => X + $ADP + $NADP; c*k2*ATP; v1: X + ATP => $Y + $ADP; c*k1*X; + // Interactions: + _I0: $NADP -o v3; ; + // Species initializations: NADPH = 0.7; ATP = 0.5; @@ -72,9 +75,13 @@ model *Rovers1995_Photsynthetic_Oscillations() k3.sboTerm = 36 k4.sboTerm = 35 v4.sboTerm = 202 + v4.kineticLaw.sboTerm = 49 v3.sboTerm = 216 + v3.kineticLaw.sboTerm = 54 v2.sboTerm = 182 + v2.kineticLaw.sboTerm = 49 v1.sboTerm = 216 + v1.kineticLaw.sboTerm = 49 // CV terms: c identity "http://identifiers.org/go/GO:0009570" diff --git a/doc/examples/biomodels/BIOMD0000000293_url.txt b/doc/examples/biomodels/BIOMD0000000293/BIOMD0000000293_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000293_url.txt rename to doc/examples/biomodels/BIOMD0000000293/BIOMD0000000293_url.txt index 83b973535..1b0f4e091 100644 --- a/doc/examples/biomodels/BIOMD0000000293_url.txt +++ b/doc/examples/biomodels/BIOMD0000000293/BIOMD0000000293_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Proctor2010_UCHL1_ProteinAggregation() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000294_url.txt b/doc/examples/biomodels/BIOMD0000000294/BIOMD0000000294_url.txt similarity index 94% rename from doc/examples/biomodels/BIOMD0000000294_url.txt rename to doc/examples/biomodels/BIOMD0000000294/BIOMD0000000294_url.txt index 6e580a9be..3b0eed308 100644 --- a/doc/examples/biomodels/BIOMD0000000294_url.txt +++ b/doc/examples/biomodels/BIOMD0000000294/BIOMD0000000294_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *restif07() // Compartments and Species: @@ -301,19 +301,18 @@ To be compatible with older software tools, the english letter names instead of the greek symbols were used for parameter names: -| | -||----------------------------------------------------|-------------|--------| -| - | - | - | -| | -| | transmission rate | β | beta | | -| | recovery rate | γ | gamma | | -| | birth/death rate | μ | mu | | -| | rate of loss of natural immunity | σ | sigma | | -| | rate of loss of vaccine immunity | σ v | sigmaV | | -| | reduction of susceptibility by primary infection | θ | theta | | -| | reduction of infection period by primary infection | ν | nu | | -| | reduction of susceptibility by vaccination | τ | tau | | -| | reduction of infection period by vaccination | η | eta | | +| parameter | symbol | name | +|----------------------------------------------------|-------------|--------| +| transmission rate | β | beta | +| recovery rate | γ | gamma | +| birth/death rate | μ | mu | +| rate of loss of natural immunity | σ | sigma | +| rate of loss of vaccine immunity | σ v | sigmaV | +| reduction of susceptibility by primary infection | θ | theta | +| reduction of infection period by primary infection | ν | nu | +| reduction of susceptibility by vaccination | τ | tau | +| reduction of infection period by vaccination | η | eta | + Originally created by libAntimony v1.4 (using libSBML 3.4.1) diff --git a/doc/examples/biomodels/BIOMD0000000295_url.txt b/doc/examples/biomodels/BIOMD0000000295/BIOMD0000000295_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000295_url.txt rename to doc/examples/biomodels/BIOMD0000000295/BIOMD0000000295_url.txt index 58269b025..0873f7d05 100644 --- a/doc/examples/biomodels/BIOMD0000000295_url.txt +++ b/doc/examples/biomodels/BIOMD0000000295/BIOMD0000000295_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Akman2008_Circadian_Clock_Model1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000296_url.txt b/doc/examples/biomodels/BIOMD0000000296/BIOMD0000000296_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000296_url.txt rename to doc/examples/biomodels/BIOMD0000000296/BIOMD0000000296_url.txt index defef8dbe..2d1bf8b25 100644 --- a/doc/examples/biomodels/BIOMD0000000296_url.txt +++ b/doc/examples/biomodels/BIOMD0000000296/BIOMD0000000296_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *blub() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000297_url.txt b/doc/examples/biomodels/BIOMD0000000297/BIOMD0000000297_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000297_url.txt rename to doc/examples/biomodels/BIOMD0000000297/BIOMD0000000297_url.txt index 371090329..66cb374d1 100644 --- a/doc/examples/biomodels/BIOMD0000000297_url.txt +++ b/doc/examples/biomodels/BIOMD0000000297/BIOMD0000000297_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ciliberto2003_Morphogenesis() // Compartments and Species: @@ -75,7 +75,7 @@ model *Ciliberto2003_Morphogenesis() // Events: event_0000002: at Clb > 0.2: flag = 1; - event_0000004: at (Clb < 0.2) && (flag > 0): mass = 0.5*mass, BE = 0; + event_0000004: at (Clb < 0.2) && (flag > 0): BE = 0, mass = 0.5*mass; event_0000003: at (Clb >= 0.2) || (BE >= 0.6): BUD = 1; event_0000005: at (Clb < 0.2) && (BE < 0.6): BUD = 0; diff --git a/doc/examples/biomodels/BIOMD0000000298_url.txt b/doc/examples/biomodels/BIOMD0000000298/BIOMD0000000298_url.txt similarity index 96% rename from doc/examples/biomodels/BIOMD0000000298_url.txt rename to doc/examples/biomodels/BIOMD0000000298/BIOMD0000000298_url.txt index ec8370a29..cb25ec7b6 100644 --- a/doc/examples/biomodels/BIOMD0000000298_url.txt +++ b/doc/examples/biomodels/BIOMD0000000298/BIOMD0000000298_url.txt @@ -1,11 +1,11 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Leloup1999_CircadianRhythms_Drosophila() // Compartments and Species: compartment Compartment; - species $MP in Compartment, $CN in Compartment, $C in Compartment, $P2 in Compartment; - species $T2 in Compartment, $T1 in Compartment, $T0 in Compartment, $MT in Compartment; - species $P0 in Compartment, $P1 in Compartment; + species MP in Compartment, CN in Compartment, C in Compartment, P2 in Compartment; + species T2 in Compartment, T1 in Compartment, T0 in Compartment, MT in Compartment; + species P0 in Compartment, P1 in Compartment; // Assignment Rules: Pt := P0 + P1 + P2 + C + CN; diff --git a/doc/examples/biomodels/BIOMD0000000299_url.txt b/doc/examples/biomodels/BIOMD0000000299/BIOMD0000000299_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000299_url.txt rename to doc/examples/biomodels/BIOMD0000000299/BIOMD0000000299_url.txt index 3ac1366b3..1788c34bc 100644 --- a/doc/examples/biomodels/BIOMD0000000299_url.txt +++ b/doc/examples/biomodels/BIOMD0000000299/BIOMD0000000299_url.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Leloup1999_CircadianRhythms_Neurospora() // Compartments and Species: compartment Cytoplasm, Nucleus; - species $M in Nucleus, $FN in Nucleus, $FC in Cytoplasm; + species M in Nucleus, FN in Nucleus, FC in Cytoplasm; // Assignment Rules: Ft := FC + FN; diff --git a/doc/examples/biomodels/BIOMD0000000300_url.txt b/doc/examples/biomodels/BIOMD0000000300/BIOMD0000000300_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000300_url.txt rename to doc/examples/biomodels/BIOMD0000000300/BIOMD0000000300_url.txt index 909c4b1e7..7ce3d105f 100644 --- a/doc/examples/biomodels/BIOMD0000000300_url.txt +++ b/doc/examples/biomodels/BIOMD0000000300/BIOMD0000000300_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Schmierer2010_FIH_Ankyrins() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000301_url.txt b/doc/examples/biomodels/BIOMD0000000301/BIOMD0000000301_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000301_url.txt rename to doc/examples/biomodels/BIOMD0000000301/BIOMD0000000301_url.txt index c7cdc145d..955ec9090 100644 --- a/doc/examples/biomodels/BIOMD0000000301_url.txt +++ b/doc/examples/biomodels/BIOMD0000000301/BIOMD0000000301_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Friedland2009_Ara_Counter_RC3_events() // Compartments and Species: @@ -28,9 +28,9 @@ model *Friedland2009_Ara_Counter_RC3_events() r12: pT3 => ; cell*d_pT3*pT3; // Events: - pulse_start1: at (time >= pulse1_start) && (time <= (pulse1_start + pulse1_length)): ara = pulse_conc, pulse_flag = 1; - pulse_start2: at (time >= pulse2_start) && (time <= (pulse2_start + pulse2_length)): ara = pulse_conc, pulse_flag = 1; - pulse_start3: at (time >= pulse3_start) && (time <= (pulse3_start + pulse3_length)): ara = pulse_conc, pulse_flag = 1; + pulse_start1: at (time >= pulse1_start) && (time <= (pulse1_start + pulse1_length)): pulse_flag = 1, ara = pulse_conc; + pulse_start2: at (time >= pulse2_start) && (time <= (pulse2_start + pulse2_length)): pulse_flag = 1, ara = pulse_conc; + pulse_start3: at (time >= pulse3_start) && (time <= (pulse3_start + pulse3_length)): pulse_flag = 1, ara = pulse_conc; pulse_end1: at (time < pulse2_start) && (time > (pulse1_start + pulse1_length)): pulse_flag = 0; pulse_end2: at (time < pulse3_start) && (time > (pulse2_start + pulse2_length)): pulse_flag = 0; pulse_end3: at time > (pulse3_start + pulse3_length): pulse_flag = 0; diff --git a/doc/examples/biomodels/BIOMD0000000302_url.txt b/doc/examples/biomodels/BIOMD0000000302/BIOMD0000000302_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000302_url.txt rename to doc/examples/biomodels/BIOMD0000000302/BIOMD0000000302_url.txt index 58233ecab..388972477 100644 --- a/doc/examples/biomodels/BIOMD0000000302_url.txt +++ b/doc/examples/biomodels/BIOMD0000000302/BIOMD0000000302_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wang1996_Single_Neuron() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000303_url.txt b/doc/examples/biomodels/BIOMD0000000303/BIOMD0000000303_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000303_url.txt rename to doc/examples/biomodels/BIOMD0000000303/BIOMD0000000303_url.txt index f1c0849c5..f8ac2ef8a 100644 --- a/doc/examples/biomodels/BIOMD0000000303_url.txt +++ b/doc/examples/biomodels/BIOMD0000000303/BIOMD0000000303_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Complement_System() // Compartments and Species: @@ -69,6 +69,24 @@ model *Complement_System() g_03: C4 => C4a + C4b; compartment_*(kg03_1*GlcNac_HF_MASP*C4/(kg03_2 + C4)); g_04: C2 => C2a + C2b; compartment_*(kg04_1*GlcNac_HF_MASP*C2/(kg04_2 + C2)); + // Interactions: + _I0: PC_CRP_C1 -o a_03; ; + _I1: PC_CRP_C1 -o a_04; ; + _I2: PC_CRP_LF_MASP -o d_03; ; + _I3: PC_CRP_LF_MASP -o d_04; ; + _I4: GlcNac_LF_MASP -o b_03; ; + _I5: GlcNac_LF_MASP -o b_04; ; + _I6: GlcNac_LF_CRP_C1 -o e_03; ; + _I7: GlcNac_LF_CRP_C1 -o e_04; ; + _I8: PC_CRP_LF_C1 -o d_06; ; + _I9: PC_CRP_LF_C1 -o d_07; ; + _I10: GlcNac_LF_CRP_MASP -o e_06; ; + _I11: GlcNac_LF_CRP_MASP -o e_07; ; + _I12: PC_CRP_LF_C1_MASP -o d_10; ; + _I13: PC_CRP_LF_C1_MASP -o d_11; ; + _I14: GlcNac_HF_MASP -o g_03; ; + _I15: GlcNac_HF_MASP -o g_04; ; + // Species initializations: CRP = 2; PC = 0.0327796; diff --git a/doc/examples/biomodels/BIOMD0000000304_url.txt b/doc/examples/biomodels/BIOMD0000000304/BIOMD0000000304_url.txt similarity index 96% rename from doc/examples/biomodels/BIOMD0000000304_url.txt rename to doc/examples/biomodels/BIOMD0000000304/BIOMD0000000304_url.txt index d2ebc18bf..20669b765 100644 --- a/doc/examples/biomodels/BIOMD0000000304_url.txt +++ b/doc/examples/biomodels/BIOMD0000000304/BIOMD0000000304_url.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Plant1981_BurstingNerveCells() // Compartments and Species: compartment COMpartment; - species $V_membrane in COMpartment, $h1 in COMpartment, $x1 in COMpartment; - species $n1 in COMpartment, $c in COMpartment; + species V_membrane in COMpartment, h1 in COMpartment, x1 in COMpartment; + species n1 in COMpartment, c in COMpartment; // Assignment Rules: i_Na := g_I*m_infinity^3*h1*(V_I - V_membrane); diff --git a/doc/examples/biomodels/BIOMD0000000305_url.txt b/doc/examples/biomodels/BIOMD0000000305/BIOMD0000000305_url.txt similarity index 95% rename from doc/examples/biomodels/BIOMD0000000305_url.txt rename to doc/examples/biomodels/BIOMD0000000305/BIOMD0000000305_url.txt index a10fbf7e4..1b82a5368 100644 --- a/doc/examples/biomodels/BIOMD0000000305_url.txt +++ b/doc/examples/biomodels/BIOMD0000000305/BIOMD0000000305_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kolomeisky2003_myosin() // Compartments and Species: @@ -22,23 +22,23 @@ model *Kolomeisky2003_myosin() // Species initializations: S0 = 10; - S0 has substance_per_volume; + S0 has substance; ATP = 20; ATP has uM; S1 = 0; - S1 has substance_per_volume; + S1 has substance; Pi_ = 0; Pi_ has uM; ADP = 0; ADP has uM; fwd_step1 = 0; - fwd_step1 has substance_per_volume; + fwd_step1 has substance; fwd_step2 = 0; - fwd_step2 has substance_per_volume; + fwd_step2 has substance; back_step1 = 0; - back_step1 has substance_per_volume; + back_step1 has substance; back_step2 = 0; - back_step2 has substance_per_volume; + back_step2 has substance; // Compartment initializations: compartment_ = 1e-15; @@ -71,7 +71,7 @@ model *Kolomeisky2003_myosin() unit length = metre; unit extent = substance; unit time_unit = second; - unit substance_per_volume = item / litre; + unit substance_volume = item * litre; // Display Names: substance is "molecules"; diff --git a/doc/examples/biomodels/BIOMD0000000306_url.txt b/doc/examples/biomodels/BIOMD0000000306/BIOMD0000000306_url.txt similarity index 93% rename from doc/examples/biomodels/BIOMD0000000306_url.txt rename to doc/examples/biomodels/BIOMD0000000306/BIOMD0000000306_url.txt index e52a9b205..98cba900e 100644 --- a/doc/examples/biomodels/BIOMD0000000306_url.txt +++ b/doc/examples/biomodels/BIOMD0000000306/BIOMD0000000306_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Tyson2003_Activator_Inhib_Oscillator() // Compartments and Species: @@ -21,6 +21,12 @@ model *Tyson2003_Activator_Inhib_Oscillator() r5: => X; env*k5*R; r6: X => ; env*k6*X; + // Interactions: + _I0: $S -o r1; ; + _I1: X -o r2_prime; ; + _I2: R -o r3; ; + _I3: R -o r5; ; + // Species initializations: R = 0; X = 0; @@ -92,13 +98,21 @@ model *Tyson2003_Activator_Inhib_Oscillator() Km3.sboTerm = 27 Km4.sboTerm = 27 r0.sboTerm = 176 + r0.kineticLaw.sboTerm = 49 r1.sboTerm = 176 + r1.kineticLaw.sboTerm = 49 r2.sboTerm = 179 + r2.kineticLaw.sboTerm = 49 r2_prime.sboTerm = 179 + r2_prime.kineticLaw.sboTerm = 54 r3.sboTerm = 216 + r3.kineticLaw.sboTerm = 430 r4.sboTerm = 330 + r4.kineticLaw.sboTerm = 199 r5.sboTerm = 176 + r5.kineticLaw.sboTerm = 49 r6.sboTerm = 179 + r6.kineticLaw.sboTerm = 49 // CV terms: env isVersionOf "http://identifiers.org/go/GO:0005623" diff --git a/doc/examples/biomodels/BIOMD0000000307_url.txt b/doc/examples/biomodels/BIOMD0000000307/BIOMD0000000307_url.txt similarity index 95% rename from doc/examples/biomodels/BIOMD0000000307_url.txt rename to doc/examples/biomodels/BIOMD0000000307/BIOMD0000000307_url.txt index 961fcd463..0e1dbfeaf 100644 --- a/doc/examples/biomodels/BIOMD0000000307_url.txt +++ b/doc/examples/biomodels/BIOMD0000000307/BIOMD0000000307_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Tyson2003_Activator_Inhibitor() // Compartments and Species: @@ -18,6 +18,11 @@ model *Tyson2003_Activator_Inhibitor() r3: $E => $Ep; env*k3*R*E/(Km3 + E); r4: $Ep => $E; env*k4*Ep/(Km4 + Ep); + // Interactions: + _I0: $Ep -o r0; ; + _I1: $S -o r1; ; + _I2: R -o r3; ; + // Species initializations: R = 0; X = 0; @@ -84,9 +89,13 @@ model *Tyson2003_Activator_Inhibitor() Km4.sboTerm = 27 r0.sboTerm = 182 r1.sboTerm = 176 + r1.kineticLaw.sboTerm = 49 r2.sboTerm = 179 + r2.kineticLaw.sboTerm = 49 r3.sboTerm = 216 + r3.kineticLaw.sboTerm = 430 r4.sboTerm = 330 + r4.kineticLaw.sboTerm = 199 // CV terms: env isVersionOf "http://identifiers.org/go/GO:0005623" diff --git a/doc/examples/biomodels/BIOMD0000000308_url.txt b/doc/examples/biomodels/BIOMD0000000308/BIOMD0000000308_url.txt similarity index 94% rename from doc/examples/biomodels/BIOMD0000000308_url.txt rename to doc/examples/biomodels/BIOMD0000000308/BIOMD0000000308_url.txt index 5dcc6934f..f5c95243d 100644 --- a/doc/examples/biomodels/BIOMD0000000308_url.txt +++ b/doc/examples/biomodels/BIOMD0000000308/BIOMD0000000308_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Tyson2003_Negative_Feedback_Oscillator() // Compartments and Species: @@ -17,6 +17,12 @@ model *Tyson2003_Negative_Feedback_Oscillator() r5: $R => Rp; env*k5*Yp*(Rt - Rp)/(Km5 + (Rt - Rp)); r6: Rp => $R; env*k6*Rp/(Km6 + Rp); + // Interactions: + _I0: $S -o r1; ; + _I1: Rp -o r2; ; + _I2: X -o r3; ; + _I3: Yp -o r5; ; + // Species initializations: Rp = 0; X = 0; @@ -95,11 +101,17 @@ model *Tyson2003_Negative_Feedback_Oscillator() k6.sboTerm = 485 Km6.sboTerm = 196 r1.sboTerm = 176 + r1.kineticLaw.sboTerm = 1 r2.sboTerm = 179 + r2.kineticLaw.sboTerm = 1 r3.sboTerm = 216 + r3.kineticLaw.sboTerm = 430 r4.sboTerm = 330 + r4.kineticLaw.sboTerm = 29 r5.sboTerm = 216 + r5.kineticLaw.sboTerm = 29 r6.sboTerm = 330 + r6.kineticLaw.sboTerm = 29 // CV terms: env isVersionOf "http://identifiers.org/go/GO:0005623" diff --git a/doc/examples/biomodels/BIOMD0000000309_url.txt b/doc/examples/biomodels/BIOMD0000000309/BIOMD0000000309_url.txt similarity index 95% rename from doc/examples/biomodels/BIOMD0000000309_url.txt rename to doc/examples/biomodels/BIOMD0000000309/BIOMD0000000309_url.txt index 2976f951f..b2e83267f 100644 --- a/doc/examples/biomodels/BIOMD0000000309_url.txt +++ b/doc/examples/biomodels/BIOMD0000000309/BIOMD0000000309_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Tyson2003_NegFB_Homeostasis() // Compartments and Species: @@ -17,6 +17,11 @@ model *Tyson2003_NegFB_Homeostasis() r3: $Ep => $E; env*k3*Ep/(Km3 + Ep); r4: $E => $Ep; env*k4*R*E/(Km4 + E); + // Interactions: + _I0: $E -o r0; ; + _I1: $S -o r2; ; + _I2: R -o r4; ; + // Species initializations: R = 0; S = 0; @@ -74,9 +79,13 @@ model *Tyson2003_NegFB_Homeostasis() Km3.sboTerm = 27 Km4.sboTerm = 27 r0.sboTerm = 176 + r0.kineticLaw.sboTerm = 49 r2.sboTerm = 179 + r2.kineticLaw.sboTerm = 54 r3.sboTerm = 330 + r3.kineticLaw.sboTerm = 29 r4.sboTerm = 216 + r4.kineticLaw.sboTerm = 29 // CV terms: env isVersionOf "http://identifiers.org/go/GO:0005623" diff --git a/doc/examples/biomodels/BIOMD0000000310_url.txt b/doc/examples/biomodels/BIOMD0000000310/BIOMD0000000310_url.txt similarity index 94% rename from doc/examples/biomodels/BIOMD0000000310_url.txt rename to doc/examples/biomodels/BIOMD0000000310/BIOMD0000000310_url.txt index 30da8c5be..fb2e7499e 100644 --- a/doc/examples/biomodels/BIOMD0000000310_url.txt +++ b/doc/examples/biomodels/BIOMD0000000310/BIOMD0000000310_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Tyson2003_Mutual_Inhibition() // Compartments and Species: @@ -19,6 +19,10 @@ model *Tyson2003_Mutual_Inhibition() r3: $Ep => $E; env*k3*Ep/(Km3 + Ep); r4: $E => $Ep; env*k4*R*E/(Km4 + E); + // Interactions: + _I0: $E -o r2_prime; ; + _I1: R -o r4; ; + // Species initializations: R = 0; S = 0; @@ -82,11 +86,17 @@ model *Tyson2003_Mutual_Inhibition() Km3.sboTerm = 27 Km4.sboTerm = 27 r0.sboTerm = 176 + r0.kineticLaw.sboTerm = 47 r1.sboTerm = 176 + r1.kineticLaw.sboTerm = 49 r2.sboTerm = 179 + r2.kineticLaw.sboTerm = 49 r2_prime.sboTerm = 179 + r2_prime.kineticLaw.sboTerm = 54 r3.sboTerm = 330 + r3.kineticLaw.sboTerm = 29 r4.sboTerm = 216 + r4.kineticLaw.sboTerm = 29 // CV terms: env isVersionOf "http://identifiers.org/go/GO:0005623" diff --git a/doc/examples/biomodels/BIOMD0000000311_url.txt b/doc/examples/biomodels/BIOMD0000000311/BIOMD0000000311_url.txt similarity index 94% rename from doc/examples/biomodels/BIOMD0000000311_url.txt rename to doc/examples/biomodels/BIOMD0000000311/BIOMD0000000311_url.txt index 162989277..a551e4132 100644 --- a/doc/examples/biomodels/BIOMD0000000311_url.txt +++ b/doc/examples/biomodels/BIOMD0000000311/BIOMD0000000311_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Tyson2003_Mutual_Activation() // Compartments and Species: @@ -16,6 +16,11 @@ model *Tyson2003_Mutual_Activation() r4: $E => $Ep; env*k3*R*E/(J3 + E); r5: $Ep => $E; env*k4*Ep/(J4 + Ep); + // Interactions: + _I0: $Ep -o r1; ; + _I1: $S -o r2; ; + _I2: R -o r4; ; + // Species initializations: R = 0; S = 0; @@ -71,10 +76,15 @@ model *Tyson2003_Mutual_Activation() k1.sboTerm = 35 k2.sboTerm = 356 r1.sboTerm = 176 + r1.kineticLaw.sboTerm = 49 r2.sboTerm = 176 + r2.kineticLaw.sboTerm = 49 r3.sboTerm = 179 + r3.kineticLaw.sboTerm = 49 r4.sboTerm = 216 + r4.kineticLaw.sboTerm = 29 r5.sboTerm = 330 + r5.kineticLaw.sboTerm = 29 // CV terms: env isVersionOf "http://identifiers.org/go/GO:0005623" diff --git a/doc/examples/biomodels/BIOMD0000000312_url.txt b/doc/examples/biomodels/BIOMD0000000312/BIOMD0000000312_url.txt similarity index 94% rename from doc/examples/biomodels/BIOMD0000000312_url.txt rename to doc/examples/biomodels/BIOMD0000000312/BIOMD0000000312_url.txt index 9671eaecd..7e666e238 100644 --- a/doc/examples/biomodels/BIOMD0000000312_url.txt +++ b/doc/examples/biomodels/BIOMD0000000312/BIOMD0000000312_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Tyson2003_Perfect_Adaption() // Compartments and Species: @@ -14,6 +14,11 @@ model *Tyson2003_Perfect_Adaption() r3: => X; env*k3*S; r4: X => ; env*k4*X; + // Interactions: + _I0: $S -o r1; ; + _I1: X -o r2; ; + _I2: $S -o r3; ; + // Species initializations: R = k1*k4/(k2*k3); X = 0; @@ -59,9 +64,13 @@ model *Tyson2003_Perfect_Adaption() S.sboTerm = 285 tau.sboTerm = 2 r1.sboTerm = 176 + r1.kineticLaw.sboTerm = 49 r2.sboTerm = 179 + r2.kineticLaw.sboTerm = 54 r3.sboTerm = 176 + r3.kineticLaw.sboTerm = 49 r4.sboTerm = 179 + r4.kineticLaw.sboTerm = 49 // CV terms: env isVersionOf "http://identifiers.org/go/GO:0005623" diff --git a/doc/examples/biomodels/BIOMD0000000313_url.txt b/doc/examples/biomodels/BIOMD0000000313/BIOMD0000000313_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000313_url.txt rename to doc/examples/biomodels/BIOMD0000000313/BIOMD0000000313_url.txt index 27d61c644..f03b9319f 100644 --- a/doc/examples/biomodels/BIOMD0000000313_url.txt +++ b/doc/examples/biomodels/BIOMD0000000313/BIOMD0000000313_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Raia2010_IL13_MedB1() // Compartments and Species: @@ -29,6 +29,9 @@ model *Raia2010_IL13_MedB1() reaction_15: SOCS3 => ; SOCS3_degradation*SOCS3*cell; reaction_16: => CD274mRNA; pSTAT5*CD274mRNA_production*cell; + // Interactions: + _I0: $IL13 -o reaction_1; ; + // Species initializations: Rec = 1.3; Rec_i = 113.194; diff --git a/doc/examples/biomodels/BIOMD0000000314_url.txt b/doc/examples/biomodels/BIOMD0000000314/BIOMD0000000314_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000314_url.txt rename to doc/examples/biomodels/BIOMD0000000314/BIOMD0000000314_url.txt index af89aa126..e3f98937f 100644 --- a/doc/examples/biomodels/BIOMD0000000314_url.txt +++ b/doc/examples/biomodels/BIOMD0000000314/BIOMD0000000314_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Raia2010_IL13_L1236() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000315_url.txt b/doc/examples/biomodels/BIOMD0000000315/BIOMD0000000315_url.txt similarity index 94% rename from doc/examples/biomodels/BIOMD0000000315_url.txt rename to doc/examples/biomodels/BIOMD0000000315/BIOMD0000000315_url.txt index 12695b0f6..3dd385346 100644 --- a/doc/examples/biomodels/BIOMD0000000315_url.txt +++ b/doc/examples/biomodels/BIOMD0000000315/BIOMD0000000315_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Oligator() // Compartments and Species: @@ -249,32 +249,59 @@ model *Oligator() beta_total.sboTerm = 196 alpha_total.sboTerm = 196 ass_aa_l.sboTerm = 177 + ass_aa_l.kineticLaw.sboTerm = 101 m_ass_aa_lr.sboTerm = 180 + m_ass_aa_lr.kineticLaw.sboTerm = 83 m_ass_aa_r.sboTerm = 180 + m_ass_aa_r.kineticLaw.sboTerm = 83 m_ass_aa_rl.sboTerm = 180 + m_ass_aa_rl.kineticLaw.sboTerm = 83 pol_aa.sboTerm = 205 + pol_aa.kineticLaw.sboTerm = 49 dis_aa.sboTerm = 180 + dis_aa.kineticLaw.sboTerm = 49 nick_aa.sboTerm = 178 + nick_aa.kineticLaw.sboTerm = 49 ass_ab_l.sboTerm = 177 + ass_ab_l.kineticLaw.sboTerm = 101 m_ass_ab_lr.sboTerm = 180 + m_ass_ab_lr.kineticLaw.sboTerm = 83 m_ass_ab_r.sboTerm = 180 + m_ass_ab_r.kineticLaw.sboTerm = 83 m_ass_ab_rl.sboTerm = 180 + m_ass_ab_rl.kineticLaw.sboTerm = 83 pol_ab.sboTerm = 205 + pol_ab.kineticLaw.sboTerm = 49 dis_ab.sboTerm = 205 + dis_ab.kineticLaw.sboTerm = 49 nick_ab.sboTerm = 178 + nick_ab.kineticLaw.sboTerm = 49 ass_bc_l.sboTerm = 177 + ass_bc_l.kineticLaw.sboTerm = 101 m_ass_bc_lr.sboTerm = 180 + m_ass_bc_lr.kineticLaw.sboTerm = 83 ass_bc_r.sboTerm = 177 + ass_bc_r.kineticLaw.sboTerm = 101 ass_bc_rl.sboTerm = 177 + ass_bc_rl.kineticLaw.sboTerm = 101 pol_bc.sboTerm = 205 + pol_bc.kineticLaw.sboTerm = 49 dis_bc.sboTerm = 205 + dis_bc.kineticLaw.sboTerm = 49 nick_bc.sboTerm = 178 + nick_bc.kineticLaw.sboTerm = 49 inh_ac.sboTerm = 177 + inh_ac.kineticLaw.sboTerm = 101 inh_displ_ac.sboTerm = 177 + inh_displ_ac.kineticLaw.sboTerm = 103 m_inh_displ_ca.sboTerm = 177 + m_inh_displ_ca.kineticLaw.sboTerm = 103 exo_a.sboTerm = 179 + exo_a.kineticLaw.sboTerm = 49 exo_b.sboTerm = 179 + exo_b.kineticLaw.sboTerm = 49 exo_c.sboTerm = 179 + exo_c.kineticLaw.sboTerm = 49 // CV terms: T1 isVersionOf "http://identifiers.org/chebi/CHEBI:16991", diff --git a/doc/examples/biomodels/BIOMD0000000316_url.txt b/doc/examples/biomodels/BIOMD0000000316/BIOMD0000000316_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000316_url.txt rename to doc/examples/biomodels/BIOMD0000000316/BIOMD0000000316_url.txt index f49215758..dd13909bd 100644 --- a/doc/examples/biomodels/BIOMD0000000316_url.txt +++ b/doc/examples/biomodels/BIOMD0000000316/BIOMD0000000316_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *shenorr02() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000317_url.txt b/doc/examples/biomodels/BIOMD0000000317/BIOMD0000000317_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000317_url.txt rename to doc/examples/biomodels/BIOMD0000000317/BIOMD0000000317_url.txt index 1a005f3da..a98fe2bed 100644 --- a/doc/examples/biomodels/BIOMD0000000317_url.txt +++ b/doc/examples/biomodels/BIOMD0000000317/BIOMD0000000317_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *shenorr02() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000318_url.txt b/doc/examples/biomodels/BIOMD0000000318/BIOMD0000000318_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000318_url.txt rename to doc/examples/biomodels/BIOMD0000000318/BIOMD0000000318_url.txt index 09d0e194a..0ab14af18 100644 --- a/doc/examples/biomodels/BIOMD0000000318_url.txt +++ b/doc/examples/biomodels/BIOMD0000000318/BIOMD0000000318_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *yao08() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000319_url.txt b/doc/examples/biomodels/BIOMD0000000319/BIOMD0000000319_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000319_url.txt rename to doc/examples/biomodels/BIOMD0000000319/BIOMD0000000319_url.txt index c9e99b0b8..00fade614 100644 --- a/doc/examples/biomodels/BIOMD0000000319_url.txt +++ b/doc/examples/biomodels/BIOMD0000000319/BIOMD0000000319_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *decroly82() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000320_url.txt b/doc/examples/biomodels/BIOMD0000000320/BIOMD0000000320_url.txt similarity index 95% rename from doc/examples/biomodels/BIOMD0000000320_url.txt rename to doc/examples/biomodels/BIOMD0000000320/BIOMD0000000320_url.txt index b9a5f5c3a..0d7eb94c9 100644 --- a/doc/examples/biomodels/BIOMD0000000320_url.txt +++ b/doc/examples/biomodels/BIOMD0000000320/BIOMD0000000320_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000320() // Compartments and Species: @@ -190,19 +190,33 @@ model *BIOMD0000000320() CL_dM.sboTerm = 35 Benserazide_per_kg_rat.sboTerm = 197 l_dopa_absorption.sboTerm = 185 + l_dopa_absorption.kineticLaw.sboTerm = 49 l_dopa_blood_hepa_clearance.sboTerm = 179 + l_dopa_blood_hepa_clearance.kineticLaw.sboTerm = 49 ro_04_5127_absorption.sboTerm = 185 + ro_04_5127_absorption.kineticLaw.sboTerm = 49 benserazide_absorption.sboTerm = 185 + benserazide_absorption.kineticLaw.sboTerm = 49 benserazide_gut_clearance.sboTerm = 179 + benserazide_gut_clearance.kineticLaw.sboTerm = 49 AADC_clearance.sboTerm = 399 + AADC_clearance.kineticLaw.sboTerm = 49 COMT_clearance.sboTerm = 214 + COMT_clearance.kineticLaw.sboTerm = 49 rest_clearance.sboTerm = 179 + rest_clearance.kineticLaw.sboTerm = 49 _3_OMD_clearance.sboTerm = 179 + _3_OMD_clearance.kineticLaw.sboTerm = 49 bens_clearance.sboTerm = 179 + bens_clearance.kineticLaw.sboTerm = 49 bens_metabolism.sboTerm = 211 + bens_metabolism.kineticLaw.sboTerm = 49 ro_clearance.sboTerm = 179 + ro_clearance.kineticLaw.sboTerm = 49 bens_distribution.sboTerm = 185 + bens_distribution.kineticLaw.sboTerm = 80 ro_distribution.sboTerm = 185 + ro_distribution.kineticLaw.sboTerm = 80 // CV terms: gut isVersionOf "http://identifiers.org/bto/BTO:0000648" diff --git a/doc/examples/biomodels/BIOMD0000000321_url.txt b/doc/examples/biomodels/BIOMD0000000321/BIOMD0000000321_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000321_url.txt rename to doc/examples/biomodels/BIOMD0000000321/BIOMD0000000321_url.txt index 90ef17bac..7d2c2baa0 100644 --- a/doc/examples/biomodels/BIOMD0000000321_url.txt +++ b/doc/examples/biomodels/BIOMD0000000321/BIOMD0000000321_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000321() // Compartments and Species: @@ -112,11 +112,17 @@ model *BIOMD0000000321() ka_b.sboTerm = 35 CL_OMD.sboTerm = 35 l_dopa_absorption.sboTerm = 185 + l_dopa_absorption.kineticLaw.sboTerm = 49 l_dopa_blood_hepa_clearance.sboTerm = 179 + l_dopa_blood_hepa_clearance.kineticLaw.sboTerm = 49 AADC_clearance.sboTerm = 399 + AADC_clearance.kineticLaw.sboTerm = 49 COMT_clearance.sboTerm = 214 + COMT_clearance.kineticLaw.sboTerm = 49 rest_clearance.sboTerm = 179 + rest_clearance.kineticLaw.sboTerm = 49 _3_OMD_clearance.sboTerm = 179 + _3_OMD_clearance.kineticLaw.sboTerm = 49 // CV terms: gut isVersionOf "http://identifiers.org/bto/BTO:0000648" diff --git a/doc/examples/biomodels/BIOMD0000000322_url.txt b/doc/examples/biomodels/BIOMD0000000322/BIOMD0000000322_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000322_url.txt rename to doc/examples/biomodels/BIOMD0000000322/BIOMD0000000322_url.txt index 4dcc83fb0..de13c04f8 100644 --- a/doc/examples/biomodels/BIOMD0000000322_url.txt +++ b/doc/examples/biomodels/BIOMD0000000322/BIOMD0000000322_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kim2011_Oscillator_SimpleI() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000323_url.txt b/doc/examples/biomodels/BIOMD0000000323/BIOMD0000000323_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000323_url.txt rename to doc/examples/biomodels/BIOMD0000000323/BIOMD0000000323_url.txt index ba7acd0b8..006c4a8f4 100644 --- a/doc/examples/biomodels/BIOMD0000000323_url.txt +++ b/doc/examples/biomodels/BIOMD0000000323/BIOMD0000000323_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kim2011_Oscillator_SimpleIII() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000324_url.txt b/doc/examples/biomodels/BIOMD0000000324/BIOMD0000000324_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000324_url.txt rename to doc/examples/biomodels/BIOMD0000000324/BIOMD0000000324_url.txt index 1b14b907f..33874f7f5 100644 --- a/doc/examples/biomodels/BIOMD0000000324_url.txt +++ b/doc/examples/biomodels/BIOMD0000000324/BIOMD0000000324_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Morris1981_MuscleFibre_Voltage() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000325_url.txt b/doc/examples/biomodels/BIOMD0000000325/BIOMD0000000325_url.txt similarity index 93% rename from doc/examples/biomodels/BIOMD0000000325_url.txt rename to doc/examples/biomodels/BIOMD0000000325/BIOMD0000000325_url.txt index 67a66ec95..4c0b7543f 100644 --- a/doc/examples/biomodels/BIOMD0000000325_url.txt +++ b/doc/examples/biomodels/BIOMD0000000325/BIOMD0000000325_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *minfb() // Compartments and Species: @@ -17,6 +17,10 @@ model *minfb() I_expression: => I; cell*(BI + TFs*A/(KD + A)); I_degradation: I => ; cell*kdegI*I; + // Interactions: + _I0: A -o R_expression; ; + _I1: A -o I_expression; ; + // Species initializations: L = 0.1; R = 1; @@ -73,15 +77,25 @@ model *minfb() TFs.sboTerm = 186 kdegI.sboTerm = 356 R_expression.sboTerm = 205 + R_expression.kineticLaw.sboTerm = 1 R_degradation.sboTerm = 179 + R_degradation.kineticLaw.sboTerm = 49 R_L_binding.sboTerm = 177 + R_L_binding.kineticLaw.sboTerm = 101 C_degradation.sboTerm = 179 + C_degradation.kineticLaw.sboTerm = 49 C_I_binding.sboTerm = 177 + C_I_binding.kineticLaw.sboTerm = 101 I_activation.sboTerm = 216 + I_activation.kineticLaw.sboTerm = 49 X_degradation.sboTerm = 179 + X_degradation.kineticLaw.sboTerm = 49 A_degradation.sboTerm = 179 + A_degradation.kineticLaw.sboTerm = 49 I_expression.sboTerm = 205 + I_expression.kineticLaw.sboTerm = 1 I_degradation.sboTerm = 179 + I_degradation.kineticLaw.sboTerm = 49 // CV terms: cell isVersionOf "http://identifiers.org/go/GO:0005623" diff --git a/doc/examples/biomodels/BIOMD0000000326_url.txt b/doc/examples/biomodels/BIOMD0000000326/BIOMD0000000326_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000326_url.txt rename to doc/examples/biomodels/BIOMD0000000326/BIOMD0000000326_url.txt index 646f0ac34..bddf7cd13 100644 --- a/doc/examples/biomodels/BIOMD0000000326_url.txt +++ b/doc/examples/biomodels/BIOMD0000000326/BIOMD0000000326_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *DellOrco2009_phototransduction() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000327_url.txt b/doc/examples/biomodels/BIOMD0000000327/BIOMD0000000327_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000327_url.txt rename to doc/examples/biomodels/BIOMD0000000327/BIOMD0000000327_url.txt index 41bdac211..2922d46ea 100644 --- a/doc/examples/biomodels/BIOMD0000000327_url.txt +++ b/doc/examples/biomodels/BIOMD0000000327/BIOMD0000000327_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *whitcomb04() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000328_url.txt b/doc/examples/biomodels/BIOMD0000000328/BIOMD0000000328_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000328_url.txt rename to doc/examples/biomodels/BIOMD0000000328/BIOMD0000000328_url.txt index 59e7f7c4a..48bf557d9 100644 --- a/doc/examples/biomodels/BIOMD0000000328_url.txt +++ b/doc/examples/biomodels/BIOMD0000000328/BIOMD0000000328_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Atorvastatin_Metabolism() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000329_url.txt b/doc/examples/biomodels/BIOMD0000000329/BIOMD0000000329_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000329_url.txt rename to doc/examples/biomodels/BIOMD0000000329/BIOMD0000000329_url.txt index dc13a0be2..d64ba45c7 100644 --- a/doc/examples/biomodels/BIOMD0000000329_url.txt +++ b/doc/examples/biomodels/BIOMD0000000329/BIOMD0000000329_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000329() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000330_url.txt b/doc/examples/biomodels/BIOMD0000000330/BIOMD0000000330_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000330_url.txt rename to doc/examples/biomodels/BIOMD0000000330/BIOMD0000000330_url.txt index d7e9306bb..2cdc3967e 100644 --- a/doc/examples/biomodels/BIOMD0000000330_url.txt +++ b/doc/examples/biomodels/BIOMD0000000330/BIOMD0000000330_url.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Larsen2004_CalciumSpiking() // Compartments and Species: compartment cytoplasm, ER, mit; - species $G_alpha in cytoplasm, $PLC in cytoplasm, $Ca_cyt in cytoplasm; - species $Ca_ER in ER, $Ca_mit in mit; + species G_alpha in cytoplasm, PLC in cytoplasm, Ca_cyt in cytoplasm, Ca_ER in ER; + species Ca_mit in mit; // Rate Rules: G_alpha' = k1 + k2*G_alpha - k3*G_alpha*PLC/(G_alpha + K4) - k5*G_alpha*Ca_cyt/(G_alpha + K6); diff --git a/doc/examples/biomodels/BIOMD0000000331_url.txt b/doc/examples/biomodels/BIOMD0000000331/BIOMD0000000331_url.txt similarity index 96% rename from doc/examples/biomodels/BIOMD0000000331_url.txt rename to doc/examples/biomodels/BIOMD0000000331/BIOMD0000000331_url.txt index 4f4e8aac9..974a5c5a9 100644 --- a/doc/examples/biomodels/BIOMD0000000331_url.txt +++ b/doc/examples/biomodels/BIOMD0000000331/BIOMD0000000331_url.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Larsen2004_CalciumSpiking_EnzymeBinding() // Compartments and Species: compartment cytoplasm, ER, mit; - species $G_alpha in cytoplasm, $PLC in cytoplasm, $Ca_cyt in cytoplasm; - species $Ca_ER in ER, $Ca_mit in mit, $Enz in cytoplasm, $Product in cytoplasm; + species G_alpha in cytoplasm, PLC in cytoplasm, Ca_cyt in cytoplasm, Ca_ER in ER; + species Ca_mit in mit, Enz in cytoplasm, Product in cytoplasm; // Rate Rules: G_alpha' = k1 + k2*G_alpha - k3*G_alpha*PLC/(G_alpha + K4) - k5*G_alpha*Ca_cyt/(G_alpha + K6); diff --git a/doc/examples/biomodels/BIOMD0000000332_url.txt b/doc/examples/biomodels/BIOMD0000000332/BIOMD0000000332_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000332_url.txt rename to doc/examples/biomodels/BIOMD0000000332/BIOMD0000000332_url.txt index d57949c57..e436acf78 100644 --- a/doc/examples/biomodels/BIOMD0000000332_url.txt +++ b/doc/examples/biomodels/BIOMD0000000332/BIOMD0000000332_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model01() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000333_url.txt b/doc/examples/biomodels/BIOMD0000000333/BIOMD0000000333_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000333_url.txt rename to doc/examples/biomodels/BIOMD0000000333/BIOMD0000000333_url.txt index 5e08e34d1..6b1f05b7c 100644 --- a/doc/examples/biomodels/BIOMD0000000333_url.txt +++ b/doc/examples/biomodels/BIOMD0000000333/BIOMD0000000333_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model01() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000334_url.txt b/doc/examples/biomodels/BIOMD0000000334/BIOMD0000000334_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000334_url.txt rename to doc/examples/biomodels/BIOMD0000000334/BIOMD0000000334_url.txt index ba2819b1b..e5884ce8d 100644 --- a/doc/examples/biomodels/BIOMD0000000334_url.txt +++ b/doc/examples/biomodels/BIOMD0000000334/BIOMD0000000334_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bungay2003_Thrombin_Generation() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000335_url.txt b/doc/examples/biomodels/BIOMD0000000335/BIOMD0000000335_url.txt similarity index 92% rename from doc/examples/biomodels/BIOMD0000000335_url.txt rename to doc/examples/biomodels/BIOMD0000000335/BIOMD0000000335_url.txt index 34389d66c..4e3d7cedc 100644 --- a/doc/examples/biomodels/BIOMD0000000335_url.txt +++ b/doc/examples/biomodels/BIOMD0000000335/BIOMD0000000335_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: @@ -188,6 +188,37 @@ model *Model_1() k40.sboTerm = 36 k41.sboTerm = 36 k42.sboTerm = 36 + R1.kineticLaw.sboTerm = 101 + R2.kineticLaw.sboTerm = 101 + R3.kineticLaw.sboTerm = 45 + R4.kineticLaw.sboTerm = 45 + R5.kineticLaw.sboTerm = 45 + R6.kineticLaw.sboTerm = 101 + R7.kineticLaw.sboTerm = 101 + R8.kineticLaw.sboTerm = 101 + R9.kineticLaw.sboTerm = 45 + R10.kineticLaw.sboTerm = 45 + R11.kineticLaw.sboTerm = 101 + R12.kineticLaw.sboTerm = 101 + R13.kineticLaw.sboTerm = 83 + R14.kineticLaw.sboTerm = 49 + R15.kineticLaw.sboTerm = 49 + R16.kineticLaw.sboTerm = 45 + R17.kineticLaw.sboTerm = 101 + R18.kineticLaw.sboTerm = 101 + R19.kineticLaw.sboTerm = 45 + R20.kineticLaw.sboTerm = 101 + R21.kineticLaw.sboTerm = 101 + R22.kineticLaw.sboTerm = 54 + R23.kineticLaw.sboTerm = 54 + R24.kineticLaw.sboTerm = 54 + R25.kineticLaw.sboTerm = 54 + R26.kineticLaw.sboTerm = 54 + R27.kineticLaw.sboTerm = 54 + R6b.kineticLaw.sboTerm = 49 + R8b.kineticLaw.sboTerm = 49 + R12b.kineticLaw.sboTerm = 49 + R18b.kineticLaw.sboTerm = 49 // CV terms: TF identity "http://identifiers.org/uniprot/P13726" diff --git a/doc/examples/biomodels/BIOMD0000000336_url.txt b/doc/examples/biomodels/BIOMD0000000336/BIOMD0000000336_url.txt similarity index 90% rename from doc/examples/biomodels/BIOMD0000000336_url.txt rename to doc/examples/biomodels/BIOMD0000000336/BIOMD0000000336_url.txt index dd22e758e..aa94d6da9 100644 --- a/doc/examples/biomodels/BIOMD0000000336_url.txt +++ b/doc/examples/biomodels/BIOMD0000000336/BIOMD0000000336_url.txt @@ -1,4 +1,8 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 + +// Warnings from automatic translation: +// An interaction was declared that claims VIIIa_IXa modifies VIIIa_IXa_degradation, but VIIIa_IXa does not appear in VIIIa_IXa_degradation's kinetic law. + model *Model_1() // Compartments and Species: @@ -38,6 +42,9 @@ model *Model_1() R4_atn: IX + Va_Xa => Va_Xa + IXa; compartment_1*k15*IX*Va_Xa; VIIIa_IXa_degradation: VIIIa_IXa => ; compartment_1*((compartment_1*abs(I - VIIIa_IXa) + (I - VIIIa_IXa))/compartment_1); + // Interactions: + _I0: VIIIa_IXa -( VIIIa_IXa_degradation; ; + // Species initializations: IX = 9e-08; IX_TF_VIIa = 0; @@ -111,6 +118,25 @@ model *Model_1() k17.sboTerm = 38 k18.sboTerm = 38 k19.sboTerm = 38 + R1.kineticLaw.sboTerm = 101 + R1b.kineticLaw.sboTerm = 49 + R2.kineticLaw.sboTerm = 101 + R2b.kineticLaw.sboTerm = 49 + R3.kineticLaw.sboTerm = 101 + R3b.kineticLaw.sboTerm = 49 + R4.kineticLaw.sboTerm = 45 + R5.kineticLaw.sboTerm = 45 + R6.kineticLaw.sboTerm = 45 + R7.kineticLaw.sboTerm = 45 + R8.kineticLaw.sboTerm = 45 + R9.kineticLaw.sboTerm = 101 + R9b.kineticLaw.sboTerm = 49 + R10.kineticLaw.sboTerm = 45 + R11.kineticLaw.sboTerm = 101 + R12.kineticLaw.sboTerm = 101 + R7_atn.kineticLaw.sboTerm = 45 + R8_atn.kineticLaw.sboTerm = 45 + R4_atn.kineticLaw.sboTerm = 45 // CV terms: IX identity "http://identifiers.org/uniprot/P00740" diff --git a/doc/examples/biomodels/BIOMD0000000337_url.txt b/doc/examples/biomodels/BIOMD0000000337/BIOMD0000000337_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000337_url.txt rename to doc/examples/biomodels/BIOMD0000000337/BIOMD0000000337_url.txt index e87a3f313..75b7d32a7 100644 --- a/doc/examples/biomodels/BIOMD0000000337_url.txt +++ b/doc/examples/biomodels/BIOMD0000000337/BIOMD0000000337_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Pfeiffer2001_ATPProducingPathways_CooperationCompetition() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000338_url.txt b/doc/examples/biomodels/BIOMD0000000338/BIOMD0000000338_url.txt similarity index 85% rename from doc/examples/biomodels/BIOMD0000000338_url.txt rename to doc/examples/biomodels/BIOMD0000000338/BIOMD0000000338_url.txt index d7fb2003d..baa654216 100644 --- a/doc/examples/biomodels/BIOMD0000000338_url.txt +++ b/doc/examples/biomodels/BIOMD0000000338/BIOMD0000000338_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: @@ -147,6 +147,51 @@ model *Model_1() pVK: => VK; compartment_1*(VK0*d_VK); dVK: VK => ; compartment_1*d_VK*VK; + // Interactions: + _I0: IIa -o r1_; ; + _I1: APC_PS -o r2_; ; + _I2: XIa -o r3_; ; + _I3: XIIa -o r4_; ; + _I4: IIa -o r5_; ; + _I5: IIa -o r6_; ; + _I6: IXa -o r7_; ; + _I7: IXa_VIIIa -o r8_; ; + _I8: VIIa -o r9_; ; + _I9: IIa -o r10; ; + _I10: APC_PS -o r11; ; + _I11: Va_Xa -o r12; ; + _I12: Xa -o r13; ; + _I13: IIa -o r14; ; + _I14: P -o r15; ; + _I15: XIIIa -o r16; ; + _I16: P -o r17; ; + _I17: P -o r18; ; + _I18: APC_PS -o r19; ; + _I19: IIa -o r20; ; + _I20: IIa -o r21; ; + _I21: F -o r22; ; + _I22: APC_PS -o r23; ; + _I23: IIa_Tmod -o r24; ; + _I24: APC_PS -o r25; ; + _I25: Xa -o r33; ; + _I26: VIIa_TF -o r34; ; + _I27: VIIa_TF -o r35; ; + _I28: TF -o r36; ; + _I29: Xa -o r38; ; + _I30: VIIa_TF -o r39; ; + _I31: IXa -o r40; ; + _I32: CA -o r41; ; + _I33: K -o r42; ; + _I34: XIIa -o r43; ; + _I35: $C_warf -( r47; ; + _I36: $C_warf -( r48; ; + _I37: VKH2 -( pII_VKH2; ; + _I38: VKH2 -( pVII_VKH2; ; + _I39: VKH2 -( pIX_VKH2; ; + _I40: VKH2 -( pX_VKH2; ; + _I41: VKH2 -( pPC_VKH2; ; + _I42: VKH2 -( pPS_VKH2; ; + // Events: clottingTime_event: at (Integral_Fibrin*3600) > 1500: clottingTime_s = time*3600; dilution_event: at time > 0: compartment_1 = compartment_1*3; @@ -445,112 +490,208 @@ model *Model_1() c45.sboTerm = 36 c46.sboTerm = 36 d_VK.sboTerm = 35 + r1_.kineticLaw.sboTerm = 28 r1__v.sboTerm = 25 r1__k.sboTerm = 371 + r2_.kineticLaw.sboTerm = 28 r2__v.sboTerm = 25 r2__k.sboTerm = 371 + r3_.kineticLaw.sboTerm = 28 r3__v.sboTerm = 25 r3__k.sboTerm = 371 + r4_.kineticLaw.sboTerm = 28 r4__v.sboTerm = 25 r4__k.sboTerm = 371 + r5_.kineticLaw.sboTerm = 28 r5__v.sboTerm = 25 r5__k.sboTerm = 371 + r6_.kineticLaw.sboTerm = 28 r6__v.sboTerm = 25 r6__k.sboTerm = 371 + r7_.kineticLaw.sboTerm = 28 r7__v.sboTerm = 25 r7__k.sboTerm = 371 + r8_.kineticLaw.sboTerm = 28 r8__v.sboTerm = 25 r8__k.sboTerm = 371 + r9_.kineticLaw.sboTerm = 28 r9__v.sboTerm = 25 r9__k.sboTerm = 371 + r10.kineticLaw.sboTerm = 28 r10_v.sboTerm = 25 r10_k.sboTerm = 371 + r11.kineticLaw.sboTerm = 28 r11_v.sboTerm = 25 r11_k.sboTerm = 371 + r12.kineticLaw.sboTerm = 28 r12_v.sboTerm = 25 r12_k.sboTerm = 371 + r13.kineticLaw.sboTerm = 28 r13_v.sboTerm = 25 r13_k.sboTerm = 371 + r14.kineticLaw.sboTerm = 28 r14_v.sboTerm = 25 r14_k.sboTerm = 371 + r15.kineticLaw.sboTerm = 28 r15_v.sboTerm = 25 r15_k.sboTerm = 371 + r16.kineticLaw.sboTerm = 28 r16_v.sboTerm = 25 r16_k.sboTerm = 371 + r17.kineticLaw.sboTerm = 28 r17_v.sboTerm = 25 r17_k.sboTerm = 371 + r18.kineticLaw.sboTerm = 28 r18_v.sboTerm = 25 r18_k.sboTerm = 371 + r19.kineticLaw.sboTerm = 28 r19_v.sboTerm = 25 r19_k.sboTerm = 371 + r20.kineticLaw.sboTerm = 28 r20_v.sboTerm = 25 r20_k.sboTerm = 371 + r21.kineticLaw.sboTerm = 28 r21_v.sboTerm = 25 r21_k.sboTerm = 371 + r22.kineticLaw.sboTerm = 28 r22_v.sboTerm = 25 r22_k.sboTerm = 371 + r23.kineticLaw.sboTerm = 28 r23_v.sboTerm = 25 r23_k.sboTerm = 371 + r24.kineticLaw.sboTerm = 28 r24_v.sboTerm = 25 r24_k.sboTerm = 371 + r25.kineticLaw.sboTerm = 28 r25_v.sboTerm = 25 r25_k.sboTerm = 371 + r26.kineticLaw.sboTerm = 28 r26_c.sboTerm = 36 + r27.kineticLaw.sboTerm = 28 r27_c.sboTerm = 36 + r28.kineticLaw.sboTerm = 28 r28_c.sboTerm = 36 + r29.kineticLaw.sboTerm = 28 r29_c.sboTerm = 36 + r30.kineticLaw.sboTerm = 28 r30_c.sboTerm = 36 + r31.kineticLaw.sboTerm = 28 r31_c.sboTerm = 36 + r32.kineticLaw.sboTerm = 28 r32_c.sboTerm = 36 + r33.kineticLaw.sboTerm = 28 r33_v.sboTerm = 25 r33_k.sboTerm = 371 + r34.kineticLaw.sboTerm = 28 r34_v.sboTerm = 25 r34_k.sboTerm = 371 + r35.kineticLaw.sboTerm = 28 r35_v.sboTerm = 25 r35_k.sboTerm = 371 + r36.kineticLaw.sboTerm = 28 r36_v.sboTerm = 25 r36_k.sboTerm = 371 + r37.kineticLaw.sboTerm = 28 r37_c.sboTerm = 36 + r38.kineticLaw.sboTerm = 28 r38_v.sboTerm = 25 r38_k.sboTerm = 371 + r39.kineticLaw.sboTerm = 28 r39_v.sboTerm = 25 r39_k.sboTerm = 371 + r40.kineticLaw.sboTerm = 28 r40_v.sboTerm = 25 r40_k.sboTerm = 371 + r41.kineticLaw.sboTerm = 28 r41_v.sboTerm = 25 r41_k.sboTerm = 371 + r42.kineticLaw.sboTerm = 28 r42_v.sboTerm = 25 r42_k.sboTerm = 371 + r43.kineticLaw.sboTerm = 28 r43_v.sboTerm = 25 r43_k.sboTerm = 371 + r44.kineticLaw.sboTerm = 28 + r45.kineticLaw.sboTerm = 28 + r46.kineticLaw.sboTerm = 28 + dFg.kineticLaw.sboTerm = 49 + dF.kineticLaw.sboTerm = 49 dF_k1.sboTerm = 35 + dXF.kineticLaw.sboTerm = 49 dXF_k1.sboTerm = 35 + dII.kineticLaw.sboTerm = 49 + dIIa.kineticLaw.sboTerm = 49 dIIa_k1.sboTerm = 35 + dTF.kineticLaw.sboTerm = 49 dTF_k1.sboTerm = 35 + dV.kineticLaw.sboTerm = 49 + dVa.kineticLaw.sboTerm = 49 dVa_k1.sboTerm = 35 + dVII.kineticLaw.sboTerm = 49 + dVIIa.kineticLaw.sboTerm = 49 dVIIa_k1.sboTerm = 35 + dVIII.kineticLaw.sboTerm = 49 + dVIIIa.kineticLaw.sboTerm = 49 dVIIIa_k1.sboTerm = 35 + dX.kineticLaw.sboTerm = 49 + dXa.kineticLaw.sboTerm = 49 dXa_k1.sboTerm = 35 + dIX.kineticLaw.sboTerm = 49 + dIXa.kineticLaw.sboTerm = 49 dIXa_k1.sboTerm = 35 + dXII.kineticLaw.sboTerm = 49 + dXIIa.kineticLaw.sboTerm = 49 dXIIa_k1.sboTerm = 35 + dXIII.kineticLaw.sboTerm = 49 + dXIIIa.kineticLaw.sboTerm = 49 dXIIIa_k1.sboTerm = 35 + dPk.kineticLaw.sboTerm = 49 + dK.kineticLaw.sboTerm = 49 dK_k1.sboTerm = 35 + dPg.kineticLaw.sboTerm = 49 + dP.kineticLaw.sboTerm = 49 dP_k1.sboTerm = 35 + dPC.kineticLaw.sboTerm = 49 + dAPC.kineticLaw.sboTerm = 49 dAPC_k1.sboTerm = 35 + dPS.kineticLaw.sboTerm = 49 + dFDP.kineticLaw.sboTerm = 49 dFDP_k1.sboTerm = 35 + dD.kineticLaw.sboTerm = 49 dD_k1.sboTerm = 35 + dTFPI.kineticLaw.sboTerm = 49 + dVIIa_TF.kineticLaw.sboTerm = 49 dVIIa_TF_k1.sboTerm = 35 + dVII_TF.kineticLaw.sboTerm = 49 dVII_TF_k1.sboTerm = 35 + dAPC_PS.kineticLaw.sboTerm = 49 dAPC_PS_k1.sboTerm = 35 + dVa_Xa.kineticLaw.sboTerm = 49 dVa_Xa_k1.sboTerm = 35 + dIXa_VIIIa.kineticLaw.sboTerm = 49 dIXa_VIIIa_k1.sboTerm = 35 + dTmod.kineticLaw.sboTerm = 49 + dIIa_Tmod.kineticLaw.sboTerm = 49 dIIa_Tmod_k1.sboTerm = 35 + dXa_TFPI.kineticLaw.sboTerm = 49 dXa_TFPI_k1.sboTerm = 35 + dVIIa_TF_Xa_TFPI.kineticLaw.sboTerm = 49 dVIIa_TF_Xa_TFPI_k1.sboTerm = 35 + dTAT.kineticLaw.sboTerm = 49 dTAT_k1.sboTerm = 35 + dCA.kineticLaw.sboTerm = 49 dCA_k1.sboTerm = 35 + dXIa.kineticLaw.sboTerm = 49 dXIa_k1.sboTerm = 35 + dVKH2.kineticLaw.sboTerm = 49 + VK_transport.kineticLaw.sboTerm = 80 + eHeparin.kineticLaw.sboTerm = 49 + eHeparinXa.kineticLaw.sboTerm = 49 + eHeparinIXa.kineticLaw.sboTerm = 49 + eHeparinIIa.kineticLaw.sboTerm = 49 + dXI.kineticLaw.sboTerm = 49 dXI_k1.sboTerm = 35 + dVK.kineticLaw.sboTerm = 49 // CV terms: IIa isVersionOf "http://identifiers.org/uniprot/P00734" diff --git a/doc/examples/biomodels/BIOMD0000000339_url.txt b/doc/examples/biomodels/BIOMD0000000339/BIOMD0000000339_url.txt similarity index 85% rename from doc/examples/biomodels/BIOMD0000000339_url.txt rename to doc/examples/biomodels/BIOMD0000000339/BIOMD0000000339_url.txt index e1faf72f1..45daee211 100644 --- a/doc/examples/biomodels/BIOMD0000000339_url.txt +++ b/doc/examples/biomodels/BIOMD0000000339/BIOMD0000000339_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: @@ -147,6 +147,51 @@ model *Model_1() pVK: => VK; compartment_1*(VK0*d_VK); dVK: VK => ; compartment_1*d_VK*VK; + // Interactions: + _I0: IIa -o r1_; ; + _I1: APC_PS -o r2_; ; + _I2: XIa -o r3_; ; + _I3: XIIa -o r4_; ; + _I4: IIa -o r5_; ; + _I5: IIa -o r6_; ; + _I6: IXa -o r7_; ; + _I7: IXa_VIIIa -o r8_; ; + _I8: VIIa -o r9_; ; + _I9: IIa -o r10; ; + _I10: APC_PS -o r11; ; + _I11: Va_Xa -o r12; ; + _I12: Xa -o r13; ; + _I13: IIa -o r14; ; + _I14: P -o r15; ; + _I15: XIIIa -o r16; ; + _I16: P -o r17; ; + _I17: P -o r18; ; + _I18: APC_PS -o r19; ; + _I19: IIa -o r20; ; + _I20: IIa -o r21; ; + _I21: F -o r22; ; + _I22: APC_PS -o r23; ; + _I23: IIa_Tmod -o r24; ; + _I24: APC_PS -o r25; ; + _I25: Xa -o r33; ; + _I26: VIIa_TF -o r34; ; + _I27: VIIa_TF -o r35; ; + _I28: TF -o r36; ; + _I29: Xa -o r38; ; + _I30: VIIa_TF -o r39; ; + _I31: IXa -o r40; ; + _I32: CA -o r41; ; + _I33: K -o r42; ; + _I34: XIIa -o r43; ; + _I35: $C_warf -( r47; ; + _I36: $C_warf -( r48; ; + _I37: VKH2 -( pII_VKH2; ; + _I38: VKH2 -( pVII_VKH2; ; + _I39: VKH2 -( pIX_VKH2; ; + _I40: VKH2 -( pX_VKH2; ; + _I41: VKH2 -( pPC_VKH2; ; + _I42: VKH2 -( pPS_VKH2; ; + // Events: clottingTime_event: at (Integral_Fibrin*3600) > 1500: clottingTime_s = time*3600; dilution_event: at time > 0: compartment_1 = compartment_1*3; @@ -445,112 +490,208 @@ model *Model_1() c45.sboTerm = 36 c46.sboTerm = 36 d_VK.sboTerm = 35 + r1_.kineticLaw.sboTerm = 28 r1__v.sboTerm = 25 r1__k.sboTerm = 371 + r2_.kineticLaw.sboTerm = 28 r2__v.sboTerm = 25 r2__k.sboTerm = 371 + r3_.kineticLaw.sboTerm = 28 r3__v.sboTerm = 25 r3__k.sboTerm = 371 + r4_.kineticLaw.sboTerm = 28 r4__v.sboTerm = 25 r4__k.sboTerm = 371 + r5_.kineticLaw.sboTerm = 28 r5__v.sboTerm = 25 r5__k.sboTerm = 371 + r6_.kineticLaw.sboTerm = 28 r6__v.sboTerm = 25 r6__k.sboTerm = 371 + r7_.kineticLaw.sboTerm = 28 r7__v.sboTerm = 25 r7__k.sboTerm = 371 + r8_.kineticLaw.sboTerm = 28 r8__v.sboTerm = 25 r8__k.sboTerm = 371 + r9_.kineticLaw.sboTerm = 28 r9__v.sboTerm = 25 r9__k.sboTerm = 371 + r10.kineticLaw.sboTerm = 28 r10_v.sboTerm = 25 r10_k.sboTerm = 371 + r11.kineticLaw.sboTerm = 28 r11_v.sboTerm = 25 r11_k.sboTerm = 371 + r12.kineticLaw.sboTerm = 28 r12_v.sboTerm = 25 r12_k.sboTerm = 371 + r13.kineticLaw.sboTerm = 28 r13_v.sboTerm = 25 r13_k.sboTerm = 371 + r14.kineticLaw.sboTerm = 28 r14_v.sboTerm = 25 r14_k.sboTerm = 371 + r15.kineticLaw.sboTerm = 28 r15_v.sboTerm = 25 r15_k.sboTerm = 371 + r16.kineticLaw.sboTerm = 28 r16_v.sboTerm = 25 r16_k.sboTerm = 371 + r17.kineticLaw.sboTerm = 28 r17_v.sboTerm = 25 r17_k.sboTerm = 371 + r18.kineticLaw.sboTerm = 28 r18_v.sboTerm = 25 r18_k.sboTerm = 371 + r19.kineticLaw.sboTerm = 28 r19_v.sboTerm = 25 r19_k.sboTerm = 371 + r20.kineticLaw.sboTerm = 28 r20_v.sboTerm = 25 r20_k.sboTerm = 371 + r21.kineticLaw.sboTerm = 28 r21_v.sboTerm = 25 r21_k.sboTerm = 371 + r22.kineticLaw.sboTerm = 28 r22_v.sboTerm = 25 r22_k.sboTerm = 371 + r23.kineticLaw.sboTerm = 28 r23_v.sboTerm = 25 r23_k.sboTerm = 371 + r24.kineticLaw.sboTerm = 28 r24_v.sboTerm = 25 r24_k.sboTerm = 371 + r25.kineticLaw.sboTerm = 28 r25_v.sboTerm = 25 r25_k.sboTerm = 371 + r26.kineticLaw.sboTerm = 28 r26_c.sboTerm = 36 + r27.kineticLaw.sboTerm = 28 r27_c.sboTerm = 36 + r28.kineticLaw.sboTerm = 28 r28_c.sboTerm = 36 + r29.kineticLaw.sboTerm = 28 r29_c.sboTerm = 36 + r30.kineticLaw.sboTerm = 28 r30_c.sboTerm = 36 + r31.kineticLaw.sboTerm = 28 r31_c.sboTerm = 36 + r32.kineticLaw.sboTerm = 28 r32_c.sboTerm = 36 + r33.kineticLaw.sboTerm = 28 r33_v.sboTerm = 25 r33_k.sboTerm = 371 + r34.kineticLaw.sboTerm = 28 r34_v.sboTerm = 25 r34_k.sboTerm = 371 + r35.kineticLaw.sboTerm = 28 r35_v.sboTerm = 25 r35_k.sboTerm = 371 + r36.kineticLaw.sboTerm = 28 r36_v.sboTerm = 25 r36_k.sboTerm = 371 + r37.kineticLaw.sboTerm = 28 r37_c.sboTerm = 36 + r38.kineticLaw.sboTerm = 28 r38_v.sboTerm = 25 r38_k.sboTerm = 371 + r39.kineticLaw.sboTerm = 28 r39_v.sboTerm = 25 r39_k.sboTerm = 371 + r40.kineticLaw.sboTerm = 28 r40_v.sboTerm = 25 r40_k.sboTerm = 371 + r41.kineticLaw.sboTerm = 28 r41_v.sboTerm = 25 r41_k.sboTerm = 371 + r42.kineticLaw.sboTerm = 28 r42_v.sboTerm = 25 r42_k.sboTerm = 371 + r43.kineticLaw.sboTerm = 28 r43_v.sboTerm = 25 r43_k.sboTerm = 371 + r44.kineticLaw.sboTerm = 28 + r45.kineticLaw.sboTerm = 28 + r46.kineticLaw.sboTerm = 28 + dFg.kineticLaw.sboTerm = 49 + dF.kineticLaw.sboTerm = 49 dF_k1.sboTerm = 35 + dXF.kineticLaw.sboTerm = 49 dXF_k1.sboTerm = 35 + dII.kineticLaw.sboTerm = 49 + dIIa.kineticLaw.sboTerm = 49 dIIa_k1.sboTerm = 35 + dTF.kineticLaw.sboTerm = 49 dTF_k1.sboTerm = 35 + dV.kineticLaw.sboTerm = 49 + dVa.kineticLaw.sboTerm = 49 dVa_k1.sboTerm = 35 + dVII.kineticLaw.sboTerm = 49 + dVIIa.kineticLaw.sboTerm = 49 dVIIa_k1.sboTerm = 35 + dVIII.kineticLaw.sboTerm = 49 + dVIIIa.kineticLaw.sboTerm = 49 dVIIIa_k1.sboTerm = 35 + dX.kineticLaw.sboTerm = 49 + dXa.kineticLaw.sboTerm = 49 dXa_k1.sboTerm = 35 + dIX.kineticLaw.sboTerm = 49 + dIXa.kineticLaw.sboTerm = 49 dIXa_k1.sboTerm = 35 + dXII.kineticLaw.sboTerm = 49 + dXIIa.kineticLaw.sboTerm = 49 dXIIa_k1.sboTerm = 35 + dXIII.kineticLaw.sboTerm = 49 + dXIIIa.kineticLaw.sboTerm = 49 dXIIIa_k1.sboTerm = 35 + dPk.kineticLaw.sboTerm = 49 + dK.kineticLaw.sboTerm = 49 dK_k1.sboTerm = 35 + dPg.kineticLaw.sboTerm = 49 + dP.kineticLaw.sboTerm = 49 dP_k1.sboTerm = 35 + dPC.kineticLaw.sboTerm = 49 + dAPC.kineticLaw.sboTerm = 49 dAPC_k1.sboTerm = 35 + dPS.kineticLaw.sboTerm = 49 + dFDP.kineticLaw.sboTerm = 49 dFDP_k1.sboTerm = 35 + dD.kineticLaw.sboTerm = 49 dD_k1.sboTerm = 35 + dTFPI.kineticLaw.sboTerm = 49 + dVIIa_TF.kineticLaw.sboTerm = 49 dVIIa_TF_k1.sboTerm = 35 + dVII_TF.kineticLaw.sboTerm = 49 dVII_TF_k1.sboTerm = 35 + dAPC_PS.kineticLaw.sboTerm = 49 dAPC_PS_k1.sboTerm = 35 + dVa_Xa.kineticLaw.sboTerm = 49 dVa_Xa_k1.sboTerm = 35 + dIXa_VIIIa.kineticLaw.sboTerm = 49 dIXa_VIIIa_k1.sboTerm = 35 + dTmod.kineticLaw.sboTerm = 49 + dIIa_Tmod.kineticLaw.sboTerm = 49 dIIa_Tmod_k1.sboTerm = 35 + dXa_TFPI.kineticLaw.sboTerm = 49 dXa_TFPI_k1.sboTerm = 35 + dVIIa_TF_Xa_TFPI.kineticLaw.sboTerm = 49 dVIIa_TF_Xa_TFPI_k1.sboTerm = 35 + dTAT.kineticLaw.sboTerm = 49 dTAT_k1.sboTerm = 35 + dCA.kineticLaw.sboTerm = 49 dCA_k1.sboTerm = 35 + dXIa.kineticLaw.sboTerm = 49 dXIa_k1.sboTerm = 35 + dVKH2.kineticLaw.sboTerm = 49 + VK_transport.kineticLaw.sboTerm = 80 + eHeparin.kineticLaw.sboTerm = 49 + eHeparinXa.kineticLaw.sboTerm = 49 + eHeparinIXa.kineticLaw.sboTerm = 49 + eHeparinIIa.kineticLaw.sboTerm = 49 + dXI.kineticLaw.sboTerm = 49 dXI_k1.sboTerm = 35 + dVK.kineticLaw.sboTerm = 49 // CV terms: IIa isVersionOf "http://identifiers.org/uniprot/P00734" diff --git a/doc/examples/biomodels/BIOMD0000000340_url.txt b/doc/examples/biomodels/BIOMD0000000340/BIOMD0000000340_url.txt similarity index 85% rename from doc/examples/biomodels/BIOMD0000000340_url.txt rename to doc/examples/biomodels/BIOMD0000000340/BIOMD0000000340_url.txt index 13f05d6a2..a0e88c6f2 100644 --- a/doc/examples/biomodels/BIOMD0000000340_url.txt +++ b/doc/examples/biomodels/BIOMD0000000340/BIOMD0000000340_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: @@ -147,6 +147,51 @@ model *Model_1() dVK: VK => ; compartment_1*d_VK*VK; pHeparin: => ATIII_Heparin; compartment_1*heparin_infusion; + // Interactions: + _I0: IIa -o r1_; ; + _I1: APC_PS -o r2_; ; + _I2: XIa -o r3_; ; + _I3: XIIa -o r4_; ; + _I4: IIa -o r5_; ; + _I5: IIa -o r6_; ; + _I6: IXa -o r7_; ; + _I7: IXa_VIIIa -o r8_; ; + _I8: VIIa -o r9_; ; + _I9: IIa -o r10; ; + _I10: APC_PS -o r11; ; + _I11: Va_Xa -o r12; ; + _I12: Xa -o r13; ; + _I13: IIa -o r14; ; + _I14: P -o r15; ; + _I15: XIIIa -o r16; ; + _I16: P -o r17; ; + _I17: P -o r18; ; + _I18: APC_PS -o r19; ; + _I19: IIa -o r20; ; + _I20: IIa -o r21; ; + _I21: F -o r22; ; + _I22: APC_PS -o r23; ; + _I23: IIa_Tmod -o r24; ; + _I24: APC_PS -o r25; ; + _I25: Xa -o r33; ; + _I26: VIIa_TF -o r34; ; + _I27: VIIa_TF -o r35; ; + _I28: TF -o r36; ; + _I29: Xa -o r38; ; + _I30: VIIa_TF -o r39; ; + _I31: IXa -o r40; ; + _I32: CA -o r41; ; + _I33: K -o r42; ; + _I34: XIIa -o r43; ; + _I35: $C_warf -( r47; ; + _I36: $C_warf -( r48; ; + _I37: VKH2 -( pII_VKH2; ; + _I38: VKH2 -( pVII_VKH2; ; + _I39: VKH2 -( pIX_VKH2; ; + _I40: VKH2 -( pX_VKH2; ; + _I41: VKH2 -( pPC_VKH2; ; + _I42: VKH2 -( pPS_VKH2; ; + // Events: warfarin_administration: at (time%24) > 1: A_warf = A_warf + warfarin_daily_dose; heparin_administration: at time > heparin_infusion_duration_hr: heparin_infusion = 0; @@ -447,112 +492,209 @@ model *Model_1() c45.sboTerm = 36 c46.sboTerm = 36 d_VK.sboTerm = 35 + r1_.kineticLaw.sboTerm = 28 r1__v.sboTerm = 25 r1__k.sboTerm = 371 + r2_.kineticLaw.sboTerm = 28 r2__v.sboTerm = 25 r2__k.sboTerm = 371 + r3_.kineticLaw.sboTerm = 28 r3__v.sboTerm = 25 r3__k.sboTerm = 371 + r4_.kineticLaw.sboTerm = 28 r4__v.sboTerm = 25 r4__k.sboTerm = 371 + r5_.kineticLaw.sboTerm = 28 r5__v.sboTerm = 25 r5__k.sboTerm = 371 + r6_.kineticLaw.sboTerm = 28 r6__v.sboTerm = 25 r6__k.sboTerm = 371 + r7_.kineticLaw.sboTerm = 28 r7__v.sboTerm = 25 r7__k.sboTerm = 371 + r8_.kineticLaw.sboTerm = 28 r8__v.sboTerm = 25 r8__k.sboTerm = 371 + r9_.kineticLaw.sboTerm = 28 r9__v.sboTerm = 25 r9__k.sboTerm = 371 + r10.kineticLaw.sboTerm = 28 r10_v.sboTerm = 25 r10_k.sboTerm = 371 + r11.kineticLaw.sboTerm = 28 r11_v.sboTerm = 25 r11_k.sboTerm = 371 + r12.kineticLaw.sboTerm = 28 r12_v.sboTerm = 25 r12_k.sboTerm = 371 + r13.kineticLaw.sboTerm = 28 r13_v.sboTerm = 25 r13_k.sboTerm = 371 + r14.kineticLaw.sboTerm = 28 r14_v.sboTerm = 25 r14_k.sboTerm = 371 + r15.kineticLaw.sboTerm = 28 r15_v.sboTerm = 25 r15_k.sboTerm = 371 + r16.kineticLaw.sboTerm = 28 r16_v.sboTerm = 25 r16_k.sboTerm = 371 + r17.kineticLaw.sboTerm = 28 r17_v.sboTerm = 25 r17_k.sboTerm = 371 + r18.kineticLaw.sboTerm = 28 r18_v.sboTerm = 25 r18_k.sboTerm = 371 + r19.kineticLaw.sboTerm = 28 r19_v.sboTerm = 25 r19_k.sboTerm = 371 + r20.kineticLaw.sboTerm = 28 r20_v.sboTerm = 25 r20_k.sboTerm = 371 + r21.kineticLaw.sboTerm = 28 r21_v.sboTerm = 25 r21_k.sboTerm = 371 + r22.kineticLaw.sboTerm = 28 r22_v.sboTerm = 25 r22_k.sboTerm = 371 + r23.kineticLaw.sboTerm = 28 r23_v.sboTerm = 25 r23_k.sboTerm = 371 + r24.kineticLaw.sboTerm = 28 r24_v.sboTerm = 25 r24_k.sboTerm = 371 + r25.kineticLaw.sboTerm = 28 r25_v.sboTerm = 25 r25_k.sboTerm = 371 + r26.kineticLaw.sboTerm = 28 r26_c.sboTerm = 36 + r27.kineticLaw.sboTerm = 28 r27_c.sboTerm = 36 + r28.kineticLaw.sboTerm = 28 r28_c.sboTerm = 36 + r29.kineticLaw.sboTerm = 28 r29_c.sboTerm = 36 + r30.kineticLaw.sboTerm = 28 r30_c.sboTerm = 36 + r31.kineticLaw.sboTerm = 28 r31_c.sboTerm = 36 + r32.kineticLaw.sboTerm = 28 r32_c.sboTerm = 36 + r33.kineticLaw.sboTerm = 28 r33_v.sboTerm = 25 r33_k.sboTerm = 371 + r34.kineticLaw.sboTerm = 28 r34_v.sboTerm = 25 r34_k.sboTerm = 371 + r35.kineticLaw.sboTerm = 28 r35_v.sboTerm = 25 r35_k.sboTerm = 371 + r36.kineticLaw.sboTerm = 28 r36_v.sboTerm = 25 r36_k.sboTerm = 371 + r37.kineticLaw.sboTerm = 28 r37_c.sboTerm = 36 + r38.kineticLaw.sboTerm = 28 r38_v.sboTerm = 25 r38_k.sboTerm = 371 + r39.kineticLaw.sboTerm = 28 r39_v.sboTerm = 25 r39_k.sboTerm = 371 + r40.kineticLaw.sboTerm = 28 r40_v.sboTerm = 25 r40_k.sboTerm = 371 + r41.kineticLaw.sboTerm = 28 r41_v.sboTerm = 25 r41_k.sboTerm = 371 + r42.kineticLaw.sboTerm = 28 r42_v.sboTerm = 25 r42_k.sboTerm = 371 + r43.kineticLaw.sboTerm = 28 r43_v.sboTerm = 25 r43_k.sboTerm = 371 + r44.kineticLaw.sboTerm = 28 + r45.kineticLaw.sboTerm = 28 + r46.kineticLaw.sboTerm = 28 + dFg.kineticLaw.sboTerm = 49 + dF.kineticLaw.sboTerm = 49 dF_k1.sboTerm = 35 + dXF.kineticLaw.sboTerm = 49 dXF_k1.sboTerm = 35 + dII.kineticLaw.sboTerm = 49 + dIIa.kineticLaw.sboTerm = 49 dIIa_k1.sboTerm = 35 + dTF.kineticLaw.sboTerm = 49 dTF_k1.sboTerm = 35 + dV.kineticLaw.sboTerm = 49 + dVa.kineticLaw.sboTerm = 49 dVa_k1.sboTerm = 35 + dVII.kineticLaw.sboTerm = 49 + dVIIa.kineticLaw.sboTerm = 49 dVIIa_k1.sboTerm = 35 + dVIII.kineticLaw.sboTerm = 49 + dVIIIa.kineticLaw.sboTerm = 49 dVIIIa_k1.sboTerm = 35 + dX.kineticLaw.sboTerm = 49 + dXa.kineticLaw.sboTerm = 49 dXa_k1.sboTerm = 35 + dIX.kineticLaw.sboTerm = 49 + dIXa.kineticLaw.sboTerm = 49 dIXa_k1.sboTerm = 35 + dXII.kineticLaw.sboTerm = 49 + dXIIa.kineticLaw.sboTerm = 49 dXIIa_k1.sboTerm = 35 + dXIII.kineticLaw.sboTerm = 49 + dXIIIa.kineticLaw.sboTerm = 49 dXIIIa_k1.sboTerm = 35 + dPk.kineticLaw.sboTerm = 49 + dK.kineticLaw.sboTerm = 49 dK_k1.sboTerm = 35 + dPg.kineticLaw.sboTerm = 49 + dP.kineticLaw.sboTerm = 49 dP_k1.sboTerm = 35 + dPC.kineticLaw.sboTerm = 49 + dAPC.kineticLaw.sboTerm = 49 dAPC_k1.sboTerm = 35 + dPS.kineticLaw.sboTerm = 49 + dFDP.kineticLaw.sboTerm = 49 dFDP_k1.sboTerm = 35 + dD.kineticLaw.sboTerm = 49 dD_k1.sboTerm = 35 + dTFPI.kineticLaw.sboTerm = 49 + dVIIa_TF.kineticLaw.sboTerm = 49 dVIIa_TF_k1.sboTerm = 35 + dVII_TF.kineticLaw.sboTerm = 49 dVII_TF_k1.sboTerm = 35 + dAPC_PS.kineticLaw.sboTerm = 49 dAPC_PS_k1.sboTerm = 35 + dVa_Xa.kineticLaw.sboTerm = 49 dVa_Xa_k1.sboTerm = 35 + dIXa_VIIIa.kineticLaw.sboTerm = 49 dIXa_VIIIa_k1.sboTerm = 35 + dTmod.kineticLaw.sboTerm = 49 + dIIa_Tmod.kineticLaw.sboTerm = 49 dIIa_Tmod_k1.sboTerm = 35 + dXa_TFPI.kineticLaw.sboTerm = 49 dXa_TFPI_k1.sboTerm = 35 + dVIIa_TF_Xa_TFPI.kineticLaw.sboTerm = 49 dVIIa_TF_Xa_TFPI_k1.sboTerm = 35 + dTAT.kineticLaw.sboTerm = 49 dTAT_k1.sboTerm = 35 + dCA.kineticLaw.sboTerm = 49 dCA_k1.sboTerm = 35 + dXIa.kineticLaw.sboTerm = 49 dXIa_k1.sboTerm = 35 + dVKH2.kineticLaw.sboTerm = 49 + VK_transport.kineticLaw.sboTerm = 80 + eHeparin.kineticLaw.sboTerm = 49 + eHeparinXa.kineticLaw.sboTerm = 49 + eHeparinIXa.kineticLaw.sboTerm = 49 + eHeparinIIa.kineticLaw.sboTerm = 49 + dXI.kineticLaw.sboTerm = 49 dXI_k1.sboTerm = 35 + dVK.kineticLaw.sboTerm = 49 + pHeparin.kineticLaw.sboTerm = 47 // CV terms: IIa isVersionOf "http://identifiers.org/uniprot/P00734" diff --git a/doc/examples/biomodels/BIOMD0000000341_url.txt b/doc/examples/biomodels/BIOMD0000000341/BIOMD0000000341_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000341_url.txt rename to doc/examples/biomodels/BIOMD0000000341/BIOMD0000000341_url.txt index 87656e46f..268c78c12 100644 --- a/doc/examples/biomodels/BIOMD0000000341_url.txt +++ b/doc/examples/biomodels/BIOMD0000000341/BIOMD0000000341_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Topp2000_BetaCellMass_Diabetes() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000342_url.txt b/doc/examples/biomodels/BIOMD0000000342/BIOMD0000000342_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000342_url.txt rename to doc/examples/biomodels/BIOMD0000000342/BIOMD0000000342_url.txt index 642a1913d..61b4078aa 100644 --- a/doc/examples/biomodels/BIOMD0000000342_url.txt +++ b/doc/examples/biomodels/BIOMD0000000342/BIOMD0000000342_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zi2011_TGFbeta_Pathway() // Compartments and Species: diff --git a/doc/examples/biomodels/Zi2011_fig1Cred.txt b/doc/examples/biomodels/BIOMD0000000342/Zi2011_fig1Cred.txt similarity index 99% rename from doc/examples/biomodels/Zi2011_fig1Cred.txt rename to doc/examples/biomodels/BIOMD0000000342/Zi2011_fig1Cred.txt index 927dbd254..6805f777d 100644 --- a/doc/examples/biomodels/Zi2011_fig1Cred.txt +++ b/doc/examples/biomodels/BIOMD0000000342/Zi2011_fig1Cred.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zi2011_TGFbeta_Pathway() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000343_url.txt b/doc/examples/biomodels/BIOMD0000000343/BIOMD0000000343_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000343_url.txt rename to doc/examples/biomodels/BIOMD0000000343/BIOMD0000000343_url.txt index 4da0ca7f9..10eb1f416 100644 --- a/doc/examples/biomodels/BIOMD0000000343_url.txt +++ b/doc/examples/biomodels/BIOMD0000000343/BIOMD0000000343_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model01() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000343_withevent.txt b/doc/examples/biomodels/BIOMD0000000343/BIOMD0000000343_withevent.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000343_withevent.txt rename to doc/examples/biomodels/BIOMD0000000343/BIOMD0000000343_withevent.txt index be28a4670..cef812ff6 100644 --- a/doc/examples/biomodels/BIOMD0000000343_withevent.txt +++ b/doc/examples/biomodels/BIOMD0000000343/BIOMD0000000343_withevent.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Brannmark2010_InsulinSignalling_Mifamodel_Fig5D() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000344_url.txt b/doc/examples/biomodels/BIOMD0000000344/BIOMD0000000344_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000344_url.txt rename to doc/examples/biomodels/BIOMD0000000344/BIOMD0000000344_url.txt index 5dd1e2962..1a636196c 100644 --- a/doc/examples/biomodels/BIOMD0000000344_url.txt +++ b/doc/examples/biomodels/BIOMD0000000344/BIOMD0000000344_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hsp70Model() // Compartments and Species: @@ -363,7 +363,7 @@ model *Hsp70Model() kbinCHIP.sboTerm = 9 krelCHIP.sboTerm = 9 ksynMkp1.sboTerm = 9 - kbinMkp1Prot.sboTerm = 9 + kbinMkp1Prot.sboTerm = 9 kdegMkp1.sboTerm = 9 kphosMkp1.sboTerm = 9 kdephosMkp1.sboTerm = 9 diff --git a/doc/examples/biomodels/MODEL1005280000_highstress.txt b/doc/examples/biomodels/BIOMD0000000344/MODEL1005280000_highstress.txt similarity index 99% rename from doc/examples/biomodels/MODEL1005280000_highstress.txt rename to doc/examples/biomodels/BIOMD0000000344/MODEL1005280000_highstress.txt index 2034b33d8..5b07da4c8 100644 --- a/doc/examples/biomodels/MODEL1005280000_highstress.txt +++ b/doc/examples/biomodels/BIOMD0000000344/MODEL1005280000_highstress.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hsp70Model() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1005280000_moderatestress.txt b/doc/examples/biomodels/BIOMD0000000344/MODEL1005280000_moderatestress.txt similarity index 99% rename from doc/examples/biomodels/MODEL1005280000_moderatestress.txt rename to doc/examples/biomodels/BIOMD0000000344/MODEL1005280000_moderatestress.txt index 02af7be2a..d7481f7eb 100644 --- a/doc/examples/biomodels/MODEL1005280000_moderatestress.txt +++ b/doc/examples/biomodels/BIOMD0000000344/MODEL1005280000_moderatestress.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hsp70Model() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000345_url.txt b/doc/examples/biomodels/BIOMD0000000345/BIOMD0000000345_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000345_url.txt rename to doc/examples/biomodels/BIOMD0000000345/BIOMD0000000345_url.txt index 9a98dad66..e3893182b 100644 --- a/doc/examples/biomodels/BIOMD0000000345_url.txt +++ b/doc/examples/biomodels/BIOMD0000000345/BIOMD0000000345_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Koschorreck2008_InsulinClearance() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000346_url.txt b/doc/examples/biomodels/BIOMD0000000346/BIOMD0000000346_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000346_url.txt rename to doc/examples/biomodels/BIOMD0000000346/BIOMD0000000346_url.txt index 256da9ee9..cfff14796 100644 --- a/doc/examples/biomodels/BIOMD0000000346_url.txt +++ b/doc/examples/biomodels/BIOMD0000000346/BIOMD0000000346_url.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *FitzHugh1961_NerveMembrane() // Compartments and Species: compartment compartment_; - species $x in compartment_, $y in compartment_; + species x in compartment_, y in compartment_; // Rate Rules: x' = c*(x + -(x^3/3) + y + z); diff --git a/doc/examples/biomodels/BIOMD0000000347_url.txt b/doc/examples/biomodels/BIOMD0000000347/BIOMD0000000347_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000347_url.txt rename to doc/examples/biomodels/BIOMD0000000347/BIOMD0000000347_url.txt index 0445f9c0d..f22b10642 100644 --- a/doc/examples/biomodels/BIOMD0000000347_url.txt +++ b/doc/examples/biomodels/BIOMD0000000347/BIOMD0000000347_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bachmann2011_JAK2STAT5_FeedbackControl() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000348_url.txt b/doc/examples/biomodels/BIOMD0000000348/BIOMD0000000348_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000348_url.txt rename to doc/examples/biomodels/BIOMD0000000348/BIOMD0000000348_url.txt index 170819200..b0ef41531 100644 --- a/doc/examples/biomodels/BIOMD0000000348_url.txt +++ b/doc/examples/biomodels/BIOMD0000000348/BIOMD0000000348_url.txt @@ -1,11 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Fridlyand2010_GlucoseSensitivity_A() // Compartments and Species: compartment compartment_; - species $G3P in compartment_, $PYR in compartment_, $ATP in compartment_; - species $NADHm in compartment_, $NADHc in compartment_, $Vm in compartment_; - species $Cam in compartment_; + species G3P in compartment_, PYR in compartment_, ATP in compartment_, NADHm in compartment_; + species NADHc in compartment_, Vm in compartment_, Cam in compartment_; // Assignment Rules: JGlu := Vmglu*Glu^hgl*ATP*(1/(Kmgl^hgl + Glu^hgl))*(1/(KmATP + ATP)); diff --git a/doc/examples/biomodels/BIOMD0000000349_url.txt b/doc/examples/biomodels/BIOMD0000000349/BIOMD0000000349_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000349_url.txt rename to doc/examples/biomodels/BIOMD0000000349/BIOMD0000000349_url.txt index 47f64a35b..48428c73c 100644 --- a/doc/examples/biomodels/BIOMD0000000349_url.txt +++ b/doc/examples/biomodels/BIOMD0000000349/BIOMD0000000349_url.txt @@ -1,11 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Fridlyand2010_GlucoseSensitivity_B() // Compartments and Species: compartment compartment_; - species $G3P in compartment_, $PYR in compartment_, $ATP in compartment_; - species $NADHm in compartment_, $NADHc in compartment_, $Vm in compartment_; - species $Cam in compartment_; + species G3P in compartment_, PYR in compartment_, ATP in compartment_, NADHm in compartment_; + species NADHc in compartment_, Vm in compartment_, Cam in compartment_; // Assignment Rules: JGlu := Vmglu*Glu^hgl*ATP*(1/(Kmgl^hgl + Glu^hgl))*(1/(KmATP + ATP)); diff --git a/doc/examples/biomodels/BIOMD0000000350_url.txt b/doc/examples/biomodels/BIOMD0000000350/BIOMD0000000350_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000350_url.txt rename to doc/examples/biomodels/BIOMD0000000350/BIOMD0000000350_url.txt index 6ffd145f5..fb7d3c266 100644 --- a/doc/examples/biomodels/BIOMD0000000350_url.txt +++ b/doc/examples/biomodels/BIOMD0000000350/BIOMD0000000350_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000351_url.txt b/doc/examples/biomodels/BIOMD0000000351/BIOMD0000000351_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000351_url.txt rename to doc/examples/biomodels/BIOMD0000000351/BIOMD0000000351_url.txt index 99ab78923..2c4eca6c2 100644 --- a/doc/examples/biomodels/BIOMD0000000351_url.txt +++ b/doc/examples/biomodels/BIOMD0000000351/BIOMD0000000351_url.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Vernoux2011_AuxinSignalling_AuxinSingleStepInput() // Compartments and Species: compartment compartment_0000001; species I in compartment_0000001, A in compartment_0000001, D_II in compartment_0000001; - species D_IA in compartment_0000001, R in compartment_0000001, $aux in compartment_0000001; + species D_IA in compartment_0000001, R in compartment_0000001, aux in compartment_0000001; // Assignment Rules: aux := piecewise(5, time > 1000, 0); diff --git a/doc/examples/biomodels/BIOMD0000000352_url.txt b/doc/examples/biomodels/BIOMD0000000352/BIOMD0000000352_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000352_url.txt rename to doc/examples/biomodels/BIOMD0000000352/BIOMD0000000352_url.txt index 12710c17d..f780c6517 100644 --- a/doc/examples/biomodels/BIOMD0000000352_url.txt +++ b/doc/examples/biomodels/BIOMD0000000352/BIOMD0000000352_url.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Vernoux2011_AuxinSignalling_AuxinFluctuating() // Compartments and Species: compartment compartment_0000001; species I in compartment_0000001, A in compartment_0000001, D_II in compartment_0000001; - species D_IA in compartment_0000001, R in compartment_0000001, $aux in compartment_0000001; + species D_IA in compartment_0000001, R in compartment_0000001, aux in compartment_0000001; // Assignment Rules: aux := 1.11*sin((2*3.1416/800)*(time - 200)) + 1.11; diff --git a/doc/examples/biomodels/BIOMD0000000353_url.txt b/doc/examples/biomodels/BIOMD0000000353/BIOMD0000000353_url.txt similarity index 96% rename from doc/examples/biomodels/BIOMD0000000353_url.txt rename to doc/examples/biomodels/BIOMD0000000353/BIOMD0000000353_url.txt index d64b17dd0..e7f5a06a2 100644 --- a/doc/examples/biomodels/BIOMD0000000353_url.txt +++ b/doc/examples/biomodels/BIOMD0000000353/BIOMD0000000353_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Nag2011_ChloroplasticStarchDegradation() // Compartments and Species: @@ -40,60 +40,60 @@ model *Nag2011_ChloroplasticStarchDegradation() // Species initializations: cpd_C00080_CY = 1.579698e-13; - cpd_C00080_CY has substance_per_volume; - cpd_C00369_CS has substance_per_volume; + cpd_C00080_CY has substance; + cpd_C00369_CS has substance; cpd_C00369Glc_CS = 3.534e-10; - cpd_C00369Glc_CS has substance_per_volume; + cpd_C00369Glc_CS has substance; cpd_C00369db_CS = 0; - cpd_C00369db_CS has substance_per_volume; + cpd_C00369db_CS has substance; ec_3_2_1_68_CS = 4.17012e-15; - ec_3_2_1_68_CS has substance_per_volume; + ec_3_2_1_68_CS has substance; cpd_C00208_CY = 1.579698e-11; - cpd_C00208_CY has substance_per_volume; + cpd_C00208_CY has substance; cpd_C00208_CS = 3.534e-12; - cpd_C00208_CS has substance_per_volume; + cpd_C00208_CS has substance; cpd_C01835_CS = 3.534e-11; - cpd_C01835_CS has substance_per_volume; + cpd_C01835_CS has substance; cpd_G00343_CS = 3.534e-10; - cpd_G00343_CS has substance_per_volume; + cpd_G00343_CS has substance; cpd_C00031_CS = 3.534e-12; - cpd_C00031_CS has substance_per_volume; + cpd_C00031_CS has substance; cpd_C00031_CY = 1.579698e-11; - cpd_C00031_CY has substance_per_volume; + cpd_C00031_CY has substance; cpd_C00569_CY = 1.579698e-08; - cpd_C00569_CY has substance_per_volume; + cpd_C00569_CY has substance; cpd_C00569Glc_CY = 1.579698e-08; - cpd_C00569Glc_CY has substance_per_volume; + cpd_C00569Glc_CY has substance; cpd_C00002tot_CY = 1.579698e-08; - cpd_C00002tot_CY has substance_per_volume; + cpd_C00002tot_CY has substance; cpd_C00008tot_CY = 1.579698e-08; - cpd_C00008tot_CY has substance_per_volume; + cpd_C00008tot_CY has substance; cpd_C00009tot_CY = 1.579698e-08; - cpd_C00009tot_CY has substance_per_volume; + cpd_C00009tot_CY has substance; cpd_C00051_CY = 1.579698e-09; - cpd_C00051_CY has substance_per_volume; + cpd_C00051_CY has substance; cpd_C00660tot_CY = 1.579698e-08; - cpd_C00660tot_CY has substance_per_volume; + cpd_C00660tot_CY has substance; cpd_C03339tot_CY = 1.579698e-08; - cpd_C03339tot_CY has substance_per_volume; + cpd_C03339tot_CY has substance; cpd_C00103tot_CY = 1.579698e-08; - cpd_C00103tot_CY has substance_per_volume; + cpd_C00103tot_CY has substance; cpd_C00092tot_CY = 1.579698e-08; - cpd_C00092tot_CY has substance_per_volume; + cpd_C00092tot_CY has substance; ec_3_2_1_2_CS = 2.767122e-15; - ec_3_2_1_2_CS has substance_per_volume; + ec_3_2_1_2_CS has substance; ec_2_4_1_25_CS = 7.068e-13; - ec_2_4_1_25_CS has substance_per_volume; + ec_2_4_1_25_CS has substance; ec_2_4_1_25_CY = 3.159396e-12; - ec_2_4_1_25_CY has substance_per_volume; + ec_2_4_1_25_CY has substance; ec_2_4_1_1_CY = 3.159396e-12; - ec_2_4_1_1_CY has substance_per_volume; + ec_2_4_1_1_CY has substance; ec_2_7_1_1_CY = 1.579698e-11; - ec_2_7_1_1_CY has substance_per_volume; + ec_2_7_1_1_CY has substance; tc_2_A_84_1_2_CIMS = 1.4136e-14; - tc_2_A_84_1_2_CIMS has substance_per_volume; + tc_2_A_84_1_2_CIMS has substance; tc_2_A_1_1_17_CIMS = 1.4136e-13; - tc_2_A_1_1_17_CIMS has substance_per_volume; + tc_2_A_1_1_17_CIMS has substance; // Compartment initializations: Cell = 3.534e-12; @@ -259,7 +259,7 @@ model *Nag2011_ChloroplasticStarchDegradation() unit length = metre; unit area = (1e-6 metre)^2; unit volume = litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = mole; unit unit_0 = gram / ((1e-6 dimensionless)^-0 * mole); unit unit_1 = 1 / dimensionless^-0; @@ -268,7 +268,7 @@ model *Nag2011_ChloroplasticStarchDegradation() unit unit_4 = gram / litre; unit unit_5 = gram^2 / litre^2; unit extent = substance; - unit substance_per_volume = mole / litre; + unit substance_volume = mole * litre; // Display Names: time_unit is "time"; diff --git a/doc/examples/biomodels/BIOMD0000000354_url.txt b/doc/examples/biomodels/BIOMD0000000354/BIOMD0000000354_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000354_url.txt rename to doc/examples/biomodels/BIOMD0000000354/BIOMD0000000354_url.txt index c2ca61fc7..63ba35f31 100644 --- a/doc/examples/biomodels/BIOMD0000000354_url.txt +++ b/doc/examples/biomodels/BIOMD0000000354/BIOMD0000000354_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Abell2011_CalciumSignaling_WithoutAdaptation() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000355_url.txt b/doc/examples/biomodels/BIOMD0000000355/BIOMD0000000355_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000355_url.txt rename to doc/examples/biomodels/BIOMD0000000355/BIOMD0000000355_url.txt index 0852ab579..304c771b7 100644 --- a/doc/examples/biomodels/BIOMD0000000355_url.txt +++ b/doc/examples/biomodels/BIOMD0000000355/BIOMD0000000355_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Abell2011_CalciumSignaling_WithAdaptation() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000356_url.txt b/doc/examples/biomodels/BIOMD0000000356/BIOMD0000000356_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000356_url.txt rename to doc/examples/biomodels/BIOMD0000000356/BIOMD0000000356_url.txt index bfe728f05..f9886c19a 100644 --- a/doc/examples/biomodels/BIOMD0000000356_url.txt +++ b/doc/examples/biomodels/BIOMD0000000356/BIOMD0000000356_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Nyman2011_M3Hierarachical_InsulinGlucosedynamics() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000357_url.txt b/doc/examples/biomodels/BIOMD0000000357/BIOMD0000000357_url.txt similarity index 92% rename from doc/examples/biomodels/BIOMD0000000357_url.txt rename to doc/examples/biomodels/BIOMD0000000357/BIOMD0000000357_url.txt index 56033b02d..68750679b 100644 --- a/doc/examples/biomodels/BIOMD0000000357_url.txt +++ b/doc/examples/biomodels/BIOMD0000000357/BIOMD0000000357_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: @@ -67,6 +67,14 @@ model *Model_1() j3a.sboTerm = 38 j5.sboTerm = 38 j7a.sboTerm = 38 + r1.kineticLaw.sboTerm = 101 + r2.kineticLaw.sboTerm = 49 + r5.kineticLaw.sboTerm = 101 + r7.kineticLaw.sboTerm = 49 + r8.kineticLaw.sboTerm = 101 + r9.kineticLaw.sboTerm = 49 + r12.kineticLaw.sboTerm = 101 + r14.kineticLaw.sboTerm = 49 // CV terms: E isVersionOf "http://identifiers.org/pr/PR:000007294" diff --git a/doc/examples/biomodels/BIOMD0000000358_url.txt b/doc/examples/biomodels/BIOMD0000000358/BIOMD0000000358_url.txt similarity index 94% rename from doc/examples/biomodels/BIOMD0000000358_url.txt rename to doc/examples/biomodels/BIOMD0000000358/BIOMD0000000358_url.txt index 0eda4fd5f..a082fae18 100644 --- a/doc/examples/biomodels/BIOMD0000000358_url.txt +++ b/doc/examples/biomodels/BIOMD0000000358/BIOMD0000000358_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000358() // Compartments and Species: @@ -21,6 +21,12 @@ model *BIOMD0000000358() R7: IIa => IIa_alpha2M; compartment_1*ki_IIaAlpha2M*IIa; R8: IIa => IIa_ATIII; compartment_1*ki_IIaATIII*IIa; + // Interactions: + _I0: RVV -o R1; ; + _I1: IIa -o R4; ; + _I2: PT -o R5; ; + _I3: Xa -o R6; ; + // Species initializations: X = 81.24998; Xa = 0; @@ -79,6 +85,14 @@ model *BIOMD0000000358() km_2.sboTerm = 371 ki_IIaAlpha2M.sboTerm = 35 ki_IIaATIII.sboTerm = 35 + R1.kineticLaw.sboTerm = 28 + R2.kineticLaw.sboTerm = 49 + R3.kineticLaw.sboTerm = 122 + R4.kineticLaw.sboTerm = 28 + R5.kineticLaw.sboTerm = 28 + R6.kineticLaw.sboTerm = 28 + R7.kineticLaw.sboTerm = 49 + R8.kineticLaw.sboTerm = 49 // CV terms: X identity "http://identifiers.org/uniprot/P00742" diff --git a/doc/examples/biomodels/BIOMD0000000359_url.txt b/doc/examples/biomodels/BIOMD0000000359/BIOMD0000000359_url.txt similarity index 94% rename from doc/examples/biomodels/BIOMD0000000359_url.txt rename to doc/examples/biomodels/BIOMD0000000359/BIOMD0000000359_url.txt index d50598fd4..b27b5c824 100644 --- a/doc/examples/biomodels/BIOMD0000000359_url.txt +++ b/doc/examples/biomodels/BIOMD0000000359/BIOMD0000000359_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: @@ -62,19 +62,27 @@ model *Model_1() reaction_8 is "reaction_9"; // SBO terms: + reaction_1.kineticLaw.sboTerm = 101 reaction_1_k1.sboTerm = 36 reaction_1_k2.sboTerm = 38 + reaction_2.kineticLaw.sboTerm = 49 reaction_2_k1.sboTerm = 35 + reaction_3.kineticLaw.sboTerm = 83 reaction_3_k1.sboTerm = 35 reaction_3_k2.sboTerm = 39 + reaction_4.kineticLaw.sboTerm = 101 reaction_4_k1.sboTerm = 36 reaction_4_k2.sboTerm = 38 + reaction_5.kineticLaw.sboTerm = 101 reaction_5_k1.sboTerm = 36 reaction_5_k2.sboTerm = 38 + reaction_6.kineticLaw.sboTerm = 101 reaction_6_k1.sboTerm = 36 reaction_6_k2.sboTerm = 38 + reaction_9.kineticLaw.sboTerm = 80 reaction_9_k1.sboTerm = 35 reaction_9_k2.sboTerm = 38 + reaction_8.kineticLaw.sboTerm = 104 reaction_8_k1.sboTerm = 36 reaction_8_k2.sboTerm = 39 diff --git a/doc/examples/biomodels/BIOMD0000000360_url.txt b/doc/examples/biomodels/BIOMD0000000360/BIOMD0000000360_url.txt similarity index 93% rename from doc/examples/biomodels/BIOMD0000000360_url.txt rename to doc/examples/biomodels/BIOMD0000000360/BIOMD0000000360_url.txt index ea57e89b4..fce28c802 100644 --- a/doc/examples/biomodels/BIOMD0000000360_url.txt +++ b/doc/examples/biomodels/BIOMD0000000360/BIOMD0000000360_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: @@ -60,19 +60,27 @@ model *Model_1() compartment_ is "compartment"; // SBO terms: + reaction_1.kineticLaw.sboTerm = 101 reaction_1_k1.sboTerm = 36 reaction_1_k2.sboTerm = 38 + reaction_2.kineticLaw.sboTerm = 49 reaction_2_k1.sboTerm = 35 + reaction_3.kineticLaw.sboTerm = 83 reaction_3_k1.sboTerm = 35 reaction_3_k2.sboTerm = 39 + reaction_4.kineticLaw.sboTerm = 101 reaction_4_k1.sboTerm = 36 reaction_4_k2.sboTerm = 38 + reaction_5.kineticLaw.sboTerm = 101 reaction_5_k1.sboTerm = 36 reaction_5_k2.sboTerm = 38 + reaction_6.kineticLaw.sboTerm = 101 reaction_6_k1.sboTerm = 36 reaction_6_k2.sboTerm = 38 + reaction_7.kineticLaw.sboTerm = 83 reaction_7_k1.sboTerm = 35 reaction_7_k2.sboTerm = 39 + reaction_8.kineticLaw.sboTerm = 80 reaction_8_k1.sboTerm = 35 reaction_8_k2.sboTerm = 38 diff --git a/doc/examples/biomodels/BIOMD0000000361_url.txt b/doc/examples/biomodels/BIOMD0000000361/BIOMD0000000361_url.txt similarity index 94% rename from doc/examples/biomodels/BIOMD0000000361_url.txt rename to doc/examples/biomodels/BIOMD0000000361/BIOMD0000000361_url.txt index d3642df6f..dc6d07a73 100644 --- a/doc/examples/biomodels/BIOMD0000000361_url.txt +++ b/doc/examples/biomodels/BIOMD0000000361/BIOMD0000000361_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: @@ -50,13 +50,18 @@ model *Model_1() compartment_ is "compartment"; // SBO terms: + reaction_1.kineticLaw.sboTerm = 101 reaction_1_k1.sboTerm = 36 reaction_1_k2.sboTerm = 38 + reaction_2.kineticLaw.sboTerm = 49 reaction_2_k1.sboTerm = 35 + reaction_3.kineticLaw.sboTerm = 83 reaction_3_k1.sboTerm = 35 reaction_3_k2.sboTerm = 39 + reaction_4.kineticLaw.sboTerm = 101 reaction_4_k1.sboTerm = 36 reaction_4_k2.sboTerm = 38 + reaction_5.kineticLaw.sboTerm = 101 reaction_5_k1.sboTerm = 36 reaction_5_k2.sboTerm = 38 diff --git a/doc/examples/biomodels/BIOMD0000000362_url.txt b/doc/examples/biomodels/BIOMD0000000362/BIOMD0000000362_url.txt similarity index 91% rename from doc/examples/biomodels/BIOMD0000000362_url.txt rename to doc/examples/biomodels/BIOMD0000000362/BIOMD0000000362_url.txt index 7ec543df2..2b245f606 100644 --- a/doc/examples/biomodels/BIOMD0000000362_url.txt +++ b/doc/examples/biomodels/BIOMD0000000362/BIOMD0000000362_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: @@ -194,6 +194,39 @@ model *Model_1() k42.sboTerm = 36 k43.sboTerm = 36 k44.sboTerm = 36 + R1.kineticLaw.sboTerm = 101 + R2.kineticLaw.sboTerm = 101 + R3.kineticLaw.sboTerm = 45 + R4.kineticLaw.sboTerm = 45 + R5.kineticLaw.sboTerm = 45 + R6.kineticLaw.sboTerm = 101 + R7.kineticLaw.sboTerm = 101 + R8.kineticLaw.sboTerm = 101 + R9.kineticLaw.sboTerm = 45 + R10.kineticLaw.sboTerm = 45 + R11.kineticLaw.sboTerm = 101 + R12.kineticLaw.sboTerm = 101 + R13.kineticLaw.sboTerm = 83 + R14.kineticLaw.sboTerm = 49 + R15.kineticLaw.sboTerm = 49 + R16.kineticLaw.sboTerm = 45 + R17.kineticLaw.sboTerm = 101 + R18.kineticLaw.sboTerm = 101 + R19.kineticLaw.sboTerm = 45 + R20.kineticLaw.sboTerm = 101 + R21.kineticLaw.sboTerm = 101 + R22.kineticLaw.sboTerm = 54 + R23.kineticLaw.sboTerm = 54 + R24.kineticLaw.sboTerm = 54 + R25.kineticLaw.sboTerm = 54 + R26.kineticLaw.sboTerm = 54 + R27.kineticLaw.sboTerm = 54 + R6b.kineticLaw.sboTerm = 49 + R8b.kineticLaw.sboTerm = 49 + R12b.kineticLaw.sboTerm = 49 + R18b.kineticLaw.sboTerm = 49 + R28.kineticLaw.sboTerm = 45 + R29.kineticLaw.sboTerm = 45 // CV terms: TF identity "http://identifiers.org/uniprot/P13726" diff --git a/doc/examples/biomodels/BIOMD0000000363_url.txt b/doc/examples/biomodels/BIOMD0000000363/BIOMD0000000363_url.txt similarity index 91% rename from doc/examples/biomodels/BIOMD0000000363_url.txt rename to doc/examples/biomodels/BIOMD0000000363/BIOMD0000000363_url.txt index e59077a91..99dd8963d 100644 --- a/doc/examples/biomodels/BIOMD0000000363_url.txt +++ b/doc/examples/biomodels/BIOMD0000000363/BIOMD0000000363_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: @@ -36,9 +36,13 @@ model *Model_1() compartment_ is "compartment"; // SBO terms: + r1.kineticLaw.sboTerm = 49 r1_k1.sboTerm = 35 + r2.kineticLaw.sboTerm = 49 r2_k1.sboTerm = 35 + r3.kineticLaw.sboTerm = 49 r3_k1.sboTerm = 35 + r4.kineticLaw.sboTerm = 49 r4_k1.sboTerm = 35 // CV terms: diff --git a/doc/examples/biomodels/BIOMD0000000364_url.txt b/doc/examples/biomodels/BIOMD0000000364/BIOMD0000000364_url.txt similarity index 90% rename from doc/examples/biomodels/BIOMD0000000364_url.txt rename to doc/examples/biomodels/BIOMD0000000364/BIOMD0000000364_url.txt index 3d36644e8..764a17b10 100644 --- a/doc/examples/biomodels/BIOMD0000000364_url.txt +++ b/doc/examples/biomodels/BIOMD0000000364/BIOMD0000000364_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: @@ -106,6 +106,22 @@ model *Model_1() j5.sboTerm = 38 j7.sboTerm = 38 j7a.sboTerm = 38 + r1.kineticLaw.sboTerm = 101 + r2.kineticLaw.sboTerm = 49 + r3.kineticLaw.sboTerm = 49 + r4.kineticLaw.sboTerm = 101 + r5.kineticLaw.sboTerm = 101 + r6.kineticLaw.sboTerm = 49 + r7.kineticLaw.sboTerm = 49 + r8.kineticLaw.sboTerm = 101 + r9.kineticLaw.sboTerm = 49 + r10.kineticLaw.sboTerm = 49 + r11.kineticLaw.sboTerm = 101 + r12.kineticLaw.sboTerm = 101 + r13.kineticLaw.sboTerm = 49 + r14.kineticLaw.sboTerm = 49 + r15.kineticLaw.sboTerm = 49 + r16.kineticLaw.sboTerm = 49 // CV terms: E hasPart "http://identifiers.org/uniprot/P12259", diff --git a/doc/examples/biomodels/BIOMD0000000365_url.txt b/doc/examples/biomodels/BIOMD0000000365/BIOMD0000000365_url.txt similarity index 84% rename from doc/examples/biomodels/BIOMD0000000365_url.txt rename to doc/examples/biomodels/BIOMD0000000365/BIOMD0000000365_url.txt index d2a08116c..8b5f79d56 100644 --- a/doc/examples/biomodels/BIOMD0000000365_url.txt +++ b/doc/examples/biomodels/BIOMD0000000365/BIOMD0000000365_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: @@ -108,6 +108,38 @@ model *Model_1() k8.sboTerm = 39 k9.sboTerm = 35 k10.sboTerm = 39 + r1.kineticLaw.sboTerm = 101 + r2.kineticLaw.sboTerm = 101 + r3.kineticLaw.sboTerm = 101 + r4.kineticLaw.sboTerm = 101 + r5.kineticLaw.sboTerm = 101 + r6.kineticLaw.sboTerm = 101 + r7.kineticLaw.sboTerm = 101 + r8.kineticLaw.sboTerm = 49 + r9.kineticLaw.sboTerm = 49 + r10.kineticLaw.sboTerm = 49 + r11.kineticLaw.sboTerm = 49 + r12.kineticLaw.sboTerm = 49 + r13.kineticLaw.sboTerm = 49 + r14.kineticLaw.sboTerm = 49 + r15.kineticLaw.sboTerm = 49 + r16.kineticLaw.sboTerm = 49 + r17.kineticLaw.sboTerm = 83 + r18.kineticLaw.sboTerm = 83 + r19.kineticLaw.sboTerm = 83 + r20.kineticLaw.sboTerm = 83 + r21.kineticLaw.sboTerm = 83 + r22.kineticLaw.sboTerm = 83 + r23.kineticLaw.sboTerm = 83 + r24.kineticLaw.sboTerm = 101 + r25.kineticLaw.sboTerm = 83 + r26.kineticLaw.sboTerm = 83 + r27.kineticLaw.sboTerm = 83 + r28.kineticLaw.sboTerm = 83 + r29.kineticLaw.sboTerm = 83 + r30.kineticLaw.sboTerm = 83 + r31.kineticLaw.sboTerm = 83 + r33.kineticLaw.sboTerm = 101 // CV terms: APC identity "http://identifiers.org/uniprot/P04070" diff --git a/doc/examples/biomodels/BIOMD0000000366_url.txt b/doc/examples/biomodels/BIOMD0000000366/BIOMD0000000366_url.txt similarity index 90% rename from doc/examples/biomodels/BIOMD0000000366_url.txt rename to doc/examples/biomodels/BIOMD0000000366/BIOMD0000000366_url.txt index aa5d81724..654f43edc 100644 --- a/doc/examples/biomodels/BIOMD0000000366_url.txt +++ b/doc/examples/biomodels/BIOMD0000000366/BIOMD0000000366_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: @@ -21,6 +21,12 @@ model *Model_1() R7: IIa => IIa_alpha2M; compartment_1*ki_IIaAlpha2M*IIa; R8: IIa => IIa_ATIII; compartment_1*ki_IIaATIII*IIa; + // Interactions: + _I0: RVV -o R1; ; + _I1: IIa -o R4; ; + _I2: PT -o R5; ; + _I3: Xa -o R6; ; + // Species initializations: X = 0.1999999; Xa = 0; @@ -79,6 +85,14 @@ model *Model_1() km_2.sboTerm = 371 ki_IIaAlpha2M.sboTerm = 35 ki_IIaATIII.sboTerm = 35 + R1.kineticLaw.sboTerm = 28 + R2.kineticLaw.sboTerm = 49 + R3.kineticLaw.sboTerm = 122 + R4.kineticLaw.sboTerm = 28 + R5.kineticLaw.sboTerm = 28 + R6.kineticLaw.sboTerm = 28 + R7.kineticLaw.sboTerm = 49 + R8.kineticLaw.sboTerm = 49 // CV terms: X identity "http://identifiers.org/uniprot/P00742" diff --git a/doc/examples/biomodels/BIOMD0000000367_url.txt b/doc/examples/biomodels/BIOMD0000000367/BIOMD0000000367_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000367_url.txt rename to doc/examples/biomodels/BIOMD0000000367/BIOMD0000000367_url.txt index c4a437575..89a7a2c66 100644 --- a/doc/examples/biomodels/BIOMD0000000367_url.txt +++ b/doc/examples/biomodels/BIOMD0000000367/BIOMD0000000367_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000368_url.txt b/doc/examples/biomodels/BIOMD0000000368/BIOMD0000000368_url.txt similarity index 89% rename from doc/examples/biomodels/BIOMD0000000368_url.txt rename to doc/examples/biomodels/BIOMD0000000368/BIOMD0000000368_url.txt index 2bdca7649..a77ff815c 100644 --- a/doc/examples/biomodels/BIOMD0000000368_url.txt +++ b/doc/examples/biomodels/BIOMD0000000368/BIOMD0000000368_url.txt @@ -1,11 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model01() // Compartments and Species: compartment compartment_1; - species $Z1 in compartment_1, $E2 in compartment_1, $E4 in compartment_1; - species $E1 in compartment_1, $Z2 in compartment_1, $Z3 in compartment_1; - species $E3 in compartment_1, $Z4 in compartment_1; + species Z1 in compartment_1, E2 in compartment_1, E4 in compartment_1, E1 in compartment_1; + species Z2 in compartment_1, Z3 in compartment_1, E3 in compartment_1, Z4 in compartment_1; // Rate Rules: Z1' = -(mu1*E2 + mu5*E4)*Z1 + k1*E1; diff --git a/doc/examples/biomodels/BIOMD0000000369_url.txt b/doc/examples/biomodels/BIOMD0000000369/BIOMD0000000369_url.txt similarity index 90% rename from doc/examples/biomodels/BIOMD0000000369_url.txt rename to doc/examples/biomodels/BIOMD0000000369/BIOMD0000000369_url.txt index 0b3e55f3a..1190ff039 100644 --- a/doc/examples/biomodels/BIOMD0000000369_url.txt +++ b/doc/examples/biomodels/BIOMD0000000369/BIOMD0000000369_url.txt @@ -1,11 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model01() // Compartments and Species: compartment compartment_1; - species $Z1 in compartment_1, $E2 in compartment_1, $E4 in compartment_1; - species $Z2 in compartment_1, $E1 in compartment_1, $Z4 in compartment_1; - species $E3 in compartment_1; + species Z1 in compartment_1, E2 in compartment_1, E4 in compartment_1, Z2 in compartment_1; + species E1 in compartment_1, Z4 in compartment_1, E3 in compartment_1; // Rate Rules: Z1' = -(mu1*E2 + mu5*E4)*Z1; diff --git a/doc/examples/biomodels/BIOMD0000000370_url.txt b/doc/examples/biomodels/BIOMD0000000370/BIOMD0000000370_url.txt similarity index 95% rename from doc/examples/biomodels/BIOMD0000000370_url.txt rename to doc/examples/biomodels/BIOMD0000000370/BIOMD0000000370_url.txt index e9e5c075d..06d77511a 100644 --- a/doc/examples/biomodels/BIOMD0000000370_url.txt +++ b/doc/examples/biomodels/BIOMD0000000370/BIOMD0000000370_url.txt @@ -1,16 +1,16 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Vinod2011_MitoticExit() // Compartments and Species: compartment cell_1; - species $Clb2T_1 in cell_1, $Mcm_1 in cell_1, $Clb5T_1 in cell_1, $MBF_1 in cell_1; - species $Cln_1 in cell_1, $Cdc20_1 in cell_1, $Cdh1_1 in cell_1, $Sic1T_1 in cell_1; - species $Swi5_1 in cell_1, $Trim2_1 in cell_1, $Clb2_2 in cell_1, $Sic1_1 in cell_1; - species $Trim5_1 in cell_1, $Clb5_1 in cell_1, $Pds1T_1 in cell_1, $Esp1T_1 in cell_1; - species $PoloT_1 in cell_1, $Polo_1 in cell_1, $Net1dep_1 in cell_1, $Net1pp_1 in cell_1; - species $RENT_1 in cell_1, $Cdc14n_1 in cell_1, $RENTp_1 in cell_1, $Cdc14c_1 in cell_1; - species $Tem1_1 in cell_1, $Esp1_1 in cell_1, $Cdc15_1 in cell_1, $MEN_1 in cell_1; - species $Pds1_1 in cell_1, $Esp1b_1 in cell_1, Net1p_1 in cell_1, $Net1_2 in cell_1; + species Clb2T_1 in cell_1, Mcm_1 in cell_1, Clb5T_1 in cell_1, MBF_1 in cell_1; + species Cln_1 in cell_1, Cdc20_1 in cell_1, Cdh1_1 in cell_1, Sic1T_1 in cell_1; + species Swi5_1 in cell_1, Trim2_1 in cell_1, Clb2_2 in cell_1, Sic1_1 in cell_1; + species Trim5_1 in cell_1, Clb5_1 in cell_1, Pds1T_1 in cell_1, Esp1T_1 in cell_1; + species PoloT_1 in cell_1, Polo_1 in cell_1, Net1dep_1 in cell_1, Net1pp_1 in cell_1; + species RENT_1 in cell_1, Cdc14n_1 in cell_1, RENTp_1 in cell_1, Cdc14c_1 in cell_1; + species Tem1_1 in cell_1, Esp1_1 in cell_1, Cdc15_1 in cell_1, MEN_1 in cell_1; + species Pds1_1 in cell_1, Esp1b_1 in cell_1, Net1p_1 in cell_1, Net1_2 in cell_1; // Assignment Rules: V2_1 := kdclb2_1 + kdclb2_2*Cdc20_1 + kdclb2_3*Cdh1_1; diff --git a/doc/examples/biomodels/BIOMD0000000371_url.txt b/doc/examples/biomodels/BIOMD0000000371/BIOMD0000000371_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000371_url.txt rename to doc/examples/biomodels/BIOMD0000000371/BIOMD0000000371_url.txt index 4f5754068..0974b21b8 100644 --- a/doc/examples/biomodels/BIOMD0000000371_url.txt +++ b/doc/examples/biomodels/BIOMD0000000371/BIOMD0000000371_url.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *DeVries2000_PancreaticBetaCells_InsulinSecretion() // Compartments and Species: compartment Compartment; - species $V_membrane in Compartment, $n in Compartment, $s in Compartment; + species V_membrane in Compartment, n in Compartment, s in Compartment; // Assignment Rules: i_Ca := g_Ca*m_infinity*(V_membrane - V_Ca); diff --git a/doc/examples/biomodels/BIOMD0000000372_url.txt b/doc/examples/biomodels/BIOMD0000000372/BIOMD0000000372_url.txt similarity index 96% rename from doc/examples/biomodels/BIOMD0000000372_url.txt rename to doc/examples/biomodels/BIOMD0000000372/BIOMD0000000372_url.txt index f04f98ea8..578557679 100644 --- a/doc/examples/biomodels/BIOMD0000000372_url.txt +++ b/doc/examples/biomodels/BIOMD0000000372/BIOMD0000000372_url.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Tolic2000_InsulinGlucoseFeedback() // Compartments and Species: compartment COMpartment; - species $x1 in COMpartment, $Ip in COMpartment, $x2 in COMpartment, $x3 in COMpartment; - species $G in COMpartment, $Ii in COMpartment; + species x1 in COMpartment, Ip in COMpartment, x2 in COMpartment, x3 in COMpartment; + species G in COMpartment, Ii in COMpartment; // Assignment Rules: f5_x3 := Rg/(1 + exp(alpha*(x3*1/Vp - C5))); diff --git a/doc/examples/biomodels/BIOMD0000000373_url.txt b/doc/examples/biomodels/BIOMD0000000373/BIOMD0000000373_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000373_url.txt rename to doc/examples/biomodels/BIOMD0000000373/BIOMD0000000373_url.txt index 80384695f..75acf1595 100644 --- a/doc/examples/biomodels/BIOMD0000000373_url.txt +++ b/doc/examples/biomodels/BIOMD0000000373/BIOMD0000000373_url.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bertram2004_PancreaticBetaCell_modelB() // Compartments and Species: compartment COMpartment; - species $V in COMpartment, $n in COMpartment, $c in COMpartment, $cer in COMpartment; - species $g6p in COMpartment, $fbp in COMpartment, $adp in COMpartment; + species V in COMpartment, n in COMpartment, c in COMpartment, cer in COMpartment; + species g6p in COMpartment, fbp in COMpartment, adp in COMpartment; // Assignment Rules: IK := gK*n*(V - VK); diff --git a/doc/examples/biomodels/BIOMD0000000374_url.txt b/doc/examples/biomodels/BIOMD0000000374/BIOMD0000000374_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000374_url.txt rename to doc/examples/biomodels/BIOMD0000000374/BIOMD0000000374_url.txt index 02d677214..e18bbce10 100644 --- a/doc/examples/biomodels/BIOMD0000000374_url.txt +++ b/doc/examples/biomodels/BIOMD0000000374/BIOMD0000000374_url.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bertram1995_PancreaticBetaCell_CRAC() // Compartments and Species: compartment COMpartment; - species $V_membrane in COMpartment, $n in COMpartment, $jm in COMpartment; - species $Ca_er_Ca_equations in COMpartment, $Ca_i in COMpartment; + species V_membrane in COMpartment, n in COMpartment, jm in COMpartment; + species Ca_er_Ca_equations in COMpartment, Ca_i in COMpartment; // Assignment Rules: i_Ca := i_Ca_f + i_Ca_s; diff --git a/doc/examples/biomodels/BIOMD0000000375_url.txt b/doc/examples/biomodels/BIOMD0000000375/BIOMD0000000375_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000375_url.txt rename to doc/examples/biomodels/BIOMD0000000375/BIOMD0000000375_url.txt index ba92e7254..3807e4d87 100644 --- a/doc/examples/biomodels/BIOMD0000000375_url.txt +++ b/doc/examples/biomodels/BIOMD0000000375/BIOMD0000000375_url.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Mears1997_CRAC_PancreaticBetaCells() // Compartments and Species: compartment COMpartment; - species $V_membrane in COMpartment, $n in COMpartment, $jm in COMpartment; - species $Ca_er_Ca_equations in COMpartment, $Ca_i in COMpartment; + species V_membrane in COMpartment, n in COMpartment, jm in COMpartment; + species Ca_er_Ca_equations in COMpartment, Ca_i in COMpartment; // Assignment Rules: i_Ca := i_Ca_f + i_Ca_s; diff --git a/doc/examples/biomodels/BIOMD0000000376_url.txt b/doc/examples/biomodels/BIOMD0000000376/BIOMD0000000376_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000376_url.txt rename to doc/examples/biomodels/BIOMD0000000376/BIOMD0000000376_url.txt index 8fc52a0da..1a9509f05 100644 --- a/doc/examples/biomodels/BIOMD0000000376_url.txt +++ b/doc/examples/biomodels/BIOMD0000000376/BIOMD0000000376_url.txt @@ -1,11 +1,11 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bertram2007_IsletCell_Oscillations() // Compartments and Species: compartment Compartment; - species $Vm in Compartment, $n in Compartment, $G6P in Compartment, $FBP in Compartment; - species $NADHm in Compartment, $delta_psi in Compartment, $Cam in Compartment; - species $ADPm in Compartment, $adp in Compartment, $c in Compartment, $Caer in Compartment; + species Vm in Compartment, n in Compartment, G6P in Compartment, FBP in Compartment; + species NADHm in Compartment, delta_psi in Compartment, Cam in Compartment; + species ADPm in Compartment, adp in Compartment, c in Compartment, Caer in Compartment; // Assignment Rules: Ik := gK*n*(Vm - VK); diff --git a/doc/examples/biomodels/BIOMD0000000377_url.txt b/doc/examples/biomodels/BIOMD0000000377/BIOMD0000000377_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000377_url.txt rename to doc/examples/biomodels/BIOMD0000000377/BIOMD0000000377_url.txt index e7d846abf..89ea4c90c 100644 --- a/doc/examples/biomodels/BIOMD0000000377_url.txt +++ b/doc/examples/biomodels/BIOMD0000000377/BIOMD0000000377_url.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bertram2000_PancreaticBetaCells_Oscillations() // Compartments and Species: compartment Compartment; - species $V in Compartment, $n in Compartment, $s1 in Compartment, $s2 in Compartment; + species V in Compartment, n in Compartment, s1 in Compartment, s2 in Compartment; // Assignment Rules: ICa := gCa*minf*(V - VCa); diff --git a/doc/examples/biomodels/BIOMD0000000378_url.txt b/doc/examples/biomodels/BIOMD0000000378/BIOMD0000000378_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000378_url.txt rename to doc/examples/biomodels/BIOMD0000000378/BIOMD0000000378_url.txt index 4cdb57033..83f9da826 100644 --- a/doc/examples/biomodels/BIOMD0000000378_url.txt +++ b/doc/examples/biomodels/BIOMD0000000378/BIOMD0000000378_url.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Chay1997_CalciumConcentration() // Compartments and Species: compartment Compartment; - species $V_membrane in Compartment, $h in Compartment, $d in Compartment; - species $n in Compartment, $Ca_i_cytosolic_calcium in Compartment, $Ca_lum in Compartment; + species V_membrane in Compartment, h in Compartment, d in Compartment, n in Compartment; + species Ca_i_cytosolic_calcium in Compartment, Ca_lum in Compartment; // Assignment Rules: i_K_dr := g_K_dr*n^4*(V_membrane - V_K); diff --git a/doc/examples/biomodels/BIOMD0000000379_url.txt b/doc/examples/biomodels/BIOMD0000000379/BIOMD0000000379_url.txt similarity index 95% rename from doc/examples/biomodels/BIOMD0000000379_url.txt rename to doc/examples/biomodels/BIOMD0000000379/BIOMD0000000379_url.txt index f199b3690..30c6fc8d4 100644 --- a/doc/examples/biomodels/BIOMD0000000379_url.txt +++ b/doc/examples/biomodels/BIOMD0000000379/BIOMD0000000379_url.txt @@ -1,12 +1,12 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *DallaMan2007_MealModel_GlucoseInsulinSystem() // Compartments and Species: compartment Compartment1; - species $G_p in Compartment1, $G_t in Compartment1, $I_l in Compartment1; - species $I_p in Compartment1, $Q_sto1 in Compartment1, $Q_gut in Compartment1; - species $Q_sto2 in Compartment1, $I_1 in Compartment1, $I_d in Compartment1; - species $X in Compartment1, $I_po in Compartment1, $Y in Compartment1; + species G_p in Compartment1, G_t in Compartment1, I_l in Compartment1, I_p in Compartment1; + species Q_sto1 in Compartment1, Q_gut in Compartment1, Q_sto2 in Compartment1; + species I_1 in Compartment1, I_d in Compartment1, X in Compartment1, I_po in Compartment1; + species Y in Compartment1; // Assignment Rules: EGP := k_p1 - k_p2*G_p - k_p3*I_d - k_p4*I_po; diff --git a/doc/examples/biomodels/BIOMD0000000380_url.txt b/doc/examples/biomodels/BIOMD0000000380/BIOMD0000000380_url.txt similarity index 96% rename from doc/examples/biomodels/BIOMD0000000380_url.txt rename to doc/examples/biomodels/BIOMD0000000380/BIOMD0000000380_url.txt index 4e084faf4..27287b653 100644 --- a/doc/examples/biomodels/BIOMD0000000380_url.txt +++ b/doc/examples/biomodels/BIOMD0000000380/BIOMD0000000380_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Smallbone2011_TrehaloseBiosynthesis() // Compartments and Species: @@ -241,12 +241,16 @@ model *Smallbone2011_TrehaloseBiosynthesis() h2o identity "http://identifiers.org/chebi/CHEBI:15377" glx identity "http://identifiers.org/chebi/CHEBI:17925" pgi isVersionOf "http://identifiers.org/ec-code/5.3.1.9" + pgi.kineticLaw publication "http://identifiers.org/biomodels.db/BIOMD0000000172" + hxt.kineticLaw publication "http://identifiers.org/biomodels.db/BIOMD0000000172" hxk isVersionOf "http://identifiers.org/ec-code/2.7.1.1" pgm isVersionOf "http://identifiers.org/ec-code/5.4.2.2" tpp isVersionOf "http://identifiers.org/ec-code/3.1.3.12" tps isVersionOf "http://identifiers.org/ec-code/2.4.1.15" nth isVersionOf "http://identifiers.org/ec-code/3.2.1.28" + nth.kineticLaw publication "http://identifiers.org/pubmed/558094" ugp isVersionOf "http://identifiers.org/ec-code/2.7.7.9" + ugp.kineticLaw publication "http://identifiers.org/pubmed/4344984" model model_source "http://identifiers.org/biomodels.db/MODEL1010010000" model model_source "http://identifiers.org/biomodels.db/BIOMD0000000380" diff --git a/doc/examples/biomodels/BIOMD0000000381_url.txt b/doc/examples/biomodels/BIOMD0000000381/BIOMD0000000381_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000381_url.txt rename to doc/examples/biomodels/BIOMD0000000381/BIOMD0000000381_url.txt index ac6ab359b..06f899e27 100644 --- a/doc/examples/biomodels/BIOMD0000000381_url.txt +++ b/doc/examples/biomodels/BIOMD0000000381/BIOMD0000000381_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Maree2006_DuCa_Type1DiabetesModel() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000382_url.txt b/doc/examples/biomodels/BIOMD0000000382/BIOMD0000000382_url.txt similarity index 96% rename from doc/examples/biomodels/BIOMD0000000382_url.txt rename to doc/examples/biomodels/BIOMD0000000382/BIOMD0000000382_url.txt index 65ca66532..da3882805 100644 --- a/doc/examples/biomodels/BIOMD0000000382_url.txt +++ b/doc/examples/biomodels/BIOMD0000000382/BIOMD0000000382_url.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Sturis1991_InsulinGlucoseModel_UltradianOscillation() // Compartments and Species: compartment compartment1; - species $x in compartment1, $y in compartment1, $z in compartment1, $h1 in compartment1; - species $h2 in compartment1, $h3 in compartment1; + species x in compartment1, y in compartment1, z in compartment1, h1 in compartment1; + species h2 in compartment1, h3 in compartment1; // Assignment Rules: f1 := 209/(1 + exp(-z/(300*v3) + 6.6)); diff --git a/doc/examples/biomodels/BIOMD0000000383_url.txt b/doc/examples/biomodels/BIOMD0000000383/BIOMD0000000383_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000383_url.txt rename to doc/examples/biomodels/BIOMD0000000383/BIOMD0000000383_url.txt index 1b4c4a55b..df28f8500 100644 --- a/doc/examples/biomodels/BIOMD0000000383_url.txt +++ b/doc/examples/biomodels/BIOMD0000000383/BIOMD0000000383_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000384_url.txt b/doc/examples/biomodels/BIOMD0000000384/BIOMD0000000384_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000384_url.txt rename to doc/examples/biomodels/BIOMD0000000384/BIOMD0000000384_url.txt index 2d3ad5dc1..10c1a50f0 100644 --- a/doc/examples/biomodels/BIOMD0000000384_url.txt +++ b/doc/examples/biomodels/BIOMD0000000384/BIOMD0000000384_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Arnold2011_Medlyn2002_RuBisCO_CalvinCycle() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000385_url.txt b/doc/examples/biomodels/BIOMD0000000385/BIOMD0000000385_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000385_url.txt rename to doc/examples/biomodels/BIOMD0000000385/BIOMD0000000385_url.txt index da9a1c45b..5a025b930 100644 --- a/doc/examples/biomodels/BIOMD0000000385_url.txt +++ b/doc/examples/biomodels/BIOMD0000000385/BIOMD0000000385_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Arnold2011_Schultz2003_RuBisCO_CalvinCycle() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000386_url.txt b/doc/examples/biomodels/BIOMD0000000386/BIOMD0000000386_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000386_url.txt rename to doc/examples/biomodels/BIOMD0000000386/BIOMD0000000386_url.txt index a62381691..dc34ecdc4 100644 --- a/doc/examples/biomodels/BIOMD0000000386_url.txt +++ b/doc/examples/biomodels/BIOMD0000000386/BIOMD0000000386_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Arnold2011_Sharkey2007_RuBisCO_CalvinCycle() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000387_url.txt b/doc/examples/biomodels/BIOMD0000000387/BIOMD0000000387_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000387_url.txt rename to doc/examples/biomodels/BIOMD0000000387/BIOMD0000000387_url.txt index c5180e785..3594ed203 100644 --- a/doc/examples/biomodels/BIOMD0000000387_url.txt +++ b/doc/examples/biomodels/BIOMD0000000387/BIOMD0000000387_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Arnold2011_Damour2007_RuBisCO_CalvinCycle() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000388_url.txt b/doc/examples/biomodels/BIOMD0000000388/BIOMD0000000388_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000388_url.txt rename to doc/examples/biomodels/BIOMD0000000388/BIOMD0000000388_url.txt index e41a493a0..b310e6812 100644 --- a/doc/examples/biomodels/BIOMD0000000388_url.txt +++ b/doc/examples/biomodels/BIOMD0000000388/BIOMD0000000388_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Arnold2011_Zhu2009_CalvinCycle() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000389_url.txt b/doc/examples/biomodels/BIOMD0000000389/BIOMD0000000389_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000389_url.txt rename to doc/examples/biomodels/BIOMD0000000389/BIOMD0000000389_url.txt index 581294ec9..5b402c44d 100644 --- a/doc/examples/biomodels/BIOMD0000000389_url.txt +++ b/doc/examples/biomodels/BIOMD0000000389/BIOMD0000000389_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Arnold2011_Hahn1986_CalvinCycle_Starch_Sucrose() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000390_url.txt b/doc/examples/biomodels/BIOMD0000000390/BIOMD0000000390_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000390_url.txt rename to doc/examples/biomodels/BIOMD0000000390/BIOMD0000000390_url.txt index 7a3ad9798..30afc8b43 100644 --- a/doc/examples/biomodels/BIOMD0000000390_url.txt +++ b/doc/examples/biomodels/BIOMD0000000390/BIOMD0000000390_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Arnold2011_Giersch1990_CalvinCycle() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000391_url.txt b/doc/examples/biomodels/BIOMD0000000391/BIOMD0000000391_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000391_url.txt rename to doc/examples/biomodels/BIOMD0000000391/BIOMD0000000391_url.txt index ede26a73c..c3d1c2272 100644 --- a/doc/examples/biomodels/BIOMD0000000391_url.txt +++ b/doc/examples/biomodels/BIOMD0000000391/BIOMD0000000391_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Arnold2011_Poolman2000_CalvinCycle_Starch() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000392_url.txt b/doc/examples/biomodels/BIOMD0000000392/BIOMD0000000392_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000392_url.txt rename to doc/examples/biomodels/BIOMD0000000392/BIOMD0000000392_url.txt index bf40e2874..2f4b12f23 100644 --- a/doc/examples/biomodels/BIOMD0000000392_url.txt +++ b/doc/examples/biomodels/BIOMD0000000392/BIOMD0000000392_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Arnold2011_Laisk2006_CalvinCycle_Starch_Sucrose() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000393_url.txt b/doc/examples/biomodels/BIOMD0000000393/BIOMD0000000393_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000393_url.txt rename to doc/examples/biomodels/BIOMD0000000393/BIOMD0000000393_url.txt index e0a72014a..13ae7af8e 100644 --- a/doc/examples/biomodels/BIOMD0000000393_url.txt +++ b/doc/examples/biomodels/BIOMD0000000393/BIOMD0000000393_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Arnold2011_Zhu2007_CalvinCycle_Starch_Sucrose_Photorespiration() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000394_url.txt b/doc/examples/biomodels/BIOMD0000000394/BIOMD0000000394_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000394_url.txt rename to doc/examples/biomodels/BIOMD0000000394/BIOMD0000000394_url.txt index 98e3402e7..e56c97c7e 100644 --- a/doc/examples/biomodels/BIOMD0000000394_url.txt +++ b/doc/examples/biomodels/BIOMD0000000394/BIOMD0000000394_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Sivakumar2011_EGFReceptorSignalingPathway() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000395_url.txt b/doc/examples/biomodels/BIOMD0000000395/BIOMD0000000395_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000395_url.txt rename to doc/examples/biomodels/BIOMD0000000395/BIOMD0000000395_url.txt index c2ec67825..2c0363758 100644 --- a/doc/examples/biomodels/BIOMD0000000395_url.txt +++ b/doc/examples/biomodels/BIOMD0000000395/BIOMD0000000395_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Sivakumar2011_HedgehogSignalingPathway() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000396_url.txt b/doc/examples/biomodels/BIOMD0000000396/BIOMD0000000396_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000396_url.txt rename to doc/examples/biomodels/BIOMD0000000396/BIOMD0000000396_url.txt index c65f80b57..aa254489c 100644 --- a/doc/examples/biomodels/BIOMD0000000396_url.txt +++ b/doc/examples/biomodels/BIOMD0000000396/BIOMD0000000396_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Sivakumar2011_NotchSignalingPathway() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000397_url.txt b/doc/examples/biomodels/BIOMD0000000397/BIOMD0000000397_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000397_url.txt rename to doc/examples/biomodels/BIOMD0000000397/BIOMD0000000397_url.txt index 80b63b6eb..94a7eed30 100644 --- a/doc/examples/biomodels/BIOMD0000000397_url.txt +++ b/doc/examples/biomodels/BIOMD0000000397/BIOMD0000000397_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Sivakumar2011_WntSignalingPathway() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000398_url.txt b/doc/examples/biomodels/BIOMD0000000398/BIOMD0000000398_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000398_url.txt rename to doc/examples/biomodels/BIOMD0000000398/BIOMD0000000398_url.txt index b2d1efcef..f2309f8f2 100644 --- a/doc/examples/biomodels/BIOMD0000000398_url.txt +++ b/doc/examples/biomodels/BIOMD0000000398/BIOMD0000000398_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Sivakumar2011_NeuralStemCellDifferentiation_Crosstalk() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000399_url.txt b/doc/examples/biomodels/BIOMD0000000399/BIOMD0000000399_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000399_url.txt rename to doc/examples/biomodels/BIOMD0000000399/BIOMD0000000399_url.txt index 87439559b..c74890a4e 100644 --- a/doc/examples/biomodels/BIOMD0000000399_url.txt +++ b/doc/examples/biomodels/BIOMD0000000399/BIOMD0000000399_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Jenkinson2011_EGF_MAPK() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000400_url.txt b/doc/examples/biomodels/BIOMD0000000400/BIOMD0000000400_url.txt similarity index 96% rename from doc/examples/biomodels/BIOMD0000000400_url.txt rename to doc/examples/biomodels/BIOMD0000000400/BIOMD0000000400_url.txt index 949e37c3f..bd972eb82 100644 --- a/doc/examples/biomodels/BIOMD0000000400_url.txt +++ b/doc/examples/biomodels/BIOMD0000000400/BIOMD0000000400_url.txt @@ -1,12 +1,12 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Cooling2007_IP3transients_CardiacMyocyte() // Compartments and Species: compartment Compartment; - species $Gd in Compartment, $Gt in Compartment, $R in Compartment, $Rl in Compartment; - species $Rg in Compartment, $Rlg in Compartment, $Rlgp in Compartment, $IP3 in Compartment; - species $Pc in Compartment, $Pcg in Compartment, $P in Compartment, $Pg in Compartment; - species $Ca in Compartment; + species Gd in Compartment, Gt in Compartment, R in Compartment, Rl in Compartment; + species Rg in Compartment, Rlg in Compartment, Rlgp in Compartment, IP3 in Compartment; + species Pc in Compartment, Pcg in Compartment, P in Compartment, Pg in Compartment; + species Ca in Compartment; // Assignment Rules: J7 := kf7*Gt; diff --git a/doc/examples/biomodels/BIOMD0000000401_url.txt b/doc/examples/biomodels/BIOMD0000000401/BIOMD0000000401_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000401_url.txt rename to doc/examples/biomodels/BIOMD0000000401/BIOMD0000000401_url.txt index 560161ab7..4fbeacf54 100644 --- a/doc/examples/biomodels/BIOMD0000000401_url.txt +++ b/doc/examples/biomodels/BIOMD0000000401/BIOMD0000000401_url.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ayati2010_BoneRemodelingDynamics_NormalCondition() // Compartments and Species: compartment Compartment; - species $C in Compartment, $B in Compartment, $z in Compartment; + species C in Compartment, B in Compartment, z in Compartment; // Assignment Rules: y2 := piecewise(B - B_bar, B > B_bar, 0); diff --git a/doc/examples/biomodels/BIOMD0000000402_url.txt b/doc/examples/biomodels/BIOMD0000000402/BIOMD0000000402_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000402_url.txt rename to doc/examples/biomodels/BIOMD0000000402/BIOMD0000000402_url.txt index b4814f7da..7ebcc2489 100644 --- a/doc/examples/biomodels/BIOMD0000000402_url.txt +++ b/doc/examples/biomodels/BIOMD0000000402/BIOMD0000000402_url.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ayati2010_BoneRemodelingDynamics_WithTumour() // Compartments and Species: compartment Compartment; - species $C in Compartment, $Tumour in Compartment, $B in Compartment, $z in Compartment; + species C in Compartment, Tumour in Compartment, B in Compartment, z in Compartment; // Assignment Rules: y2 := piecewise(B - B_bar, B > B_bar, 0); diff --git a/doc/examples/biomodels/BIOMD0000000403_url.txt b/doc/examples/biomodels/BIOMD0000000403/BIOMD0000000403_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000403_url.txt rename to doc/examples/biomodels/BIOMD0000000403/BIOMD0000000403_url.txt index 9cd308f1d..7845af530 100644 --- a/doc/examples/biomodels/BIOMD0000000403_url.txt +++ b/doc/examples/biomodels/BIOMD0000000403/BIOMD0000000403_url.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ayati2010_BoneRemodelingDynamics_WithTumourDrugTreatment() // Compartments and Species: compartment Compartment; - species $C in Compartment, $Tumour in Compartment, $B in Compartment, $z in Compartment; + species C in Compartment, Tumour in Compartment, B in Compartment, z in Compartment; // Assignment Rules: V1 := piecewise(v1, time >= 600, 0); diff --git a/doc/examples/biomodels/BIOMD0000000404_url.txt b/doc/examples/biomodels/BIOMD0000000404/BIOMD0000000404_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000404_url.txt rename to doc/examples/biomodels/BIOMD0000000404/BIOMD0000000404_url.txt index 57c131d97..ca15107b4 100644 --- a/doc/examples/biomodels/BIOMD0000000404_url.txt +++ b/doc/examples/biomodels/BIOMD0000000404/BIOMD0000000404_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bray1993_chemotaxis() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000405_url.txt b/doc/examples/biomodels/BIOMD0000000405/BIOMD0000000405_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000405_url.txt rename to doc/examples/biomodels/BIOMD0000000405/BIOMD0000000405_url.txt index 16dee8cb1..71650f56a 100644 --- a/doc/examples/biomodels/BIOMD0000000405_url.txt +++ b/doc/examples/biomodels/BIOMD0000000405/BIOMD0000000405_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Cookson2011_EnzymaticQueueingCoupling() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000406_url.txt b/doc/examples/biomodels/BIOMD0000000406/BIOMD0000000406_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000406_url.txt rename to doc/examples/biomodels/BIOMD0000000406/BIOMD0000000406_url.txt index bbc7e0ef6..daf90611a 100644 --- a/doc/examples/biomodels/BIOMD0000000406_url.txt +++ b/doc/examples/biomodels/BIOMD0000000406/BIOMD0000000406_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Moriya2011_CellCycle_FissionYeast() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000407_url.txt b/doc/examples/biomodels/BIOMD0000000407/BIOMD0000000407_url.txt similarity index 95% rename from doc/examples/biomodels/BIOMD0000000407_url.txt rename to doc/examples/biomodels/BIOMD0000000407/BIOMD0000000407_url.txt index 425b35e08..fec365e74 100644 --- a/doc/examples/biomodels/BIOMD0000000407_url.txt +++ b/doc/examples/biomodels/BIOMD0000000407/BIOMD0000000407_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Schliemann2011_TNF_ProAntiApoptosis() // Compartments and Species: @@ -113,99 +113,99 @@ model *Schliemann2011_TNF_ProAntiApoptosis() // Species initializations: TNFR_E = 0.005; - TNFR_E has a_mole_per_pl; + TNFR_E has a_mole; TNF_E = 0.2688; - TNF_E has a_mole_per_pl; + TNF_E has a_mole; TNF_TNFR_E = 0; - TNF_TNFR_E has a_mole_per_pl; + TNF_TNFR_E has a_mole; TNFR = 0.00028; - TNFR has a_mole_per_pl; + TNFR has a_mole; RIP = 0.20256; - RIP has a_mole_per_pl; + RIP has a_mole; TRADD = 0.29344; - TRADD has a_mole_per_pl; + TRADD has a_mole; TRAF2 = 0.33056; - TRAF2 has a_mole_per_pl; + TRAF2 has a_mole; FADD = 0.30944; - FADD has a_mole_per_pl; + FADD has a_mole; TNF_TNFR_TRADD = 0; - TNF_TNFR_TRADD has a_mole_per_pl; + TNF_TNFR_TRADD has a_mole; TNFRC1 = 0; - TNFRC1 has a_mole_per_pl; + TNFRC1 has a_mole; TNFRCint1 = 0; - TNFRCint1 has a_mole_per_pl; + TNFRCint1 has a_mole; TNFRCint2 = 0; - TNFRCint2 has a_mole_per_pl; + TNFRCint2 has a_mole; TNFRCint3 = 0; - TNFRCint3 has a_mole_per_pl; + TNFRCint3 has a_mole; TNFRC2 = 0; - TNFRC2 has a_mole_per_pl; + TNFRC2 has a_mole; FLIP = 0.0320472; - FLIP has a_mole_per_pl; + FLIP has a_mole; TNFRC2_FLIP = 0; - TNFRC2_FLIP has a_mole_per_pl; + TNFRC2_FLIP has a_mole; TNFRC2_pCasp8 = 0; - TNFRC2_pCasp8 has a_mole_per_pl; + TNFRC2_pCasp8 has a_mole; TNFRC2_FLIP_FLIP = 0; - TNFRC2_FLIP_FLIP has a_mole_per_pl; + TNFRC2_FLIP_FLIP has a_mole; TNFRC2_pCasp8_pCasp8 = 0; - TNFRC2_pCasp8_pCasp8 has a_mole_per_pl; + TNFRC2_pCasp8_pCasp8 has a_mole; TNFRC2_FLIP_pCasp8 = 0; - TNFRC2_FLIP_pCasp8 has a_mole_per_pl; + TNFRC2_FLIP_pCasp8 has a_mole; TNFRC2_FLIP_pCasp8_RIP_TRAF2 = 0; - TNFRC2_FLIP_pCasp8_RIP_TRAF2 has a_mole_per_pl; + TNFRC2_FLIP_pCasp8_RIP_TRAF2 has a_mole; IKK = 0.64; - IKK has a_mole_per_pl; + IKK has a_mole; IKKa = 0; - IKKa has a_mole_per_pl; + IKKa has a_mole; A20 = 0.104434; - A20 has a_mole_per_pl; + A20 has a_mole; NFkB = 0.000115365; - NFkB has a_mole_per_pl; + NFkB has a_mole; IkBa = 0.00101518; - IkBa has a_mole_per_pl; + IkBa has a_mole; IkBa_NFkB = 0.0151032; - IkBa_NFkB has a_mole_per_pl; + IkBa_NFkB has a_mole; PIkBa = 0; - PIkBa has a_mole_per_pl; + PIkBa has a_mole; NFkB_N = 0.000691431; - NFkB_N has a_mole_per_pl; + NFkB_N has a_mole; IkBa_N = 0.0013839; - IkBa_N has a_mole_per_pl; + IkBa_N has a_mole; IkBa_NFkB_N = 9.00189e-05; - IkBa_NFkB_N has a_mole_per_pl; + IkBa_NFkB_N has a_mole; A20_mRNA = 5.56657e-05; - A20_mRNA has a_mole_per_pl; + A20_mRNA has a_mole; IkBa_mRNA = 5.31517e-05; - IkBa_mRNA has a_mole_per_pl; + IkBa_mRNA has a_mole; XIAP_mRNA = 0.000219646; - XIAP_mRNA has a_mole_per_pl; + XIAP_mRNA has a_mole; FLIP_mRNA = 0.000139056; - FLIP_mRNA has a_mole_per_pl; + FLIP_mRNA has a_mole; BAR = 0.28789; - BAR has a_mole_per_pl; + BAR has a_mole; XIAP = 7.83371; - XIAP has a_mole_per_pl; + XIAP has a_mole; pCasp8 = 3.2; - pCasp8 has a_mole_per_pl; + pCasp8 has a_mole; pCasp3 = 0.8; - pCasp3 has a_mole_per_pl; + pCasp3 has a_mole; pCasp6 = 0.064; - pCasp6 has a_mole_per_pl; + pCasp6 has a_mole; Casp8 = 0; - Casp8 has a_mole_per_pl; + Casp8 has a_mole; Casp3 = 0; - Casp3 has a_mole_per_pl; + Casp3 has a_mole; Casp6 = 0; - Casp6 has a_mole_per_pl; + Casp6 has a_mole; BAR_Casp8 = 0; - BAR_Casp8 has a_mole_per_pl; + BAR_Casp8 has a_mole; XIAP_Casp3 = 0; - XIAP_Casp3 has a_mole_per_pl; + XIAP_Casp3 has a_mole; PARP = 1.66667; - PARP has a_mole_per_pl; + PARP has a_mole; cPARP = 0; - cPARP has a_mole_per_pl; + cPARP has a_mole; // Compartment initializations: cytoplasm = 3.2; @@ -439,7 +439,7 @@ model *Schliemann2011_TNF_ProAntiApoptosis() unit a_mole_per_second = 1e-18 mole / second; unit per_a_mole_per_second = 1 / (1e-18 mole * second); unit per_a_mole_squared_per_second = 1 / ((1e-18 mole)^2 * second); - unit a_mole_per_pl = 1e-18 mole / 1e-12 litre; + unit a_mole_pl = 1e-18 mole * 1e-12 litre; // Display Names: TNF_TNFR_E is "TNF:TNFR_E"; diff --git a/doc/examples/biomodels/BIOMD0000000408_url.txt b/doc/examples/biomodels/BIOMD0000000408/BIOMD0000000408_url.txt similarity index 95% rename from doc/examples/biomodels/BIOMD0000000408_url.txt rename to doc/examples/biomodels/BIOMD0000000408/BIOMD0000000408_url.txt index 4e5432e8a..f46d3825f 100644 --- a/doc/examples/biomodels/BIOMD0000000408_url.txt +++ b/doc/examples/biomodels/BIOMD0000000408/BIOMD0000000408_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hettling2011() // Compartments and Species: @@ -42,9 +42,9 @@ model *Hettling2011() J_diff_ATP: ATPi -> ATP; j_diff_atp; // Events: - pulsatile_test: at 0 after ((time >= time_Jhyd_step) && ((time - last_time_fired) > stepsize)) && (pulsatility == 1): last_time_fired = time, Jhyd = piecewise((1 - (phase - fracSysUp)/fracSysDown)*VhydAmp_test, (phase > fracSysUp) && (phase <= (1 - fracDia)), (phase/fracSysUp)*VhydAmp_test, phase <= fracSysUp, 0, phase >= (1 - fracDia), Jhyd); - pulsatile_basis: at 0 after ((time < time_Jhyd_step) && ((time - last_time_fired) >= stepsize)) && (pulsatility == 1): last_time_fired = time, Jhyd = piecewise(0, phase <= fracDia, ((phase - fracDia)/fracSysDown)*VhydAmp_basis, (phase > fracDia) && (phase <= (1 - fracSysUp)), (1 - phase)*VhydAmp_basis/fracSysUp, phase > (1 - fracSysUp), Jhyd); - nonpulsatile_step: at 0 after time >= time_Jhyd_step: tmito_factor = 1, heartrate_bpm = heartrate_test, Jhyd = piecewise(Jhyd_test, pulsatility == 0, Jhyd); + pulsatile_test: at 0 after ((time >= time_Jhyd_step) && ((time - last_time_fired) > stepsize)) && (pulsatility == 1): Jhyd = piecewise((1 - (phase - fracSysUp)/fracSysDown)*VhydAmp_test, (phase > fracSysUp) && (phase <= (1 - fracDia)), (phase/fracSysUp)*VhydAmp_test, phase <= fracSysUp, 0, phase >= (1 - fracDia), Jhyd), last_time_fired = time; + pulsatile_basis: at 0 after ((time < time_Jhyd_step) && ((time - last_time_fired) >= stepsize)) && (pulsatility == 1): Jhyd = piecewise(0, phase <= fracDia, ((phase - fracDia)/fracSysDown)*VhydAmp_basis, (phase > fracDia) && (phase <= (1 - fracSysUp)), (1 - phase)*VhydAmp_basis/fracSysUp, phase > (1 - fracSysUp), Jhyd), last_time_fired = time; + nonpulsatile_step: at 0 after time >= time_Jhyd_step: Jhyd = piecewise(Jhyd_test, pulsatility == 0, Jhyd), heartrate_bpm = heartrate_test, tmito_factor = 1; // Species initializations: ADPi = 39; diff --git a/doc/examples/biomodels/BIOMD0000000409_url.txt b/doc/examples/biomodels/BIOMD0000000409/BIOMD0000000409_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000409_url.txt rename to doc/examples/biomodels/BIOMD0000000409/BIOMD0000000409_url.txt index 20f6797d7..e2b597221 100644 --- a/doc/examples/biomodels/BIOMD0000000409_url.txt +++ b/doc/examples/biomodels/BIOMD0000000409/BIOMD0000000409_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Queralt2006_MitoticExit_Cdc55DownregulationBySeparase() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000410_url.txt b/doc/examples/biomodels/BIOMD0000000410/BIOMD0000000410_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000410_url.txt rename to doc/examples/biomodels/BIOMD0000000410/BIOMD0000000410_url.txt index 9dd6c69ce..0bcf98185 100644 --- a/doc/examples/biomodels/BIOMD0000000410_url.txt +++ b/doc/examples/biomodels/BIOMD0000000410/BIOMD0000000410_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000411_url.txt b/doc/examples/biomodels/BIOMD0000000411/BIOMD0000000411_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000411_url.txt rename to doc/examples/biomodels/BIOMD0000000411/BIOMD0000000411_url.txt index 4090ca081..1694008fe 100644 --- a/doc/examples/biomodels/BIOMD0000000411_url.txt +++ b/doc/examples/biomodels/BIOMD0000000411/BIOMD0000000411_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000412_url.txt b/doc/examples/biomodels/BIOMD0000000412/BIOMD0000000412_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000412_url.txt rename to doc/examples/biomodels/BIOMD0000000412/BIOMD0000000412_url.txt index ec8d385a4..70326d9c3 100644 --- a/doc/examples/biomodels/BIOMD0000000412_url.txt +++ b/doc/examples/biomodels/BIOMD0000000412/BIOMD0000000412_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000413_url.txt b/doc/examples/biomodels/BIOMD0000000413/BIOMD0000000413_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000413_url.txt rename to doc/examples/biomodels/BIOMD0000000413/BIOMD0000000413_url.txt index e93a48c8e..efc82239d 100644 --- a/doc/examples/biomodels/BIOMD0000000413_url.txt +++ b/doc/examples/biomodels/BIOMD0000000413/BIOMD0000000413_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *DIIVENUS_fullmodel() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000414_url.txt b/doc/examples/biomodels/BIOMD0000000414/BIOMD0000000414_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000414_url.txt rename to doc/examples/biomodels/BIOMD0000000414/BIOMD0000000414_url.txt index f35c410ef..7566b794c 100644 --- a/doc/examples/biomodels/BIOMD0000000414_url.txt +++ b/doc/examples/biomodels/BIOMD0000000414/BIOMD0000000414_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *DIIVENUS_reducedmodel() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000415_url.txt b/doc/examples/biomodels/BIOMD0000000415/BIOMD0000000415_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000415_url.txt rename to doc/examples/biomodels/BIOMD0000000415/BIOMD0000000415_url.txt index d782e9c98..d36f7e996 100644 --- a/doc/examples/biomodels/BIOMD0000000415_url.txt +++ b/doc/examples/biomodels/BIOMD0000000415/BIOMD0000000415_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000416_url.txt b/doc/examples/biomodels/BIOMD0000000416/BIOMD0000000416_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000416_url.txt rename to doc/examples/biomodels/BIOMD0000000416/BIOMD0000000416_url.txt index db7ebebeb..fa0677360 100644 --- a/doc/examples/biomodels/BIOMD0000000416_url.txt +++ b/doc/examples/biomodels/BIOMD0000000416/BIOMD0000000416_url.txt @@ -1,15 +1,15 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Muraro2011_CytokininAuxin_CrossRegulation() // Compartments and Species: compartment cell; species IAAm in cell, IAAp in cell, AuxTIR1 in cell, AuxTIAA in cell, IAAs in cell; species ARFIAA in cell, ARF2 in cell, Aux in cell, PINm in cell, PINp in cell; - species ARm in cell, ARp in cell, $TIR1 in cell, $ARF in cell, CRm in cell; + species ARm in cell, ARp in cell, TIR1 in cell, ARF in cell, CRm in cell; species CRp in cell, AHKph in cell, Ck in cell, ARRBph in cell, ARRAph in cell; - species ARRAm in cell, ARRAp in cell, $ARRBp in cell, $CkAHKph in cell; - species $CkAHK in cell, $F1 in cell, $F2 in cell, $F3 in cell, $F4 in cell; - species $F5a in cell, $F5b in cell, $F6 in cell; + species ARRAm in cell, ARRAp in cell, ARRBp in cell, CkAHKph in cell, CkAHK in cell; + species F1 in cell, F2 in cell, F3 in cell, F4 in cell, F5a in cell, F5b in cell; + species F6 in cell; // Assignment Rules: TIR1 := alphaTIR1 - AuxTIR1 - AuxTIAA; diff --git a/doc/examples/biomodels/BIOMD0000000417_url.txt b/doc/examples/biomodels/BIOMD0000000417/BIOMD0000000417_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000417_url.txt rename to doc/examples/biomodels/BIOMD0000000417/BIOMD0000000417_url.txt index bfa5387b9..82d89e441 100644 --- a/doc/examples/biomodels/BIOMD0000000417_url.txt +++ b/doc/examples/biomodels/BIOMD0000000417/BIOMD0000000417_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ratushny2012_NF() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000418_url.txt b/doc/examples/biomodels/BIOMD0000000418/BIOMD0000000418_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000418_url.txt rename to doc/examples/biomodels/BIOMD0000000418/BIOMD0000000418_url.txt index 955750de9..3a8a26e73 100644 --- a/doc/examples/biomodels/BIOMD0000000418_url.txt +++ b/doc/examples/biomodels/BIOMD0000000418/BIOMD0000000418_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ratushny2012_SPF() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000419_url.txt b/doc/examples/biomodels/BIOMD0000000419/BIOMD0000000419_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000419_url.txt rename to doc/examples/biomodels/BIOMD0000000419/BIOMD0000000419_url.txt index 4b58edd82..f186968ee 100644 --- a/doc/examples/biomodels/BIOMD0000000419_url.txt +++ b/doc/examples/biomodels/BIOMD0000000419/BIOMD0000000419_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ratushny2012_SPF_I() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000420_url.txt b/doc/examples/biomodels/BIOMD0000000420/BIOMD0000000420_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000420_url.txt rename to doc/examples/biomodels/BIOMD0000000420/BIOMD0000000420_url.txt index ba2ceb814..89e07d5bb 100644 --- a/doc/examples/biomodels/BIOMD0000000420_url.txt +++ b/doc/examples/biomodels/BIOMD0000000420/BIOMD0000000420_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ratushny2012_ASSURE_I() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000421_url.txt b/doc/examples/biomodels/BIOMD0000000421/BIOMD0000000421_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000421_url.txt rename to doc/examples/biomodels/BIOMD0000000421/BIOMD0000000421_url.txt index e028dc57e..f90e92c87 100644 --- a/doc/examples/biomodels/BIOMD0000000421_url.txt +++ b/doc/examples/biomodels/BIOMD0000000421/BIOMD0000000421_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ratushny2012_ASSURE_II() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000422_url.txt b/doc/examples/biomodels/BIOMD0000000422/BIOMD0000000422_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000422_url.txt rename to doc/examples/biomodels/BIOMD0000000422/BIOMD0000000422_url.txt index a0bc02fd6..38a37bf9c 100644 --- a/doc/examples/biomodels/BIOMD0000000422_url.txt +++ b/doc/examples/biomodels/BIOMD0000000422/BIOMD0000000422_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Middleton2012_GibberellinSignalling() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000423_url.txt b/doc/examples/biomodels/BIOMD0000000423/BIOMD0000000423_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000423_url.txt rename to doc/examples/biomodels/BIOMD0000000423/BIOMD0000000423_url.txt index ded00f33e..eb7311833 100644 --- a/doc/examples/biomodels/BIOMD0000000423_url.txt +++ b/doc/examples/biomodels/BIOMD0000000423/BIOMD0000000423_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Nyman2012_InsulinSignalling() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000424_url.txt b/doc/examples/biomodels/BIOMD0000000424/BIOMD0000000424_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000424_url.txt rename to doc/examples/biomodels/BIOMD0000000424/BIOMD0000000424_url.txt index e99d6d7dd..707b7e54d 100644 --- a/doc/examples/biomodels/BIOMD0000000424_url.txt +++ b/doc/examples/biomodels/BIOMD0000000424/BIOMD0000000424_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Faratian2009_PTENrole_TrastuzumabResistance() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000425_url.txt b/doc/examples/biomodels/BIOMD0000000425/BIOMD0000000425_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000425_url.txt rename to doc/examples/biomodels/BIOMD0000000425/BIOMD0000000425_url.txt index b23a4973b..8aa334c81 100644 --- a/doc/examples/biomodels/BIOMD0000000425_url.txt +++ b/doc/examples/biomodels/BIOMD0000000425/BIOMD0000000425_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1208300000() // Compartments and Species: @@ -9,7 +9,7 @@ model *MODEL1208300000() reaction_1: => c; reaction_1_alpha; reaction_3: c => ; reaction_3_kd*c; reaction_2: => c; c/(reaction_2_kappa + c); - reaction_4: c => ; reaction_4_phi*c/(reaction_4_delta + reaction_4_gamma*c); + reaction_4: c => ; reaction_4_phi*c/(reaction_4_delta + reaction_4_gamma_*c); // Species initializations: c = 1/cell; @@ -23,7 +23,7 @@ model *MODEL1208300000() reaction_2_kappa = 0.5; reaction_4_phi = 5e-06; reaction_4_delta = 1e-05; - reaction_4_gamma = 1e-05; + reaction_4_gamma_ = 1e-05; // Other declarations: const cell; @@ -112,7 +112,7 @@ with decreasing rates of intrinsic or antibiotic-induced degradation of C (ribos increasing dissociation between the antibiotic and C, and increasing export rate of the antibiotic. ``` - reaction_4_gamma notes "gamma represents the bacterial density" + reaction_4_gamma_ notes "gamma represents the bacterial density" end MODEL1208300000 is "Tan2012 - Antibiotic Treatment, Inoculum Effect" diff --git a/doc/examples/biomodels/BIOMD0000000426_url.txt b/doc/examples/biomodels/BIOMD0000000426/BIOMD0000000426_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000426_url.txt rename to doc/examples/biomodels/BIOMD0000000426/BIOMD0000000426_url.txt index efdebcab9..978ee9c1b 100644 --- a/doc/examples/biomodels/BIOMD0000000426_url.txt +++ b/doc/examples/biomodels/BIOMD0000000426/BIOMD0000000426_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1210150000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000427_url.txt b/doc/examples/biomodels/BIOMD0000000427/BIOMD0000000427_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000427_url.txt rename to doc/examples/biomodels/BIOMD0000000427/BIOMD0000000427_url.txt index 1c6b09b48..321350d66 100644 --- a/doc/examples/biomodels/BIOMD0000000427_url.txt +++ b/doc/examples/biomodels/BIOMD0000000427/BIOMD0000000427_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1209230000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000428_url.txt b/doc/examples/biomodels/BIOMD0000000428/BIOMD0000000428_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000428_url.txt rename to doc/examples/biomodels/BIOMD0000000428/BIOMD0000000428_url.txt index 4255e9c66..8a5794c3d 100644 --- a/doc/examples/biomodels/BIOMD0000000428_url.txt +++ b/doc/examples/biomodels/BIOMD0000000428/BIOMD0000000428_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1209130000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000429_url.txt b/doc/examples/biomodels/BIOMD0000000429/BIOMD0000000429_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000429_url.txt rename to doc/examples/biomodels/BIOMD0000000429/BIOMD0000000429_url.txt index 72c484b7c..6db29b0f7 100644 --- a/doc/examples/biomodels/BIOMD0000000429_url.txt +++ b/doc/examples/biomodels/BIOMD0000000429/BIOMD0000000429_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1209110001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000430_url.txt b/doc/examples/biomodels/BIOMD0000000430/BIOMD0000000430_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000430_url.txt rename to doc/examples/biomodels/BIOMD0000000430/BIOMD0000000430_url.txt index 0250099f2..e4aeaa33c 100644 --- a/doc/examples/biomodels/BIOMD0000000430_url.txt +++ b/doc/examples/biomodels/BIOMD0000000430/BIOMD0000000430_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1204280020() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000431_url.txt b/doc/examples/biomodels/BIOMD0000000431/BIOMD0000000431_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000431_url.txt rename to doc/examples/biomodels/BIOMD0000000431/BIOMD0000000431_url.txt index bc7b1c014..6373ce792 100644 --- a/doc/examples/biomodels/BIOMD0000000431_url.txt +++ b/doc/examples/biomodels/BIOMD0000000431/BIOMD0000000431_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1204280024() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000432_url.txt b/doc/examples/biomodels/BIOMD0000000432/BIOMD0000000432_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000432_url.txt rename to doc/examples/biomodels/BIOMD0000000432/BIOMD0000000432_url.txt index 6983615de..d1833c735 100644 --- a/doc/examples/biomodels/BIOMD0000000432_url.txt +++ b/doc/examples/biomodels/BIOMD0000000432/BIOMD0000000432_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1204280036() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000433_url.txt b/doc/examples/biomodels/BIOMD0000000433/BIOMD0000000433_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000433_url.txt rename to doc/examples/biomodels/BIOMD0000000433/BIOMD0000000433_url.txt index 6faa729ff..687656d3a 100644 --- a/doc/examples/biomodels/BIOMD0000000433_url.txt +++ b/doc/examples/biomodels/BIOMD0000000433/BIOMD0000000433_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1204280040() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000434_url.txt b/doc/examples/biomodels/BIOMD0000000434/BIOMD0000000434_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000434_url.txt rename to doc/examples/biomodels/BIOMD0000000434/BIOMD0000000434_url.txt index 22ee5ddcf..6bdd8a877 100644 --- a/doc/examples/biomodels/BIOMD0000000434_url.txt +++ b/doc/examples/biomodels/BIOMD0000000434/BIOMD0000000434_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1206010000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000435_url.txt b/doc/examples/biomodels/BIOMD0000000435/BIOMD0000000435_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000435_url.txt rename to doc/examples/biomodels/BIOMD0000000435/BIOMD0000000435_url.txt index ca4aba4c3..c43a6d148 100644 --- a/doc/examples/biomodels/BIOMD0000000435_url.txt +++ b/doc/examples/biomodels/BIOMD0000000435/BIOMD0000000435_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1211010000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000436_url.txt b/doc/examples/biomodels/BIOMD0000000436/BIOMD0000000436_url.txt similarity index 90% rename from doc/examples/biomodels/BIOMD0000000436_url.txt rename to doc/examples/biomodels/BIOMD0000000436/BIOMD0000000436_url.txt index 7493ba8c3..bea42e5d2 100644 --- a/doc/examples/biomodels/BIOMD0000000436_url.txt +++ b/doc/examples/biomodels/BIOMD0000000436/BIOMD0000000436_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000436() // Compartments and Species: @@ -39,40 +39,40 @@ model *BIOMD0000000436() r12: AA => PGH2; k12*AA*LPSactivity; // Events: - _E0: at timevalue > t0: GPChoslope = GPChoslopezero, GPChoint = GPChointzero, DGslope = DGslopezero, DGint = DGintzero, LPSslope = LPSslopezero, LPSint = LPSintzero; - _E1: at timevalue >= t1: GPChoslope = GPChoslope1, GPChoint = GPChoint1, DGslope = DGslope1, DGint = DGint1, LPSslope = LPSslope1, LPSint = LPSint1; - _E2: at timevalue >= t2: GPChoslope = GPChoslope2, GPChoint = GPChoint2, DGslope = DGslope2, DGint = DGint2; - _E3: at timevalue >= t3: GPChoslope = GPChoslope3, GPChoint = GPChoint3, DGslope = DGslope3, DGint = DGint3, LPSslope = LPSslope3, LPSint = LPSint3; - _E4: at timevalue >= t4: GPChoslope = GPChoslope4, GPChoint = GPChoint4, DGslope = DGslope4, DGint = DGint4; - _E5: at timevalue >= t5: GPChoslope = GPChoslope5, GPChoint = GPChoint5, DGslope = DGslope5, DGint = DGint5; - _E6: at timevalue >= t6: GPChoslope = GPChoslope6, GPChoint = GPChoint6, DGslope = DGslope6, DGint = DGint6; + _E0: at timevalue > t0: LPSint = LPSintzero, LPSslope = LPSslopezero, DGint = DGintzero, DGslope = DGslopezero, GPChoint = GPChointzero, GPChoslope = GPChoslopezero; + _E1: at timevalue >= t1: LPSint = LPSint1, LPSslope = LPSslope1, DGint = DGint1, DGslope = DGslope1, GPChoint = GPChoint1, GPChoslope = GPChoslope1; + _E2: at timevalue >= t2: DGint = DGint2, DGslope = DGslope2, GPChoint = GPChoint2, GPChoslope = GPChoslope2; + _E3: at timevalue >= t3: LPSint = LPSint3, LPSslope = LPSslope3, DGint = DGint3, DGslope = DGslope3, GPChoint = GPChoint3, GPChoslope = GPChoslope3; + _E4: at timevalue >= t4: DGint = DGint4, DGslope = DGslope4, GPChoint = GPChoint4, GPChoslope = GPChoslope4; + _E5: at timevalue >= t5: DGint = DGint5, DGslope = DGslope5, GPChoint = GPChoint5, GPChoslope = GPChoslope5; + _E6: at timevalue >= t6: DGint = DGint6, DGslope = DGslope6, GPChoint = GPChoint6, GPChoslope = GPChoslope6; // Species initializations: FA = 1; - FA has pmol_per_litre; + FA has pmol; HETE = 0; - HETE has pmol_per_litre; + HETE has pmol; PGH2 = 0; - PGH2 has pmol_per_litre; + PGH2 has pmol; PGE2 = 0; - PGE2 has pmol_per_litre; + PGE2 has pmol; PGF2a = 0; - PGF2a has pmol_per_litre; + PGF2a has pmol; PGD2 = 0; PGJ2 = 0; - PGJ2 has pmol_per_litre; + PGJ2 has pmol; dPGJ2 = 0; - dPGJ2 has pmol_per_litre; + dPGJ2 has pmol; AA = 25; - AA has pmol_per_litre; + AA has pmol; LPS = 0.5/c1; LPS has dimensionless_per_litre; DG = 0; DG has dimensionless_per_litre; GPCho = 1; - GPCho has pmol_per_litre; + GPCho has pmol; dPGD2 = 0; - dPGD2 has pmol_per_litre; + dPGD2 has pmol; // Compartment initializations: c1 = 1; @@ -250,8 +250,8 @@ model *BIOMD0000000436() unit pmol = 1e-12 mole; unit pmolperh = 1e-12 mole / 0.0002778 second; unit ugDNAperh = 1e-6 gram / 3600 second; - unit pmol_per_litre = 1e-12 mole / litre; unit dimensionless_per_litre = dimensionless / litre; + unit pmol_litre = 1e-12 mole * litre; // Display Names: AA is "Arachidonic acid"; @@ -281,6 +281,8 @@ model *BIOMD0000000436() k22.sboTerm = 9 DNA_.sboTerm = 2 DGperDNA.sboTerm = 2 + r14.kineticLaw.sboTerm = 44 + r22.kineticLaw.sboTerm = 1 // CV terms: c1 isVersionOf "http://identifiers.org/go/GO:0005623" diff --git a/doc/examples/biomodels/BIOMD0000000437_url.txt b/doc/examples/biomodels/BIOMD0000000437/BIOMD0000000437_url.txt similarity index 74% rename from doc/examples/biomodels/BIOMD0000000437_url.txt rename to doc/examples/biomodels/BIOMD0000000437/BIOMD0000000437_url.txt index 68c302a34..293b272a6 100644 --- a/doc/examples/biomodels/BIOMD0000000437_url.txt +++ b/doc/examples/biomodels/BIOMD0000000437/BIOMD0000000437_url.txt @@ -1,24 +1,23 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1212150000() // Compartments and Species: compartment default, c1, c2; - species L_WCC in c2, L_WCCVVDn in c2, $Period in default, Y in default; - species X in default, T in default, VVDc in c1, VVDn in c2, WC1c in c1; - species WC2c in c1, active_hypoWCCn in c2, $c_hypoFRQ_to_hyperFRQ in default; - species hypoFRQc in c1, hyperFRQc in c1, cycle in default, degraded_L_WCCCVVDn in c2; - species degraded_VVDc in c1, degraded_VVDn in c2, degraded_WC1c in c1, degraded_WC2c in c1; - species degraded_active_hypoWCCn in c2, degraded_frq_mRNA in c1, degraded_hyperFFCn in c2; - species degraded_hyperFRQc in c1, degraded_hyperWCCc in c1, degraded_hyperWCCn in c2; - species degraded_vvd_mRNA in c1, degraded_wc1_mRNA in c1, degraded_wc2_mRNA in c1; - species frq_level_A in default, frq_mRNA in c1, hyperFRQn in c2, hyperWCCc in c1; - species hyperWCCn in c2, hypoFRQn in c2, hypoWCCc in c1, hypoWCCn in c2; - species $n_hypoFRQ_to_hyperFRQ in default, time_ in default, $total_FRQ in default; - species $total_FRQc in default, $total_FRQn in default, $total_VVD in default; - species $total_WC1 in default, $total_WC2 in default, $total_WCCn in default; - species $total_hyper_FRQ in default, $total_hypoWCC in default, $total_hypo_FRQ in default; - species vvd_gene in c2, vvd_mRNA in c1, wc1_mRNA in c1, wc2_mRNA in c1; - species $total_hyperWCC in default, $s61 in default; + species L_WCC in c2, L_WCCVVDn in c2, Period in default, Y in default, X in default; + species T in default, VVDc in c1, VVDn in c2, WC1c in c1, WC2c in c1, active_hypoWCCn in c2; + species c_hypoFRQ_to_hyperFRQ in default, hypoFRQc in c1, hyperFRQc in c1; + species cycle in default, degraded_L_WCCCVVDn in c2, degraded_VVDc in c1; + species degraded_VVDn in c2, degraded_WC1c in c1, degraded_WC2c in c1, degraded_active_hypoWCCn in c2; + species degraded_frq_mRNA in c1, degraded_hyperFFCn in c2, degraded_hyperFRQc in c1; + species degraded_hyperWCCc in c1, degraded_hyperWCCn in c2, degraded_vvd_mRNA in c1; + species degraded_wc1_mRNA in c1, degraded_wc2_mRNA in c1, frq_level_A in default; + species frq_mRNA in c1, hyperFRQn in c2, hyperWCCc in c1, hyperWCCn in c2; + species hypoFRQn in c2, hypoWCCc in c1, hypoWCCn in c2, n_hypoFRQ_to_hyperFRQ in default; + species time_ in default, total_FRQ in default, total_FRQc in default, total_FRQn in default; + species total_VVD in default, total_WC1 in default, total_WC2 in default; + species total_WCCn in default, total_hyper_FRQ in default, total_hypoWCC in default; + species total_hypo_FRQ in default, vvd_gene in c2, vvd_mRNA in c1, wc1_mRNA in c1; + species wc2_mRNA in c1, total_hyperWCC in default, s61 in default; substanceOnly species $frq_gene in c2, $wc1_gene in c2, $wc2_gene in c2; substanceOnly species line in default, line2 in default, line3 in default; @@ -38,45 +37,45 @@ model *MODEL1212150000() total_hypo_FRQ := hypoFRQn + hypoFRQc; total_hyperWCC := hyperWCCn + hyperWCCc; s61 := total_hyperWCC/total_hypoWCC; - re45_time__stoichiometry := 0; - frq_transcription_frq_gene_stoichiometry := 0; - wc1_transcription_wc1_gene_stoichiometry := 0; - wc2_transcription_wc2_gene_stoichiometry := 0; - vvd_transcription_vvd_gene_stoichiometry := 0; - frq_translation_frq_mRNA_stoichiometry := 0; - wc1_translation_wc1_mRNA_stoichiometry := 0; - wc2_translation_wc2_mRNA_stoichiometry := 0; - vvd_translation_vvd_mRNA_stoichiometry := 0; - frq_mRNA_degraded_frq_mRNA_stoichiometry := 0; - wc1_mRNA_degraded_wc1_mRNA_stoichiometry := 0; - wc2_mRNA_degraded_wc2_mRNA_stoichiometry := 0; - vvd_mRNA_degraded_vvd_mRNA_stoichiometry := 0; - hyperFRQc_degraded_hyperFRQc_stoichiometry := 0; - hyperFRQn_degraded_hyperFFCn_stoichiometry := 0; - WC1c_degraded_WC1c_stoichiometry := 0; - WC2c_degraded_WC2c_stoichiometry := 0; - hyperWCCc_degraded_hyperWCCc_stoichiometry := 0; - hyperWCCn_degraded_hyperWCCn_stoichiometry := 0; - active_hypoWCCn_degraded_active_hypoWCCn_stoichiometry := 0; - L_WCC_degraded_L_WCCCVVDn_stoichiometry := 0; - VVDc_degraded_VVDc_stoichiometry := 0; - VVDn_degraded_VVDn_stoichiometry := 0; - L_WCCVVDn_degraded_L_WCCCVVDn_stoichiometry := 0; + re45_time__stoichiometry0 := 0; + frq_transcription_frq_gene_stoichiometry0 := 0; + wc1_transcription_wc1_gene_stoichiometry0 := 0; + wc2_transcription_wc2_gene_stoichiometry0 := 0; + vvd_transcription_vvd_gene_stoichiometry0 := 0; + frq_translation_frq_mRNA_stoichiometry0 := 0; + wc1_translation_wc1_mRNA_stoichiometry0 := 0; + wc2_translation_wc2_mRNA_stoichiometry0 := 0; + vvd_translation_vvd_mRNA_stoichiometry0 := 0; + frq_mRNA_degradation_degraded_frq_mRNA_stoichiometry0 := 0; + wc1_mRNA_degradation_degraded_wc1_mRNA_stoichiometry0 := 0; + wc2_mRNA_degradation_degraded_wc2_mRNA_stoichiometry0 := 0; + vvd_mRNA_degradation_degraded_vvd_mRNA_stoichiometry0 := 0; + hyperFRQc_degradation_degraded_hyperFRQc_stoichiometry0 := 0; + hyperFFCn_degradation_degraded_hyperFFCn_stoichiometry0 := 0; + WC1c_degradation_degraded_WC1c_stoichiometry0 := 0; + WC2c_degradation_degraded_WC2c_stoichiometry0 := 0; + hyperWCCc_degradation_degraded_hyperWCCc_stoichiometry0 := 0; + hyperWCCn_degradation_degraded_hyperWCCn_stoichiometry0 := 0; + active_hypoWCCn_degradation_degraded_active_hypoWCCn_stoichiometry0 := 0; + L_WCC_degradation_degraded_L_WCCCVVDn_stoichiometry0 := 0; + VVDc_degradation_degraded_VVDc_stoichiometry0 := 0; + VVDn_degradation_degraded_VVDn_stoichiometry0 := 0; + L_WCCVVD_degradation_degraded_L_WCCCVVDn_stoichiometry0 := 0; // Reactions: - re45: re45_time__stoichiometry time_ => T; 1; - frq_transcription: frq_transcription_frq_gene_stoichiometry $frq_gene => frq_mRNA; kmax_frq*(active_hypoWCCn^A_active_hypoWCCn_frq/(Km_frq^A_active_hypoWCCn_frq + active_hypoWCCn^A_active_hypoWCCn_frq)) + kadd_light_frq*L_WCC; - wc1_transcription: wc1_transcription_wc1_gene_stoichiometry $wc1_gene => wc1_mRNA; k_min_wc1 + kadd_wc1*active_hypoWCCn + kadd_L_wc1*L_WCC; - wc2_transcription: wc2_transcription_wc2_gene_stoichiometry $wc2_gene => wc2_mRNA; kmax_wc2*(1/(1 + hypoWCCn*ki_wc2_transcription)) + hypoFRQn*kadd_wc2_transcription_hypoFRQn; - vvd_transcription: vvd_transcription_vvd_gene_stoichiometry vvd_gene => vvd_mRNA; kadd_vvd_light_mRNA*L_WCC; - frq_translation: frq_translation_frq_mRNA_stoichiometry frq_mRNA => hypoFRQc; frq_mRNA*k_hypoFRQc; - wc1_translation: wc1_translation_wc1_mRNA_stoichiometry wc1_mRNA => WC1c; k_WC1c*wc1_mRNA; - wc2_translation: wc2_translation_wc2_mRNA_stoichiometry wc2_mRNA => WC2c; wc2_mRNA*k_WC2c; - vvd_translation: vvd_translation_vvd_mRNA_stoichiometry vvd_mRNA => VVDc; k_VVDc*vvd_mRNA; - frq_mRNA_degradation: frq_mRNA => frq_mRNA_degraded_frq_mRNA_stoichiometry degraded_frq_mRNA; frq_mRNA*(kd_frq + hypoFRQc*kdfrq_hypoFRQc); - wc1_mRNA_degradation: wc1_mRNA => wc1_mRNA_degraded_wc1_mRNA_stoichiometry degraded_wc1_mRNA; wc1_mRNA*kd_wc1; - wc2_mRNA_degradation: wc2_mRNA => wc2_mRNA_degraded_wc2_mRNA_stoichiometry degraded_wc2_mRNA; wc2_mRNA*kd_wc2; - vvd_mRNA_degradation: vvd_mRNA => vvd_mRNA_degraded_vvd_mRNA_stoichiometry degraded_vvd_mRNA; kd_vvd_mRNA*vvd_mRNA; + re45: re45_time__stoichiometry0 time_ => T; 1; + frq_transcription: frq_transcription_frq_gene_stoichiometry0 $frq_gene => frq_mRNA; kmax_frq*(active_hypoWCCn^A_active_hypoWCCn_frq/(Km_frq^A_active_hypoWCCn_frq + active_hypoWCCn^A_active_hypoWCCn_frq)) + kadd_light_frq*L_WCC; + wc1_transcription: wc1_transcription_wc1_gene_stoichiometry0 $wc1_gene => wc1_mRNA; k_min_wc1 + kadd_wc1*active_hypoWCCn + kadd_L_wc1*L_WCC; + wc2_transcription: wc2_transcription_wc2_gene_stoichiometry0 $wc2_gene => wc2_mRNA; kmax_wc2*(1/(1 + hypoWCCn*ki_wc2_transcription)) + hypoFRQn*kadd_wc2_transcription_hypoFRQn; + vvd_transcription: vvd_transcription_vvd_gene_stoichiometry0 vvd_gene => vvd_mRNA; kadd_vvd_light_mRNA*L_WCC; + frq_translation: frq_translation_frq_mRNA_stoichiometry0 frq_mRNA => hypoFRQc; frq_mRNA*k_hypoFRQc; + wc1_translation: wc1_translation_wc1_mRNA_stoichiometry0 wc1_mRNA => WC1c; k_WC1c*wc1_mRNA; + wc2_translation: wc2_translation_wc2_mRNA_stoichiometry0 wc2_mRNA => WC2c; wc2_mRNA*k_WC2c; + vvd_translation: vvd_translation_vvd_mRNA_stoichiometry0 vvd_mRNA => VVDc; k_VVDc*vvd_mRNA; + frq_mRNA_degradation: frq_mRNA => frq_mRNA_degradation_degraded_frq_mRNA_stoichiometry0 degraded_frq_mRNA; frq_mRNA*(kd_frq + hypoFRQc*kdfrq_hypoFRQc); + wc1_mRNA_degradation: wc1_mRNA => wc1_mRNA_degradation_degraded_wc1_mRNA_stoichiometry0 degraded_wc1_mRNA; wc1_mRNA*kd_wc1; + wc2_mRNA_degradation: wc2_mRNA => wc2_mRNA_degradation_degraded_wc2_mRNA_stoichiometry0 degraded_wc2_mRNA; wc2_mRNA*kd_wc2; + vvd_mRNA_degradation: vvd_mRNA => vvd_mRNA_degradation_degraded_vvd_mRNA_stoichiometry0 degraded_vvd_mRNA; kd_vvd_mRNA*vvd_mRNA; hypoWCCc_formation: WC1c + WC2c => hypoWCCc; WC1c*WC2c*k_hypoWCCc; hypoFRQc_translocation_in_nucleus: hypoFRQc => hypoFRQn; kin_hypoFRQc*hypoFRQc; hypoWCCc_translocation_in_nucleus: hypoWCCc => hypoWCCn; hypoWCCc*kin_hypoWCCc; @@ -93,17 +92,17 @@ model *MODEL1212150000() L_WCC_formation: hypoWCCn => L_WCC; kact_L_WCC*hypoWCCn; WCCVVD_complex_formation: VVDn + L_WCC => L_WCCVVDn; VVDn*L_WCC*k_WCCVVD; WCCVVD_complex_disassociation: L_WCCVVDn => hypoWCCn + VVDn; L_WCCVVDn*k_dis_WCCVVD; - hyperFRQc_degradation: hyperFRQc => hyperFRQc_degraded_hyperFRQc_stoichiometry degraded_hyperFRQc; hyperFRQc*kd_hyperFRQc; - hyperFFCn_degradation: hyperFRQn => hyperFRQn_degraded_hyperFFCn_stoichiometry degraded_hyperFFCn; hyperFRQn*kd_hyperFRQn; - WC1c_degradation: WC1c => WC1c_degraded_WC1c_stoichiometry degraded_WC1c; WC1c*kd_WC1c; - WC2c_degradation: WC2c => WC2c_degraded_WC2c_stoichiometry degraded_WC2c; WC2c*kd_WC2c; - hyperWCCc_degradation: hyperWCCc => hyperWCCc_degraded_hyperWCCc_stoichiometry degraded_hyperWCCc; hyperWCCc*kd_hyperWCCc; - hyperWCCn_degradation: hyperWCCn => hyperWCCn_degraded_hyperWCCn_stoichiometry degraded_hyperWCCn; hyperWCCn*kd_hyperWCCn; - active_hypoWCCn_degradation: active_hypoWCCn => active_hypoWCCn_degraded_active_hypoWCCn_stoichiometry degraded_active_hypoWCCn; active_hypoWCCn*kd_active_hypoWCCn; - L_WCC_degradation: L_WCC => L_WCC_degraded_L_WCCCVVDn_stoichiometry degraded_L_WCCCVVDn; L_WCC*kd_L_WCC; - VVDc_degradation: VVDc => VVDc_degraded_VVDc_stoichiometry degraded_VVDc; VVDc*kd_VVDc; - VVDn_degradation: VVDn => VVDn_degraded_VVDn_stoichiometry degraded_VVDn; VVDn*kd_VVDn; - L_WCCVVD_degradation: L_WCCVVDn => L_WCCVVDn_degraded_L_WCCCVVDn_stoichiometry degraded_L_WCCCVVDn; L_WCCVVDn*kd_WCCVVD; + hyperFRQc_degradation: hyperFRQc => hyperFRQc_degradation_degraded_hyperFRQc_stoichiometry0 degraded_hyperFRQc; hyperFRQc*kd_hyperFRQc; + hyperFFCn_degradation: hyperFRQn => hyperFFCn_degradation_degraded_hyperFFCn_stoichiometry0 degraded_hyperFFCn; hyperFRQn*kd_hyperFRQn; + WC1c_degradation: WC1c => WC1c_degradation_degraded_WC1c_stoichiometry0 degraded_WC1c; WC1c*kd_WC1c; + WC2c_degradation: WC2c => WC2c_degradation_degraded_WC2c_stoichiometry0 degraded_WC2c; WC2c*kd_WC2c; + hyperWCCc_degradation: hyperWCCc => hyperWCCc_degradation_degraded_hyperWCCc_stoichiometry0 degraded_hyperWCCc; hyperWCCc*kd_hyperWCCc; + hyperWCCn_degradation: hyperWCCn => hyperWCCn_degradation_degraded_hyperWCCn_stoichiometry0 degraded_hyperWCCn; hyperWCCn*kd_hyperWCCn; + active_hypoWCCn_degradation: active_hypoWCCn => active_hypoWCCn_degradation_degraded_active_hypoWCCn_stoichiometry0 degraded_active_hypoWCCn; active_hypoWCCn*kd_active_hypoWCCn; + L_WCC_degradation: L_WCC => L_WCC_degradation_degraded_L_WCCCVVDn_stoichiometry0 degraded_L_WCCCVVDn; L_WCC*kd_L_WCC; + VVDc_degradation: VVDc => VVDc_degradation_degraded_VVDc_stoichiometry0 degraded_VVDc; VVDc*kd_VVDc; + VVDn_degradation: VVDn => VVDn_degradation_degraded_VVDn_stoichiometry0 degraded_VVDn; VVDn*kd_VVDn; + L_WCCVVD_degradation: L_WCCVVDn => L_WCCVVD_degradation_degraded_L_WCCCVVDn_stoichiometry0 degraded_L_WCCCVVDn; L_WCCVVDn*kd_WCCVVD; // Events: n_CYCLE: at 0 after (time > 125) && (frq_mRNA > frq_level_A): cycle = cycle + 1; @@ -141,7 +140,7 @@ model *MODEL1212150000() degraded_vvd_mRNA = 0; degraded_wc1_mRNA = 0; degraded_wc2_mRNA = 0; - frq_gene = 1/c2; + frq_gene = 1*c2; frq_level_A = 0; frq_mRNA = 0.22321; hyperFRQn = 0.07298/c2; @@ -153,9 +152,9 @@ model *MODEL1212150000() time_ = 0; vvd_gene = 1/c2; vvd_mRNA = 0; - wc1_gene = 1/c2; + wc1_gene = 1*c2; wc1_mRNA = 0.5218; - wc2_gene = 1/c2; + wc2_gene = 1*c2; wc2_mRNA = 0.636098; line = 1.8728; line2 = 0.985; diff --git a/doc/examples/biomodels/BIOMD0000000438_url.txt b/doc/examples/biomodels/BIOMD0000000438/BIOMD0000000438_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000438_url.txt rename to doc/examples/biomodels/BIOMD0000000438/BIOMD0000000438_url.txt index 39e3740f9..6706e0c84 100644 --- a/doc/examples/biomodels/BIOMD0000000438_url.txt +++ b/doc/examples/biomodels/BIOMD0000000438/BIOMD0000000438_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1301110000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000439_url.txt b/doc/examples/biomodels/BIOMD0000000439/BIOMD0000000439_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000439_url.txt rename to doc/examples/biomodels/BIOMD0000000439/BIOMD0000000439_url.txt index 2c8fbd309..3256b7af7 100644 --- a/doc/examples/biomodels/BIOMD0000000439_url.txt +++ b/doc/examples/biomodels/BIOMD0000000439/BIOMD0000000439_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1212040001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000440_url.txt b/doc/examples/biomodels/BIOMD0000000440/BIOMD0000000440_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000440_url.txt rename to doc/examples/biomodels/BIOMD0000000440/BIOMD0000000440_url.txt index 770650d49..a045a1862 100644 --- a/doc/examples/biomodels/BIOMD0000000440_url.txt +++ b/doc/examples/biomodels/BIOMD0000000440/BIOMD0000000440_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1112190003() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000441_url.txt b/doc/examples/biomodels/BIOMD0000000441/BIOMD0000000441_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000441_url.txt rename to doc/examples/biomodels/BIOMD0000000441/BIOMD0000000441_url.txt index 8c46ea3aa..a4bf023f0 100644 --- a/doc/examples/biomodels/BIOMD0000000441_url.txt +++ b/doc/examples/biomodels/BIOMD0000000441/BIOMD0000000441_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1112190004() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000442_url.txt b/doc/examples/biomodels/BIOMD0000000442/BIOMD0000000442_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000442_url.txt rename to doc/examples/biomodels/BIOMD0000000442/BIOMD0000000442_url.txt index 2cde20122..34093f9af 100644 --- a/doc/examples/biomodels/BIOMD0000000442_url.txt +++ b/doc/examples/biomodels/BIOMD0000000442/BIOMD0000000442_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1112190005() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000443_url.txt b/doc/examples/biomodels/BIOMD0000000443/BIOMD0000000443_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000443_url.txt rename to doc/examples/biomodels/BIOMD0000000443/BIOMD0000000443_url.txt index 27f2e83d1..f6f9af96a 100644 --- a/doc/examples/biomodels/BIOMD0000000443_url.txt +++ b/doc/examples/biomodels/BIOMD0000000443/BIOMD0000000443_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1112190006() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000444_url.txt b/doc/examples/biomodels/BIOMD0000000444/BIOMD0000000444_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000444_url.txt rename to doc/examples/biomodels/BIOMD0000000444/BIOMD0000000444_url.txt index 2d057987d..e1f24d614 100644 --- a/doc/examples/biomodels/BIOMD0000000444_url.txt +++ b/doc/examples/biomodels/BIOMD0000000444/BIOMD0000000444_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1112190007() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000445_url.txt b/doc/examples/biomodels/BIOMD0000000445/BIOMD0000000445_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000445_url.txt rename to doc/examples/biomodels/BIOMD0000000445/BIOMD0000000445_url.txt index e44476741..8a0899b78 100644 --- a/doc/examples/biomodels/BIOMD0000000445_url.txt +++ b/doc/examples/biomodels/BIOMD0000000445/BIOMD0000000445_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1209110002() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000446_url.txt b/doc/examples/biomodels/BIOMD0000000446/BIOMD0000000446_url.txt similarity index 93% rename from doc/examples/biomodels/BIOMD0000000446_url.txt rename to doc/examples/biomodels/BIOMD0000000446/BIOMD0000000446_url.txt index bb7cc65ea..4c100d286 100644 --- a/doc/examples/biomodels/BIOMD0000000446_url.txt +++ b/doc/examples/biomodels/BIOMD0000000446/BIOMD0000000446_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1302180000() // Compartments and Species: @@ -92,59 +92,59 @@ model *MODEL1302180000() // Species initializations: UFPT = 0; - UFPT has substance_per_volume; + UFPT has substance; BiUFP = 0; - BiUFP has substance_per_volume; + BiUFP has substance; BiRE1 = 0; - BiRE1 has substance_per_volume; + BiRE1 has substance; BiATF = 0; - BiATF has substance_per_volume; + BiATF has substance; BiPER = 0; - BiPER has substance_per_volume; + BiPER has substance; IRE1A = 0; - IRE1A has substance_per_volume; + IRE1A has substance; PERKA = 0; - PERKA has substance_per_volume; + PERKA has substance; mXbp1u = 0; - mXbp1u has substance_per_volume; + mXbp1u has substance; mXbp1s = 0; - mXbp1s has substance_per_volume; + mXbp1s has substance; Xbp1s = 0; - Xbp1s has substance_per_volume; + Xbp1s has substance; mBiPT = 0; - mBiPT has substance_per_volume; + mBiPT has substance; BiPT = 0; - BiPT has substance_per_volume; + BiPT has substance; ATF6T = 0; - ATF6T has substance_per_volume; + ATF6T has substance; ATF6GB = 0; - ATF6GB has substance_per_volume; + ATF6GB has substance; ATF6p50 = 0; - ATF6p50 has substance_per_volume; + ATF6p50 has substance; mWFS1 = 0; - mWFS1 has substance_per_volume; + mWFS1 has substance; WFS1 = 0; - WFS1 has substance_per_volume; + WFS1 has substance; ATF4 = 0; - ATF4 has substance_per_volume; + ATF4 has substance; mCHOP = 0; - mCHOP has substance_per_volume; + mCHOP has substance; CHOP = 0; - CHOP has substance_per_volume; + CHOP has substance; mGADD34 = 0; - mGADD34 has substance_per_volume; + mGADD34 has substance; GADD34 = 0; - GADD34 has substance_per_volume; + GADD34 has substance; BCL2T = 0; - BCL2T has substance_per_volume; + BCL2T has substance; BAXmT = 0; - BAXmT has substance_per_volume; + BAXmT has substance; BH3T = 0; - BH3T has substance_per_volume; + BH3T has substance; BAXmBCL2 = 0; - BAXmBCL2 has substance_per_volume; + BAXmBCL2 has substance; BH3BCL2 = 0; - BH3BCL2 has substance_per_volume; + BH3BCL2 has substance; // Compartment initializations: ERlumen = 1; @@ -357,7 +357,7 @@ model *MODEL1302180000() unit rate1 = 1 / second; unit substance1 = 1 / mole; unit rate3 = 1 / (mole^3 * second); - unit substance_per_volume = mole / litre; + unit substance_volume = mole * litre; // Display Names: substance is "acu"; diff --git a/doc/examples/biomodels/BIOMD0000000447_url.txt b/doc/examples/biomodels/BIOMD0000000447/BIOMD0000000447_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000447_url.txt rename to doc/examples/biomodels/BIOMD0000000447/BIOMD0000000447_url.txt index b8e45e4fa..00c916682 100644 --- a/doc/examples/biomodels/BIOMD0000000447_url.txt +++ b/doc/examples/biomodels/BIOMD0000000447/BIOMD0000000447_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1303130000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000448_url.txt b/doc/examples/biomodels/BIOMD0000000448/BIOMD0000000448_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000448_url.txt rename to doc/examples/biomodels/BIOMD0000000448/BIOMD0000000448_url.txt index f600c5e60..5dd86b098 100644 --- a/doc/examples/biomodels/BIOMD0000000448_url.txt +++ b/doc/examples/biomodels/BIOMD0000000448/BIOMD0000000448_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1304190000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000449_url.txt b/doc/examples/biomodels/BIOMD0000000449/BIOMD0000000449_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000449_url.txt rename to doc/examples/biomodels/BIOMD0000000449/BIOMD0000000449_url.txt index a283f16d1..cccfae2d4 100644 --- a/doc/examples/biomodels/BIOMD0000000449_url.txt +++ b/doc/examples/biomodels/BIOMD0000000449/BIOMD0000000449_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1304160000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000450_url.txt b/doc/examples/biomodels/BIOMD0000000450/BIOMD0000000450_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000450_url.txt rename to doc/examples/biomodels/BIOMD0000000450/BIOMD0000000450_url.txt index 8399abb80..1e34e7b38 100644 --- a/doc/examples/biomodels/BIOMD0000000450_url.txt +++ b/doc/examples/biomodels/BIOMD0000000450/BIOMD0000000450_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1305060001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000451_url.txt b/doc/examples/biomodels/BIOMD0000000451/BIOMD0000000451_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000451_url.txt rename to doc/examples/biomodels/BIOMD0000000451/BIOMD0000000451_url.txt index 112c5e451..422161983 100644 --- a/doc/examples/biomodels/BIOMD0000000451_url.txt +++ b/doc/examples/biomodels/BIOMD0000000451/BIOMD0000000451_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1304230001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000452_url.txt b/doc/examples/biomodels/BIOMD0000000452/BIOMD0000000452_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000452_url.txt rename to doc/examples/biomodels/BIOMD0000000452/BIOMD0000000452_url.txt index 797e46663..07a17eda7 100644 --- a/doc/examples/biomodels/BIOMD0000000452_url.txt +++ b/doc/examples/biomodels/BIOMD0000000452/BIOMD0000000452_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1304020000() // Compartments and Species: @@ -90,7 +90,7 @@ model *MODEL1304020000() species mw9b937ca3_0d82_46d5_8f5a_0f9701002797 in mw1637dd35_5f09_4a8d_bb7f_58717cdf1612; species mw57a44eb0_ace7_4294_905a_219e87d3c281 in mw1637dd35_5f09_4a8d_bb7f_58717cdf1612; species mwd746a5d5_5e65_4a4c_9f84_0e4a3cb7d2fc in mw1637dd35_5f09_4a8d_bb7f_58717cdf1612; - species $mwa6994523_5d45_4000_af0c_3e94073bf183 in mw1637dd35_5f09_4a8d_bb7f_58717cdf1612; + species mwa6994523_5d45_4000_af0c_3e94073bf183 in mw1637dd35_5f09_4a8d_bb7f_58717cdf1612; species mwdf92bdc0_f426_45b0_9ad0_876521f41312 in mw1637dd35_5f09_4a8d_bb7f_58717cdf1612; species mw13abe2a6_9905_40e5_8c23_3fc8834b572a in mw1637dd35_5f09_4a8d_bb7f_58717cdf1612; species mw2fd710a6_7fe2_4484_bca6_59c187bade8b in mw1637dd35_5f09_4a8d_bb7f_58717cdf1612; diff --git a/doc/examples/biomodels/BIOMD0000000453_url.txt b/doc/examples/biomodels/BIOMD0000000453/BIOMD0000000453_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000453_url.txt rename to doc/examples/biomodels/BIOMD0000000453/BIOMD0000000453_url.txt index c89701f13..6d29bcd15 100644 --- a/doc/examples/biomodels/BIOMD0000000453_url.txt +++ b/doc/examples/biomodels/BIOMD0000000453/BIOMD0000000453_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1304020001() // Compartments and Species: @@ -90,7 +90,7 @@ model *MODEL1304020001() species mw9b937ca3_0d82_46d5_8f5a_0f9701002797 in mw1637dd35_5f09_4a8d_bb7f_58717cdf1612; species mw57a44eb0_ace7_4294_905a_219e87d3c281 in mw1637dd35_5f09_4a8d_bb7f_58717cdf1612; species mwd746a5d5_5e65_4a4c_9f84_0e4a3cb7d2fc in mw1637dd35_5f09_4a8d_bb7f_58717cdf1612; - species $mwa6994523_5d45_4000_af0c_3e94073bf183 in mw1637dd35_5f09_4a8d_bb7f_58717cdf1612; + species mwa6994523_5d45_4000_af0c_3e94073bf183 in mw1637dd35_5f09_4a8d_bb7f_58717cdf1612; species mwdf92bdc0_f426_45b0_9ad0_876521f41312 in mw1637dd35_5f09_4a8d_bb7f_58717cdf1612; species mw13abe2a6_9905_40e5_8c23_3fc8834b572a in mw1637dd35_5f09_4a8d_bb7f_58717cdf1612; species mw2fd710a6_7fe2_4484_bca6_59c187bade8b in mw1637dd35_5f09_4a8d_bb7f_58717cdf1612; diff --git a/doc/examples/biomodels/BIOMD0000000454_url.txt b/doc/examples/biomodels/BIOMD0000000454/BIOMD0000000454_url.txt similarity index 96% rename from doc/examples/biomodels/BIOMD0000000454_url.txt rename to doc/examples/biomodels/BIOMD0000000454/BIOMD0000000454_url.txt index 917f73c76..d4077d4a9 100644 --- a/doc/examples/biomodels/BIOMD0000000454_url.txt +++ b/doc/examples/biomodels/BIOMD0000000454/BIOMD0000000454_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1305030000() // Compartments and Species: @@ -62,9 +62,13 @@ model *MODEL1305030000() y4.sboTerm = 247 y5.sboTerm = 247 v1.sboTerm = 176 + v1.kineticLaw.sboTerm = 430 v2.sboTerm = 176 + v2.kineticLaw.sboTerm = 430 v3.sboTerm = 176 + v3.kineticLaw.sboTerm = 430 v4.sboTerm = 176 + v4.kineticLaw.sboTerm = 430 // CV terms: cell identity "http://identifiers.org/go/GO:0005623" diff --git a/doc/examples/biomodels/BIOMD0000000455_url.txt b/doc/examples/biomodels/BIOMD0000000455/BIOMD0000000455_url.txt similarity index 96% rename from doc/examples/biomodels/BIOMD0000000455_url.txt rename to doc/examples/biomodels/BIOMD0000000455/BIOMD0000000455_url.txt index 5e6165fc5..0c2405117 100644 --- a/doc/examples/biomodels/BIOMD0000000455_url.txt +++ b/doc/examples/biomodels/BIOMD0000000455/BIOMD0000000455_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1305030001() // Compartments and Species: @@ -69,10 +69,15 @@ model *MODEL1305030001() y5.sboTerm = 247 y6.sboTerm = 247 v1.sboTerm = 176 + v1.kineticLaw.sboTerm = 430 v2.sboTerm = 176 + v2.kineticLaw.sboTerm = 430 v3.sboTerm = 176 + v3.kineticLaw.sboTerm = 430 v4.sboTerm = 176 + v4.kineticLaw.sboTerm = 430 v5.sboTerm = 176 + v5.kineticLaw.sboTerm = 430 // CV terms: cell identity "http://identifiers.org/go/GO:0005623" diff --git a/doc/examples/biomodels/BIOMD0000000456_url.txt b/doc/examples/biomodels/BIOMD0000000456/BIOMD0000000456_url.txt similarity index 95% rename from doc/examples/biomodels/BIOMD0000000456_url.txt rename to doc/examples/biomodels/BIOMD0000000456/BIOMD0000000456_url.txt index e195eee4e..26c100763 100644 --- a/doc/examples/biomodels/BIOMD0000000456_url.txt +++ b/doc/examples/biomodels/BIOMD0000000456/BIOMD0000000456_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1305030002() // Compartments and Species: @@ -78,11 +78,17 @@ model *MODEL1305030002() x4.sboTerm = 247 y8.sboTerm = 247 v1.sboTerm = 176 + v1.kineticLaw.sboTerm = 430 v2.sboTerm = 176 + v2.kineticLaw.sboTerm = 430 v3.sboTerm = 176 + v3.kineticLaw.sboTerm = 430 v4.sboTerm = 176 + v4.kineticLaw.sboTerm = 430 v6.sboTerm = 176 + v6.kineticLaw.sboTerm = 430 v7.sboTerm = 176 + v7.kineticLaw.sboTerm = 430 // CV terms: cell identity "http://identifiers.org/go/GO:0005623" diff --git a/doc/examples/biomodels/BIOMD0000000457_url.txt b/doc/examples/biomodels/BIOMD0000000457/BIOMD0000000457_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000457_url.txt rename to doc/examples/biomodels/BIOMD0000000457/BIOMD0000000457_url.txt index 864cb8819..ea8f03206 100644 --- a/doc/examples/biomodels/BIOMD0000000457_url.txt +++ b/doc/examples/biomodels/BIOMD0000000457/BIOMD0000000457_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000457() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000458_url.txt b/doc/examples/biomodels/BIOMD0000000458/BIOMD0000000458_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000458_url.txt rename to doc/examples/biomodels/BIOMD0000000458/BIOMD0000000458_url.txt index 30bcc3939..7dc0816e2 100644 --- a/doc/examples/biomodels/BIOMD0000000458_url.txt +++ b/doc/examples/biomodels/BIOMD0000000458/BIOMD0000000458_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000458() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000459_url.txt b/doc/examples/biomodels/BIOMD0000000459/BIOMD0000000459_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000459_url.txt rename to doc/examples/biomodels/BIOMD0000000459/BIOMD0000000459_url.txt index 66ce5e894..bfed37dfd 100644 --- a/doc/examples/biomodels/BIOMD0000000459_url.txt +++ b/doc/examples/biomodels/BIOMD0000000459/BIOMD0000000459_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1302080001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000460_url.txt b/doc/examples/biomodels/BIOMD0000000460/BIOMD0000000460_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000460_url.txt rename to doc/examples/biomodels/BIOMD0000000460/BIOMD0000000460_url.txt index bb0247b92..d94ec0827 100644 --- a/doc/examples/biomodels/BIOMD0000000460_url.txt +++ b/doc/examples/biomodels/BIOMD0000000460/BIOMD0000000460_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1302080000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000461_url.txt b/doc/examples/biomodels/BIOMD0000000461/BIOMD0000000461_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000461_url.txt rename to doc/examples/biomodels/BIOMD0000000461/BIOMD0000000461_url.txt index 87b80f80c..2782747c8 100644 --- a/doc/examples/biomodels/BIOMD0000000461_url.txt +++ b/doc/examples/biomodels/BIOMD0000000461/BIOMD0000000461_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1212180000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000462_url.txt b/doc/examples/biomodels/BIOMD0000000462/BIOMD0000000462_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000462_url.txt rename to doc/examples/biomodels/BIOMD0000000462/BIOMD0000000462_url.txt index 4c139bb39..86ea3b96f 100644 --- a/doc/examples/biomodels/BIOMD0000000462_url.txt +++ b/doc/examples/biomodels/BIOMD0000000462/BIOMD0000000462_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000462() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000463_url.txt b/doc/examples/biomodels/BIOMD0000000463/BIOMD0000000463_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000463_url.txt rename to doc/examples/biomodels/BIOMD0000000463/BIOMD0000000463_url.txt index 5ffbe05c9..cd9d2beeb 100644 --- a/doc/examples/biomodels/BIOMD0000000463_url.txt +++ b/doc/examples/biomodels/BIOMD0000000463/BIOMD0000000463_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1307270000() // Compartments and Species: @@ -228,7 +228,7 @@ model *MODEL1307270000() unit length = metre; unit area = metre^2; unit volume = dimensionless; - unit time_unit = time_unit; + unit time_unit = 3600 second; unit substance = dimensionless; unit extent = substance; unit mole_per_litre = mole / litre; diff --git a/doc/examples/biomodels/BIOMD0000000464_url.txt b/doc/examples/biomodels/BIOMD0000000464/BIOMD0000000464_url.txt similarity index 90% rename from doc/examples/biomodels/BIOMD0000000464_url.txt rename to doc/examples/biomodels/BIOMD0000000464/BIOMD0000000464_url.txt index 66c686248..d7dc9a6bf 100644 --- a/doc/examples/biomodels/BIOMD0000000464_url.txt +++ b/doc/examples/biomodels/BIOMD0000000464/BIOMD0000000464_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1302180003() // Compartments and Species: @@ -21,33 +21,33 @@ model *MODEL1302180003() // Species initializations: s1 = 1500000; - s1 has substance_per_volume; + s1 has substance; s2 = 2830000; - s2 has substance_per_volume; + s2 has substance; s3 = 117.2; - s3 has substance_per_volume; + s3 has substance; s4 = 3870; - s4 has substance_per_volume; + s4 has substance; s5 = 0; - s5 has substance_per_volume; + s5 has substance; s6 = 0; - s6 has substance_per_volume; + s6 has substance; s7 = 0; - s7 has substance_per_volume; + s7 has substance; s8 = 0; - s8 has substance_per_volume; + s8 has substance; s9 = 0; - s9 has substance_per_volume; + s9 has substance; s10 = 0; - s10 has substance_per_volume; + s10 has substance; s11 = 0; - s11 has substance_per_volume; + s11 has substance; s12 = 0; - s12 has substance_per_volume; + s12 has substance; s13 = 0; - s13 has substance_per_volume; + s13 has substance; s119 = 0; - s119 has substance_per_volume; + s119 has substance; // Compartment initializations: default = 1; @@ -131,7 +131,7 @@ model *MODEL1302180003() unit inv_sec_sub = 1 / (1e-09 mole * second); unit nM_inv_s = 1e-9 mole / second; unit inv_nM_s = 1 / (1e-9 mole * second); - unit substance_per_volume = 1e-09 mole / litre; + unit substance_volume = 1e-09 mole * litre; // Display Names: time_unit is "time"; diff --git a/doc/examples/biomodels/BIOMD0000000465_url.txt b/doc/examples/biomodels/BIOMD0000000465/BIOMD0000000465_url.txt similarity index 88% rename from doc/examples/biomodels/BIOMD0000000465_url.txt rename to doc/examples/biomodels/BIOMD0000000465/BIOMD0000000465_url.txt index 8d6945fcb..037153e61 100644 --- a/doc/examples/biomodels/BIOMD0000000465_url.txt +++ b/doc/examples/biomodels/BIOMD0000000465/BIOMD0000000465_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1302180004() // Compartments and Species: @@ -9,7 +9,7 @@ model *MODEL1302180004() substanceOnly species s119 in default; // Reactions: - re57: s22 -> s20; exp(re57_unity - (s23/re57_tf)^1.8)*re57_normal*(s23/re57_unimol)^0.8*(re57_unity - (s23/re57_tf)^1.8); + re57: s22 -> s20; exp(re57_unity - (s23/re57_tf)^1.8)*re57_normal_*(s23/re57_unimol)^0.8*(re57_unity - (s23/re57_tf)^1.8); re58: s19 => s17; re58_k2*s19*s20/(re58_Km2 + s19); re59: s17 => s19; re59_k3*s17*s18/(re59_Km3 + s17); re60: s17 + s16 -> s28; re60_k4*s17*s16 - re60_kr4*s28; @@ -24,37 +24,37 @@ model *MODEL1302180004() // Species initializations: s14 = 0.246; - s14 has substance_per_volume; + s14 has substance; s15 = 150; - s15 has substance_per_volume; + s15 has substance; s16 = 167.616; - s16 has substance_per_volume; + s16 has substance; s17 = 0.345; - s17 has substance_per_volume; + s17 has substance; s18 = 0.1; - s18 has substance_per_volume; + s18 has substance; s19 = 6967.271; - s19 has substance_per_volume; + s19 has substance; s20 = 0.03; - s20 has substance_per_volume; + s20 has substance; s21 = 0; - s21 has substance_per_volume; + s21 has substance; s22 = 99.97; - s22 has substance_per_volume; + s22 has substance; s23 = 0; - s23 has substance_per_volume; + s23 has substance; s24 = 3; - s24 has substance_per_volume; + s24 has substance; s25 = 999.754; - s25 has substance_per_volume; + s25 has substance; s26 = 1.457; - s26 has substance_per_volume; + s26 has substance; s27 = 1.723; - s27 has substance_per_volume; + s27 has substance; s28 = 29.203; - s28 has substance_per_volume; + s28 has substance; s119 = 0; - s119 has substance_per_volume; + s119 has substance; // Compartment initializations: default = 1; @@ -63,8 +63,8 @@ model *MODEL1302180004() c1 has volume; // Variable initializations: - re57_normal = 0.907; - re57_normal has sub_sec; + re57_normal_ = 0.907; + re57_normal_ has sub_sec; re57_unity = 1; re57_unity has dimensionless; re57_unimol = 1; @@ -124,7 +124,7 @@ model *MODEL1302180004() unit inv_sec_sub = 1 / (1e-09 mole * second); unit nM_inv_s = 1e-9 mole / second; unit inv_nM_s = 1 / (1e-9 mole * second); - unit substance_per_volume = 1e-09 mole / litre; + unit substance_volume = 1e-09 mole * litre; // Display Names: time_unit is "time"; diff --git a/doc/examples/biomodels/BIOMD0000000466_url.txt b/doc/examples/biomodels/BIOMD0000000466/BIOMD0000000466_url.txt similarity index 86% rename from doc/examples/biomodels/BIOMD0000000466_url.txt rename to doc/examples/biomodels/BIOMD0000000466/BIOMD0000000466_url.txt index ba4700cd2..532550025 100644 --- a/doc/examples/biomodels/BIOMD0000000466_url.txt +++ b/doc/examples/biomodels/BIOMD0000000466/BIOMD0000000466_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1302180005() // Compartments and Species: @@ -12,8 +12,8 @@ model *MODEL1302180005() substanceOnly species s113 in c1, s114 in c1, s115 in c3, s119 in default; // Reactions: - re102: s95 -> s93; exp(re102_unity - (s39/re102_tf)^0.35)*re102_normal*((s39 + re102_tiny_num)/re102_unimol)^-0.65*(re102_unity - (s39/re102_tf)^0.35); - re103: s94 -> s92; exp(re103_unity - (s39/re103_tf)^1.3)*re103_normal*(s39/re103_unimol)^0.3*(re103_unity - (s39/re103_tf)^1.3); + re102: s95 -> s93; exp(re102_unity - (s39/re102_tf)^0.35)*re102_normal_*((s39 + re102_tiny_num)/re102_unimol)^-0.65*(re102_unity - (s39/re102_tf)^0.35); + re103: s94 -> s92; exp(re103_unity - (s39/re103_tf)^1.3)*re103_normal_*(s39/re103_unimol)^0.3*(re103_unity - (s39/re103_tf)^1.3); re104: s91 + s93 -> s110; re104_k3*s91*s93 - re104_kr3*s110; re105: s110 -> s112; re105_k4*s110*s92 - re105_kr4*s112; re106: s112 + s111 -> s113; re106_k5*s111*s112 - re106_kr5*s113; @@ -39,77 +39,77 @@ model *MODEL1302180005() re126: s104 => s44; re126_k19*s104*s43/(re126_Km19 + s104); re127: s42 => s107; s44*s42*re127_k21/(re127_Km21 + s42); re128: s107 => s42; re128_V22*s107/(s107 + re128_Km22); - re129: s105 => s49; (exp(re129_tau*(re129_delay - s39/re129_tc))/(1 + 2*exp(re129_tau*(re129_delay - s39/re129_tc)) + exp(2*re129_tau*(re129_delay - s39/re129_tc)))/re129_uc)*29.256; + re129: s105 => s49; (exp(re129_tau*(re129_delay_ - s39/re129_tc))/(1 + 2*exp(re129_tau*(re129_delay_ - s39/re129_tc)) + exp(2*re129_tau*(re129_delay_ - s39/re129_tc)))/re129_uc)*29.256; // Species initializations: s35 = 0; - s35 has substance_per_volume; + s35 has substance; s37 = 10000; - s37 has substance_per_volume; + s37 has substance; s38 = 0; - s38 has substance_per_volume; + s38 has substance; s39 = 0; - s39 has substance_per_volume; + s39 has substance; s42 = 50; - s42 has substance_per_volume; + s42 has substance; s43 = 0.006; - s43 has substance_per_volume; + s43 has substance; s44 = 0; - s44 has substance_per_volume; + s44 has substance; s49 = 10; - s49 has substance_per_volume; + s49 has substance; s51 = 34.98; - s51 has substance_per_volume; + s51 has substance; s91 = 819.25; - s91 has substance_per_volume; + s91 has substance; s92 = 18; - s92 has substance_per_volume; + s92 has substance; s93 = 0.605; - s93 has substance_per_volume; + s93 has substance; s94 = 72; - s94 has substance_per_volume; + s94 has substance; s95 = 57; - s95 has substance_per_volume; + s95 has substance; s96 = 299.706; - s96 has substance_per_volume; + s96 has substance; s97 = 98.514; - s97 has substance_per_volume; + s97 has substance; s98 = 157.162; - s98 has substance_per_volume; + s98 has substance; s99 = 299.997; - s99 has substance_per_volume; + s99 has substance; s100 = 0.288; - s100 has substance_per_volume; + s100 has substance; s101 = 1.486; - s101 has substance_per_volume; + s101 has substance; s102 = 0.616; - s102 has substance_per_volume; + s102 has substance; s103 = 119.384; - s103 has substance_per_volume; + s103 has substance; s104 = 0.003; - s104 has substance_per_volume; + s104 has substance; s105 = 0; - s105 has substance_per_volume; + s105 has substance; s106 = 3.214; - s106 has substance_per_volume; + s106 has substance; s107 = 0; - s107 has substance_per_volume; + s107 has substance; s108 = 0; - s108 has substance_per_volume; + s108 has substance; s110 = 0.857; - s110 has substance_per_volume; + s110 has substance; s111 = 3.23; - s111 has substance_per_volume; + s111 has substance; s112 = 15.962; - s112 has substance_per_volume; + s112 has substance; s113 = 5.577; - s113 has substance_per_volume; + s113 has substance; s114 = 1.193; - s114 has substance_per_volume; + s114 has substance; s115 = 0.09; - s115 has substance_per_volume; + s115 has substance; s119 = 0; - s119 has substance_per_volume; + s119 has substance; // Compartment initializations: default = 1; @@ -120,8 +120,8 @@ model *MODEL1302180005() c3 has volume; // Variable initializations: - re102_normal = 4; - re102_normal has nM_inv_s; + re102_normal_ = 4; + re102_normal_ has nM_inv_s; re102_tf = 60; re102_tf has substance; re102_unity = 1; @@ -130,8 +130,8 @@ model *MODEL1302180005() re102_unimol has substance; re102_tiny_num = 1e-06; re102_tiny_num has substance; - re103_normal = 0.026; - re103_normal has nM_inv_s; + re103_normal_ = 0.026; + re103_normal_ has nM_inv_s; re103_tf = 540; re103_tf has substance; re103_unity = 1; @@ -236,8 +236,8 @@ model *MODEL1302180005() re129_tc has substance; re129_uc = 3600; re129_uc has dimensionless; - re129_delay = 5; - re129_delay has dimensionless; + re129_delay_ = 5; + re129_delay_ has dimensionless; re129_unity = 20; re129_unity has nM_inv_s; @@ -255,7 +255,7 @@ model *MODEL1302180005() unit inv_sec_sub = 1 / (1e-09 mole * second); unit nM_inv_s = 1e-9 mole / second; unit inv_nM_s = 1 / (1e-9 mole * second); - unit substance_per_volume = 1e-09 mole / litre; + unit substance_volume = 1e-09 mole * litre; // Display Names: time_unit is "time"; diff --git a/doc/examples/biomodels/BIOMD0000000467_url.txt b/doc/examples/biomodels/BIOMD0000000467/BIOMD0000000467_url.txt similarity index 90% rename from doc/examples/biomodels/BIOMD0000000467_url.txt rename to doc/examples/biomodels/BIOMD0000000467/BIOMD0000000467_url.txt index 66253f1de..e11484820 100644 --- a/doc/examples/biomodels/BIOMD0000000467_url.txt +++ b/doc/examples/biomodels/BIOMD0000000467/BIOMD0000000467_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1302180006() // Compartments and Species: @@ -36,45 +36,45 @@ model *MODEL1302180006() // Species initializations: s3 = 117.2; - s3 has substance_per_volume; + s3 has substance; s27 = 1.723; - s27 has substance_per_volume; + s27 has substance; s45 = 0.0415; - s45 has substance_per_volume; + s45 has substance; s47 = 2.827; - s47 has substance_per_volume; + s47 has substance; s48 = 347.52; - s48 has substance_per_volume; + s48 has substance; s50 = 2.12; - s50 has substance_per_volume; + s50 has substance; s51 = 34.98; - s51 has substance_per_volume; + s51 has substance; s52 = 7635.36; - s52 has substance_per_volume; + s52 has substance; s57 = 199987; - s57 has substance_per_volume; + s57 has substance; s58 = 1.037; - s58 has substance_per_volume; + s58 has substance; s60 = 0.0089; - s60 has substance_per_volume; + s60 has substance; s61 = 10.98; - s61 has substance_per_volume; + s61 has substance; s62 = 0.106; - s62 has substance_per_volume; + s62 has substance; s63 = 500000; - s63 has substance_per_volume; + s63 has substance; s64 = 0; - s64 has substance_per_volume; + s64 has substance; s65 = 0.643; - s65 has substance_per_volume; + s65 has substance; s66 = 0.083; - s66 has substance_per_volume; + s66 has substance; s116 = 0; - s116 has substance_per_volume; + s116 has substance; s117 = 0; - s117 has substance_per_volume; + s117 has substance; s118 = 0; - s118 has substance_per_volume; + s118 has substance; // Compartment initializations: default = 1; @@ -135,7 +135,7 @@ model *MODEL1302180006() unit inv_sec_sub = 1 / (1e-09 mole * second); unit nM_inv_s = 1e-9 mole / second; unit inv_nM_s = 1 / (1e-9 mole * second); - unit substance_per_volume = 1e-09 mole / litre; + unit substance_volume = 1e-09 mole * litre; // Display Names: time_unit is "time"; diff --git a/doc/examples/biomodels/BIOMD0000000468_url.txt b/doc/examples/biomodels/BIOMD0000000468/BIOMD0000000468_url.txt similarity index 87% rename from doc/examples/biomodels/BIOMD0000000468_url.txt rename to doc/examples/biomodels/BIOMD0000000468/BIOMD0000000468_url.txt index e1eccc0b8..715173b7f 100644 --- a/doc/examples/biomodels/BIOMD0000000468_url.txt +++ b/doc/examples/biomodels/BIOMD0000000468/BIOMD0000000468_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1308190000() // Compartments and Species: @@ -42,7 +42,7 @@ model *MODEL1308190000() re54: s60 -> s62; gam*k14*s60 - k13*s3*s62; re55: s58 -> s60; kp*s58*s27/(s58 + Kmp) - Vdp*s60/(s60 + Kmdp); re56: s61 -> s62; kp*s61*s27/(s61 + Kmp) - Vdp*s62/(s62 + Kmdp); - re57: s22 -> s20; exp(re57_unity - (s23/re57_tf)^1.8)*re57_normal*(s23/re57_unimol)^0.8*(re57_unity - (s23/re57_tf)^1.8); + re57: s22 -> s20; exp(re57_unity - (s23/re57_tf)^1.8)*re57_normal_*(s23/re57_unimol)^0.8*(re57_unity - (s23/re57_tf)^1.8); re58: s19 => s17; re58_k58*s19*s20/(re58_Km58 + s19); re59: s17 => s19; re59_k59*s17*s18/(re59_Km59 + s17); re60: s17 + s16 -> s28; re60_k60*s17*s16 - re60_kr60*s28; @@ -58,8 +58,8 @@ model *MODEL1308190000() re70: s65 => s66; Vdp*s65/(s65 + Kmdp); re71: s66 => s51 + s57; kr90*s66; re72: s62 -> s65 + s48; k18*s62 - k17*s65*s48; - re102: s95 -> s93; exp(re102_unity - (s39/re102_tf)^0.35)*re102_normal*((s39 + re102_tiny_num)/re102_unimol)^-0.65*(re102_unity - (s39/re102_tf)^0.35); - re103: s94 -> s92; exp(re103_unity - (s39/re103_tf)^1.3)*re103_normal*(s39/re103_unimol)^0.3*(re103_unity - (s39/re103_tf)^1.3); + re102: s95 -> s93; exp(re102_unity - (s39/re102_tf)^0.35)*re102_normal_*((s39 + re102_tiny_num)/re102_unimol)^-0.65*(re102_unity - (s39/re102_tf)^0.35); + re103: s94 -> s92; exp(re103_unity - (s39/re103_tf)^1.3)*re103_normal_*(s39/re103_unimol)^0.3*(re103_unity - (s39/re103_tf)^1.3); re104: s91 + s93 -> s110; re104_k105*s91*s93 - re104_k_105*s110; re105: s110 -> s112; re105_kcat_src*s110*s92 - re105_k_6*s112; re106: s112 + s111 -> s113; re106_k107*s111*s112 - re106_k_107*s113; @@ -85,7 +85,7 @@ model *MODEL1308190000() re126: s104 => s44; re126_k40*s104*s43/(re126_K40 + s104); re127: s42 => s107; s44*s42*re127_k43/(re127_K43 + s42); re128: s107 => s42; re128_V44*s107/(s107 + re128_K44); - re129: s105 => s49; (exp(re129_tau*(re129_delay - s39/re129_tc))/(1 + 2*exp(re129_tau*(re129_delay - s39/re129_tc)) + exp(2*re129_tau*(re129_delay - s39/re129_tc)))/re129_uc)*29.256; + re129: s105 => s49; (exp(re129_tau*(re129_delay_ - s39/re129_tc))/(1 + 2*exp(re129_tau*(re129_delay_ - s39/re129_tc)) + exp(2*re129_tau*(re129_delay_ - s39/re129_tc)))/re129_uc)*29.256; re131: s51 => s116; kDD*s51; re132: s45 => s117 + s47; kDD*s45; re133: s50 => s117 + s48; kDD*s50; @@ -98,163 +98,163 @@ model *MODEL1308190000() // Species initializations: s1 = 1500000; - s1 has substance_per_volume; + s1 has substance; s2 = 2830000; - s2 has substance_per_volume; + s2 has substance; s3 = 117.2; - s3 has substance_per_volume; + s3 has substance; s4 = 3870; - s4 has substance_per_volume; + s4 has substance; s5 = 0; - s5 has substance_per_volume; + s5 has substance; s6 = 0; - s6 has substance_per_volume; + s6 has substance; s7 = 0; - s7 has substance_per_volume; + s7 has substance; s8 = 0; - s8 has substance_per_volume; + s8 has substance; s9 = 0; - s9 has substance_per_volume; + s9 has substance; s10 = 0; - s10 has substance_per_volume; + s10 has substance; s11 = 0; - s11 has substance_per_volume; + s11 has substance; s12 = 0; - s12 has substance_per_volume; + s12 has substance; s13 = 0; - s13 has substance_per_volume; + s13 has substance; s14 = 0.246; - s14 has substance_per_volume; + s14 has substance; s15 = 150; - s15 has substance_per_volume; + s15 has substance; s16 = 167.616; - s16 has substance_per_volume; + s16 has substance; s17 = 0.345; - s17 has substance_per_volume; + s17 has substance; s18 = 0.1; - s18 has substance_per_volume; + s18 has substance; s19 = 6967.271; - s19 has substance_per_volume; + s19 has substance; s20 = 0.03; - s20 has substance_per_volume; + s20 has substance; s21 = 0; - s21 has substance_per_volume; + s21 has substance; s22 = 99.97; - s22 has substance_per_volume; + s22 has substance; s23 = 0; - s23 has substance_per_volume; + s23 has substance; s24 = 3; - s24 has substance_per_volume; + s24 has substance; s25 = 999.754; - s25 has substance_per_volume; + s25 has substance; s26 = 1.457; - s26 has substance_per_volume; + s26 has substance; s27 = 1.723; - s27 has substance_per_volume; + s27 has substance; s28 = 29.203; - s28 has substance_per_volume; + s28 has substance; s35 = 0; - s35 has substance_per_volume; + s35 has substance; s37 = 10000; - s37 has substance_per_volume; + s37 has substance; s38 = 0; - s38 has substance_per_volume; + s38 has substance; s39 = 0; - s39 has substance_per_volume; + s39 has substance; s42 = 50; - s42 has substance_per_volume; + s42 has substance; s43 = 0.006; - s43 has substance_per_volume; + s43 has substance; s44 = 0; - s44 has substance_per_volume; + s44 has substance; s45 = 0.0415; - s45 has substance_per_volume; + s45 has substance; s47 = 2.827; - s47 has substance_per_volume; + s47 has substance; s48 = 347.52; - s48 has substance_per_volume; + s48 has substance; s49 = 10; - s49 has substance_per_volume; + s49 has substance; s50 = 2.12; - s50 has substance_per_volume; + s50 has substance; s51 = 34.98; - s51 has substance_per_volume; + s51 has substance; s52 = 7635.36; - s52 has substance_per_volume; + s52 has substance; s57 = 199987; - s57 has substance_per_volume; + s57 has substance; s58 = 1.037; - s58 has substance_per_volume; + s58 has substance; s60 = 0.0089; - s60 has substance_per_volume; + s60 has substance; s61 = 10.98; - s61 has substance_per_volume; + s61 has substance; s62 = 0.106; - s62 has substance_per_volume; + s62 has substance; s63 = 500000; - s63 has substance_per_volume; + s63 has substance; s64 = 0; - s64 has substance_per_volume; + s64 has substance; s65 = 0.643; - s65 has substance_per_volume; + s65 has substance; s66 = 0.083; - s66 has substance_per_volume; + s66 has substance; s91 = 819.25; - s91 has substance_per_volume; + s91 has substance; s92 = 18; - s92 has substance_per_volume; + s92 has substance; s93 = 0.605; - s93 has substance_per_volume; + s93 has substance; s94 = 72; - s94 has substance_per_volume; + s94 has substance; s95 = 57; - s95 has substance_per_volume; + s95 has substance; s96 = 299.706; - s96 has substance_per_volume; + s96 has substance; s97 = 98.514; - s97 has substance_per_volume; + s97 has substance; s98 = 157.162; - s98 has substance_per_volume; + s98 has substance; s99 = 299.997; - s99 has substance_per_volume; + s99 has substance; s100 = 0.288; - s100 has substance_per_volume; + s100 has substance; s101 = 1.486; - s101 has substance_per_volume; + s101 has substance; s102 = 0.616; - s102 has substance_per_volume; + s102 has substance; s103 = 119.384; - s103 has substance_per_volume; + s103 has substance; s104 = 0.003; - s104 has substance_per_volume; + s104 has substance; s105 = 0; - s105 has substance_per_volume; + s105 has substance; s106 = 3.214; - s106 has substance_per_volume; + s106 has substance; s107 = 0; - s107 has substance_per_volume; + s107 has substance; s108 = 0; - s108 has substance_per_volume; + s108 has substance; s110 = 0.857; - s110 has substance_per_volume; + s110 has substance; s111 = 3.23; - s111 has substance_per_volume; + s111 has substance; s112 = 15.962; - s112 has substance_per_volume; + s112 has substance; s113 = 5.577; - s113 has substance_per_volume; + s113 has substance; s114 = 1.193; - s114 has substance_per_volume; + s114 has substance; s115 = 0.09; - s115 has substance_per_volume; + s115 has substance; s116 = 0; - s116 has substance_per_volume; + s116 has substance; s117 = 0; - s117 has substance_per_volume; + s117 has substance; s118 = 0; - s118 has substance_per_volume; + s118 has substance; s119 = 0; - s119 has substance_per_volume; + s119 has substance; // Compartment initializations: default = 1; @@ -363,8 +363,8 @@ model *MODEL1308190000() kDD has inv_sec; re11_unisec = 1; re11_unisec has sub_sec; - re57_normal = 0.907; - re57_normal has sub_sec; + re57_normal_ = 0.907; + re57_normal_ has sub_sec; re57_unity = 1; re57_unity has dimensionless; re57_unimol = 1; @@ -415,8 +415,8 @@ model *MODEL1308190000() re69_K_p_no has inv_sec; re69_K_pcam_no = 17; re69_K_pcam_no has inv_sec; - re102_normal = 4; - re102_normal has nM_inv_s; + re102_normal_ = 4; + re102_normal_ has nM_inv_s; re102_tf = 60; re102_tf has substance; re102_unity = 1; @@ -425,8 +425,8 @@ model *MODEL1308190000() re102_unimol has substance; re102_tiny_num = 1e-06; re102_tiny_num has substance; - re103_normal = 0.026; - re103_normal has nM_inv_s; + re103_normal_ = 0.026; + re103_normal_ has nM_inv_s; re103_tf = 540; re103_tf has substance; re103_unity = 1; @@ -533,8 +533,8 @@ model *MODEL1308190000() re129_tc has substance; re129_uc = 3600; re129_uc has dimensionless; - re129_delay = 5; - re129_delay has dimensionless; + re129_delay_ = 5; + re129_delay_ has dimensionless; re129_unity = 20; re129_unity has nM_inv_s; @@ -556,7 +556,7 @@ model *MODEL1308190000() unit inv_sec_sub = 1 / (1e-09 mole * second); unit nM_inv_s = 1e-9 mole / second; unit inv_nM_s = 1 / (1e-9 mole * second); - unit substance_per_volume = 1e-09 mole / litre; + unit substance_volume = 1e-09 mole * litre; // Display Names: time_unit is "time"; diff --git a/doc/examples/biomodels/BIOMD0000000469_url.txt b/doc/examples/biomodels/BIOMD0000000469/BIOMD0000000469_url.txt similarity index 85% rename from doc/examples/biomodels/BIOMD0000000469_url.txt rename to doc/examples/biomodels/BIOMD0000000469/BIOMD0000000469_url.txt index 6f4297cd8..5cb3f2b0c 100644 --- a/doc/examples/biomodels/BIOMD0000000469_url.txt +++ b/doc/examples/biomodels/BIOMD0000000469/BIOMD0000000469_url.txt @@ -1,4 +1,529 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 + +// Warnings from automatic translation: +// An interaction was declared that claims e_0610 modifies r_0008, but e_0610 does not appear in r_0008's kinetic law. +// An interaction was declared that claims e_0149 modifies r_0009, but e_0149 does not appear in r_0009's kinetic law. +// An interaction was declared that claims e_0078 modifies r_0011, but e_0078 does not appear in r_0011's kinetic law. +// An interaction was declared that claims e_0953 modifies r_0012, but e_0953 does not appear in r_0012's kinetic law. +// An interaction was declared that claims e_0953 modifies r_0013, but e_0953 does not appear in r_0013's kinetic law. +// An interaction was declared that claims e_0010 modifies r_0014, but e_0010 does not appear in r_0014's kinetic law. +// An interaction was declared that claims e_0010 modifies r_0015, but e_0010 does not appear in r_0015's kinetic law. +// An interaction was declared that claims e_1137 modifies r_0038, but e_1137 does not appear in r_0038's kinetic law. +// An interaction was declared that claims e_0034 modifies r_0038, but e_0034 does not appear in r_0038's kinetic law. +// An interaction was declared that claims e_0035 modifies r_0038, but e_0035 does not appear in r_0038's kinetic law. +// An interaction was declared that claims e_1136 modifies r_0038, but e_1136 does not appear in r_0038's kinetic law. +// An interaction was declared that claims e_0866 modifies r_0053, but e_0866 does not appear in r_0053's kinetic law. +// An interaction was declared that claims e_0867 modifies r_0054, but e_0867 does not appear in r_0054's kinetic law. +// An interaction was declared that claims e_0578 modifies r_0056, but e_0578 does not appear in r_0056's kinetic law. +// An interaction was declared that claims e_0152 modifies r_0063, but e_0152 does not appear in r_0063's kinetic law. +// An interaction was declared that claims e_1170 modifies r_0063, but e_1170 does not appear in r_0063's kinetic law. +// An interaction was declared that claims e_0031 modifies r_0066, but e_0031 does not appear in r_0066's kinetic law. +// An interaction was declared that claims e_0030 modifies r_0066, but e_0030 does not appear in r_0066's kinetic law. +// An interaction was declared that claims e_0033 modifies r_0067, but e_0033 does not appear in r_0067's kinetic law. +// An interaction was declared that claims e_0238 modifies r_0084, but e_0238 does not appear in r_0084's kinetic law. +// An interaction was declared that claims e_0798 modifies r_0084, but e_0798 does not appear in r_0084's kinetic law. +// An interaction was declared that claims e_0911 modifies r_0084, but e_0911 does not appear in r_0084's kinetic law. +// An interaction was declared that claims e_1326 modifies r_0085, but e_1326 does not appear in r_0085's kinetic law. +// An interaction was declared that claims e_0960 modifies r_0092, but e_0960 does not appear in r_0092's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0096, but e_1203 does not appear in r_0096's kinetic law. +// An interaction was declared that claims e_0541 modifies r_0098, but e_0541 does not appear in r_0098's kinetic law. +// An interaction was declared that claims e_1027 modifies r_0099, but e_1027 does not appear in r_0099's kinetic law. +// An interaction was declared that claims e_0406 modifies r_0100, but e_0406 does not appear in r_0100's kinetic law. +// An interaction was declared that claims e_0544 modifies r_0101, but e_0544 does not appear in r_0101's kinetic law. +// An interaction was declared that claims e_0827 modifies r_0101, but e_0827 does not appear in r_0101's kinetic law. +// An interaction was declared that claims e_0263 modifies r_0101, but e_0263 does not appear in r_0101's kinetic law. +// An interaction was declared that claims e_1125 modifies r_0102, but e_1125 does not appear in r_0102's kinetic law. +// An interaction was declared that claims e_1125 modifies r_0103, but e_1125 does not appear in r_0103's kinetic law. +// An interaction was declared that claims e_0331 modifies r_0105, but e_0331 does not appear in r_0105's kinetic law. +// An interaction was declared that claims e_0994 modifies r_0106, but e_0994 does not appear in r_0106's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0120, but e_1203 does not appear in r_0120's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0120, but e_0735 does not appear in r_0120's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0121, but e_1203 does not appear in r_0121's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0121, but e_0735 does not appear in r_0121's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0122, but e_1203 does not appear in r_0122's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0122, but e_0735 does not appear in r_0122's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0123, but e_1203 does not appear in r_0123's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0123, but e_0735 does not appear in r_0123's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0124, but e_1203 does not appear in r_0124's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0124, but e_0735 does not appear in r_0124's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0126, but e_1203 does not appear in r_0126's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0126, but e_0735 does not appear in r_0126's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0127, but e_1203 does not appear in r_0127's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0127, but e_0735 does not appear in r_0127's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0128, but e_1203 does not appear in r_0128's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0128, but e_0735 does not appear in r_0128's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0129, but e_1203 does not appear in r_0129's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0129, but e_0735 does not appear in r_0129's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0130, but e_1203 does not appear in r_0130's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0130, but e_0735 does not appear in r_0130's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0131, but e_1203 does not appear in r_0131's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0131, but e_0735 does not appear in r_0131's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0133, but e_1203 does not appear in r_0133's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0133, but e_0735 does not appear in r_0133's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0134, but e_1203 does not appear in r_0134's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0134, but e_0735 does not appear in r_0134's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0135, but e_1203 does not appear in r_0135's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0135, but e_0735 does not appear in r_0135's kinetic law. +// An interaction was declared that claims e_0031 modifies r_0138, but e_0031 does not appear in r_0138's kinetic law. +// An interaction was declared that claims e_0030 modifies r_0138, but e_0030 does not appear in r_0138's kinetic law. +// An interaction was declared that claims e_0032 modifies r_0139, but e_0032 does not appear in r_0139's kinetic law. +// An interaction was declared that claims e_0063 modifies r_0143, but e_0063 does not appear in r_0143's kinetic law. +// An interaction was declared that claims e_0082 modifies r_0145, but e_0082 does not appear in r_0145's kinetic law. +// An interaction was declared that claims e_0374 modifies r_0146, but e_0374 does not appear in r_0146's kinetic law. +// An interaction was declared that claims e_0372 modifies r_0147, but e_0372 does not appear in r_0147's kinetic law. +// An interaction was declared that claims e_0082 modifies r_0148, but e_0082 does not appear in r_0148's kinetic law. +// An interaction was declared that claims e_0374 modifies r_0149, but e_0374 does not appear in r_0149's kinetic law. +// An interaction was declared that claims e_0732 modifies r_0150, but e_0732 does not appear in r_0150's kinetic law. +// An interaction was declared that claims e_0374 modifies r_0154, but e_0374 does not appear in r_0154's kinetic law. +// An interaction was declared that claims e_0376 modifies r_0166, but e_0376 does not appear in r_0166's kinetic law. +// An interaction was declared that claims e_0732 modifies r_0166, but e_0732 does not appear in r_0166's kinetic law. +// An interaction was declared that claims e_0327 modifies r_0175, but e_0327 does not appear in r_0175's kinetic law. +// An interaction was declared that claims e_0404 modifies r_0178, but e_0404 does not appear in r_0178's kinetic law. +// An interaction was declared that claims e_1254 modifies r_0179, but e_1254 does not appear in r_0179's kinetic law. +// An interaction was declared that claims e_1015 modifies r_0181, but e_1015 does not appear in r_0181's kinetic law. +// An interaction was declared that claims e_0572 modifies r_0181, but e_0572 does not appear in r_0181's kinetic law. +// An interaction was declared that claims e_0377 modifies r_0182, but e_0377 does not appear in r_0182's kinetic law. +// An interaction was declared that claims e_0074 modifies r_0186, but e_0074 does not appear in r_0186's kinetic law. +// An interaction was declared that claims e_1234 modifies r_0211, but e_1234 does not appear in r_0211's kinetic law. +// An interaction was declared that claims e_0144 modifies r_0212, but e_0144 does not appear in r_0212's kinetic law. +// An interaction was declared that claims e_0064 modifies r_0216, but e_0064 does not appear in r_0216's kinetic law. +// An interaction was declared that claims e_0579 modifies r_0217, but e_0579 does not appear in r_0217's kinetic law. +// An interaction was declared that claims e_0273 modifies r_0218, but e_0273 does not appear in r_0218's kinetic law. +// An interaction was declared that claims e_0276 modifies r_0222, but e_0276 does not appear in r_0222's kinetic law. +// An interaction was declared that claims e_0125 modifies r_0224, but e_0125 does not appear in r_0224's kinetic law. +// An interaction was declared that claims e_0416 modifies r_0224, but e_0416 does not appear in r_0224's kinetic law. +// An interaction was declared that claims e_0975 modifies r_0225, but e_0975 does not appear in r_0225's kinetic law. +// An interaction was declared that claims e_0719 modifies r_0225, but e_0719 does not appear in r_0225's kinetic law. +// An interaction was declared that claims e_0577 modifies r_0225, but e_0577 does not appear in r_0225's kinetic law. +// An interaction was declared that claims e_1137 modifies r_0227, but e_1137 does not appear in r_0227's kinetic law. +// An interaction was declared that claims e_0034 modifies r_0227, but e_0034 does not appear in r_0227's kinetic law. +// An interaction was declared that claims e_0035 modifies r_0227, but e_0035 does not appear in r_0227's kinetic law. +// An interaction was declared that claims e_1136 modifies r_0227, but e_1136 does not appear in r_0227's kinetic law. +// An interaction was declared that claims e_0682 modifies r_0230, but e_0682 does not appear in r_0230's kinetic law. +// An interaction was declared that claims e_1202 modifies r_0230, but e_1202 does not appear in r_0230's kinetic law. +// An interaction was declared that claims e_0736 modifies r_0230, but e_0736 does not appear in r_0230's kinetic law. +// An interaction was declared that claims e_1202 modifies r_0231, but e_1202 does not appear in r_0231's kinetic law. +// An interaction was declared that claims e_0736 modifies r_0231, but e_0736 does not appear in r_0231's kinetic law. +// An interaction was declared that claims e_1202 modifies r_0232, but e_1202 does not appear in r_0232's kinetic law. +// An interaction was declared that claims e_0736 modifies r_0232, but e_0736 does not appear in r_0232's kinetic law. +// An interaction was declared that claims e_1202 modifies r_0233, but e_1202 does not appear in r_0233's kinetic law. +// An interaction was declared that claims e_0736 modifies r_0233, but e_0736 does not appear in r_0233's kinetic law. +// An interaction was declared that claims e_1202 modifies r_0234, but e_1202 does not appear in r_0234's kinetic law. +// An interaction was declared that claims e_0736 modifies r_0234, but e_0736 does not appear in r_0234's kinetic law. +// An interaction was declared that claims e_1202 modifies r_0235, but e_1202 does not appear in r_0235's kinetic law. +// An interaction was declared that claims e_0736 modifies r_0235, but e_0736 does not appear in r_0235's kinetic law. +// An interaction was declared that claims e_1202 modifies r_0236, but e_1202 does not appear in r_0236's kinetic law. +// An interaction was declared that claims e_0736 modifies r_0236, but e_0736 does not appear in r_0236's kinetic law. +// An interaction was declared that claims e_0085 modifies r_0237, but e_0085 does not appear in r_0237's kinetic law. +// An interaction was declared that claims e_1006 modifies r_0237, but e_1006 does not appear in r_0237's kinetic law. +// An interaction was declared that claims e_1005 modifies r_0237, but e_1005 does not appear in r_0237's kinetic law. +// An interaction was declared that claims e_0730 modifies r_0237, but e_0730 does not appear in r_0237's kinetic law. +// An interaction was declared that claims e_1243 modifies r_0243, but e_1243 does not appear in r_0243's kinetic law. +// An interaction was declared that claims e_1241 modifies r_0244, but e_1241 does not appear in r_0244's kinetic law. +// An interaction was declared that claims e_0559 modifies r_0245, but e_0559 does not appear in r_0245's kinetic law. +// An interaction was declared that claims e_1014 modifies r_0245, but e_1014 does not appear in r_0245's kinetic law. +// An interaction was declared that claims e_0431 modifies r_0246, but e_0431 does not appear in r_0246's kinetic law. +// An interaction was declared that claims e_0054 modifies r_0246, but e_0054 does not appear in r_0246's kinetic law. +// An interaction was declared that claims e_0431 modifies r_0247, but e_0431 does not appear in r_0247's kinetic law. +// An interaction was declared that claims e_0054 modifies r_0247, but e_0054 does not appear in r_0247's kinetic law. +// An interaction was declared that claims e_0375 modifies r_0257, but e_0375 does not appear in r_0257's kinetic law. +// An interaction was declared that claims e_0896 modifies r_0257, but e_0896 does not appear in r_0257's kinetic law. +// An interaction was declared that claims e_0375 modifies r_0259, but e_0375 does not appear in r_0259's kinetic law. +// An interaction was declared that claims e_0896 modifies r_0259, but e_0896 does not appear in r_0259's kinetic law. +// An interaction was declared that claims e_0375 modifies r_0260, but e_0375 does not appear in r_0260's kinetic law. +// An interaction was declared that claims e_0896 modifies r_0260, but e_0896 does not appear in r_0260's kinetic law. +// An interaction was declared that claims e_0094 modifies r_0266, but e_0094 does not appear in r_0266's kinetic law. +// An interaction was declared that claims e_0094 modifies r_0267, but e_0094 does not appear in r_0267's kinetic law. +// An interaction was declared that claims e_0094 modifies r_0268, but e_0094 does not appear in r_0268's kinetic law. +// An interaction was declared that claims e_0094 modifies r_0269, but e_0094 does not appear in r_0269's kinetic law. +// An interaction was declared that claims e_0094 modifies r_0270, but e_0094 does not appear in r_0270's kinetic law. +// An interaction was declared that claims e_0094 modifies r_0272, but e_0094 does not appear in r_0272's kinetic law. +// An interaction was declared that claims e_0094 modifies r_0273, but e_0094 does not appear in r_0273's kinetic law. +// An interaction was declared that claims e_0167 modifies r_0292, but e_0167 does not appear in r_0292's kinetic law. +// An interaction was declared that claims e_0274 modifies r_0297, but e_0274 does not appear in r_0297's kinetic law. +// An interaction was declared that claims e_0167 modifies r_0301, but e_0167 does not appear in r_0301's kinetic law. +// An interaction was declared that claims e_0389 modifies r_0302, but e_0389 does not appear in r_0302's kinetic law. +// An interaction was declared that claims e_1315 modifies r_0303, but e_1315 does not appear in r_0303's kinetic law. +// An interaction was declared that claims e_0389 modifies r_0304, but e_0389 does not appear in r_0304's kinetic law. +// An interaction was declared that claims e_0868 modifies r_0305, but e_0868 does not appear in r_0305's kinetic law. +// An interaction was declared that claims e_0395 modifies r_0310, but e_0395 does not appear in r_0310's kinetic law. +// An interaction was declared that claims e_1275 modifies r_0310, but e_1275 does not appear in r_0310's kinetic law. +// An interaction was declared that claims e_0428 modifies r_0348, but e_0428 does not appear in r_0348's kinetic law. +// An interaction was declared that claims e_0429 modifies r_0349, but e_0429 does not appear in r_0349's kinetic law. +// An interaction was declared that claims e_0428 modifies r_0349, but e_0428 does not appear in r_0349's kinetic law. +// An interaction was declared that claims e_0993 modifies r_0355, but e_0993 does not appear in r_0355's kinetic law. +// An interaction was declared that claims e_0848 modifies r_0355, but e_0848 does not appear in r_0355's kinetic law. +// An interaction was declared that claims e_1244 modifies r_0360, but e_1244 does not appear in r_0360's kinetic law. +// An interaction was declared that claims e_0986 modifies r_0361, but e_0986 does not appear in r_0361's kinetic law. +// An interaction was declared that claims e_1160 modifies r_0365, but e_1160 does not appear in r_0365's kinetic law. +// An interaction was declared that claims e_0061 modifies r_0367, but e_0061 does not appear in r_0367's kinetic law. +// An interaction was declared that claims e_1340 modifies r_0368, but e_1340 does not appear in r_0368's kinetic law. +// An interaction was declared that claims e_1339 modifies r_0368, but e_1339 does not appear in r_0368's kinetic law. +// An interaction was declared that claims e_1263 modifies r_0369, but e_1263 does not appear in r_0369's kinetic law. +// An interaction was declared that claims e_0001 modifies r_0369, but e_0001 does not appear in r_0369's kinetic law. +// An interaction was declared that claims e_1233 modifies r_0369, but e_1233 does not appear in r_0369's kinetic law. +// An interaction was declared that claims e_0332 modifies r_0370, but e_0332 does not appear in r_0370's kinetic law. +// An interaction was declared that claims e_1045 modifies r_0371, but e_1045 does not appear in r_0371's kinetic law. +// An interaction was declared that claims e_0605 modifies r_0374, but e_0605 does not appear in r_0374's kinetic law. +// An interaction was declared that claims e_0275 modifies r_0383, but e_0275 does not appear in r_0383's kinetic law. +// An interaction was declared that claims e_0292 modifies r_0384, but e_0292 does not appear in r_0384's kinetic law. +// An interaction was declared that claims e_1207 modifies r_0385, but e_1207 does not appear in r_0385's kinetic law. +// An interaction was declared that claims e_1206 modifies r_0385, but e_1206 does not appear in r_0385's kinetic law. +// An interaction was declared that claims e_1207 modifies r_0386, but e_1207 does not appear in r_0386's kinetic law. +// An interaction was declared that claims e_1206 modifies r_0386, but e_1206 does not appear in r_0386's kinetic law. +// An interaction was declared that claims e_0903 modifies r_0388, but e_0903 does not appear in r_0388's kinetic law. +// An interaction was declared that claims e_0183 modifies r_0388, but e_0183 does not appear in r_0388's kinetic law. +// An interaction was declared that claims e_0110 modifies r_0388, but e_0110 does not appear in r_0388's kinetic law. +// An interaction was declared that claims e_0080 modifies r_0418, but e_0080 does not appear in r_0418's kinetic law. +// An interaction was declared that claims e_0080 modifies r_0419, but e_0080 does not appear in r_0419's kinetic law. +// An interaction was declared that claims e_0825 modifies r_0423, but e_0825 does not appear in r_0423's kinetic law. +// An interaction was declared that claims e_0826 modifies r_0423, but e_0826 does not appear in r_0423's kinetic law. +// An interaction was declared that claims e_1271 modifies r_0424, but e_1271 does not appear in r_0424's kinetic law. +// An interaction was declared that claims e_0734 modifies r_0425, but e_0734 does not appear in r_0425's kinetic law. +// An interaction was declared that claims e_0246 modifies r_0428, but e_0246 does not appear in r_0428's kinetic law. +// An interaction was declared that claims e_0765 modifies r_0436, but e_0765 does not appear in r_0436's kinetic law. +// An interaction was declared that claims e_0876 modifies r_0440, but e_0876 does not appear in r_0440's kinetic law. +// An interaction was declared that claims e_0279 modifies r_0445, but e_0279 does not appear in r_0445's kinetic law. +// An interaction was declared that claims e_0280 modifies r_0445, but e_0280 does not appear in r_0445's kinetic law. +// An interaction was declared that claims e_0951 modifies r_0450, but e_0951 does not appear in r_0450's kinetic law. +// An interaction was declared that claims e_0519 modifies r_0450, but e_0519 does not appear in r_0450's kinetic law. +// An interaction was declared that claims e_0757 modifies r_0452, but e_0757 does not appear in r_0452's kinetic law. +// An interaction was declared that claims e_0750 modifies r_0452, but e_0750 does not appear in r_0452's kinetic law. +// An interaction was declared that claims e_0328 modifies r_0457, but e_0328 does not appear in r_0457's kinetic law. +// An interaction was declared that claims e_0043 modifies r_0463, but e_0043 does not appear in r_0463's kinetic law. +// An interaction was declared that claims e_0135 modifies r_0463, but e_0135 does not appear in r_0463's kinetic law. +// An interaction was declared that claims e_0046 modifies r_0488, but e_0046 does not appear in r_0488's kinetic law. +// An interaction was declared that claims e_0278 modifies r_0489, but e_0278 does not appear in r_0489's kinetic law. +// An interaction was declared that claims e_0144 modifies r_0498, but e_0144 does not appear in r_0498's kinetic law. +// An interaction was declared that claims e_0897 modifies r_0499, but e_0897 does not appear in r_0499's kinetic law. +// An interaction was declared that claims e_1189 modifies r_0500, but e_1189 does not appear in r_0500's kinetic law. +// An interaction was declared that claims e_0342 modifies r_0501, but e_0342 does not appear in r_0501's kinetic law. +// An interaction was declared that claims e_0012 modifies r_0502, but e_0012 does not appear in r_0502's kinetic law. +// An interaction was declared that claims e_0776 modifies r_0503, but e_0776 does not appear in r_0503's kinetic law. +// An interaction was declared that claims e_0514 modifies r_0504, but e_0514 does not appear in r_0504's kinetic law. +// An interaction was declared that claims e_0020 modifies r_0504, but e_0020 does not appear in r_0504's kinetic law. +// An interaction was declared that claims e_0729 modifies r_0505, but e_0729 does not appear in r_0505's kinetic law. +// An interaction was declared that claims e_0964 modifies r_0507, but e_0964 does not appear in r_0507's kinetic law. +// An interaction was declared that claims e_0045 modifies r_0510, but e_0045 does not appear in r_0510's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0510, but e_0586 does not appear in r_0510's kinetic law. +// An interaction was declared that claims e_0368 modifies r_0511, but e_0368 does not appear in r_0511's kinetic law. +// An interaction was declared that claims e_0342 modifies r_0512, but e_0342 does not appear in r_0512's kinetic law. +// An interaction was declared that claims e_0988 modifies r_0515, but e_0988 does not appear in r_0515's kinetic law. +// An interaction was declared that claims e_1168 modifies r_0517, but e_1168 does not appear in r_0517's kinetic law. +// An interaction was declared that claims e_1168 modifies r_0518, but e_1168 does not appear in r_0518's kinetic law. +// An interaction was declared that claims e_0150 modifies r_0522, but e_0150 does not appear in r_0522's kinetic law. +// An interaction was declared that claims e_0378 modifies r_0532, but e_0378 does not appear in r_0532's kinetic law. +// An interaction was declared that claims e_1128 modifies r_0533, but e_1128 does not appear in r_0533's kinetic law. +// An interaction was declared that claims e_0691 modifies r_0533, but e_0691 does not appear in r_0533's kinetic law. +// An interaction was declared that claims e_0875 modifies r_0538, but e_0875 does not appear in r_0538's kinetic law. +// An interaction was declared that claims e_0436 modifies r_0563, but e_0436 does not appear in r_0563's kinetic law. +// An interaction was declared that claims e_0436 modifies r_0564, but e_0436 does not appear in r_0564's kinetic law. +// An interaction was declared that claims e_0731 modifies r_0573, but e_0731 does not appear in r_0573's kinetic law. +// An interaction was declared that claims e_0926 modifies r_0574, but e_0926 does not appear in r_0574's kinetic law. +// An interaction was declared that claims e_0567 modifies r_0574, but e_0567 does not appear in r_0574's kinetic law. +// An interaction was declared that claims e_1201 modifies r_0576, but e_1201 does not appear in r_0576's kinetic law. +// An interaction was declared that claims e_0162 modifies r_0579, but e_0162 does not appear in r_0579's kinetic law. +// An interaction was declared that claims e_0162 modifies r_0580, but e_0162 does not appear in r_0580's kinetic law. +// An interaction was declared that claims e_0162 modifies r_0581, but e_0162 does not appear in r_0581's kinetic law. +// An interaction was declared that claims e_0168 modifies r_0602, but e_0168 does not appear in r_0602's kinetic law. +// An interaction was declared that claims e_0008 modifies r_0611, but e_0008 does not appear in r_0611's kinetic law. +// An interaction was declared that claims e_1298 modifies r_0632, but e_1298 does not appear in r_0632's kinetic law. +// An interaction was declared that claims e_0515 modifies r_0632, but e_0515 does not appear in r_0632's kinetic law. +// An interaction was declared that claims e_0516 modifies r_0632, but e_0516 does not appear in r_0632's kinetic law. +// An interaction was declared that claims e_0577 modifies r_0648, but e_0577 does not appear in r_0648's kinetic law. +// An interaction was declared that claims e_0150 modifies r_0655, but e_0150 does not appear in r_0655's kinetic law. +// An interaction was declared that claims e_1150 modifies r_0658, but e_1150 does not appear in r_0658's kinetic law. +// An interaction was declared that claims e_0580 modifies r_0660, but e_0580 does not appear in r_0660's kinetic law. +// An interaction was declared that claims e_1264 modifies r_0664, but e_1264 does not appear in r_0664's kinetic law. +// An interaction was declared that claims e_0099 modifies r_0673, but e_0099 does not appear in r_0673's kinetic law. +// An interaction was declared that claims e_0561 modifies r_0675, but e_0561 does not appear in r_0675's kinetic law. +// An interaction was declared that claims e_1247 modifies r_0676, but e_1247 does not appear in r_0676's kinetic law. +// An interaction was declared that claims e_0071 modifies r_0678, but e_0071 does not appear in r_0678's kinetic law. +// An interaction was declared that claims e_0100 modifies r_0679, but e_0100 does not appear in r_0679's kinetic law. +// An interaction was declared that claims e_0728 modifies r_0682, but e_0728 does not appear in r_0682's kinetic law. +// An interaction was declared that claims e_1210 modifies r_0683, but e_1210 does not appear in r_0683's kinetic law. +// An interaction was declared that claims e_0439 modifies r_0683, but e_0439 does not appear in r_0683's kinetic law. +// An interaction was declared that claims e_1149 modifies r_0684, but e_1149 does not appear in r_0684's kinetic law. +// An interaction was declared that claims e_0405 modifies r_0686, but e_0405 does not appear in r_0686's kinetic law. +// An interaction was declared that claims e_0746 modifies r_0687, but e_0746 does not appear in r_0687's kinetic law. +// An interaction was declared that claims e_0567 modifies r_0695, but e_0567 does not appear in r_0695's kinetic law. +// An interaction was declared that claims e_0978 modifies r_0697, but e_0978 does not appear in r_0697's kinetic law. +// An interaction was declared that claims e_0375 modifies r_0706, but e_0375 does not appear in r_0706's kinetic law. +// An interaction was declared that claims e_1273 modifies r_0706, but e_1273 does not appear in r_0706's kinetic law. +// An interaction was declared that claims e_0375 modifies r_0707, but e_0375 does not appear in r_0707's kinetic law. +// An interaction was declared that claims e_1273 modifies r_0707, but e_1273 does not appear in r_0707's kinetic law. +// An interaction was declared that claims e_1106 modifies r_0712, but e_1106 does not appear in r_0712's kinetic law. +// An interaction was declared that claims e_1110 modifies r_0724, but e_1110 does not appear in r_0724's kinetic law. +// An interaction was declared that claims e_0813 modifies r_0726, but e_0813 does not appear in r_0726's kinetic law. +// An interaction was declared that claims e_0466 modifies r_0731, but e_0466 does not appear in r_0731's kinetic law. +// An interaction was declared that claims e_1376 modifies r_0734, but e_1376 does not appear in r_0734's kinetic law. +// An interaction was declared that claims e_0941 modifies r_0734, but e_0941 does not appear in r_0734's kinetic law. +// An interaction was declared that claims e_1377 modifies r_0734, but e_1377 does not appear in r_0734's kinetic law. +// An interaction was declared that claims e_1376 modifies r_0735, but e_1376 does not appear in r_0735's kinetic law. +// An interaction was declared that claims e_0941 modifies r_0735, but e_0941 does not appear in r_0735's kinetic law. +// An interaction was declared that claims e_1377 modifies r_0735, but e_1377 does not appear in r_0735's kinetic law. +// An interaction was declared that claims e_0175 modifies r_0739, but e_0175 does not appear in r_0739's kinetic law. +// An interaction was declared that claims e_0795 modifies r_0741, but e_0795 does not appear in r_0741's kinetic law. +// An interaction was declared that claims e_0657 modifies r_0744, but e_0657 does not appear in r_0744's kinetic law. +// An interaction was declared that claims e_0432 modifies r_0745, but e_0432 does not appear in r_0745's kinetic law. +// An interaction was declared that claims e_1130 modifies r_0754, but e_1130 does not appear in r_0754's kinetic law. +// An interaction was declared that claims e_0060 modifies r_0755, but e_0060 does not appear in r_0755's kinetic law. +// An interaction was declared that claims e_0116 modifies r_0755, but e_0116 does not appear in r_0755's kinetic law. +// An interaction was declared that claims e_0139 modifies r_0761, but e_0139 does not appear in r_0761's kinetic law. +// An interaction was declared that claims e_0743 modifies r_0762, but e_0743 does not appear in r_0762's kinetic law. +// An interaction was declared that claims e_0606 modifies r_0763, but e_0606 does not appear in r_0763's kinetic law. +// An interaction was declared that claims e_0608 modifies r_0764, but e_0608 does not appear in r_0764's kinetic law. +// An interaction was declared that claims e_0607 modifies r_0765, but e_0607 does not appear in r_0765's kinetic law. +// An interaction was declared that claims e_0001 modifies r_0769, but e_0001 does not appear in r_0769's kinetic law. +// An interaction was declared that claims e_1233 modifies r_0769, but e_1233 does not appear in r_0769's kinetic law. +// An interaction was declared that claims e_0002 modifies r_0770, but e_0002 does not appear in r_0770's kinetic law. +// An interaction was declared that claims e_1259 modifies r_0771, but e_1259 does not appear in r_0771's kinetic law. +// An interaction was declared that claims e_1272 modifies r_0775, but e_1272 does not appear in r_0775's kinetic law. +// An interaction was declared that claims e_1186 modifies r_0777, but e_1186 does not appear in r_0777's kinetic law. +// An interaction was declared that claims e_0611 modifies r_0784, but e_0611 does not appear in r_0784's kinetic law. +// An interaction was declared that claims e_0609 modifies r_0784, but e_0609 does not appear in r_0784's kinetic law. +// An interaction was declared that claims e_0608 modifies r_0785, but e_0608 does not appear in r_0785's kinetic law. +// An interaction was declared that claims e_1258 modifies r_0786, but e_1258 does not appear in r_0786's kinetic law. +// An interaction was declared that claims e_0796 modifies r_0787, but e_0796 does not appear in r_0787's kinetic law. +// An interaction was declared that claims e_0427 modifies r_0788, but e_0427 does not appear in r_0788's kinetic law. +// An interaction was declared that claims e_0805 modifies r_0796, but e_0805 does not appear in r_0796's kinetic law. +// An interaction was declared that claims e_0804 modifies r_0796, but e_0804 does not appear in r_0796's kinetic law. +// An interaction was declared that claims e_0804 modifies r_0797, but e_0804 does not appear in r_0797's kinetic law. +// An interaction was declared that claims e_1188 modifies r_0797, but e_1188 does not appear in r_0797's kinetic law. +// An interaction was declared that claims e_0805 modifies r_0797, but e_0805 does not appear in r_0797's kinetic law. +// An interaction was declared that claims e_0804 modifies r_0798, but e_0804 does not appear in r_0798's kinetic law. +// An interaction was declared that claims e_1188 modifies r_0798, but e_1188 does not appear in r_0798's kinetic law. +// An interaction was declared that claims e_0805 modifies r_0798, but e_0805 does not appear in r_0798's kinetic law. +// An interaction was declared that claims e_0803 modifies r_0799, but e_0803 does not appear in r_0799's kinetic law. +// An interaction was declared that claims e_0804 modifies r_0799, but e_0804 does not appear in r_0799's kinetic law. +// An interaction was declared that claims e_0804 modifies r_0800, but e_0804 does not appear in r_0800's kinetic law. +// An interaction was declared that claims e_0803 modifies r_0801, but e_0803 does not appear in r_0801's kinetic law. +// An interaction was declared that claims e_0804 modifies r_0801, but e_0804 does not appear in r_0801's kinetic law. +// An interaction was declared that claims e_0805 modifies r_0802, but e_0805 does not appear in r_0802's kinetic law. +// An interaction was declared that claims e_0391 modifies r_0806, but e_0391 does not appear in r_0806's kinetic law. +// An interaction was declared that claims e_1167 modifies r_0808, but e_1167 does not appear in r_0808's kinetic law. +// An interaction was declared that claims e_1170 modifies r_0811, but e_1170 does not appear in r_0811's kinetic law. +// An interaction was declared that claims e_1170 modifies r_0812, but e_1170 does not appear in r_0812's kinetic law. +// An interaction was declared that claims e_0742 modifies r_0815, but e_0742 does not appear in r_0815's kinetic law. +// An interaction was declared that claims e_0717 modifies r_0815, but e_0717 does not appear in r_0815's kinetic law. +// An interaction was declared that claims e_0819 modifies r_0829, but e_0819 does not appear in r_0829's kinetic law. +// An interaction was declared that claims e_1169 modifies r_0847, but e_1169 does not appear in r_0847's kinetic law. +// An interaction was declared that claims e_0977 modifies r_0847, but e_0977 does not appear in r_0847's kinetic law. +// An interaction was declared that claims e_1109 modifies r_0848, but e_1109 does not appear in r_0848's kinetic law. +// An interaction was declared that claims e_1167 modifies r_0854, but e_1167 does not appear in r_0854's kinetic law. +// An interaction was declared that claims e_1276 modifies r_0854, but e_1276 does not appear in r_0854's kinetic law. +// An interaction was declared that claims e_0084 modifies r_0857, but e_0084 does not appear in r_0857's kinetic law. +// An interaction was declared that claims e_1004 modifies r_0925, but e_1004 does not appear in r_0925's kinetic law. +// An interaction was declared that claims e_0277 modifies r_0934, but e_0277 does not appear in r_0934's kinetic law. +// An interaction was declared that claims e_0375 modifies r_0935, but e_0375 does not appear in r_0935's kinetic law. +// An interaction was declared that claims e_0373 modifies r_0935, but e_0373 does not appear in r_0935's kinetic law. +// An interaction was declared that claims e_0188 modifies r_0950, but e_0188 does not appear in r_0950's kinetic law. +// An interaction was declared that claims e_0931 modifies r_0951, but e_0931 does not appear in r_0951's kinetic law. +// An interaction was declared that claims e_1196 modifies r_0954, but e_1196 does not appear in r_0954's kinetic law. +// An interaction was declared that claims e_1262 modifies r_0954, but e_1262 does not appear in r_0954's kinetic law. +// An interaction was declared that claims e_0188 modifies r_0957, but e_0188 does not appear in r_0957's kinetic law. +// An interaction was declared that claims e_0281 modifies r_0963, but e_0281 does not appear in r_0963's kinetic law. +// An interaction was declared that claims e_0805 modifies r_0963, but e_0805 does not appear in r_0963's kinetic law. +// An interaction was declared that claims e_0292 modifies r_0964, but e_0292 does not appear in r_0964's kinetic law. +// An interaction was declared that claims e_0006 modifies r_0965, but e_0006 does not appear in r_0965's kinetic law. +// An interaction was declared that claims e_0281 modifies r_0968, but e_0281 does not appear in r_0968's kinetic law. +// An interaction was declared that claims e_0282 modifies r_0968, but e_0282 does not appear in r_0968's kinetic law. +// An interaction was declared that claims e_0291 modifies r_0969, but e_0291 does not appear in r_0969's kinetic law. +// An interaction was declared that claims e_0036 modifies r_0970, but e_0036 does not appear in r_0970's kinetic law. +// An interaction was declared that claims e_1029 modifies r_0970, but e_1029 does not appear in r_0970's kinetic law. +// An interaction was declared that claims e_0221 modifies r_0970, but e_0221 does not appear in r_0970's kinetic law. +// An interaction was declared that claims e_0065 modifies r_0970, but e_0065 does not appear in r_0970's kinetic law. +// An interaction was declared that claims e_1242 modifies r_0996, but e_1242 does not appear in r_0996's kinetic law. +// An interaction was declared that claims e_0893 modifies r_0999, but e_0893 does not appear in r_0999's kinetic law. +// An interaction was declared that claims e_0828 modifies r_1006, but e_0828 does not appear in r_1006's kinetic law. +// An interaction was declared that claims e_0554 modifies r_1008, but e_0554 does not appear in r_1008's kinetic law. +// An interaction was declared that claims e_0223 modifies r_1019, but e_0223 does not appear in r_1019's kinetic law. +// An interaction was declared that claims e_0048 modifies r_1021, but e_0048 does not appear in r_1021's kinetic law. +// An interaction was declared that claims e_0799 modifies r_1039, but e_0799 does not appear in r_1039's kinetic law. +// An interaction was declared that claims e_0167 modifies r_1039, but e_0167 does not appear in r_1039's kinetic law. +// An interaction was declared that claims e_0799 modifies r_1043, but e_0799 does not appear in r_1043's kinetic law. +// An interaction was declared that claims e_0167 modifies r_1043, but e_0167 does not appear in r_1043's kinetic law. +// An interaction was declared that claims e_0799 modifies r_1045, but e_0799 does not appear in r_1045's kinetic law. +// An interaction was declared that claims e_0167 modifies r_1045, but e_0167 does not appear in r_1045's kinetic law. +// An interaction was declared that claims e_0799 modifies r_1046, but e_0799 does not appear in r_1046's kinetic law. +// An interaction was declared that claims e_0167 modifies r_1046, but e_0167 does not appear in r_1046's kinetic law. +// An interaction was declared that claims e_1313 modifies r_1047, but e_1313 does not appear in r_1047's kinetic law. +// An interaction was declared that claims e_0225 modifies r_1047, but e_0225 does not appear in r_1047's kinetic law. +// An interaction was declared that claims e_0326 modifies r_1054, but e_0326 does not appear in r_1054's kinetic law. +// An interaction was declared that claims e_1232 modifies r_1057, but e_1232 does not appear in r_1057's kinetic law. +// An interaction was declared that claims e_0990 modifies r_1063, but e_0990 does not appear in r_1063's kinetic law. +// An interaction was declared that claims e_0727 modifies r_1064, but e_0727 does not appear in r_1064's kinetic law. +// An interaction was declared that claims e_1200 modifies r_1064, but e_1200 does not appear in r_1064's kinetic law. +// An interaction was declared that claims e_1341 modifies r_1065, but e_1341 does not appear in r_1065's kinetic law. +// An interaction was declared that claims e_0103 modifies r_1065, but e_0103 does not appear in r_1065's kinetic law. +// An interaction was declared that claims e_1129 modifies r_1067, but e_1129 does not appear in r_1067's kinetic law. +// An interaction was declared that claims e_0435 modifies r_1068, but e_0435 does not appear in r_1068's kinetic law. +// An interaction was declared that claims e_1126 modifies r_1074, but e_1126 does not appear in r_1074's kinetic law. +// An interaction was declared that claims e_1249 modifies r_1075, but e_1249 does not appear in r_1075's kinetic law. +// An interaction was declared that claims e_0062 modifies r_1076, but e_0062 does not appear in r_1076's kinetic law. +// An interaction was declared that claims e_1167 modifies r_1081, but e_1167 does not appear in r_1081's kinetic law. +// An interaction was declared that claims e_1276 modifies r_1081, but e_1276 does not appear in r_1081's kinetic law. +// An interaction was declared that claims e_0332 modifies r_1081, but e_0332 does not appear in r_1081's kinetic law. +// An interaction was declared that claims e_1312 modifies r_1123, but e_1312 does not appear in r_1123's kinetic law. +// An interaction was declared that claims e_1312 modifies r_1124, but e_1312 does not appear in r_1124's kinetic law. +// An interaction was declared that claims e_0823 modifies r_1130, but e_0823 does not appear in r_1130's kinetic law. +// An interaction was declared that claims e_0823 modifies r_1131, but e_0823 does not appear in r_1131's kinetic law. +// An interaction was declared that claims e_1277 modifies r_1134, but e_1277 does not appear in r_1134's kinetic law. +// An interaction was declared that claims e_1369 modifies r_1134, but e_1369 does not appear in r_1134's kinetic law. +// An interaction was declared that claims e_0039 modifies r_1137, but e_0039 does not appear in r_1137's kinetic law. +// An interaction was declared that claims e_0871 modifies r_1139, but e_0871 does not appear in r_1139's kinetic law. +// An interaction was declared that claims e_1172 modifies r_1139, but e_1172 does not appear in r_1139's kinetic law. +// An interaction was declared that claims e_0822 modifies r_1139, but e_0822 does not appear in r_1139's kinetic law. +// An interaction was declared that claims e_1240 modifies r_1141, but e_1240 does not appear in r_1141's kinetic law. +// An interaction was declared that claims e_0987 modifies r_1150, but e_0987 does not appear in r_1150's kinetic law. +// An interaction was declared that claims e_0918 modifies r_1151, but e_0918 does not appear in r_1151's kinetic law. +// An interaction was declared that claims e_0925 modifies r_1152, but e_0925 does not appear in r_1152's kinetic law. +// An interaction was declared that claims e_1108 modifies r_1153, but e_1108 does not appear in r_1153's kinetic law. +// An interaction was declared that claims e_1373 modifies r_1153, but e_1373 does not appear in r_1153's kinetic law. +// An interaction was declared that claims e_0264 modifies r_1153, but e_0264 does not appear in r_1153's kinetic law. +// An interaction was declared that claims e_0641 modifies r_1198, but e_0641 does not appear in r_1198's kinetic law. +// An interaction was declared that claims e_1127 modifies r_1200, but e_1127 does not appear in r_1200's kinetic law. +// An interaction was declared that claims e_1127 modifies r_1201, but e_1127 does not appear in r_1201's kinetic law. +// An interaction was declared that claims e_1023 modifies r_1202, but e_1023 does not appear in r_1202's kinetic law. +// An interaction was declared that claims e_1366 modifies r_1202, but e_1366 does not appear in r_1202's kinetic law. +// An interaction was declared that claims e_0612 modifies r_1204, but e_0612 does not appear in r_1204's kinetic law. +// An interaction was declared that claims e_0612 modifies r_1205, but e_0612 does not appear in r_1205's kinetic law. +// An interaction was declared that claims e_0184 modifies r_1206, but e_0184 does not appear in r_1206's kinetic law. +// An interaction was declared that claims e_0185 modifies r_1207, but e_0185 does not appear in r_1207's kinetic law. +// An interaction was declared that claims e_0791 modifies r_1208, but e_0791 does not appear in r_1208's kinetic law. +// An interaction was declared that claims e_1258 modifies r_1209, but e_1258 does not appear in r_1209's kinetic law. +// An interaction was declared that claims e_0775 modifies r_1210, but e_0775 does not appear in r_1210's kinetic law. +// An interaction was declared that claims e_0427 modifies r_1211, but e_0427 does not appear in r_1211's kinetic law. +// An interaction was declared that claims e_0815 modifies r_1212, but e_0815 does not appear in r_1212's kinetic law. +// An interaction was declared that claims e_1257 modifies r_1214, but e_1257 does not appear in r_1214's kinetic law. +// An interaction was declared that claims e_0403 modifies r_1215, but e_0403 does not appear in r_1215's kinetic law. +// An interaction was declared that claims e_0326 modifies r_1217, but e_0326 does not appear in r_1217's kinetic law. +// An interaction was declared that claims e_0768 modifies r_1218, but e_0768 does not appear in r_1218's kinetic law. +// An interaction was declared that claims e_0720 modifies r_1218, but e_0720 does not appear in r_1218's kinetic law. +// An interaction was declared that claims e_1034 modifies r_1220, but e_1034 does not appear in r_1220's kinetic law. +// An interaction was declared that claims e_0793 modifies r_1222, but e_0793 does not appear in r_1222's kinetic law. +// An interaction was declared that claims e_0134 modifies r_1223, but e_0134 does not appear in r_1223's kinetic law. +// An interaction was declared that claims e_0825 modifies r_1224, but e_0825 does not appear in r_1224's kinetic law. +// An interaction was declared that claims e_0826 modifies r_1225, but e_0826 does not appear in r_1225's kinetic law. +// An interaction was declared that claims e_1205 modifies r_1230, but e_1205 does not appear in r_1230's kinetic law. +// An interaction was declared that claims e_1367 modifies r_1232, but e_1367 does not appear in r_1232's kinetic law. +// An interaction was declared that claims e_0818 modifies r_1245, but e_0818 does not appear in r_1245's kinetic law. +// An interaction was declared that claims e_0022 modifies r_1245, but e_0022 does not appear in r_1245's kinetic law. +// An interaction was declared that claims e_0137 modifies r_1250, but e_0137 does not appear in r_1250's kinetic law. +// An interaction was declared that claims e_0052 modifies r_1251, but e_0052 does not appear in r_1251's kinetic law. +// An interaction was declared that claims e_0051 modifies r_1251, but e_0051 does not appear in r_1251's kinetic law. +// An interaction was declared that claims e_0053 modifies r_1251, but e_0053 does not appear in r_1251's kinetic law. +// An interaction was declared that claims e_0974 modifies r_1252, but e_0974 does not appear in r_1252's kinetic law. +// An interaction was declared that claims e_1238 modifies r_1252, but e_1238 does not appear in r_1252's kinetic law. +// An interaction was declared that claims e_1239 modifies r_1252, but e_1239 does not appear in r_1252's kinetic law. +// An interaction was declared that claims e_0323 modifies r_1252, but e_0323 does not appear in r_1252's kinetic law. +// An interaction was declared that claims e_0324 modifies r_1252, but e_0324 does not appear in r_1252's kinetic law. +// An interaction was declared that claims e_0821 modifies r_1252, but e_0821 does not appear in r_1252's kinetic law. +// An interaction was declared that claims e_0451 modifies r_1255, but e_0451 does not appear in r_1255's kinetic law. +// An interaction was declared that claims e_0238 modifies r_1255, but e_0238 does not appear in r_1255's kinetic law. +// An interaction was declared that claims e_0911 modifies r_1255, but e_0911 does not appear in r_1255's kinetic law. +// An interaction was declared that claims e_0260 modifies r_1259, but e_0260 does not appear in r_1259's kinetic law. +// An interaction was declared that claims e_0008 modifies r_1264, but e_0008 does not appear in r_1264's kinetic law. +// An interaction was declared that claims e_0531 modifies r_1265, but e_0531 does not appear in r_1265's kinetic law. +// An interaction was declared that claims e_0145 modifies r_1266, but e_0145 does not appear in r_1266's kinetic law. +// An interaction was declared that claims e_1335 modifies r_1276, but e_1335 does not appear in r_1276's kinetic law. +// An interaction was declared that claims e_1227 modifies r_1276, but e_1227 does not appear in r_1276's kinetic law. +// An interaction was declared that claims e_1334 modifies r_1276, but e_1334 does not appear in r_1276's kinetic law. +// An interaction was declared that claims e_0238 modifies r_1276, but e_0238 does not appear in r_1276's kinetic law. +// An interaction was declared that claims e_0911 modifies r_1276, but e_0911 does not appear in r_1276's kinetic law. +// An interaction was declared that claims e_1335 modifies r_1277, but e_1335 does not appear in r_1277's kinetic law. +// An interaction was declared that claims e_1227 modifies r_1277, but e_1227 does not appear in r_1277's kinetic law. +// An interaction was declared that claims e_1334 modifies r_1277, but e_1334 does not appear in r_1277's kinetic law. +// An interaction was declared that claims e_0238 modifies r_1277, but e_0238 does not appear in r_1277's kinetic law. +// An interaction was declared that claims e_0911 modifies r_1277, but e_0911 does not appear in r_1277's kinetic law. +// An interaction was declared that claims e_1335 modifies r_1278, but e_1335 does not appear in r_1278's kinetic law. +// An interaction was declared that claims e_1227 modifies r_1278, but e_1227 does not appear in r_1278's kinetic law. +// An interaction was declared that claims e_1334 modifies r_1278, but e_1334 does not appear in r_1278's kinetic law. +// An interaction was declared that claims e_0238 modifies r_1278, but e_0238 does not appear in r_1278's kinetic law. +// An interaction was declared that claims e_0911 modifies r_1278, but e_0911 does not appear in r_1278's kinetic law. +// An interaction was declared that claims e_1335 modifies r_1279, but e_1335 does not appear in r_1279's kinetic law. +// An interaction was declared that claims e_1227 modifies r_1279, but e_1227 does not appear in r_1279's kinetic law. +// An interaction was declared that claims e_1334 modifies r_1279, but e_1334 does not appear in r_1279's kinetic law. +// An interaction was declared that claims e_0238 modifies r_1279, but e_0238 does not appear in r_1279's kinetic law. +// An interaction was declared that claims e_0911 modifies r_1279, but e_0911 does not appear in r_1279's kinetic law. +// An interaction was declared that claims e_0919 modifies r_1284, but e_0919 does not appear in r_1284's kinetic law. +// An interaction was declared that claims e_1291 modifies r_1284, but e_1291 does not appear in r_1284's kinetic law. +// An interaction was declared that claims e_1355 modifies r_1285, but e_1355 does not appear in r_1285's kinetic law. +// An interaction was declared that claims e_1026 modifies r_1285, but e_1026 does not appear in r_1285's kinetic law. +// An interaction was declared that claims e_0074 modifies r_1288, but e_0074 does not appear in r_1288's kinetic law. +// An interaction was declared that claims e_0839 modifies r_1291, but e_0839 does not appear in r_1291's kinetic law. +// An interaction was declared that claims e_1105 modifies r_1301, but e_1105 does not appear in r_1301's kinetic law. +// An interaction was declared that claims e_1010 modifies r_1304, but e_1010 does not appear in r_1304's kinetic law. +// An interaction was declared that claims e_0540 modifies r_1304, but e_0540 does not appear in r_1304's kinetic law. +// An interaction was declared that claims e_1028 modifies r_1305, but e_1028 does not appear in r_1305's kinetic law. +// An interaction was declared that claims e_0138 modifies r_1305, but e_0138 does not appear in r_1305's kinetic law. +// An interaction was declared that claims e_1019 modifies r_1306, but e_1019 does not appear in r_1306's kinetic law. +// An interaction was declared that claims e_1019 modifies r_1307, but e_1019 does not appear in r_1307's kinetic law. +// An interaction was declared that claims e_0253 modifies r_1315, but e_0253 does not appear in r_1315's kinetic law. +// An interaction was declared that claims e_0254 modifies r_1315, but e_0254 does not appear in r_1315's kinetic law. +// An interaction was declared that claims e_0774 modifies r_1316, but e_0774 does not appear in r_1316's kinetic law. +// An interaction was declared that claims e_1014 modifies r_1318, but e_1014 does not appear in r_1318's kinetic law. +// An interaction was declared that claims e_0869 modifies r_1329, but e_0869 does not appear in r_1329's kinetic law. +// An interaction was declared that claims e_0870 modifies r_1329, but e_0870 does not appear in r_1329's kinetic law. +// An interaction was declared that claims e_0872 modifies r_1330, but e_0872 does not appear in r_1330's kinetic law. +// An interaction was declared that claims e_0873 modifies r_1330, but e_0873 does not appear in r_1330's kinetic law. +// An interaction was declared that claims e_0979 modifies r_1335, but e_0979 does not appear in r_1335's kinetic law. +// An interaction was declared that claims e_0177 modifies r_1335, but e_0177 does not appear in r_1335's kinetic law. +// An interaction was declared that claims e_0330 modifies r_1337, but e_0330 does not appear in r_1337's kinetic law. +// An interaction was declared that claims e_0076 modifies r_1338, but e_0076 does not appear in r_1338's kinetic law. +// An interaction was declared that claims e_1253 modifies r_1344, but e_1253 does not appear in r_1344's kinetic law. +// An interaction was declared that claims e_0146 modifies r_1345, but e_0146 does not appear in r_1345's kinetic law. +// An interaction was declared that claims e_1374 modifies r_1346, but e_1374 does not appear in r_1346's kinetic law. +// An interaction was declared that claims e_1250 modifies r_1346, but e_1250 does not appear in r_1346's kinetic law. +// An interaction was declared that claims e_0805 modifies r_1346, but e_0805 does not appear in r_1346's kinetic law. +// An interaction was declared that claims e_0151 modifies r_1346, but e_0151 does not appear in r_1346's kinetic law. +// An interaction was declared that claims e_1252 modifies r_1346, but e_1252 does not appear in r_1346's kinetic law. +// An interaction was declared that claims e_1172 modifies r_1347, but e_1172 does not appear in r_1347's kinetic law. +// An interaction was declared that claims e_0822 modifies r_1347, but e_0822 does not appear in r_1347's kinetic law. +// An interaction was declared that claims e_0318 modifies r_1347, but e_0318 does not appear in r_1347's kinetic law. +// An interaction was declared that claims e_0313 modifies r_1348, but e_0313 does not appear in r_1348's kinetic law. +// An interaction was declared that claims e_0813 modifies r_1348, but e_0813 does not appear in r_1348's kinetic law. +// An interaction was declared that claims e_0003 modifies r_1349, but e_0003 does not appear in r_1349's kinetic law. +// An interaction was declared that claims e_0894 modifies r_1353, but e_0894 does not appear in r_1353's kinetic law. +// An interaction was declared that claims e_0770 modifies r_1356, but e_0770 does not appear in r_1356's kinetic law. +// An interaction was declared that claims e_0005 modifies r_1356, but e_0005 does not appear in r_1356's kinetic law. +// An interaction was declared that claims e_0771 modifies r_1357, but e_0771 does not appear in r_1357's kinetic law. +// An interaction was declared that claims e_0928 modifies r_1357, but e_0928 does not appear in r_1357's kinetic law. +// An interaction was declared that claims e_0771 modifies r_1358, but e_0771 does not appear in r_1358's kinetic law. +// An interaction was declared that claims e_0928 modifies r_1358, but e_0928 does not appear in r_1358's kinetic law. +// An interaction was declared that claims e_1226 modifies r_1363, but e_1226 does not appear in r_1363's kinetic law. +// An interaction was declared that claims e_0425 modifies r_1367, but e_0425 does not appear in r_1367's kinetic law. +// An interaction was declared that claims e_0426 modifies r_1367, but e_0426 does not appear in r_1367's kinetic law. +// An interaction was declared that claims e_1141 modifies r_1368, but e_1141 does not appear in r_1368's kinetic law. +// An interaction was declared that claims e_1251 modifies r_1375, but e_1251 does not appear in r_1375's kinetic law. +// An interaction was declared that claims e_1276 modifies r_1376, but e_1276 does not appear in r_1376's kinetic law. +// An interaction was declared that claims e_0332 modifies r_1376, but e_0332 does not appear in r_1376's kinetic law. +// An interaction was declared that claims e_0081 modifies r_1378, but e_0081 does not appear in r_1378's kinetic law. +// An interaction was declared that claims e_0044 modifies r_1379, but e_0044 does not appear in r_1379's kinetic law. +// An interaction was declared that claims e_1248 modifies r_1388, but e_1248 does not appear in r_1388's kinetic law. +// An interaction was declared that claims e_0991 modifies r_1389, but e_0991 does not appear in r_1389's kinetic law. +// An interaction was declared that claims e_0375 modifies r_1391, but e_0375 does not appear in r_1391's kinetic law. +// An interaction was declared that claims e_0083 modifies r_1391, but e_0083 does not appear in r_1391's kinetic law. +// An interaction was declared that claims e_1150 modifies r_1392, but e_1150 does not appear in r_1392's kinetic law. +// An interaction was declared that claims e_0041 modifies r_1393, but e_0041 does not appear in r_1393's kinetic law. +// An interaction was declared that claims e_0042 modifies r_1397, but e_0042 does not appear in r_1397's kinetic law. +// An interaction was declared that claims e_0040 modifies r_1399, but e_0040 does not appear in r_1399's kinetic law. +// An interaction was declared that claims e_0037 modifies r_1400, but e_0037 does not appear in r_1400's kinetic law. +// An interaction was declared that claims e_0038 modifies r_1401, but e_0038 does not appear in r_1401's kinetic law. +// An interaction was declared that claims e_0186 modifies r_1402, but e_0186 does not appear in r_1402's kinetic law. +// An interaction was declared that claims e_0328 modifies r_1409, but e_0328 does not appear in r_1409's kinetic law. +// An interaction was declared that claims e_0077 modifies r_1409, but e_0077 does not appear in r_1409's kinetic law. +// An interaction was declared that claims e_0079 modifies r_1410, but e_0079 does not appear in r_1410's kinetic law. +// An interaction was declared that claims e_0962 modifies r_1413, but e_0962 does not appear in r_1413's kinetic law. +// An interaction was declared that claims e_0433 modifies r_1413, but e_0433 does not appear in r_1413's kinetic law. +// An interaction was declared that claims e_0300 modifies r_1413, but e_0300 does not appear in r_1413's kinetic law. +// An interaction was declared that claims e_1256 modifies r_1421, but e_1256 does not appear in r_1421's kinetic law. +// An interaction was declared that claims e_1184 modifies r_1422, but e_1184 does not appear in r_1422's kinetic law. +// An interaction was declared that claims e_1019 modifies r_1422, but e_1019 does not appear in r_1422's kinetic law. +// An interaction was declared that claims e_1185 modifies r_1423, but e_1185 does not appear in r_1423's kinetic law. +// An interaction was declared that claims e_1167 modifies r_1425, but e_1167 does not appear in r_1425's kinetic law. +// An interaction was declared that claims e_1086 modifies r_1432, but e_1086 does not appear in r_1432's kinetic law. + model *MODEL1302140001() // Compartments and Species: @@ -602,6 +1127,530 @@ model *MODEL1302140001() r_2538: s_1550 => $s_2093; cell*((r_2538_v0*(1 + r_2538_ep1550*ln(s_1550/ic1550)) + zero_flux + abs(r_2538_v0*(1 + r_2538_ep1550*ln(s_1550/ic1550)) - zero_flux))/2); r_2584: 0.000223 s_0133 + 2.6e-05 s_0378 + 0.000223 s_0226 + 0.00026 s_0380 + 0.5137 s_1041 + 0.000223 s_1552 + 0.2958 s_1061 + 0.2411 s_1068 + 0.2411 s_1072 + 54.12 s_0467 + 0.000122 s_0480 + 2e-06 s_0476 + 0.005205 s_0497 + 0.005205 s_0520 + 0.000576 s_0555 + 2.5e-05 s_0546 + 0.1335 s_0575 + 0.000709 s_0579 + 0.09158 s_1083 + 0.02617 s_0726 + 0.02702 s_0731 + 0.02702 s_0760 + 0.02617 s_0805 + 0.000223 s_0859 + 0.006715 s_0838 + 0.007808 s_0841 + 0.2632 s_1101 + 0.2632 s_1095 + 0.6126 s_0929 + 0.2151 s_0945 + 0.09474 s_1106 + 0.2905 s_1119 + 0.1952 s_1494 + 0.4505 s_1127 + 0.3432 s_1131 + 0.1537 s_1141 + 0.008675 s_1212 + 0.000223 s_0336 + 0.000691 s_1255 + 7e-06 s_1261 + 0.001831 s_1333 + 0.000447 s_1335 + 0.01301 s_0451 + 0.000323 s_1329 + 0.06382 s_1437 + 0.07521 s_1435 + 0.1853 s_1151 + 0.000223 s_1508 + 0.2211 s_1155 + 0.000223 s_1522 + 0.000223 s_1546 + 0.2158 s_1170 + 0.000223 s_1577 + 0.004338 s_1609 + 0.000223 s_0337 + 0.000223 s_1644 + 0.2537 s_1179 + 0.05684 s_1185 + 0.1379 s_1189 + 5.5e-05 s_1765 + 0.1441 s_1792 + 0.4232 s_1193 + 0.000341 s_1804 + 0.01946 s_1033 + 0.01389 s_1719 => 53.95 s_0421 + 53.95 s_1430 + 0.7739 s_0783; cell*((r_2584_v0*(1 + r_2584_ep0133*ln(s_0133/ic0133) + r_2584_ep0378*ln(s_0378/ic0378) + r_2584_ep0226*ln(s_0226/ic0226) + r_2584_ep0380*ln(s_0380/ic0380) + r_2584_ep1041*ln(s_1041/ic1041) + r_2584_ep1552*ln(s_1552/ic1552) + r_2584_ep1061*ln(s_1061/ic1061) + r_2584_ep1068*ln(s_1068/ic1068) + r_2584_ep1072*ln(s_1072/ic1072) + r_2584_ep0467*ln(s_0467/ic0467) + r_2584_ep0480*ln(s_0480/ic0480) + r_2584_ep0476*ln(s_0476/ic0476) + r_2584_ep0497*ln(s_0497/ic0497) + r_2584_ep0520*ln(s_0520/ic0520) + r_2584_ep0555*ln(s_0555/ic0555) + r_2584_ep0546*ln(s_0546/ic0546) + r_2584_ep0575*ln(s_0575/ic0575) + r_2584_ep0579*ln(s_0579/ic0579) + r_2584_ep1083*ln(s_1083/ic1083) + r_2584_ep0726*ln(s_0726/ic0726) + r_2584_ep0731*ln(s_0731/ic0731) + r_2584_ep0760*ln(s_0760/ic0760) + r_2584_ep0805*ln(s_0805/ic0805) + r_2584_ep0859*ln(s_0859/ic0859) + r_2584_ep0838*ln(s_0838/ic0838) + r_2584_ep0841*ln(s_0841/ic0841) + r_2584_ep1101*ln(s_1101/ic1101) + r_2584_ep1095*ln(s_1095/ic1095) + r_2584_ep0929*ln(s_0929/ic0929) + r_2584_ep0945*ln(s_0945/ic0945) + r_2584_ep1106*ln(s_1106/ic1106) + r_2584_ep1119*ln(s_1119/ic1119) + r_2584_ep1494*ln(s_1494/ic1494) + r_2584_ep1127*ln(s_1127/ic1127) + r_2584_ep1131*ln(s_1131/ic1131) + r_2584_ep1141*ln(s_1141/ic1141) + r_2584_ep1212*ln(s_1212/ic1212) + r_2584_ep0336*ln(s_0336/ic0336) + r_2584_ep1255*ln(s_1255/ic1255) + r_2584_ep1261*ln(s_1261/ic1261) + r_2584_ep1333*ln(s_1333/ic1333) + r_2584_ep1335*ln(s_1335/ic1335) + r_2584_ep0451*ln(s_0451/ic0451) + r_2584_ep1329*ln(s_1329/ic1329) + r_2584_ep1437*ln(s_1437/ic1437) + r_2584_ep1435*ln(s_1435/ic1435) + r_2584_ep1151*ln(s_1151/ic1151) + r_2584_ep1508*ln(s_1508/ic1508) + r_2584_ep1155*ln(s_1155/ic1155) + r_2584_ep1522*ln(s_1522/ic1522) + r_2584_ep1546*ln(s_1546/ic1546) + r_2584_ep1170*ln(s_1170/ic1170) + r_2584_ep1577*ln(s_1577/ic1577) + r_2584_ep1609*ln(s_1609/ic1609) + r_2584_ep0337*ln(s_0337/ic0337) + r_2584_ep1644*ln(s_1644/ic1644) + r_2584_ep1179*ln(s_1179/ic1179) + r_2584_ep1185*ln(s_1185/ic1185) + r_2584_ep1189*ln(s_1189/ic1189) + r_2584_ep1765*ln(s_1765/ic1765) + r_2584_ep1792*ln(s_1792/ic1792) + r_2584_ep1193*ln(s_1193/ic1193) + r_2584_ep1804*ln(s_1804/ic1804) + r_2584_ep1033*ln(s_1033/ic1033) + r_2584_ep1719*ln(s_1719/ic1719)) + zero_flux + abs(r_2584_v0*(1 + r_2584_ep0133*ln(s_0133/ic0133) + r_2584_ep0378*ln(s_0378/ic0378) + r_2584_ep0226*ln(s_0226/ic0226) + r_2584_ep0380*ln(s_0380/ic0380) + r_2584_ep1041*ln(s_1041/ic1041) + r_2584_ep1552*ln(s_1552/ic1552) + r_2584_ep1061*ln(s_1061/ic1061) + r_2584_ep1068*ln(s_1068/ic1068) + r_2584_ep1072*ln(s_1072/ic1072) + r_2584_ep0467*ln(s_0467/ic0467) + r_2584_ep0480*ln(s_0480/ic0480) + r_2584_ep0476*ln(s_0476/ic0476) + r_2584_ep0497*ln(s_0497/ic0497) + r_2584_ep0520*ln(s_0520/ic0520) + r_2584_ep0555*ln(s_0555/ic0555) + r_2584_ep0546*ln(s_0546/ic0546) + r_2584_ep0575*ln(s_0575/ic0575) + r_2584_ep0579*ln(s_0579/ic0579) + r_2584_ep1083*ln(s_1083/ic1083) + r_2584_ep0726*ln(s_0726/ic0726) + r_2584_ep0731*ln(s_0731/ic0731) + r_2584_ep0760*ln(s_0760/ic0760) + r_2584_ep0805*ln(s_0805/ic0805) + r_2584_ep0859*ln(s_0859/ic0859) + r_2584_ep0838*ln(s_0838/ic0838) + r_2584_ep0841*ln(s_0841/ic0841) + r_2584_ep1101*ln(s_1101/ic1101) + r_2584_ep1095*ln(s_1095/ic1095) + r_2584_ep0929*ln(s_0929/ic0929) + r_2584_ep0945*ln(s_0945/ic0945) + r_2584_ep1106*ln(s_1106/ic1106) + r_2584_ep1119*ln(s_1119/ic1119) + r_2584_ep1494*ln(s_1494/ic1494) + r_2584_ep1127*ln(s_1127/ic1127) + r_2584_ep1131*ln(s_1131/ic1131) + r_2584_ep1141*ln(s_1141/ic1141) + r_2584_ep1212*ln(s_1212/ic1212) + r_2584_ep0336*ln(s_0336/ic0336) + r_2584_ep1255*ln(s_1255/ic1255) + r_2584_ep1261*ln(s_1261/ic1261) + r_2584_ep1333*ln(s_1333/ic1333) + r_2584_ep1335*ln(s_1335/ic1335) + r_2584_ep0451*ln(s_0451/ic0451) + r_2584_ep1329*ln(s_1329/ic1329) + r_2584_ep1437*ln(s_1437/ic1437) + r_2584_ep1435*ln(s_1435/ic1435) + r_2584_ep1151*ln(s_1151/ic1151) + r_2584_ep1508*ln(s_1508/ic1508) + r_2584_ep1155*ln(s_1155/ic1155) + r_2584_ep1522*ln(s_1522/ic1522) + r_2584_ep1546*ln(s_1546/ic1546) + r_2584_ep1170*ln(s_1170/ic1170) + r_2584_ep1577*ln(s_1577/ic1577) + r_2584_ep1609*ln(s_1609/ic1609) + r_2584_ep0337*ln(s_0337/ic0337) + r_2584_ep1644*ln(s_1644/ic1644) + r_2584_ep1179*ln(s_1179/ic1179) + r_2584_ep1185*ln(s_1185/ic1185) + r_2584_ep1189*ln(s_1189/ic1189) + r_2584_ep1765*ln(s_1765/ic1765) + r_2584_ep1792*ln(s_1792/ic1792) + r_2584_ep1193*ln(s_1193/ic1193) + r_2584_ep1804*ln(s_1804/ic1804) + r_2584_ep1033*ln(s_1033/ic1033) + r_2584_ep1719*ln(s_1719/ic1719)) - zero_flux))/2); + // Interactions: + _I0: $e_0610 -o r_0008; ; + _I1: $e_0149 -o r_0009; ; + _I2: $e_0078 -o r_0011; ; + _I3: $e_0953 -o r_0012; ; + _I4: $e_0953 -o r_0013; ; + _I5: $e_0010 -o r_0014; ; + _I6: $e_0010 -o r_0015; ; + _I7: $e_1137 -o r_0038; ; + _I8: $e_0034 -o r_0038; ; + _I9: $e_0035 -o r_0038; ; + _I10: $e_1136 -o r_0038; ; + _I11: $e_0866 -o r_0053; ; + _I12: $e_0867 -o r_0054; ; + _I13: $e_0578 -o r_0056; ; + _I14: $e_0152 -o r_0063; ; + _I15: $e_1170 -o r_0063; ; + _I16: $e_0031 -o r_0066; ; + _I17: $e_0030 -o r_0066; ; + _I18: $e_0033 -o r_0067; ; + _I19: $e_0238 -o r_0084; ; + _I20: $e_0798 -o r_0084; ; + _I21: $e_0911 -o r_0084; ; + _I22: $e_1326 -o r_0085; ; + _I23: $e_0960 -o r_0092; ; + _I24: $e_1203 -o r_0096; ; + _I25: $e_0541 -o r_0098; ; + _I26: $e_1027 -o r_0099; ; + _I27: $e_0406 -o r_0100; ; + _I28: $e_0544 -o r_0101; ; + _I29: $e_0827 -o r_0101; ; + _I30: $e_0263 -o r_0101; ; + _I31: $e_1125 -o r_0102; ; + _I32: $e_1125 -o r_0103; ; + _I33: $e_0331 -o r_0105; ; + _I34: $e_0994 -o r_0106; ; + _I35: $e_1203 -o r_0120; ; + _I36: $e_0735 -o r_0120; ; + _I37: $e_1203 -o r_0121; ; + _I38: $e_0735 -o r_0121; ; + _I39: $e_1203 -o r_0122; ; + _I40: $e_0735 -o r_0122; ; + _I41: $e_1203 -o r_0123; ; + _I42: $e_0735 -o r_0123; ; + _I43: $e_1203 -o r_0124; ; + _I44: $e_0735 -o r_0124; ; + _I45: $e_1203 -o r_0126; ; + _I46: $e_0735 -o r_0126; ; + _I47: $e_1203 -o r_0127; ; + _I48: $e_0735 -o r_0127; ; + _I49: $e_1203 -o r_0128; ; + _I50: $e_0735 -o r_0128; ; + _I51: $e_1203 -o r_0129; ; + _I52: $e_0735 -o r_0129; ; + _I53: $e_1203 -o r_0130; ; + _I54: $e_0735 -o r_0130; ; + _I55: $e_1203 -o r_0131; ; + _I56: $e_0735 -o r_0131; ; + _I57: $e_1203 -o r_0133; ; + _I58: $e_0735 -o r_0133; ; + _I59: $e_1203 -o r_0134; ; + _I60: $e_0735 -o r_0134; ; + _I61: $e_1203 -o r_0135; ; + _I62: $e_0735 -o r_0135; ; + _I63: $e_0031 -o r_0138; ; + _I64: $e_0030 -o r_0138; ; + _I65: $e_0032 -o r_0139; ; + _I66: $e_0063 -o r_0143; ; + _I67: $e_0082 -o r_0145; ; + _I68: $e_0374 -o r_0146; ; + _I69: $e_0372 -o r_0147; ; + _I70: $e_0082 -o r_0148; ; + _I71: $e_0374 -o r_0149; ; + _I72: $e_0732 -o r_0150; ; + _I73: $e_0374 -o r_0154; ; + _I74: $e_0376 -o r_0166; ; + _I75: $e_0732 -o r_0166; ; + _I76: $e_0327 -o r_0175; ; + _I77: $e_0404 -o r_0178; ; + _I78: $e_1254 -o r_0179; ; + _I79: $e_1015 -o r_0181; ; + _I80: $e_0572 -o r_0181; ; + _I81: $e_0377 -o r_0182; ; + _I82: $e_0074 -o r_0186; ; + _I83: $e_1234 -o r_0211; ; + _I84: $e_0144 -o r_0212; ; + _I85: $e_0064 -o r_0216; ; + _I86: $e_0579 -o r_0217; ; + _I87: $e_0273 -o r_0218; ; + _I88: $e_0276 -o r_0222; ; + _I89: $e_0125 -o r_0224; ; + _I90: $e_0416 -o r_0224; ; + _I91: $e_0975 -o r_0225; ; + _I92: $e_0719 -o r_0225; ; + _I93: $e_0577 -o r_0225; ; + _I94: $e_1137 -o r_0227; ; + _I95: $e_0034 -o r_0227; ; + _I96: $e_0035 -o r_0227; ; + _I97: $e_1136 -o r_0227; ; + _I98: $e_0682 -o r_0230; ; + _I99: $e_1202 -o r_0230; ; + _I100: $e_0736 -o r_0230; ; + _I101: $e_1202 -o r_0231; ; + _I102: $e_0736 -o r_0231; ; + _I103: $e_1202 -o r_0232; ; + _I104: $e_0736 -o r_0232; ; + _I105: $e_1202 -o r_0233; ; + _I106: $e_0736 -o r_0233; ; + _I107: $e_1202 -o r_0234; ; + _I108: $e_0736 -o r_0234; ; + _I109: $e_1202 -o r_0235; ; + _I110: $e_0736 -o r_0235; ; + _I111: $e_1202 -o r_0236; ; + _I112: $e_0736 -o r_0236; ; + _I113: $e_0085 -o r_0237; ; + _I114: $e_1006 -o r_0237; ; + _I115: $e_1005 -o r_0237; ; + _I116: $e_0730 -o r_0237; ; + _I117: $e_1243 -o r_0243; ; + _I118: $e_1241 -o r_0244; ; + _I119: $e_0559 -o r_0245; ; + _I120: $e_1014 -o r_0245; ; + _I121: $e_0431 -o r_0246; ; + _I122: $e_0054 -o r_0246; ; + _I123: $e_0431 -o r_0247; ; + _I124: $e_0054 -o r_0247; ; + _I125: $e_0375 -o r_0257; ; + _I126: $e_0896 -o r_0257; ; + _I127: $e_0375 -o r_0259; ; + _I128: $e_0896 -o r_0259; ; + _I129: $e_0375 -o r_0260; ; + _I130: $e_0896 -o r_0260; ; + _I131: $e_0094 -o r_0266; ; + _I132: $e_0094 -o r_0267; ; + _I133: $e_0094 -o r_0268; ; + _I134: $e_0094 -o r_0269; ; + _I135: $e_0094 -o r_0270; ; + _I136: $e_0094 -o r_0272; ; + _I137: $e_0094 -o r_0273; ; + _I138: $e_0167 -o r_0292; ; + _I139: $e_0274 -o r_0297; ; + _I140: $e_0167 -o r_0301; ; + _I141: $e_0389 -o r_0302; ; + _I142: $e_1315 -o r_0303; ; + _I143: $e_0389 -o r_0304; ; + _I144: $e_0868 -o r_0305; ; + _I145: $e_0395 -o r_0310; ; + _I146: $e_1275 -o r_0310; ; + _I147: $e_0428 -o r_0348; ; + _I148: $e_0429 -o r_0349; ; + _I149: $e_0428 -o r_0349; ; + _I150: $e_0993 -o r_0355; ; + _I151: $e_0848 -o r_0355; ; + _I152: $e_1244 -o r_0360; ; + _I153: $e_0986 -o r_0361; ; + _I154: $e_1160 -o r_0365; ; + _I155: $e_0061 -o r_0367; ; + _I156: $e_1340 -o r_0368; ; + _I157: $e_1339 -o r_0368; ; + _I158: $e_1263 -o r_0369; ; + _I159: $e_0001 -o r_0369; ; + _I160: $e_1233 -o r_0369; ; + _I161: $e_0332 -o r_0370; ; + _I162: $e_1045 -o r_0371; ; + _I163: $e_0605 -o r_0374; ; + _I164: $e_0275 -o r_0383; ; + _I165: $e_0292 -o r_0384; ; + _I166: $e_1207 -o r_0385; ; + _I167: $e_1206 -o r_0385; ; + _I168: $e_1207 -o r_0386; ; + _I169: $e_1206 -o r_0386; ; + _I170: $e_0903 -o r_0388; ; + _I171: $e_0183 -o r_0388; ; + _I172: $e_0110 -o r_0388; ; + _I173: $e_0080 -o r_0418; ; + _I174: $e_0080 -o r_0419; ; + _I175: $e_0825 -o r_0423; ; + _I176: $e_0826 -o r_0423; ; + _I177: $e_1271 -o r_0424; ; + _I178: $e_0734 -o r_0425; ; + _I179: $e_0246 -o r_0428; ; + _I180: $e_0765 -o r_0436; ; + _I181: $e_0876 -o r_0440; ; + _I182: $e_0279 -o r_0445; ; + _I183: $e_0280 -o r_0445; ; + _I184: $e_0951 -o r_0450; ; + _I185: $e_0519 -o r_0450; ; + _I186: $e_0757 -o r_0452; ; + _I187: $e_0750 -o r_0452; ; + _I188: $e_0328 -o r_0457; ; + _I189: $e_0043 -o r_0463; ; + _I190: $e_0135 -o r_0463; ; + _I191: $e_0046 -o r_0488; ; + _I192: $e_0278 -o r_0489; ; + _I193: $e_0144 -o r_0498; ; + _I194: $e_0897 -o r_0499; ; + _I195: $e_1189 -o r_0500; ; + _I196: $e_0342 -o r_0501; ; + _I197: $e_0012 -o r_0502; ; + _I198: $e_0776 -o r_0503; ; + _I199: $e_0514 -o r_0504; ; + _I200: $e_0020 -o r_0504; ; + _I201: $e_0729 -o r_0505; ; + _I202: $e_0964 -o r_0507; ; + _I203: $e_0045 -o r_0510; ; + _I204: $e_0586 -o r_0510; ; + _I205: $e_0368 -o r_0511; ; + _I206: $e_0342 -o r_0512; ; + _I207: $e_0988 -o r_0515; ; + _I208: $e_1168 -o r_0517; ; + _I209: $e_1168 -o r_0518; ; + _I210: $e_0150 -o r_0522; ; + _I211: $e_0378 -o r_0532; ; + _I212: $e_1128 -o r_0533; ; + _I213: $e_0691 -o r_0533; ; + _I214: $e_0875 -o r_0538; ; + _I215: $e_0436 -o r_0563; ; + _I216: $e_0436 -o r_0564; ; + _I217: $e_0731 -o r_0573; ; + _I218: $e_0926 -o r_0574; ; + _I219: $e_0567 -o r_0574; ; + _I220: $e_1201 -o r_0576; ; + _I221: $e_0162 -o r_0579; ; + _I222: $e_0162 -o r_0580; ; + _I223: $e_0162 -o r_0581; ; + _I224: $e_0168 -o r_0602; ; + _I225: $e_0008 -o r_0611; ; + _I226: $e_1298 -o r_0632; ; + _I227: $e_0515 -o r_0632; ; + _I228: $e_0516 -o r_0632; ; + _I229: $e_0577 -o r_0648; ; + _I230: $e_0150 -o r_0655; ; + _I231: $e_1150 -o r_0658; ; + _I232: $e_0580 -o r_0660; ; + _I233: $e_1264 -o r_0664; ; + _I234: $e_0099 -o r_0673; ; + _I235: $e_0561 -o r_0675; ; + _I236: $e_1247 -o r_0676; ; + _I237: $e_0071 -o r_0678; ; + _I238: $e_0100 -o r_0679; ; + _I239: $e_0728 -o r_0682; ; + _I240: $e_1210 -o r_0683; ; + _I241: $e_0439 -o r_0683; ; + _I242: $e_1149 -o r_0684; ; + _I243: $e_0405 -o r_0686; ; + _I244: $e_0746 -o r_0687; ; + _I245: $e_0567 -o r_0695; ; + _I246: $e_0978 -o r_0697; ; + _I247: $e_0375 -o r_0706; ; + _I248: $e_1273 -o r_0706; ; + _I249: $e_0375 -o r_0707; ; + _I250: $e_1273 -o r_0707; ; + _I251: $e_1106 -o r_0712; ; + _I252: $e_1110 -o r_0724; ; + _I253: $e_0813 -o r_0726; ; + _I254: $e_0466 -o r_0731; ; + _I255: $e_1376 -o r_0734; ; + _I256: $e_0941 -o r_0734; ; + _I257: $e_1377 -o r_0734; ; + _I258: $e_1376 -o r_0735; ; + _I259: $e_0941 -o r_0735; ; + _I260: $e_1377 -o r_0735; ; + _I261: $e_0175 -o r_0739; ; + _I262: $e_0795 -o r_0741; ; + _I263: $e_0657 -o r_0744; ; + _I264: $e_0432 -o r_0745; ; + _I265: $e_1130 -o r_0754; ; + _I266: $e_0060 -o r_0755; ; + _I267: $e_0116 -o r_0755; ; + _I268: $e_0139 -o r_0761; ; + _I269: $e_0743 -o r_0762; ; + _I270: $e_0606 -o r_0763; ; + _I271: $e_0608 -o r_0764; ; + _I272: $e_0607 -o r_0765; ; + _I273: $e_0001 -o r_0769; ; + _I274: $e_1233 -o r_0769; ; + _I275: $e_0002 -o r_0770; ; + _I276: $e_1259 -o r_0771; ; + _I277: $e_1272 -o r_0775; ; + _I278: $e_1186 -o r_0777; ; + _I279: $e_0611 -o r_0784; ; + _I280: $e_0609 -o r_0784; ; + _I281: $e_0608 -o r_0785; ; + _I282: $e_1258 -o r_0786; ; + _I283: $e_0796 -o r_0787; ; + _I284: $e_0427 -o r_0788; ; + _I285: $e_0805 -o r_0796; ; + _I286: $e_0804 -o r_0796; ; + _I287: $e_0804 -o r_0797; ; + _I288: $e_1188 -o r_0797; ; + _I289: $e_0805 -o r_0797; ; + _I290: $e_0804 -o r_0798; ; + _I291: $e_1188 -o r_0798; ; + _I292: $e_0805 -o r_0798; ; + _I293: $e_0803 -o r_0799; ; + _I294: $e_0804 -o r_0799; ; + _I295: $e_0804 -o r_0800; ; + _I296: $e_0803 -o r_0801; ; + _I297: $e_0804 -o r_0801; ; + _I298: $e_0805 -o r_0802; ; + _I299: $e_0391 -o r_0806; ; + _I300: $e_1167 -o r_0808; ; + _I301: $e_1170 -o r_0811; ; + _I302: $e_1170 -o r_0812; ; + _I303: $e_0742 -o r_0815; ; + _I304: $e_0717 -o r_0815; ; + _I305: $e_0819 -o r_0829; ; + _I306: $e_1169 -o r_0847; ; + _I307: $e_0977 -o r_0847; ; + _I308: $e_1109 -o r_0848; ; + _I309: $e_1167 -o r_0854; ; + _I310: $e_1276 -o r_0854; ; + _I311: $e_0084 -o r_0857; ; + _I312: $e_1004 -o r_0925; ; + _I313: $e_0277 -o r_0934; ; + _I314: $e_0375 -o r_0935; ; + _I315: $e_0373 -o r_0935; ; + _I316: $e_0188 -o r_0950; ; + _I317: $e_0931 -o r_0951; ; + _I318: $e_1196 -o r_0954; ; + _I319: $e_1262 -o r_0954; ; + _I320: $e_0188 -o r_0957; ; + _I321: $e_0281 -o r_0963; ; + _I322: $e_0805 -o r_0963; ; + _I323: $e_0292 -o r_0964; ; + _I324: $e_0006 -o r_0965; ; + _I325: $e_0281 -o r_0968; ; + _I326: $e_0282 -o r_0968; ; + _I327: $e_0291 -o r_0969; ; + _I328: $e_0036 -o r_0970; ; + _I329: $e_1029 -o r_0970; ; + _I330: $e_0221 -o r_0970; ; + _I331: $e_0065 -o r_0970; ; + _I332: $e_1242 -o r_0996; ; + _I333: $e_0893 -o r_0999; ; + _I334: $e_0828 -o r_1006; ; + _I335: $e_0554 -o r_1008; ; + _I336: $e_0223 -o r_1019; ; + _I337: $e_0048 -o r_1021; ; + _I338: $e_0799 -o r_1039; ; + _I339: $e_0167 -o r_1039; ; + _I340: $e_0799 -o r_1043; ; + _I341: $e_0167 -o r_1043; ; + _I342: $e_0799 -o r_1045; ; + _I343: $e_0167 -o r_1045; ; + _I344: $e_0799 -o r_1046; ; + _I345: $e_0167 -o r_1046; ; + _I346: $e_1313 -o r_1047; ; + _I347: $e_0225 -o r_1047; ; + _I348: $e_0326 -o r_1054; ; + _I349: $e_1232 -o r_1057; ; + _I350: $e_0990 -o r_1063; ; + _I351: $e_0727 -o r_1064; ; + _I352: $e_1200 -o r_1064; ; + _I353: $e_1341 -o r_1065; ; + _I354: $e_0103 -o r_1065; ; + _I355: $e_1129 -o r_1067; ; + _I356: $e_0435 -o r_1068; ; + _I357: $e_1126 -o r_1074; ; + _I358: $e_1249 -o r_1075; ; + _I359: $e_0062 -o r_1076; ; + _I360: $e_1167 -o r_1081; ; + _I361: $e_1276 -o r_1081; ; + _I362: $e_0332 -o r_1081; ; + _I363: $e_1312 -o r_1123; ; + _I364: $e_1312 -o r_1124; ; + _I365: $e_0823 -o r_1130; ; + _I366: $e_0823 -o r_1131; ; + _I367: $e_1277 -o r_1134; ; + _I368: $e_1369 -o r_1134; ; + _I369: $e_0039 -o r_1137; ; + _I370: $e_0871 -o r_1139; ; + _I371: $e_1172 -o r_1139; ; + _I372: $e_0822 -o r_1139; ; + _I373: $e_1240 -o r_1141; ; + _I374: $e_0987 -o r_1150; ; + _I375: $e_0918 -o r_1151; ; + _I376: $e_0925 -o r_1152; ; + _I377: $e_1108 -o r_1153; ; + _I378: $e_1373 -o r_1153; ; + _I379: $e_0264 -o r_1153; ; + _I380: $e_0641 -o r_1198; ; + _I381: $e_1127 -o r_1200; ; + _I382: $e_1127 -o r_1201; ; + _I383: $e_1023 -o r_1202; ; + _I384: $e_1366 -o r_1202; ; + _I385: $e_0612 -o r_1204; ; + _I386: $e_0612 -o r_1205; ; + _I387: $e_0184 -o r_1206; ; + _I388: $e_0185 -o r_1207; ; + _I389: $e_0791 -o r_1208; ; + _I390: $e_1258 -o r_1209; ; + _I391: $e_0775 -o r_1210; ; + _I392: $e_0427 -o r_1211; ; + _I393: $e_0815 -o r_1212; ; + _I394: $e_1257 -o r_1214; ; + _I395: $e_0403 -o r_1215; ; + _I396: $e_0326 -o r_1217; ; + _I397: $e_0768 -o r_1218; ; + _I398: $e_0720 -o r_1218; ; + _I399: $e_1034 -o r_1220; ; + _I400: $e_0793 -o r_1222; ; + _I401: $e_0134 -o r_1223; ; + _I402: $e_0825 -o r_1224; ; + _I403: $e_0826 -o r_1225; ; + _I404: $e_1205 -o r_1230; ; + _I405: $e_1367 -o r_1232; ; + _I406: $e_0818 -o r_1245; ; + _I407: $e_0022 -o r_1245; ; + _I408: $e_0137 -o r_1250; ; + _I409: $e_0052 -o r_1251; ; + _I410: $e_0051 -o r_1251; ; + _I411: $e_0053 -o r_1251; ; + _I412: $e_0974 -o r_1252; ; + _I413: $e_1238 -o r_1252; ; + _I414: $e_1239 -o r_1252; ; + _I415: $e_0323 -o r_1252; ; + _I416: $e_0324 -o r_1252; ; + _I417: $e_0821 -o r_1252; ; + _I418: $e_0451 -o r_1255; ; + _I419: $e_0238 -o r_1255; ; + _I420: $e_0911 -o r_1255; ; + _I421: $e_0260 -o r_1259; ; + _I422: $e_0008 -o r_1264; ; + _I423: $e_0531 -o r_1265; ; + _I424: $e_0145 -o r_1266; ; + _I425: $e_1335 -o r_1276; ; + _I426: $e_1227 -o r_1276; ; + _I427: $e_1334 -o r_1276; ; + _I428: $e_0238 -o r_1276; ; + _I429: $e_0911 -o r_1276; ; + _I430: $e_1335 -o r_1277; ; + _I431: $e_1227 -o r_1277; ; + _I432: $e_1334 -o r_1277; ; + _I433: $e_0238 -o r_1277; ; + _I434: $e_0911 -o r_1277; ; + _I435: $e_1335 -o r_1278; ; + _I436: $e_1227 -o r_1278; ; + _I437: $e_1334 -o r_1278; ; + _I438: $e_0238 -o r_1278; ; + _I439: $e_0911 -o r_1278; ; + _I440: $e_1335 -o r_1279; ; + _I441: $e_1227 -o r_1279; ; + _I442: $e_1334 -o r_1279; ; + _I443: $e_0238 -o r_1279; ; + _I444: $e_0911 -o r_1279; ; + _I445: $e_0919 -o r_1284; ; + _I446: $e_1291 -o r_1284; ; + _I447: $e_1355 -o r_1285; ; + _I448: $e_1026 -o r_1285; ; + _I449: $e_0074 -o r_1288; ; + _I450: $e_0839 -o r_1291; ; + _I451: $e_1105 -o r_1301; ; + _I452: $e_1010 -o r_1304; ; + _I453: $e_0540 -o r_1304; ; + _I454: $e_1028 -o r_1305; ; + _I455: $e_0138 -o r_1305; ; + _I456: $e_1019 -o r_1306; ; + _I457: $e_1019 -o r_1307; ; + _I458: $e_0253 -o r_1315; ; + _I459: $e_0254 -o r_1315; ; + _I460: $e_0774 -o r_1316; ; + _I461: $e_1014 -o r_1318; ; + _I462: $e_0869 -o r_1329; ; + _I463: $e_0870 -o r_1329; ; + _I464: $e_0872 -o r_1330; ; + _I465: $e_0873 -o r_1330; ; + _I466: $e_0979 -o r_1335; ; + _I467: $e_0177 -o r_1335; ; + _I468: $e_0330 -o r_1337; ; + _I469: $e_0076 -o r_1338; ; + _I470: $e_1253 -o r_1344; ; + _I471: $e_0146 -o r_1345; ; + _I472: $e_1374 -o r_1346; ; + _I473: $e_1250 -o r_1346; ; + _I474: $e_0805 -o r_1346; ; + _I475: $e_0151 -o r_1346; ; + _I476: $e_1252 -o r_1346; ; + _I477: $e_1172 -o r_1347; ; + _I478: $e_0822 -o r_1347; ; + _I479: $e_0318 -o r_1347; ; + _I480: $e_0313 -o r_1348; ; + _I481: $e_0813 -o r_1348; ; + _I482: $e_0003 -o r_1349; ; + _I483: $e_0894 -o r_1353; ; + _I484: $e_0770 -o r_1356; ; + _I485: $e_0005 -o r_1356; ; + _I486: $e_0771 -o r_1357; ; + _I487: $e_0928 -o r_1357; ; + _I488: $e_0771 -o r_1358; ; + _I489: $e_0928 -o r_1358; ; + _I490: $e_1226 -o r_1363; ; + _I491: $e_0425 -o r_1367; ; + _I492: $e_0426 -o r_1367; ; + _I493: $e_1141 -o r_1368; ; + _I494: $e_1251 -o r_1375; ; + _I495: $e_1276 -o r_1376; ; + _I496: $e_0332 -o r_1376; ; + _I497: $e_0081 -o r_1378; ; + _I498: $e_0044 -o r_1379; ; + _I499: $e_1248 -o r_1388; ; + _I500: $e_0991 -o r_1389; ; + _I501: $e_0375 -o r_1391; ; + _I502: $e_0083 -o r_1391; ; + _I503: $e_1150 -o r_1392; ; + _I504: $e_0041 -o r_1393; ; + _I505: $e_0042 -o r_1397; ; + _I506: $e_0040 -o r_1399; ; + _I507: $e_0037 -o r_1400; ; + _I508: $e_0038 -o r_1401; ; + _I509: $e_0186 -o r_1402; ; + _I510: $e_0328 -o r_1409; ; + _I511: $e_0077 -o r_1409; ; + _I512: $e_0079 -o r_1410; ; + _I513: $e_0962 -o r_1413; ; + _I514: $e_0433 -o r_1413; ; + _I515: $e_0300 -o r_1413; ; + _I516: $e_1256 -o r_1421; ; + _I517: $e_1184 -o r_1422; ; + _I518: $e_1019 -o r_1422; ; + _I519: $e_1185 -o r_1423; ; + _I520: $e_1167 -o r_1425; ; + _I521: $e_1086 -o r_1432; ; + // Species initializations: s_0003 = 0.1; s_0004 = 0.1; diff --git a/doc/examples/biomodels/BIOMD0000000470_url.txt b/doc/examples/biomodels/BIOMD0000000470/BIOMD0000000470_url.txt similarity index 87% rename from doc/examples/biomodels/BIOMD0000000470_url.txt rename to doc/examples/biomodels/BIOMD0000000470/BIOMD0000000470_url.txt index d51aac67d..9ca5ffb58 100644 --- a/doc/examples/biomodels/BIOMD0000000470_url.txt +++ b/doc/examples/biomodels/BIOMD0000000470/BIOMD0000000470_url.txt @@ -1,4 +1,529 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 + +// Warnings from automatic translation: +// An interaction was declared that claims e_0610 modifies r_0008, but e_0610 does not appear in r_0008's kinetic law. +// An interaction was declared that claims e_0149 modifies r_0009, but e_0149 does not appear in r_0009's kinetic law. +// An interaction was declared that claims e_0078 modifies r_0011, but e_0078 does not appear in r_0011's kinetic law. +// An interaction was declared that claims e_0953 modifies r_0012, but e_0953 does not appear in r_0012's kinetic law. +// An interaction was declared that claims e_0953 modifies r_0013, but e_0953 does not appear in r_0013's kinetic law. +// An interaction was declared that claims e_0010 modifies r_0014, but e_0010 does not appear in r_0014's kinetic law. +// An interaction was declared that claims e_0010 modifies r_0015, but e_0010 does not appear in r_0015's kinetic law. +// An interaction was declared that claims e_1137 modifies r_0038, but e_1137 does not appear in r_0038's kinetic law. +// An interaction was declared that claims e_0034 modifies r_0038, but e_0034 does not appear in r_0038's kinetic law. +// An interaction was declared that claims e_0035 modifies r_0038, but e_0035 does not appear in r_0038's kinetic law. +// An interaction was declared that claims e_1136 modifies r_0038, but e_1136 does not appear in r_0038's kinetic law. +// An interaction was declared that claims e_0866 modifies r_0053, but e_0866 does not appear in r_0053's kinetic law. +// An interaction was declared that claims e_0867 modifies r_0054, but e_0867 does not appear in r_0054's kinetic law. +// An interaction was declared that claims e_0578 modifies r_0056, but e_0578 does not appear in r_0056's kinetic law. +// An interaction was declared that claims e_0152 modifies r_0063, but e_0152 does not appear in r_0063's kinetic law. +// An interaction was declared that claims e_1170 modifies r_0063, but e_1170 does not appear in r_0063's kinetic law. +// An interaction was declared that claims e_0031 modifies r_0066, but e_0031 does not appear in r_0066's kinetic law. +// An interaction was declared that claims e_0030 modifies r_0066, but e_0030 does not appear in r_0066's kinetic law. +// An interaction was declared that claims e_0033 modifies r_0067, but e_0033 does not appear in r_0067's kinetic law. +// An interaction was declared that claims e_0238 modifies r_0084, but e_0238 does not appear in r_0084's kinetic law. +// An interaction was declared that claims e_0798 modifies r_0084, but e_0798 does not appear in r_0084's kinetic law. +// An interaction was declared that claims e_0911 modifies r_0084, but e_0911 does not appear in r_0084's kinetic law. +// An interaction was declared that claims e_1326 modifies r_0085, but e_1326 does not appear in r_0085's kinetic law. +// An interaction was declared that claims e_0960 modifies r_0092, but e_0960 does not appear in r_0092's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0096, but e_1203 does not appear in r_0096's kinetic law. +// An interaction was declared that claims e_0541 modifies r_0098, but e_0541 does not appear in r_0098's kinetic law. +// An interaction was declared that claims e_1027 modifies r_0099, but e_1027 does not appear in r_0099's kinetic law. +// An interaction was declared that claims e_0406 modifies r_0100, but e_0406 does not appear in r_0100's kinetic law. +// An interaction was declared that claims e_0544 modifies r_0101, but e_0544 does not appear in r_0101's kinetic law. +// An interaction was declared that claims e_0827 modifies r_0101, but e_0827 does not appear in r_0101's kinetic law. +// An interaction was declared that claims e_0263 modifies r_0101, but e_0263 does not appear in r_0101's kinetic law. +// An interaction was declared that claims e_1125 modifies r_0102, but e_1125 does not appear in r_0102's kinetic law. +// An interaction was declared that claims e_1125 modifies r_0103, but e_1125 does not appear in r_0103's kinetic law. +// An interaction was declared that claims e_0331 modifies r_0105, but e_0331 does not appear in r_0105's kinetic law. +// An interaction was declared that claims e_0994 modifies r_0106, but e_0994 does not appear in r_0106's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0120, but e_1203 does not appear in r_0120's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0120, but e_0735 does not appear in r_0120's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0121, but e_1203 does not appear in r_0121's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0121, but e_0735 does not appear in r_0121's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0122, but e_1203 does not appear in r_0122's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0122, but e_0735 does not appear in r_0122's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0123, but e_1203 does not appear in r_0123's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0123, but e_0735 does not appear in r_0123's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0124, but e_1203 does not appear in r_0124's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0124, but e_0735 does not appear in r_0124's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0126, but e_1203 does not appear in r_0126's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0126, but e_0735 does not appear in r_0126's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0127, but e_1203 does not appear in r_0127's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0127, but e_0735 does not appear in r_0127's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0128, but e_1203 does not appear in r_0128's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0128, but e_0735 does not appear in r_0128's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0129, but e_1203 does not appear in r_0129's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0129, but e_0735 does not appear in r_0129's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0130, but e_1203 does not appear in r_0130's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0130, but e_0735 does not appear in r_0130's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0131, but e_1203 does not appear in r_0131's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0131, but e_0735 does not appear in r_0131's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0133, but e_1203 does not appear in r_0133's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0133, but e_0735 does not appear in r_0133's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0134, but e_1203 does not appear in r_0134's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0134, but e_0735 does not appear in r_0134's kinetic law. +// An interaction was declared that claims e_1203 modifies r_0135, but e_1203 does not appear in r_0135's kinetic law. +// An interaction was declared that claims e_0735 modifies r_0135, but e_0735 does not appear in r_0135's kinetic law. +// An interaction was declared that claims e_0031 modifies r_0138, but e_0031 does not appear in r_0138's kinetic law. +// An interaction was declared that claims e_0030 modifies r_0138, but e_0030 does not appear in r_0138's kinetic law. +// An interaction was declared that claims e_0032 modifies r_0139, but e_0032 does not appear in r_0139's kinetic law. +// An interaction was declared that claims e_0063 modifies r_0143, but e_0063 does not appear in r_0143's kinetic law. +// An interaction was declared that claims e_0082 modifies r_0145, but e_0082 does not appear in r_0145's kinetic law. +// An interaction was declared that claims e_0374 modifies r_0146, but e_0374 does not appear in r_0146's kinetic law. +// An interaction was declared that claims e_0372 modifies r_0147, but e_0372 does not appear in r_0147's kinetic law. +// An interaction was declared that claims e_0082 modifies r_0148, but e_0082 does not appear in r_0148's kinetic law. +// An interaction was declared that claims e_0374 modifies r_0149, but e_0374 does not appear in r_0149's kinetic law. +// An interaction was declared that claims e_0732 modifies r_0150, but e_0732 does not appear in r_0150's kinetic law. +// An interaction was declared that claims e_0374 modifies r_0154, but e_0374 does not appear in r_0154's kinetic law. +// An interaction was declared that claims e_0376 modifies r_0166, but e_0376 does not appear in r_0166's kinetic law. +// An interaction was declared that claims e_0732 modifies r_0166, but e_0732 does not appear in r_0166's kinetic law. +// An interaction was declared that claims e_0327 modifies r_0175, but e_0327 does not appear in r_0175's kinetic law. +// An interaction was declared that claims e_0404 modifies r_0178, but e_0404 does not appear in r_0178's kinetic law. +// An interaction was declared that claims e_1254 modifies r_0179, but e_1254 does not appear in r_0179's kinetic law. +// An interaction was declared that claims e_1015 modifies r_0181, but e_1015 does not appear in r_0181's kinetic law. +// An interaction was declared that claims e_0572 modifies r_0181, but e_0572 does not appear in r_0181's kinetic law. +// An interaction was declared that claims e_0377 modifies r_0182, but e_0377 does not appear in r_0182's kinetic law. +// An interaction was declared that claims e_0074 modifies r_0186, but e_0074 does not appear in r_0186's kinetic law. +// An interaction was declared that claims e_1234 modifies r_0211, but e_1234 does not appear in r_0211's kinetic law. +// An interaction was declared that claims e_0144 modifies r_0212, but e_0144 does not appear in r_0212's kinetic law. +// An interaction was declared that claims e_0064 modifies r_0216, but e_0064 does not appear in r_0216's kinetic law. +// An interaction was declared that claims e_0579 modifies r_0217, but e_0579 does not appear in r_0217's kinetic law. +// An interaction was declared that claims e_0273 modifies r_0218, but e_0273 does not appear in r_0218's kinetic law. +// An interaction was declared that claims e_0276 modifies r_0222, but e_0276 does not appear in r_0222's kinetic law. +// An interaction was declared that claims e_0125 modifies r_0224, but e_0125 does not appear in r_0224's kinetic law. +// An interaction was declared that claims e_0416 modifies r_0224, but e_0416 does not appear in r_0224's kinetic law. +// An interaction was declared that claims e_0975 modifies r_0225, but e_0975 does not appear in r_0225's kinetic law. +// An interaction was declared that claims e_0719 modifies r_0225, but e_0719 does not appear in r_0225's kinetic law. +// An interaction was declared that claims e_0577 modifies r_0225, but e_0577 does not appear in r_0225's kinetic law. +// An interaction was declared that claims e_1137 modifies r_0227, but e_1137 does not appear in r_0227's kinetic law. +// An interaction was declared that claims e_0034 modifies r_0227, but e_0034 does not appear in r_0227's kinetic law. +// An interaction was declared that claims e_0035 modifies r_0227, but e_0035 does not appear in r_0227's kinetic law. +// An interaction was declared that claims e_1136 modifies r_0227, but e_1136 does not appear in r_0227's kinetic law. +// An interaction was declared that claims e_0682 modifies r_0230, but e_0682 does not appear in r_0230's kinetic law. +// An interaction was declared that claims e_1202 modifies r_0230, but e_1202 does not appear in r_0230's kinetic law. +// An interaction was declared that claims e_0736 modifies r_0230, but e_0736 does not appear in r_0230's kinetic law. +// An interaction was declared that claims e_1202 modifies r_0231, but e_1202 does not appear in r_0231's kinetic law. +// An interaction was declared that claims e_0736 modifies r_0231, but e_0736 does not appear in r_0231's kinetic law. +// An interaction was declared that claims e_1202 modifies r_0232, but e_1202 does not appear in r_0232's kinetic law. +// An interaction was declared that claims e_0736 modifies r_0232, but e_0736 does not appear in r_0232's kinetic law. +// An interaction was declared that claims e_1202 modifies r_0233, but e_1202 does not appear in r_0233's kinetic law. +// An interaction was declared that claims e_0736 modifies r_0233, but e_0736 does not appear in r_0233's kinetic law. +// An interaction was declared that claims e_1202 modifies r_0234, but e_1202 does not appear in r_0234's kinetic law. +// An interaction was declared that claims e_0736 modifies r_0234, but e_0736 does not appear in r_0234's kinetic law. +// An interaction was declared that claims e_1202 modifies r_0235, but e_1202 does not appear in r_0235's kinetic law. +// An interaction was declared that claims e_0736 modifies r_0235, but e_0736 does not appear in r_0235's kinetic law. +// An interaction was declared that claims e_1202 modifies r_0236, but e_1202 does not appear in r_0236's kinetic law. +// An interaction was declared that claims e_0736 modifies r_0236, but e_0736 does not appear in r_0236's kinetic law. +// An interaction was declared that claims e_0085 modifies r_0237, but e_0085 does not appear in r_0237's kinetic law. +// An interaction was declared that claims e_1006 modifies r_0237, but e_1006 does not appear in r_0237's kinetic law. +// An interaction was declared that claims e_1005 modifies r_0237, but e_1005 does not appear in r_0237's kinetic law. +// An interaction was declared that claims e_0730 modifies r_0237, but e_0730 does not appear in r_0237's kinetic law. +// An interaction was declared that claims e_1243 modifies r_0243, but e_1243 does not appear in r_0243's kinetic law. +// An interaction was declared that claims e_1241 modifies r_0244, but e_1241 does not appear in r_0244's kinetic law. +// An interaction was declared that claims e_0559 modifies r_0245, but e_0559 does not appear in r_0245's kinetic law. +// An interaction was declared that claims e_1014 modifies r_0245, but e_1014 does not appear in r_0245's kinetic law. +// An interaction was declared that claims e_0431 modifies r_0246, but e_0431 does not appear in r_0246's kinetic law. +// An interaction was declared that claims e_0054 modifies r_0246, but e_0054 does not appear in r_0246's kinetic law. +// An interaction was declared that claims e_0431 modifies r_0247, but e_0431 does not appear in r_0247's kinetic law. +// An interaction was declared that claims e_0054 modifies r_0247, but e_0054 does not appear in r_0247's kinetic law. +// An interaction was declared that claims e_0375 modifies r_0257, but e_0375 does not appear in r_0257's kinetic law. +// An interaction was declared that claims e_0896 modifies r_0257, but e_0896 does not appear in r_0257's kinetic law. +// An interaction was declared that claims e_0375 modifies r_0259, but e_0375 does not appear in r_0259's kinetic law. +// An interaction was declared that claims e_0896 modifies r_0259, but e_0896 does not appear in r_0259's kinetic law. +// An interaction was declared that claims e_0375 modifies r_0260, but e_0375 does not appear in r_0260's kinetic law. +// An interaction was declared that claims e_0896 modifies r_0260, but e_0896 does not appear in r_0260's kinetic law. +// An interaction was declared that claims e_0094 modifies r_0266, but e_0094 does not appear in r_0266's kinetic law. +// An interaction was declared that claims e_0094 modifies r_0267, but e_0094 does not appear in r_0267's kinetic law. +// An interaction was declared that claims e_0094 modifies r_0268, but e_0094 does not appear in r_0268's kinetic law. +// An interaction was declared that claims e_0094 modifies r_0269, but e_0094 does not appear in r_0269's kinetic law. +// An interaction was declared that claims e_0094 modifies r_0270, but e_0094 does not appear in r_0270's kinetic law. +// An interaction was declared that claims e_0094 modifies r_0272, but e_0094 does not appear in r_0272's kinetic law. +// An interaction was declared that claims e_0094 modifies r_0273, but e_0094 does not appear in r_0273's kinetic law. +// An interaction was declared that claims e_0167 modifies r_0292, but e_0167 does not appear in r_0292's kinetic law. +// An interaction was declared that claims e_0274 modifies r_0297, but e_0274 does not appear in r_0297's kinetic law. +// An interaction was declared that claims e_0167 modifies r_0301, but e_0167 does not appear in r_0301's kinetic law. +// An interaction was declared that claims e_0389 modifies r_0302, but e_0389 does not appear in r_0302's kinetic law. +// An interaction was declared that claims e_1315 modifies r_0303, but e_1315 does not appear in r_0303's kinetic law. +// An interaction was declared that claims e_0389 modifies r_0304, but e_0389 does not appear in r_0304's kinetic law. +// An interaction was declared that claims e_0868 modifies r_0305, but e_0868 does not appear in r_0305's kinetic law. +// An interaction was declared that claims e_0395 modifies r_0310, but e_0395 does not appear in r_0310's kinetic law. +// An interaction was declared that claims e_1275 modifies r_0310, but e_1275 does not appear in r_0310's kinetic law. +// An interaction was declared that claims e_0428 modifies r_0348, but e_0428 does not appear in r_0348's kinetic law. +// An interaction was declared that claims e_0429 modifies r_0349, but e_0429 does not appear in r_0349's kinetic law. +// An interaction was declared that claims e_0428 modifies r_0349, but e_0428 does not appear in r_0349's kinetic law. +// An interaction was declared that claims e_0993 modifies r_0355, but e_0993 does not appear in r_0355's kinetic law. +// An interaction was declared that claims e_0848 modifies r_0355, but e_0848 does not appear in r_0355's kinetic law. +// An interaction was declared that claims e_1244 modifies r_0360, but e_1244 does not appear in r_0360's kinetic law. +// An interaction was declared that claims e_0986 modifies r_0361, but e_0986 does not appear in r_0361's kinetic law. +// An interaction was declared that claims e_1160 modifies r_0365, but e_1160 does not appear in r_0365's kinetic law. +// An interaction was declared that claims e_0061 modifies r_0367, but e_0061 does not appear in r_0367's kinetic law. +// An interaction was declared that claims e_1340 modifies r_0368, but e_1340 does not appear in r_0368's kinetic law. +// An interaction was declared that claims e_1339 modifies r_0368, but e_1339 does not appear in r_0368's kinetic law. +// An interaction was declared that claims e_1263 modifies r_0369, but e_1263 does not appear in r_0369's kinetic law. +// An interaction was declared that claims e_0001 modifies r_0369, but e_0001 does not appear in r_0369's kinetic law. +// An interaction was declared that claims e_1233 modifies r_0369, but e_1233 does not appear in r_0369's kinetic law. +// An interaction was declared that claims e_0332 modifies r_0370, but e_0332 does not appear in r_0370's kinetic law. +// An interaction was declared that claims e_1045 modifies r_0371, but e_1045 does not appear in r_0371's kinetic law. +// An interaction was declared that claims e_0605 modifies r_0374, but e_0605 does not appear in r_0374's kinetic law. +// An interaction was declared that claims e_0275 modifies r_0383, but e_0275 does not appear in r_0383's kinetic law. +// An interaction was declared that claims e_0292 modifies r_0384, but e_0292 does not appear in r_0384's kinetic law. +// An interaction was declared that claims e_1207 modifies r_0385, but e_1207 does not appear in r_0385's kinetic law. +// An interaction was declared that claims e_1206 modifies r_0385, but e_1206 does not appear in r_0385's kinetic law. +// An interaction was declared that claims e_1207 modifies r_0386, but e_1207 does not appear in r_0386's kinetic law. +// An interaction was declared that claims e_1206 modifies r_0386, but e_1206 does not appear in r_0386's kinetic law. +// An interaction was declared that claims e_0903 modifies r_0388, but e_0903 does not appear in r_0388's kinetic law. +// An interaction was declared that claims e_0183 modifies r_0388, but e_0183 does not appear in r_0388's kinetic law. +// An interaction was declared that claims e_0110 modifies r_0388, but e_0110 does not appear in r_0388's kinetic law. +// An interaction was declared that claims e_0080 modifies r_0418, but e_0080 does not appear in r_0418's kinetic law. +// An interaction was declared that claims e_0080 modifies r_0419, but e_0080 does not appear in r_0419's kinetic law. +// An interaction was declared that claims e_0825 modifies r_0423, but e_0825 does not appear in r_0423's kinetic law. +// An interaction was declared that claims e_0826 modifies r_0423, but e_0826 does not appear in r_0423's kinetic law. +// An interaction was declared that claims e_1271 modifies r_0424, but e_1271 does not appear in r_0424's kinetic law. +// An interaction was declared that claims e_0734 modifies r_0425, but e_0734 does not appear in r_0425's kinetic law. +// An interaction was declared that claims e_0246 modifies r_0428, but e_0246 does not appear in r_0428's kinetic law. +// An interaction was declared that claims e_0765 modifies r_0436, but e_0765 does not appear in r_0436's kinetic law. +// An interaction was declared that claims e_0876 modifies r_0440, but e_0876 does not appear in r_0440's kinetic law. +// An interaction was declared that claims e_0279 modifies r_0445, but e_0279 does not appear in r_0445's kinetic law. +// An interaction was declared that claims e_0280 modifies r_0445, but e_0280 does not appear in r_0445's kinetic law. +// An interaction was declared that claims e_0951 modifies r_0450, but e_0951 does not appear in r_0450's kinetic law. +// An interaction was declared that claims e_0519 modifies r_0450, but e_0519 does not appear in r_0450's kinetic law. +// An interaction was declared that claims e_0757 modifies r_0452, but e_0757 does not appear in r_0452's kinetic law. +// An interaction was declared that claims e_0750 modifies r_0452, but e_0750 does not appear in r_0452's kinetic law. +// An interaction was declared that claims e_0328 modifies r_0457, but e_0328 does not appear in r_0457's kinetic law. +// An interaction was declared that claims e_0043 modifies r_0463, but e_0043 does not appear in r_0463's kinetic law. +// An interaction was declared that claims e_0135 modifies r_0463, but e_0135 does not appear in r_0463's kinetic law. +// An interaction was declared that claims e_0046 modifies r_0488, but e_0046 does not appear in r_0488's kinetic law. +// An interaction was declared that claims e_0278 modifies r_0489, but e_0278 does not appear in r_0489's kinetic law. +// An interaction was declared that claims e_0144 modifies r_0498, but e_0144 does not appear in r_0498's kinetic law. +// An interaction was declared that claims e_0897 modifies r_0499, but e_0897 does not appear in r_0499's kinetic law. +// An interaction was declared that claims e_1189 modifies r_0500, but e_1189 does not appear in r_0500's kinetic law. +// An interaction was declared that claims e_0342 modifies r_0501, but e_0342 does not appear in r_0501's kinetic law. +// An interaction was declared that claims e_0012 modifies r_0502, but e_0012 does not appear in r_0502's kinetic law. +// An interaction was declared that claims e_0776 modifies r_0503, but e_0776 does not appear in r_0503's kinetic law. +// An interaction was declared that claims e_0514 modifies r_0504, but e_0514 does not appear in r_0504's kinetic law. +// An interaction was declared that claims e_0020 modifies r_0504, but e_0020 does not appear in r_0504's kinetic law. +// An interaction was declared that claims e_0729 modifies r_0505, but e_0729 does not appear in r_0505's kinetic law. +// An interaction was declared that claims e_0964 modifies r_0507, but e_0964 does not appear in r_0507's kinetic law. +// An interaction was declared that claims e_0045 modifies r_0510, but e_0045 does not appear in r_0510's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0510, but e_0586 does not appear in r_0510's kinetic law. +// An interaction was declared that claims e_0368 modifies r_0511, but e_0368 does not appear in r_0511's kinetic law. +// An interaction was declared that claims e_0342 modifies r_0512, but e_0342 does not appear in r_0512's kinetic law. +// An interaction was declared that claims e_0988 modifies r_0515, but e_0988 does not appear in r_0515's kinetic law. +// An interaction was declared that claims e_1168 modifies r_0517, but e_1168 does not appear in r_0517's kinetic law. +// An interaction was declared that claims e_1168 modifies r_0518, but e_1168 does not appear in r_0518's kinetic law. +// An interaction was declared that claims e_0150 modifies r_0522, but e_0150 does not appear in r_0522's kinetic law. +// An interaction was declared that claims e_0378 modifies r_0532, but e_0378 does not appear in r_0532's kinetic law. +// An interaction was declared that claims e_1128 modifies r_0533, but e_1128 does not appear in r_0533's kinetic law. +// An interaction was declared that claims e_0691 modifies r_0533, but e_0691 does not appear in r_0533's kinetic law. +// An interaction was declared that claims e_0875 modifies r_0538, but e_0875 does not appear in r_0538's kinetic law. +// An interaction was declared that claims e_0436 modifies r_0563, but e_0436 does not appear in r_0563's kinetic law. +// An interaction was declared that claims e_0436 modifies r_0564, but e_0436 does not appear in r_0564's kinetic law. +// An interaction was declared that claims e_0731 modifies r_0573, but e_0731 does not appear in r_0573's kinetic law. +// An interaction was declared that claims e_0926 modifies r_0574, but e_0926 does not appear in r_0574's kinetic law. +// An interaction was declared that claims e_0567 modifies r_0574, but e_0567 does not appear in r_0574's kinetic law. +// An interaction was declared that claims e_1201 modifies r_0576, but e_1201 does not appear in r_0576's kinetic law. +// An interaction was declared that claims e_0162 modifies r_0579, but e_0162 does not appear in r_0579's kinetic law. +// An interaction was declared that claims e_0162 modifies r_0580, but e_0162 does not appear in r_0580's kinetic law. +// An interaction was declared that claims e_0162 modifies r_0581, but e_0162 does not appear in r_0581's kinetic law. +// An interaction was declared that claims e_0168 modifies r_0602, but e_0168 does not appear in r_0602's kinetic law. +// An interaction was declared that claims e_0008 modifies r_0611, but e_0008 does not appear in r_0611's kinetic law. +// An interaction was declared that claims e_1298 modifies r_0632, but e_1298 does not appear in r_0632's kinetic law. +// An interaction was declared that claims e_0515 modifies r_0632, but e_0515 does not appear in r_0632's kinetic law. +// An interaction was declared that claims e_0516 modifies r_0632, but e_0516 does not appear in r_0632's kinetic law. +// An interaction was declared that claims e_0577 modifies r_0648, but e_0577 does not appear in r_0648's kinetic law. +// An interaction was declared that claims e_0150 modifies r_0655, but e_0150 does not appear in r_0655's kinetic law. +// An interaction was declared that claims e_1150 modifies r_0658, but e_1150 does not appear in r_0658's kinetic law. +// An interaction was declared that claims e_0580 modifies r_0660, but e_0580 does not appear in r_0660's kinetic law. +// An interaction was declared that claims e_1264 modifies r_0664, but e_1264 does not appear in r_0664's kinetic law. +// An interaction was declared that claims e_0099 modifies r_0673, but e_0099 does not appear in r_0673's kinetic law. +// An interaction was declared that claims e_0561 modifies r_0675, but e_0561 does not appear in r_0675's kinetic law. +// An interaction was declared that claims e_1247 modifies r_0676, but e_1247 does not appear in r_0676's kinetic law. +// An interaction was declared that claims e_0071 modifies r_0678, but e_0071 does not appear in r_0678's kinetic law. +// An interaction was declared that claims e_0100 modifies r_0679, but e_0100 does not appear in r_0679's kinetic law. +// An interaction was declared that claims e_0728 modifies r_0682, but e_0728 does not appear in r_0682's kinetic law. +// An interaction was declared that claims e_1210 modifies r_0683, but e_1210 does not appear in r_0683's kinetic law. +// An interaction was declared that claims e_0439 modifies r_0683, but e_0439 does not appear in r_0683's kinetic law. +// An interaction was declared that claims e_1149 modifies r_0684, but e_1149 does not appear in r_0684's kinetic law. +// An interaction was declared that claims e_0405 modifies r_0686, but e_0405 does not appear in r_0686's kinetic law. +// An interaction was declared that claims e_0746 modifies r_0687, but e_0746 does not appear in r_0687's kinetic law. +// An interaction was declared that claims e_0567 modifies r_0695, but e_0567 does not appear in r_0695's kinetic law. +// An interaction was declared that claims e_0978 modifies r_0697, but e_0978 does not appear in r_0697's kinetic law. +// An interaction was declared that claims e_0375 modifies r_0706, but e_0375 does not appear in r_0706's kinetic law. +// An interaction was declared that claims e_1273 modifies r_0706, but e_1273 does not appear in r_0706's kinetic law. +// An interaction was declared that claims e_0375 modifies r_0707, but e_0375 does not appear in r_0707's kinetic law. +// An interaction was declared that claims e_1273 modifies r_0707, but e_1273 does not appear in r_0707's kinetic law. +// An interaction was declared that claims e_1106 modifies r_0712, but e_1106 does not appear in r_0712's kinetic law. +// An interaction was declared that claims e_1110 modifies r_0724, but e_1110 does not appear in r_0724's kinetic law. +// An interaction was declared that claims e_0813 modifies r_0726, but e_0813 does not appear in r_0726's kinetic law. +// An interaction was declared that claims e_0466 modifies r_0731, but e_0466 does not appear in r_0731's kinetic law. +// An interaction was declared that claims e_1376 modifies r_0734, but e_1376 does not appear in r_0734's kinetic law. +// An interaction was declared that claims e_0941 modifies r_0734, but e_0941 does not appear in r_0734's kinetic law. +// An interaction was declared that claims e_1377 modifies r_0734, but e_1377 does not appear in r_0734's kinetic law. +// An interaction was declared that claims e_1376 modifies r_0735, but e_1376 does not appear in r_0735's kinetic law. +// An interaction was declared that claims e_0941 modifies r_0735, but e_0941 does not appear in r_0735's kinetic law. +// An interaction was declared that claims e_1377 modifies r_0735, but e_1377 does not appear in r_0735's kinetic law. +// An interaction was declared that claims e_0175 modifies r_0739, but e_0175 does not appear in r_0739's kinetic law. +// An interaction was declared that claims e_0795 modifies r_0741, but e_0795 does not appear in r_0741's kinetic law. +// An interaction was declared that claims e_0657 modifies r_0744, but e_0657 does not appear in r_0744's kinetic law. +// An interaction was declared that claims e_0432 modifies r_0745, but e_0432 does not appear in r_0745's kinetic law. +// An interaction was declared that claims e_1130 modifies r_0754, but e_1130 does not appear in r_0754's kinetic law. +// An interaction was declared that claims e_0060 modifies r_0755, but e_0060 does not appear in r_0755's kinetic law. +// An interaction was declared that claims e_0116 modifies r_0755, but e_0116 does not appear in r_0755's kinetic law. +// An interaction was declared that claims e_0139 modifies r_0761, but e_0139 does not appear in r_0761's kinetic law. +// An interaction was declared that claims e_0743 modifies r_0762, but e_0743 does not appear in r_0762's kinetic law. +// An interaction was declared that claims e_0606 modifies r_0763, but e_0606 does not appear in r_0763's kinetic law. +// An interaction was declared that claims e_0608 modifies r_0764, but e_0608 does not appear in r_0764's kinetic law. +// An interaction was declared that claims e_0607 modifies r_0765, but e_0607 does not appear in r_0765's kinetic law. +// An interaction was declared that claims e_0001 modifies r_0769, but e_0001 does not appear in r_0769's kinetic law. +// An interaction was declared that claims e_1233 modifies r_0769, but e_1233 does not appear in r_0769's kinetic law. +// An interaction was declared that claims e_0002 modifies r_0770, but e_0002 does not appear in r_0770's kinetic law. +// An interaction was declared that claims e_1259 modifies r_0771, but e_1259 does not appear in r_0771's kinetic law. +// An interaction was declared that claims e_1272 modifies r_0775, but e_1272 does not appear in r_0775's kinetic law. +// An interaction was declared that claims e_1186 modifies r_0777, but e_1186 does not appear in r_0777's kinetic law. +// An interaction was declared that claims e_0611 modifies r_0784, but e_0611 does not appear in r_0784's kinetic law. +// An interaction was declared that claims e_0609 modifies r_0784, but e_0609 does not appear in r_0784's kinetic law. +// An interaction was declared that claims e_0608 modifies r_0785, but e_0608 does not appear in r_0785's kinetic law. +// An interaction was declared that claims e_1258 modifies r_0786, but e_1258 does not appear in r_0786's kinetic law. +// An interaction was declared that claims e_0796 modifies r_0787, but e_0796 does not appear in r_0787's kinetic law. +// An interaction was declared that claims e_0427 modifies r_0788, but e_0427 does not appear in r_0788's kinetic law. +// An interaction was declared that claims e_0805 modifies r_0796, but e_0805 does not appear in r_0796's kinetic law. +// An interaction was declared that claims e_0804 modifies r_0796, but e_0804 does not appear in r_0796's kinetic law. +// An interaction was declared that claims e_0804 modifies r_0797, but e_0804 does not appear in r_0797's kinetic law. +// An interaction was declared that claims e_1188 modifies r_0797, but e_1188 does not appear in r_0797's kinetic law. +// An interaction was declared that claims e_0805 modifies r_0797, but e_0805 does not appear in r_0797's kinetic law. +// An interaction was declared that claims e_0804 modifies r_0798, but e_0804 does not appear in r_0798's kinetic law. +// An interaction was declared that claims e_1188 modifies r_0798, but e_1188 does not appear in r_0798's kinetic law. +// An interaction was declared that claims e_0805 modifies r_0798, but e_0805 does not appear in r_0798's kinetic law. +// An interaction was declared that claims e_0803 modifies r_0799, but e_0803 does not appear in r_0799's kinetic law. +// An interaction was declared that claims e_0804 modifies r_0799, but e_0804 does not appear in r_0799's kinetic law. +// An interaction was declared that claims e_0804 modifies r_0800, but e_0804 does not appear in r_0800's kinetic law. +// An interaction was declared that claims e_0803 modifies r_0801, but e_0803 does not appear in r_0801's kinetic law. +// An interaction was declared that claims e_0804 modifies r_0801, but e_0804 does not appear in r_0801's kinetic law. +// An interaction was declared that claims e_0805 modifies r_0802, but e_0805 does not appear in r_0802's kinetic law. +// An interaction was declared that claims e_0391 modifies r_0806, but e_0391 does not appear in r_0806's kinetic law. +// An interaction was declared that claims e_1167 modifies r_0808, but e_1167 does not appear in r_0808's kinetic law. +// An interaction was declared that claims e_1170 modifies r_0811, but e_1170 does not appear in r_0811's kinetic law. +// An interaction was declared that claims e_1170 modifies r_0812, but e_1170 does not appear in r_0812's kinetic law. +// An interaction was declared that claims e_0742 modifies r_0815, but e_0742 does not appear in r_0815's kinetic law. +// An interaction was declared that claims e_0717 modifies r_0815, but e_0717 does not appear in r_0815's kinetic law. +// An interaction was declared that claims e_0819 modifies r_0829, but e_0819 does not appear in r_0829's kinetic law. +// An interaction was declared that claims e_1169 modifies r_0847, but e_1169 does not appear in r_0847's kinetic law. +// An interaction was declared that claims e_0977 modifies r_0847, but e_0977 does not appear in r_0847's kinetic law. +// An interaction was declared that claims e_1109 modifies r_0848, but e_1109 does not appear in r_0848's kinetic law. +// An interaction was declared that claims e_1167 modifies r_0854, but e_1167 does not appear in r_0854's kinetic law. +// An interaction was declared that claims e_1276 modifies r_0854, but e_1276 does not appear in r_0854's kinetic law. +// An interaction was declared that claims e_0084 modifies r_0857, but e_0084 does not appear in r_0857's kinetic law. +// An interaction was declared that claims e_1004 modifies r_0925, but e_1004 does not appear in r_0925's kinetic law. +// An interaction was declared that claims e_0277 modifies r_0934, but e_0277 does not appear in r_0934's kinetic law. +// An interaction was declared that claims e_0375 modifies r_0935, but e_0375 does not appear in r_0935's kinetic law. +// An interaction was declared that claims e_0373 modifies r_0935, but e_0373 does not appear in r_0935's kinetic law. +// An interaction was declared that claims e_0188 modifies r_0950, but e_0188 does not appear in r_0950's kinetic law. +// An interaction was declared that claims e_0931 modifies r_0951, but e_0931 does not appear in r_0951's kinetic law. +// An interaction was declared that claims e_1196 modifies r_0954, but e_1196 does not appear in r_0954's kinetic law. +// An interaction was declared that claims e_1262 modifies r_0954, but e_1262 does not appear in r_0954's kinetic law. +// An interaction was declared that claims e_0188 modifies r_0957, but e_0188 does not appear in r_0957's kinetic law. +// An interaction was declared that claims e_0281 modifies r_0963, but e_0281 does not appear in r_0963's kinetic law. +// An interaction was declared that claims e_0805 modifies r_0963, but e_0805 does not appear in r_0963's kinetic law. +// An interaction was declared that claims e_0292 modifies r_0964, but e_0292 does not appear in r_0964's kinetic law. +// An interaction was declared that claims e_0006 modifies r_0965, but e_0006 does not appear in r_0965's kinetic law. +// An interaction was declared that claims e_0281 modifies r_0968, but e_0281 does not appear in r_0968's kinetic law. +// An interaction was declared that claims e_0282 modifies r_0968, but e_0282 does not appear in r_0968's kinetic law. +// An interaction was declared that claims e_0291 modifies r_0969, but e_0291 does not appear in r_0969's kinetic law. +// An interaction was declared that claims e_0036 modifies r_0970, but e_0036 does not appear in r_0970's kinetic law. +// An interaction was declared that claims e_1029 modifies r_0970, but e_1029 does not appear in r_0970's kinetic law. +// An interaction was declared that claims e_0221 modifies r_0970, but e_0221 does not appear in r_0970's kinetic law. +// An interaction was declared that claims e_0065 modifies r_0970, but e_0065 does not appear in r_0970's kinetic law. +// An interaction was declared that claims e_1242 modifies r_0996, but e_1242 does not appear in r_0996's kinetic law. +// An interaction was declared that claims e_0893 modifies r_0999, but e_0893 does not appear in r_0999's kinetic law. +// An interaction was declared that claims e_0828 modifies r_1006, but e_0828 does not appear in r_1006's kinetic law. +// An interaction was declared that claims e_0554 modifies r_1008, but e_0554 does not appear in r_1008's kinetic law. +// An interaction was declared that claims e_0223 modifies r_1019, but e_0223 does not appear in r_1019's kinetic law. +// An interaction was declared that claims e_0048 modifies r_1021, but e_0048 does not appear in r_1021's kinetic law. +// An interaction was declared that claims e_0799 modifies r_1039, but e_0799 does not appear in r_1039's kinetic law. +// An interaction was declared that claims e_0167 modifies r_1039, but e_0167 does not appear in r_1039's kinetic law. +// An interaction was declared that claims e_0799 modifies r_1043, but e_0799 does not appear in r_1043's kinetic law. +// An interaction was declared that claims e_0167 modifies r_1043, but e_0167 does not appear in r_1043's kinetic law. +// An interaction was declared that claims e_0799 modifies r_1045, but e_0799 does not appear in r_1045's kinetic law. +// An interaction was declared that claims e_0167 modifies r_1045, but e_0167 does not appear in r_1045's kinetic law. +// An interaction was declared that claims e_0799 modifies r_1046, but e_0799 does not appear in r_1046's kinetic law. +// An interaction was declared that claims e_0167 modifies r_1046, but e_0167 does not appear in r_1046's kinetic law. +// An interaction was declared that claims e_1313 modifies r_1047, but e_1313 does not appear in r_1047's kinetic law. +// An interaction was declared that claims e_0225 modifies r_1047, but e_0225 does not appear in r_1047's kinetic law. +// An interaction was declared that claims e_0326 modifies r_1054, but e_0326 does not appear in r_1054's kinetic law. +// An interaction was declared that claims e_1232 modifies r_1057, but e_1232 does not appear in r_1057's kinetic law. +// An interaction was declared that claims e_0990 modifies r_1063, but e_0990 does not appear in r_1063's kinetic law. +// An interaction was declared that claims e_0727 modifies r_1064, but e_0727 does not appear in r_1064's kinetic law. +// An interaction was declared that claims e_1200 modifies r_1064, but e_1200 does not appear in r_1064's kinetic law. +// An interaction was declared that claims e_1341 modifies r_1065, but e_1341 does not appear in r_1065's kinetic law. +// An interaction was declared that claims e_0103 modifies r_1065, but e_0103 does not appear in r_1065's kinetic law. +// An interaction was declared that claims e_1129 modifies r_1067, but e_1129 does not appear in r_1067's kinetic law. +// An interaction was declared that claims e_0435 modifies r_1068, but e_0435 does not appear in r_1068's kinetic law. +// An interaction was declared that claims e_1126 modifies r_1074, but e_1126 does not appear in r_1074's kinetic law. +// An interaction was declared that claims e_1249 modifies r_1075, but e_1249 does not appear in r_1075's kinetic law. +// An interaction was declared that claims e_0062 modifies r_1076, but e_0062 does not appear in r_1076's kinetic law. +// An interaction was declared that claims e_1167 modifies r_1081, but e_1167 does not appear in r_1081's kinetic law. +// An interaction was declared that claims e_1276 modifies r_1081, but e_1276 does not appear in r_1081's kinetic law. +// An interaction was declared that claims e_0332 modifies r_1081, but e_0332 does not appear in r_1081's kinetic law. +// An interaction was declared that claims e_1312 modifies r_1123, but e_1312 does not appear in r_1123's kinetic law. +// An interaction was declared that claims e_1312 modifies r_1124, but e_1312 does not appear in r_1124's kinetic law. +// An interaction was declared that claims e_0823 modifies r_1130, but e_0823 does not appear in r_1130's kinetic law. +// An interaction was declared that claims e_0823 modifies r_1131, but e_0823 does not appear in r_1131's kinetic law. +// An interaction was declared that claims e_1277 modifies r_1134, but e_1277 does not appear in r_1134's kinetic law. +// An interaction was declared that claims e_1369 modifies r_1134, but e_1369 does not appear in r_1134's kinetic law. +// An interaction was declared that claims e_0039 modifies r_1137, but e_0039 does not appear in r_1137's kinetic law. +// An interaction was declared that claims e_0871 modifies r_1139, but e_0871 does not appear in r_1139's kinetic law. +// An interaction was declared that claims e_1172 modifies r_1139, but e_1172 does not appear in r_1139's kinetic law. +// An interaction was declared that claims e_0822 modifies r_1139, but e_0822 does not appear in r_1139's kinetic law. +// An interaction was declared that claims e_1240 modifies r_1141, but e_1240 does not appear in r_1141's kinetic law. +// An interaction was declared that claims e_0987 modifies r_1150, but e_0987 does not appear in r_1150's kinetic law. +// An interaction was declared that claims e_0918 modifies r_1151, but e_0918 does not appear in r_1151's kinetic law. +// An interaction was declared that claims e_0925 modifies r_1152, but e_0925 does not appear in r_1152's kinetic law. +// An interaction was declared that claims e_1108 modifies r_1153, but e_1108 does not appear in r_1153's kinetic law. +// An interaction was declared that claims e_1373 modifies r_1153, but e_1373 does not appear in r_1153's kinetic law. +// An interaction was declared that claims e_0264 modifies r_1153, but e_0264 does not appear in r_1153's kinetic law. +// An interaction was declared that claims e_0641 modifies r_1198, but e_0641 does not appear in r_1198's kinetic law. +// An interaction was declared that claims e_1127 modifies r_1200, but e_1127 does not appear in r_1200's kinetic law. +// An interaction was declared that claims e_1127 modifies r_1201, but e_1127 does not appear in r_1201's kinetic law. +// An interaction was declared that claims e_1023 modifies r_1202, but e_1023 does not appear in r_1202's kinetic law. +// An interaction was declared that claims e_1366 modifies r_1202, but e_1366 does not appear in r_1202's kinetic law. +// An interaction was declared that claims e_0612 modifies r_1204, but e_0612 does not appear in r_1204's kinetic law. +// An interaction was declared that claims e_0612 modifies r_1205, but e_0612 does not appear in r_1205's kinetic law. +// An interaction was declared that claims e_0184 modifies r_1206, but e_0184 does not appear in r_1206's kinetic law. +// An interaction was declared that claims e_0185 modifies r_1207, but e_0185 does not appear in r_1207's kinetic law. +// An interaction was declared that claims e_0791 modifies r_1208, but e_0791 does not appear in r_1208's kinetic law. +// An interaction was declared that claims e_1258 modifies r_1209, but e_1258 does not appear in r_1209's kinetic law. +// An interaction was declared that claims e_0775 modifies r_1210, but e_0775 does not appear in r_1210's kinetic law. +// An interaction was declared that claims e_0427 modifies r_1211, but e_0427 does not appear in r_1211's kinetic law. +// An interaction was declared that claims e_0815 modifies r_1212, but e_0815 does not appear in r_1212's kinetic law. +// An interaction was declared that claims e_1257 modifies r_1214, but e_1257 does not appear in r_1214's kinetic law. +// An interaction was declared that claims e_0403 modifies r_1215, but e_0403 does not appear in r_1215's kinetic law. +// An interaction was declared that claims e_0326 modifies r_1217, but e_0326 does not appear in r_1217's kinetic law. +// An interaction was declared that claims e_0768 modifies r_1218, but e_0768 does not appear in r_1218's kinetic law. +// An interaction was declared that claims e_0720 modifies r_1218, but e_0720 does not appear in r_1218's kinetic law. +// An interaction was declared that claims e_1034 modifies r_1220, but e_1034 does not appear in r_1220's kinetic law. +// An interaction was declared that claims e_0793 modifies r_1222, but e_0793 does not appear in r_1222's kinetic law. +// An interaction was declared that claims e_0134 modifies r_1223, but e_0134 does not appear in r_1223's kinetic law. +// An interaction was declared that claims e_0825 modifies r_1224, but e_0825 does not appear in r_1224's kinetic law. +// An interaction was declared that claims e_0826 modifies r_1225, but e_0826 does not appear in r_1225's kinetic law. +// An interaction was declared that claims e_1205 modifies r_1230, but e_1205 does not appear in r_1230's kinetic law. +// An interaction was declared that claims e_1367 modifies r_1232, but e_1367 does not appear in r_1232's kinetic law. +// An interaction was declared that claims e_0818 modifies r_1245, but e_0818 does not appear in r_1245's kinetic law. +// An interaction was declared that claims e_0022 modifies r_1245, but e_0022 does not appear in r_1245's kinetic law. +// An interaction was declared that claims e_0137 modifies r_1250, but e_0137 does not appear in r_1250's kinetic law. +// An interaction was declared that claims e_0052 modifies r_1251, but e_0052 does not appear in r_1251's kinetic law. +// An interaction was declared that claims e_0051 modifies r_1251, but e_0051 does not appear in r_1251's kinetic law. +// An interaction was declared that claims e_0053 modifies r_1251, but e_0053 does not appear in r_1251's kinetic law. +// An interaction was declared that claims e_0974 modifies r_1252, but e_0974 does not appear in r_1252's kinetic law. +// An interaction was declared that claims e_1238 modifies r_1252, but e_1238 does not appear in r_1252's kinetic law. +// An interaction was declared that claims e_1239 modifies r_1252, but e_1239 does not appear in r_1252's kinetic law. +// An interaction was declared that claims e_0323 modifies r_1252, but e_0323 does not appear in r_1252's kinetic law. +// An interaction was declared that claims e_0324 modifies r_1252, but e_0324 does not appear in r_1252's kinetic law. +// An interaction was declared that claims e_0821 modifies r_1252, but e_0821 does not appear in r_1252's kinetic law. +// An interaction was declared that claims e_0451 modifies r_1255, but e_0451 does not appear in r_1255's kinetic law. +// An interaction was declared that claims e_0238 modifies r_1255, but e_0238 does not appear in r_1255's kinetic law. +// An interaction was declared that claims e_0911 modifies r_1255, but e_0911 does not appear in r_1255's kinetic law. +// An interaction was declared that claims e_0260 modifies r_1259, but e_0260 does not appear in r_1259's kinetic law. +// An interaction was declared that claims e_0008 modifies r_1264, but e_0008 does not appear in r_1264's kinetic law. +// An interaction was declared that claims e_0531 modifies r_1265, but e_0531 does not appear in r_1265's kinetic law. +// An interaction was declared that claims e_0145 modifies r_1266, but e_0145 does not appear in r_1266's kinetic law. +// An interaction was declared that claims e_1335 modifies r_1276, but e_1335 does not appear in r_1276's kinetic law. +// An interaction was declared that claims e_1227 modifies r_1276, but e_1227 does not appear in r_1276's kinetic law. +// An interaction was declared that claims e_1334 modifies r_1276, but e_1334 does not appear in r_1276's kinetic law. +// An interaction was declared that claims e_0238 modifies r_1276, but e_0238 does not appear in r_1276's kinetic law. +// An interaction was declared that claims e_0911 modifies r_1276, but e_0911 does not appear in r_1276's kinetic law. +// An interaction was declared that claims e_1335 modifies r_1277, but e_1335 does not appear in r_1277's kinetic law. +// An interaction was declared that claims e_1227 modifies r_1277, but e_1227 does not appear in r_1277's kinetic law. +// An interaction was declared that claims e_1334 modifies r_1277, but e_1334 does not appear in r_1277's kinetic law. +// An interaction was declared that claims e_0238 modifies r_1277, but e_0238 does not appear in r_1277's kinetic law. +// An interaction was declared that claims e_0911 modifies r_1277, but e_0911 does not appear in r_1277's kinetic law. +// An interaction was declared that claims e_1335 modifies r_1278, but e_1335 does not appear in r_1278's kinetic law. +// An interaction was declared that claims e_1227 modifies r_1278, but e_1227 does not appear in r_1278's kinetic law. +// An interaction was declared that claims e_1334 modifies r_1278, but e_1334 does not appear in r_1278's kinetic law. +// An interaction was declared that claims e_0238 modifies r_1278, but e_0238 does not appear in r_1278's kinetic law. +// An interaction was declared that claims e_0911 modifies r_1278, but e_0911 does not appear in r_1278's kinetic law. +// An interaction was declared that claims e_1335 modifies r_1279, but e_1335 does not appear in r_1279's kinetic law. +// An interaction was declared that claims e_1227 modifies r_1279, but e_1227 does not appear in r_1279's kinetic law. +// An interaction was declared that claims e_1334 modifies r_1279, but e_1334 does not appear in r_1279's kinetic law. +// An interaction was declared that claims e_0238 modifies r_1279, but e_0238 does not appear in r_1279's kinetic law. +// An interaction was declared that claims e_0911 modifies r_1279, but e_0911 does not appear in r_1279's kinetic law. +// An interaction was declared that claims e_0919 modifies r_1284, but e_0919 does not appear in r_1284's kinetic law. +// An interaction was declared that claims e_1291 modifies r_1284, but e_1291 does not appear in r_1284's kinetic law. +// An interaction was declared that claims e_1355 modifies r_1285, but e_1355 does not appear in r_1285's kinetic law. +// An interaction was declared that claims e_1026 modifies r_1285, but e_1026 does not appear in r_1285's kinetic law. +// An interaction was declared that claims e_0074 modifies r_1288, but e_0074 does not appear in r_1288's kinetic law. +// An interaction was declared that claims e_0839 modifies r_1291, but e_0839 does not appear in r_1291's kinetic law. +// An interaction was declared that claims e_1105 modifies r_1301, but e_1105 does not appear in r_1301's kinetic law. +// An interaction was declared that claims e_1010 modifies r_1304, but e_1010 does not appear in r_1304's kinetic law. +// An interaction was declared that claims e_0540 modifies r_1304, but e_0540 does not appear in r_1304's kinetic law. +// An interaction was declared that claims e_1028 modifies r_1305, but e_1028 does not appear in r_1305's kinetic law. +// An interaction was declared that claims e_0138 modifies r_1305, but e_0138 does not appear in r_1305's kinetic law. +// An interaction was declared that claims e_1019 modifies r_1306, but e_1019 does not appear in r_1306's kinetic law. +// An interaction was declared that claims e_1019 modifies r_1307, but e_1019 does not appear in r_1307's kinetic law. +// An interaction was declared that claims e_0253 modifies r_1315, but e_0253 does not appear in r_1315's kinetic law. +// An interaction was declared that claims e_0254 modifies r_1315, but e_0254 does not appear in r_1315's kinetic law. +// An interaction was declared that claims e_0774 modifies r_1316, but e_0774 does not appear in r_1316's kinetic law. +// An interaction was declared that claims e_1014 modifies r_1318, but e_1014 does not appear in r_1318's kinetic law. +// An interaction was declared that claims e_0869 modifies r_1329, but e_0869 does not appear in r_1329's kinetic law. +// An interaction was declared that claims e_0870 modifies r_1329, but e_0870 does not appear in r_1329's kinetic law. +// An interaction was declared that claims e_0872 modifies r_1330, but e_0872 does not appear in r_1330's kinetic law. +// An interaction was declared that claims e_0873 modifies r_1330, but e_0873 does not appear in r_1330's kinetic law. +// An interaction was declared that claims e_0979 modifies r_1335, but e_0979 does not appear in r_1335's kinetic law. +// An interaction was declared that claims e_0177 modifies r_1335, but e_0177 does not appear in r_1335's kinetic law. +// An interaction was declared that claims e_0330 modifies r_1337, but e_0330 does not appear in r_1337's kinetic law. +// An interaction was declared that claims e_0076 modifies r_1338, but e_0076 does not appear in r_1338's kinetic law. +// An interaction was declared that claims e_1253 modifies r_1344, but e_1253 does not appear in r_1344's kinetic law. +// An interaction was declared that claims e_0146 modifies r_1345, but e_0146 does not appear in r_1345's kinetic law. +// An interaction was declared that claims e_1374 modifies r_1346, but e_1374 does not appear in r_1346's kinetic law. +// An interaction was declared that claims e_1250 modifies r_1346, but e_1250 does not appear in r_1346's kinetic law. +// An interaction was declared that claims e_0805 modifies r_1346, but e_0805 does not appear in r_1346's kinetic law. +// An interaction was declared that claims e_0151 modifies r_1346, but e_0151 does not appear in r_1346's kinetic law. +// An interaction was declared that claims e_1252 modifies r_1346, but e_1252 does not appear in r_1346's kinetic law. +// An interaction was declared that claims e_1172 modifies r_1347, but e_1172 does not appear in r_1347's kinetic law. +// An interaction was declared that claims e_0822 modifies r_1347, but e_0822 does not appear in r_1347's kinetic law. +// An interaction was declared that claims e_0318 modifies r_1347, but e_0318 does not appear in r_1347's kinetic law. +// An interaction was declared that claims e_0313 modifies r_1348, but e_0313 does not appear in r_1348's kinetic law. +// An interaction was declared that claims e_0813 modifies r_1348, but e_0813 does not appear in r_1348's kinetic law. +// An interaction was declared that claims e_0003 modifies r_1349, but e_0003 does not appear in r_1349's kinetic law. +// An interaction was declared that claims e_0894 modifies r_1353, but e_0894 does not appear in r_1353's kinetic law. +// An interaction was declared that claims e_0770 modifies r_1356, but e_0770 does not appear in r_1356's kinetic law. +// An interaction was declared that claims e_0005 modifies r_1356, but e_0005 does not appear in r_1356's kinetic law. +// An interaction was declared that claims e_0771 modifies r_1357, but e_0771 does not appear in r_1357's kinetic law. +// An interaction was declared that claims e_0928 modifies r_1357, but e_0928 does not appear in r_1357's kinetic law. +// An interaction was declared that claims e_0771 modifies r_1358, but e_0771 does not appear in r_1358's kinetic law. +// An interaction was declared that claims e_0928 modifies r_1358, but e_0928 does not appear in r_1358's kinetic law. +// An interaction was declared that claims e_1226 modifies r_1363, but e_1226 does not appear in r_1363's kinetic law. +// An interaction was declared that claims e_0425 modifies r_1367, but e_0425 does not appear in r_1367's kinetic law. +// An interaction was declared that claims e_0426 modifies r_1367, but e_0426 does not appear in r_1367's kinetic law. +// An interaction was declared that claims e_1141 modifies r_1368, but e_1141 does not appear in r_1368's kinetic law. +// An interaction was declared that claims e_1251 modifies r_1375, but e_1251 does not appear in r_1375's kinetic law. +// An interaction was declared that claims e_1276 modifies r_1376, but e_1276 does not appear in r_1376's kinetic law. +// An interaction was declared that claims e_0332 modifies r_1376, but e_0332 does not appear in r_1376's kinetic law. +// An interaction was declared that claims e_0081 modifies r_1378, but e_0081 does not appear in r_1378's kinetic law. +// An interaction was declared that claims e_0044 modifies r_1379, but e_0044 does not appear in r_1379's kinetic law. +// An interaction was declared that claims e_1248 modifies r_1388, but e_1248 does not appear in r_1388's kinetic law. +// An interaction was declared that claims e_0991 modifies r_1389, but e_0991 does not appear in r_1389's kinetic law. +// An interaction was declared that claims e_0375 modifies r_1391, but e_0375 does not appear in r_1391's kinetic law. +// An interaction was declared that claims e_0083 modifies r_1391, but e_0083 does not appear in r_1391's kinetic law. +// An interaction was declared that claims e_1150 modifies r_1392, but e_1150 does not appear in r_1392's kinetic law. +// An interaction was declared that claims e_0041 modifies r_1393, but e_0041 does not appear in r_1393's kinetic law. +// An interaction was declared that claims e_0042 modifies r_1397, but e_0042 does not appear in r_1397's kinetic law. +// An interaction was declared that claims e_0040 modifies r_1399, but e_0040 does not appear in r_1399's kinetic law. +// An interaction was declared that claims e_0037 modifies r_1400, but e_0037 does not appear in r_1400's kinetic law. +// An interaction was declared that claims e_0038 modifies r_1401, but e_0038 does not appear in r_1401's kinetic law. +// An interaction was declared that claims e_0186 modifies r_1402, but e_0186 does not appear in r_1402's kinetic law. +// An interaction was declared that claims e_0328 modifies r_1409, but e_0328 does not appear in r_1409's kinetic law. +// An interaction was declared that claims e_0077 modifies r_1409, but e_0077 does not appear in r_1409's kinetic law. +// An interaction was declared that claims e_0079 modifies r_1410, but e_0079 does not appear in r_1410's kinetic law. +// An interaction was declared that claims e_0962 modifies r_1413, but e_0962 does not appear in r_1413's kinetic law. +// An interaction was declared that claims e_0433 modifies r_1413, but e_0433 does not appear in r_1413's kinetic law. +// An interaction was declared that claims e_0300 modifies r_1413, but e_0300 does not appear in r_1413's kinetic law. +// An interaction was declared that claims e_1256 modifies r_1421, but e_1256 does not appear in r_1421's kinetic law. +// An interaction was declared that claims e_1184 modifies r_1422, but e_1184 does not appear in r_1422's kinetic law. +// An interaction was declared that claims e_1019 modifies r_1422, but e_1019 does not appear in r_1422's kinetic law. +// An interaction was declared that claims e_1185 modifies r_1423, but e_1185 does not appear in r_1423's kinetic law. +// An interaction was declared that claims e_1167 modifies r_1425, but e_1167 does not appear in r_1425's kinetic law. +// An interaction was declared that claims e_1086 modifies r_1432, but e_1086 does not appear in r_1432's kinetic law. + model *MODEL1302140002() // Compartments and Species: @@ -602,6 +1127,530 @@ model *MODEL1302140002() r_2538: s_1550 => $s_2093; cell*r_2538_Vmax*s_1550/r_2538_Km1550/(1 + s_1550/r_2538_Km1550); r_2584: 0.000223 s_0133 + 2.6e-05 s_0378 + 0.000223 s_0226 + 0.00026 s_0380 + 0.5137 s_1041 + 0.000223 s_1552 + 0.2958 s_1061 + 0.2411 s_1068 + 0.2411 s_1072 + 54.12 s_0467 + 0.000122 s_0480 + 2e-06 s_0476 + 0.005205 s_0497 + 0.005205 s_0520 + 0.000576 s_0555 + 2.5e-05 s_0546 + 0.1335 s_0575 + 0.000709 s_0579 + 0.09158 s_1083 + 0.02617 s_0726 + 0.02702 s_0731 + 0.02702 s_0760 + 0.02617 s_0805 + 0.000223 s_0859 + 0.006715 s_0838 + 0.007808 s_0841 + 0.2632 s_1101 + 0.2632 s_1095 + 0.6126 s_0929 + 0.2151 s_0945 + 0.09474 s_1106 + 0.2905 s_1119 + 0.1952 s_1494 + 0.4505 s_1127 + 0.3432 s_1131 + 0.1537 s_1141 + 0.008675 s_1212 + 0.000223 s_0336 + 0.000691 s_1255 + 7e-06 s_1261 + 0.001831 s_1333 + 0.000447 s_1335 + 0.01301 s_0451 + 0.000323 s_1329 + 0.06382 s_1437 + 0.07521 s_1435 + 0.1853 s_1151 + 0.000223 s_1508 + 0.2211 s_1155 + 0.000223 s_1522 + 0.000223 s_1546 + 0.2158 s_1170 + 0.000223 s_1577 + 0.004338 s_1609 + 0.000223 s_0337 + 0.000223 s_1644 + 0.2537 s_1179 + 0.05684 s_1185 + 0.1379 s_1189 + 5.5e-05 s_1765 + 0.1441 s_1792 + 0.4232 s_1193 + 0.000341 s_1804 + 0.01946 s_1033 + 0.01389 s_1719 => 53.95 s_0421 + 53.95 s_1430 + 0.7739 s_0783; cell*((r_2584_V0*(1 + r_2584_ep0133*ln(s_0133/r_2584_ic0133) + r_2584_ep0378*ln(s_0378/r_2584_ic0378) + r_2584_ep0226*ln(s_0226/r_2584_ic0226) + r_2584_ep0380*ln(s_0380/r_2584_ic0380) + r_2584_ep1041*ln(s_1041/r_2584_ic1041) + r_2584_ep1552*ln(s_1552/r_2584_ic1552) + r_2584_ep1061*ln(s_1061/r_2584_ic1061) + r_2584_ep1068*ln(s_1068/r_2584_ic1068) + r_2584_ep1072*ln(s_1072/r_2584_ic1072) + r_2584_ep0467*ln(s_0467/r_2584_ic0467) + r_2584_ep0480*ln(s_0480/r_2584_ic0480) + r_2584_ep0476*ln(s_0476/r_2584_ic0476) + r_2584_ep0497*ln(s_0497/r_2584_ic0497) + r_2584_ep0520*ln(s_0520/r_2584_ic0520) + r_2584_ep0555*ln(s_0555/r_2584_ic0555) + r_2584_ep0546*ln(s_0546/r_2584_ic0546) + r_2584_ep0575*ln(s_0575/r_2584_ic0575) + r_2584_ep0579*ln(s_0579/r_2584_ic0579) + r_2584_ep1083*ln(s_1083/r_2584_ic1083) + r_2584_ep0726*ln(s_0726/r_2584_ic0726) + r_2584_ep0731*ln(s_0731/r_2584_ic0731) + r_2584_ep0760*ln(s_0760/r_2584_ic0760) + r_2584_ep0805*ln(s_0805/r_2584_ic0805) + r_2584_ep0859*ln(s_0859/r_2584_ic0859) + r_2584_ep0838*ln(s_0838/r_2584_ic0838) + r_2584_ep0841*ln(s_0841/r_2584_ic0841) + r_2584_ep1101*ln(s_1101/r_2584_ic1101) + r_2584_ep1095*ln(s_1095/r_2584_ic1095) + r_2584_ep0929*ln(s_0929/r_2584_ic0929) + r_2584_ep0945*ln(s_0945/r_2584_ic0945) + r_2584_ep1106*ln(s_1106/r_2584_ic1106) + r_2584_ep1119*ln(s_1119/r_2584_ic1119) + r_2584_ep1494*ln(s_1494/r_2584_ic1494) + r_2584_ep1127*ln(s_1127/r_2584_ic1127) + r_2584_ep1131*ln(s_1131/r_2584_ic1131) + r_2584_ep1141*ln(s_1141/r_2584_ic1141) + r_2584_ep1212*ln(s_1212/r_2584_ic1212) + r_2584_ep0336*ln(s_0336/r_2584_ic0336) + r_2584_ep1255*ln(s_1255/r_2584_ic1255) + r_2584_ep1261*ln(s_1261/r_2584_ic1261) + r_2584_ep1333*ln(s_1333/r_2584_ic1333) + r_2584_ep1335*ln(s_1335/r_2584_ic1335) + r_2584_ep0451*ln(s_0451/r_2584_ic0451) + r_2584_ep1329*ln(s_1329/r_2584_ic1329) + r_2584_ep1437*ln(s_1437/r_2584_ic1437) + r_2584_ep1435*ln(s_1435/r_2584_ic1435) + r_2584_ep1151*ln(s_1151/r_2584_ic1151) + r_2584_ep1508*ln(s_1508/r_2584_ic1508) + r_2584_ep1155*ln(s_1155/r_2584_ic1155) + r_2584_ep1522*ln(s_1522/r_2584_ic1522) + r_2584_ep1546*ln(s_1546/r_2584_ic1546) + r_2584_ep1170*ln(s_1170/r_2584_ic1170) + r_2584_ep1577*ln(s_1577/r_2584_ic1577) + r_2584_ep1609*ln(s_1609/r_2584_ic1609) + r_2584_ep0337*ln(s_0337/r_2584_ic0337) + r_2584_ep1644*ln(s_1644/r_2584_ic1644) + r_2584_ep1179*ln(s_1179/r_2584_ic1179) + r_2584_ep1185*ln(s_1185/r_2584_ic1185) + r_2584_ep1189*ln(s_1189/r_2584_ic1189) + r_2584_ep1765*ln(s_1765/r_2584_ic1765) + r_2584_ep1792*ln(s_1792/r_2584_ic1792) + r_2584_ep1193*ln(s_1193/r_2584_ic1193) + r_2584_ep1804*ln(s_1804/r_2584_ic1804) + r_2584_ep1033*ln(s_1033/r_2584_ic1033) + r_2584_ep1719*ln(s_1719/r_2584_ic1719)) + r_2584_zero_flux + abs(r_2584_V0*(1 + r_2584_ep0133*ln(s_0133/r_2584_ic0133) + r_2584_ep0378*ln(s_0378/r_2584_ic0378) + r_2584_ep0226*ln(s_0226/r_2584_ic0226) + r_2584_ep0380*ln(s_0380/r_2584_ic0380) + r_2584_ep1041*ln(s_1041/r_2584_ic1041) + r_2584_ep1552*ln(s_1552/r_2584_ic1552) + r_2584_ep1061*ln(s_1061/r_2584_ic1061) + r_2584_ep1068*ln(s_1068/r_2584_ic1068) + r_2584_ep1072*ln(s_1072/r_2584_ic1072) + r_2584_ep0467*ln(s_0467/r_2584_ic0467) + r_2584_ep0480*ln(s_0480/r_2584_ic0480) + r_2584_ep0476*ln(s_0476/r_2584_ic0476) + r_2584_ep0497*ln(s_0497/r_2584_ic0497) + r_2584_ep0520*ln(s_0520/r_2584_ic0520) + r_2584_ep0555*ln(s_0555/r_2584_ic0555) + r_2584_ep0546*ln(s_0546/r_2584_ic0546) + r_2584_ep0575*ln(s_0575/r_2584_ic0575) + r_2584_ep0579*ln(s_0579/r_2584_ic0579) + r_2584_ep1083*ln(s_1083/r_2584_ic1083) + r_2584_ep0726*ln(s_0726/r_2584_ic0726) + r_2584_ep0731*ln(s_0731/r_2584_ic0731) + r_2584_ep0760*ln(s_0760/r_2584_ic0760) + r_2584_ep0805*ln(s_0805/r_2584_ic0805) + r_2584_ep0859*ln(s_0859/r_2584_ic0859) + r_2584_ep0838*ln(s_0838/r_2584_ic0838) + r_2584_ep0841*ln(s_0841/r_2584_ic0841) + r_2584_ep1101*ln(s_1101/r_2584_ic1101) + r_2584_ep1095*ln(s_1095/r_2584_ic1095) + r_2584_ep0929*ln(s_0929/r_2584_ic0929) + r_2584_ep0945*ln(s_0945/r_2584_ic0945) + r_2584_ep1106*ln(s_1106/r_2584_ic1106) + r_2584_ep1119*ln(s_1119/r_2584_ic1119) + r_2584_ep1494*ln(s_1494/r_2584_ic1494) + r_2584_ep1127*ln(s_1127/r_2584_ic1127) + r_2584_ep1131*ln(s_1131/r_2584_ic1131) + r_2584_ep1141*ln(s_1141/r_2584_ic1141) + r_2584_ep1212*ln(s_1212/r_2584_ic1212) + r_2584_ep0336*ln(s_0336/r_2584_ic0336) + r_2584_ep1255*ln(s_1255/r_2584_ic1255) + r_2584_ep1261*ln(s_1261/r_2584_ic1261) + r_2584_ep1333*ln(s_1333/r_2584_ic1333) + r_2584_ep1335*ln(s_1335/r_2584_ic1335) + r_2584_ep0451*ln(s_0451/r_2584_ic0451) + r_2584_ep1329*ln(s_1329/r_2584_ic1329) + r_2584_ep1437*ln(s_1437/r_2584_ic1437) + r_2584_ep1435*ln(s_1435/r_2584_ic1435) + r_2584_ep1151*ln(s_1151/r_2584_ic1151) + r_2584_ep1508*ln(s_1508/r_2584_ic1508) + r_2584_ep1155*ln(s_1155/r_2584_ic1155) + r_2584_ep1522*ln(s_1522/r_2584_ic1522) + r_2584_ep1546*ln(s_1546/r_2584_ic1546) + r_2584_ep1170*ln(s_1170/r_2584_ic1170) + r_2584_ep1577*ln(s_1577/r_2584_ic1577) + r_2584_ep1609*ln(s_1609/r_2584_ic1609) + r_2584_ep0337*ln(s_0337/r_2584_ic0337) + r_2584_ep1644*ln(s_1644/r_2584_ic1644) + r_2584_ep1179*ln(s_1179/r_2584_ic1179) + r_2584_ep1185*ln(s_1185/r_2584_ic1185) + r_2584_ep1189*ln(s_1189/r_2584_ic1189) + r_2584_ep1765*ln(s_1765/r_2584_ic1765) + r_2584_ep1792*ln(s_1792/r_2584_ic1792) + r_2584_ep1193*ln(s_1193/r_2584_ic1193) + r_2584_ep1804*ln(s_1804/r_2584_ic1804) + r_2584_ep1033*ln(s_1033/r_2584_ic1033) + r_2584_ep1719*ln(s_1719/r_2584_ic1719)) - r_2584_zero_flux))/2); + // Interactions: + _I0: $e_0610 -o r_0008; ; + _I1: $e_0149 -o r_0009; ; + _I2: $e_0078 -o r_0011; ; + _I3: $e_0953 -o r_0012; ; + _I4: $e_0953 -o r_0013; ; + _I5: $e_0010 -o r_0014; ; + _I6: $e_0010 -o r_0015; ; + _I7: $e_1137 -o r_0038; ; + _I8: $e_0034 -o r_0038; ; + _I9: $e_0035 -o r_0038; ; + _I10: $e_1136 -o r_0038; ; + _I11: $e_0866 -o r_0053; ; + _I12: $e_0867 -o r_0054; ; + _I13: $e_0578 -o r_0056; ; + _I14: $e_0152 -o r_0063; ; + _I15: $e_1170 -o r_0063; ; + _I16: $e_0031 -o r_0066; ; + _I17: $e_0030 -o r_0066; ; + _I18: $e_0033 -o r_0067; ; + _I19: $e_0238 -o r_0084; ; + _I20: $e_0798 -o r_0084; ; + _I21: $e_0911 -o r_0084; ; + _I22: $e_1326 -o r_0085; ; + _I23: $e_0960 -o r_0092; ; + _I24: $e_1203 -o r_0096; ; + _I25: $e_0541 -o r_0098; ; + _I26: $e_1027 -o r_0099; ; + _I27: $e_0406 -o r_0100; ; + _I28: $e_0544 -o r_0101; ; + _I29: $e_0827 -o r_0101; ; + _I30: $e_0263 -o r_0101; ; + _I31: $e_1125 -o r_0102; ; + _I32: $e_1125 -o r_0103; ; + _I33: $e_0331 -o r_0105; ; + _I34: $e_0994 -o r_0106; ; + _I35: $e_1203 -o r_0120; ; + _I36: $e_0735 -o r_0120; ; + _I37: $e_1203 -o r_0121; ; + _I38: $e_0735 -o r_0121; ; + _I39: $e_1203 -o r_0122; ; + _I40: $e_0735 -o r_0122; ; + _I41: $e_1203 -o r_0123; ; + _I42: $e_0735 -o r_0123; ; + _I43: $e_1203 -o r_0124; ; + _I44: $e_0735 -o r_0124; ; + _I45: $e_1203 -o r_0126; ; + _I46: $e_0735 -o r_0126; ; + _I47: $e_1203 -o r_0127; ; + _I48: $e_0735 -o r_0127; ; + _I49: $e_1203 -o r_0128; ; + _I50: $e_0735 -o r_0128; ; + _I51: $e_1203 -o r_0129; ; + _I52: $e_0735 -o r_0129; ; + _I53: $e_1203 -o r_0130; ; + _I54: $e_0735 -o r_0130; ; + _I55: $e_1203 -o r_0131; ; + _I56: $e_0735 -o r_0131; ; + _I57: $e_1203 -o r_0133; ; + _I58: $e_0735 -o r_0133; ; + _I59: $e_1203 -o r_0134; ; + _I60: $e_0735 -o r_0134; ; + _I61: $e_1203 -o r_0135; ; + _I62: $e_0735 -o r_0135; ; + _I63: $e_0031 -o r_0138; ; + _I64: $e_0030 -o r_0138; ; + _I65: $e_0032 -o r_0139; ; + _I66: $e_0063 -o r_0143; ; + _I67: $e_0082 -o r_0145; ; + _I68: $e_0374 -o r_0146; ; + _I69: $e_0372 -o r_0147; ; + _I70: $e_0082 -o r_0148; ; + _I71: $e_0374 -o r_0149; ; + _I72: $e_0732 -o r_0150; ; + _I73: $e_0374 -o r_0154; ; + _I74: $e_0376 -o r_0166; ; + _I75: $e_0732 -o r_0166; ; + _I76: $e_0327 -o r_0175; ; + _I77: $e_0404 -o r_0178; ; + _I78: $e_1254 -o r_0179; ; + _I79: $e_1015 -o r_0181; ; + _I80: $e_0572 -o r_0181; ; + _I81: $e_0377 -o r_0182; ; + _I82: $e_0074 -o r_0186; ; + _I83: $e_1234 -o r_0211; ; + _I84: $e_0144 -o r_0212; ; + _I85: $e_0064 -o r_0216; ; + _I86: $e_0579 -o r_0217; ; + _I87: $e_0273 -o r_0218; ; + _I88: $e_0276 -o r_0222; ; + _I89: $e_0125 -o r_0224; ; + _I90: $e_0416 -o r_0224; ; + _I91: $e_0975 -o r_0225; ; + _I92: $e_0719 -o r_0225; ; + _I93: $e_0577 -o r_0225; ; + _I94: $e_1137 -o r_0227; ; + _I95: $e_0034 -o r_0227; ; + _I96: $e_0035 -o r_0227; ; + _I97: $e_1136 -o r_0227; ; + _I98: $e_0682 -o r_0230; ; + _I99: $e_1202 -o r_0230; ; + _I100: $e_0736 -o r_0230; ; + _I101: $e_1202 -o r_0231; ; + _I102: $e_0736 -o r_0231; ; + _I103: $e_1202 -o r_0232; ; + _I104: $e_0736 -o r_0232; ; + _I105: $e_1202 -o r_0233; ; + _I106: $e_0736 -o r_0233; ; + _I107: $e_1202 -o r_0234; ; + _I108: $e_0736 -o r_0234; ; + _I109: $e_1202 -o r_0235; ; + _I110: $e_0736 -o r_0235; ; + _I111: $e_1202 -o r_0236; ; + _I112: $e_0736 -o r_0236; ; + _I113: $e_0085 -o r_0237; ; + _I114: $e_1006 -o r_0237; ; + _I115: $e_1005 -o r_0237; ; + _I116: $e_0730 -o r_0237; ; + _I117: $e_1243 -o r_0243; ; + _I118: $e_1241 -o r_0244; ; + _I119: $e_0559 -o r_0245; ; + _I120: $e_1014 -o r_0245; ; + _I121: $e_0431 -o r_0246; ; + _I122: $e_0054 -o r_0246; ; + _I123: $e_0431 -o r_0247; ; + _I124: $e_0054 -o r_0247; ; + _I125: $e_0375 -o r_0257; ; + _I126: $e_0896 -o r_0257; ; + _I127: $e_0375 -o r_0259; ; + _I128: $e_0896 -o r_0259; ; + _I129: $e_0375 -o r_0260; ; + _I130: $e_0896 -o r_0260; ; + _I131: $e_0094 -o r_0266; ; + _I132: $e_0094 -o r_0267; ; + _I133: $e_0094 -o r_0268; ; + _I134: $e_0094 -o r_0269; ; + _I135: $e_0094 -o r_0270; ; + _I136: $e_0094 -o r_0272; ; + _I137: $e_0094 -o r_0273; ; + _I138: $e_0167 -o r_0292; ; + _I139: $e_0274 -o r_0297; ; + _I140: $e_0167 -o r_0301; ; + _I141: $e_0389 -o r_0302; ; + _I142: $e_1315 -o r_0303; ; + _I143: $e_0389 -o r_0304; ; + _I144: $e_0868 -o r_0305; ; + _I145: $e_0395 -o r_0310; ; + _I146: $e_1275 -o r_0310; ; + _I147: $e_0428 -o r_0348; ; + _I148: $e_0429 -o r_0349; ; + _I149: $e_0428 -o r_0349; ; + _I150: $e_0993 -o r_0355; ; + _I151: $e_0848 -o r_0355; ; + _I152: $e_1244 -o r_0360; ; + _I153: $e_0986 -o r_0361; ; + _I154: $e_1160 -o r_0365; ; + _I155: $e_0061 -o r_0367; ; + _I156: $e_1340 -o r_0368; ; + _I157: $e_1339 -o r_0368; ; + _I158: $e_1263 -o r_0369; ; + _I159: $e_0001 -o r_0369; ; + _I160: $e_1233 -o r_0369; ; + _I161: $e_0332 -o r_0370; ; + _I162: $e_1045 -o r_0371; ; + _I163: $e_0605 -o r_0374; ; + _I164: $e_0275 -o r_0383; ; + _I165: $e_0292 -o r_0384; ; + _I166: $e_1207 -o r_0385; ; + _I167: $e_1206 -o r_0385; ; + _I168: $e_1207 -o r_0386; ; + _I169: $e_1206 -o r_0386; ; + _I170: $e_0903 -o r_0388; ; + _I171: $e_0183 -o r_0388; ; + _I172: $e_0110 -o r_0388; ; + _I173: $e_0080 -o r_0418; ; + _I174: $e_0080 -o r_0419; ; + _I175: $e_0825 -o r_0423; ; + _I176: $e_0826 -o r_0423; ; + _I177: $e_1271 -o r_0424; ; + _I178: $e_0734 -o r_0425; ; + _I179: $e_0246 -o r_0428; ; + _I180: $e_0765 -o r_0436; ; + _I181: $e_0876 -o r_0440; ; + _I182: $e_0279 -o r_0445; ; + _I183: $e_0280 -o r_0445; ; + _I184: $e_0951 -o r_0450; ; + _I185: $e_0519 -o r_0450; ; + _I186: $e_0757 -o r_0452; ; + _I187: $e_0750 -o r_0452; ; + _I188: $e_0328 -o r_0457; ; + _I189: $e_0043 -o r_0463; ; + _I190: $e_0135 -o r_0463; ; + _I191: $e_0046 -o r_0488; ; + _I192: $e_0278 -o r_0489; ; + _I193: $e_0144 -o r_0498; ; + _I194: $e_0897 -o r_0499; ; + _I195: $e_1189 -o r_0500; ; + _I196: $e_0342 -o r_0501; ; + _I197: $e_0012 -o r_0502; ; + _I198: $e_0776 -o r_0503; ; + _I199: $e_0514 -o r_0504; ; + _I200: $e_0020 -o r_0504; ; + _I201: $e_0729 -o r_0505; ; + _I202: $e_0964 -o r_0507; ; + _I203: $e_0045 -o r_0510; ; + _I204: $e_0586 -o r_0510; ; + _I205: $e_0368 -o r_0511; ; + _I206: $e_0342 -o r_0512; ; + _I207: $e_0988 -o r_0515; ; + _I208: $e_1168 -o r_0517; ; + _I209: $e_1168 -o r_0518; ; + _I210: $e_0150 -o r_0522; ; + _I211: $e_0378 -o r_0532; ; + _I212: $e_1128 -o r_0533; ; + _I213: $e_0691 -o r_0533; ; + _I214: $e_0875 -o r_0538; ; + _I215: $e_0436 -o r_0563; ; + _I216: $e_0436 -o r_0564; ; + _I217: $e_0731 -o r_0573; ; + _I218: $e_0926 -o r_0574; ; + _I219: $e_0567 -o r_0574; ; + _I220: $e_1201 -o r_0576; ; + _I221: $e_0162 -o r_0579; ; + _I222: $e_0162 -o r_0580; ; + _I223: $e_0162 -o r_0581; ; + _I224: $e_0168 -o r_0602; ; + _I225: $e_0008 -o r_0611; ; + _I226: $e_1298 -o r_0632; ; + _I227: $e_0515 -o r_0632; ; + _I228: $e_0516 -o r_0632; ; + _I229: $e_0577 -o r_0648; ; + _I230: $e_0150 -o r_0655; ; + _I231: $e_1150 -o r_0658; ; + _I232: $e_0580 -o r_0660; ; + _I233: $e_1264 -o r_0664; ; + _I234: $e_0099 -o r_0673; ; + _I235: $e_0561 -o r_0675; ; + _I236: $e_1247 -o r_0676; ; + _I237: $e_0071 -o r_0678; ; + _I238: $e_0100 -o r_0679; ; + _I239: $e_0728 -o r_0682; ; + _I240: $e_1210 -o r_0683; ; + _I241: $e_0439 -o r_0683; ; + _I242: $e_1149 -o r_0684; ; + _I243: $e_0405 -o r_0686; ; + _I244: $e_0746 -o r_0687; ; + _I245: $e_0567 -o r_0695; ; + _I246: $e_0978 -o r_0697; ; + _I247: $e_0375 -o r_0706; ; + _I248: $e_1273 -o r_0706; ; + _I249: $e_0375 -o r_0707; ; + _I250: $e_1273 -o r_0707; ; + _I251: $e_1106 -o r_0712; ; + _I252: $e_1110 -o r_0724; ; + _I253: $e_0813 -o r_0726; ; + _I254: $e_0466 -o r_0731; ; + _I255: $e_1376 -o r_0734; ; + _I256: $e_0941 -o r_0734; ; + _I257: $e_1377 -o r_0734; ; + _I258: $e_1376 -o r_0735; ; + _I259: $e_0941 -o r_0735; ; + _I260: $e_1377 -o r_0735; ; + _I261: $e_0175 -o r_0739; ; + _I262: $e_0795 -o r_0741; ; + _I263: $e_0657 -o r_0744; ; + _I264: $e_0432 -o r_0745; ; + _I265: $e_1130 -o r_0754; ; + _I266: $e_0060 -o r_0755; ; + _I267: $e_0116 -o r_0755; ; + _I268: $e_0139 -o r_0761; ; + _I269: $e_0743 -o r_0762; ; + _I270: $e_0606 -o r_0763; ; + _I271: $e_0608 -o r_0764; ; + _I272: $e_0607 -o r_0765; ; + _I273: $e_0001 -o r_0769; ; + _I274: $e_1233 -o r_0769; ; + _I275: $e_0002 -o r_0770; ; + _I276: $e_1259 -o r_0771; ; + _I277: $e_1272 -o r_0775; ; + _I278: $e_1186 -o r_0777; ; + _I279: $e_0611 -o r_0784; ; + _I280: $e_0609 -o r_0784; ; + _I281: $e_0608 -o r_0785; ; + _I282: $e_1258 -o r_0786; ; + _I283: $e_0796 -o r_0787; ; + _I284: $e_0427 -o r_0788; ; + _I285: $e_0805 -o r_0796; ; + _I286: $e_0804 -o r_0796; ; + _I287: $e_0804 -o r_0797; ; + _I288: $e_1188 -o r_0797; ; + _I289: $e_0805 -o r_0797; ; + _I290: $e_0804 -o r_0798; ; + _I291: $e_1188 -o r_0798; ; + _I292: $e_0805 -o r_0798; ; + _I293: $e_0803 -o r_0799; ; + _I294: $e_0804 -o r_0799; ; + _I295: $e_0804 -o r_0800; ; + _I296: $e_0803 -o r_0801; ; + _I297: $e_0804 -o r_0801; ; + _I298: $e_0805 -o r_0802; ; + _I299: $e_0391 -o r_0806; ; + _I300: $e_1167 -o r_0808; ; + _I301: $e_1170 -o r_0811; ; + _I302: $e_1170 -o r_0812; ; + _I303: $e_0742 -o r_0815; ; + _I304: $e_0717 -o r_0815; ; + _I305: $e_0819 -o r_0829; ; + _I306: $e_1169 -o r_0847; ; + _I307: $e_0977 -o r_0847; ; + _I308: $e_1109 -o r_0848; ; + _I309: $e_1167 -o r_0854; ; + _I310: $e_1276 -o r_0854; ; + _I311: $e_0084 -o r_0857; ; + _I312: $e_1004 -o r_0925; ; + _I313: $e_0277 -o r_0934; ; + _I314: $e_0375 -o r_0935; ; + _I315: $e_0373 -o r_0935; ; + _I316: $e_0188 -o r_0950; ; + _I317: $e_0931 -o r_0951; ; + _I318: $e_1196 -o r_0954; ; + _I319: $e_1262 -o r_0954; ; + _I320: $e_0188 -o r_0957; ; + _I321: $e_0281 -o r_0963; ; + _I322: $e_0805 -o r_0963; ; + _I323: $e_0292 -o r_0964; ; + _I324: $e_0006 -o r_0965; ; + _I325: $e_0281 -o r_0968; ; + _I326: $e_0282 -o r_0968; ; + _I327: $e_0291 -o r_0969; ; + _I328: $e_0036 -o r_0970; ; + _I329: $e_1029 -o r_0970; ; + _I330: $e_0221 -o r_0970; ; + _I331: $e_0065 -o r_0970; ; + _I332: $e_1242 -o r_0996; ; + _I333: $e_0893 -o r_0999; ; + _I334: $e_0828 -o r_1006; ; + _I335: $e_0554 -o r_1008; ; + _I336: $e_0223 -o r_1019; ; + _I337: $e_0048 -o r_1021; ; + _I338: $e_0799 -o r_1039; ; + _I339: $e_0167 -o r_1039; ; + _I340: $e_0799 -o r_1043; ; + _I341: $e_0167 -o r_1043; ; + _I342: $e_0799 -o r_1045; ; + _I343: $e_0167 -o r_1045; ; + _I344: $e_0799 -o r_1046; ; + _I345: $e_0167 -o r_1046; ; + _I346: $e_1313 -o r_1047; ; + _I347: $e_0225 -o r_1047; ; + _I348: $e_0326 -o r_1054; ; + _I349: $e_1232 -o r_1057; ; + _I350: $e_0990 -o r_1063; ; + _I351: $e_0727 -o r_1064; ; + _I352: $e_1200 -o r_1064; ; + _I353: $e_1341 -o r_1065; ; + _I354: $e_0103 -o r_1065; ; + _I355: $e_1129 -o r_1067; ; + _I356: $e_0435 -o r_1068; ; + _I357: $e_1126 -o r_1074; ; + _I358: $e_1249 -o r_1075; ; + _I359: $e_0062 -o r_1076; ; + _I360: $e_1167 -o r_1081; ; + _I361: $e_1276 -o r_1081; ; + _I362: $e_0332 -o r_1081; ; + _I363: $e_1312 -o r_1123; ; + _I364: $e_1312 -o r_1124; ; + _I365: $e_0823 -o r_1130; ; + _I366: $e_0823 -o r_1131; ; + _I367: $e_1277 -o r_1134; ; + _I368: $e_1369 -o r_1134; ; + _I369: $e_0039 -o r_1137; ; + _I370: $e_0871 -o r_1139; ; + _I371: $e_1172 -o r_1139; ; + _I372: $e_0822 -o r_1139; ; + _I373: $e_1240 -o r_1141; ; + _I374: $e_0987 -o r_1150; ; + _I375: $e_0918 -o r_1151; ; + _I376: $e_0925 -o r_1152; ; + _I377: $e_1108 -o r_1153; ; + _I378: $e_1373 -o r_1153; ; + _I379: $e_0264 -o r_1153; ; + _I380: $e_0641 -o r_1198; ; + _I381: $e_1127 -o r_1200; ; + _I382: $e_1127 -o r_1201; ; + _I383: $e_1023 -o r_1202; ; + _I384: $e_1366 -o r_1202; ; + _I385: $e_0612 -o r_1204; ; + _I386: $e_0612 -o r_1205; ; + _I387: $e_0184 -o r_1206; ; + _I388: $e_0185 -o r_1207; ; + _I389: $e_0791 -o r_1208; ; + _I390: $e_1258 -o r_1209; ; + _I391: $e_0775 -o r_1210; ; + _I392: $e_0427 -o r_1211; ; + _I393: $e_0815 -o r_1212; ; + _I394: $e_1257 -o r_1214; ; + _I395: $e_0403 -o r_1215; ; + _I396: $e_0326 -o r_1217; ; + _I397: $e_0768 -o r_1218; ; + _I398: $e_0720 -o r_1218; ; + _I399: $e_1034 -o r_1220; ; + _I400: $e_0793 -o r_1222; ; + _I401: $e_0134 -o r_1223; ; + _I402: $e_0825 -o r_1224; ; + _I403: $e_0826 -o r_1225; ; + _I404: $e_1205 -o r_1230; ; + _I405: $e_1367 -o r_1232; ; + _I406: $e_0818 -o r_1245; ; + _I407: $e_0022 -o r_1245; ; + _I408: $e_0137 -o r_1250; ; + _I409: $e_0052 -o r_1251; ; + _I410: $e_0051 -o r_1251; ; + _I411: $e_0053 -o r_1251; ; + _I412: $e_0974 -o r_1252; ; + _I413: $e_1238 -o r_1252; ; + _I414: $e_1239 -o r_1252; ; + _I415: $e_0323 -o r_1252; ; + _I416: $e_0324 -o r_1252; ; + _I417: $e_0821 -o r_1252; ; + _I418: $e_0451 -o r_1255; ; + _I419: $e_0238 -o r_1255; ; + _I420: $e_0911 -o r_1255; ; + _I421: $e_0260 -o r_1259; ; + _I422: $e_0008 -o r_1264; ; + _I423: $e_0531 -o r_1265; ; + _I424: $e_0145 -o r_1266; ; + _I425: $e_1335 -o r_1276; ; + _I426: $e_1227 -o r_1276; ; + _I427: $e_1334 -o r_1276; ; + _I428: $e_0238 -o r_1276; ; + _I429: $e_0911 -o r_1276; ; + _I430: $e_1335 -o r_1277; ; + _I431: $e_1227 -o r_1277; ; + _I432: $e_1334 -o r_1277; ; + _I433: $e_0238 -o r_1277; ; + _I434: $e_0911 -o r_1277; ; + _I435: $e_1335 -o r_1278; ; + _I436: $e_1227 -o r_1278; ; + _I437: $e_1334 -o r_1278; ; + _I438: $e_0238 -o r_1278; ; + _I439: $e_0911 -o r_1278; ; + _I440: $e_1335 -o r_1279; ; + _I441: $e_1227 -o r_1279; ; + _I442: $e_1334 -o r_1279; ; + _I443: $e_0238 -o r_1279; ; + _I444: $e_0911 -o r_1279; ; + _I445: $e_0919 -o r_1284; ; + _I446: $e_1291 -o r_1284; ; + _I447: $e_1355 -o r_1285; ; + _I448: $e_1026 -o r_1285; ; + _I449: $e_0074 -o r_1288; ; + _I450: $e_0839 -o r_1291; ; + _I451: $e_1105 -o r_1301; ; + _I452: $e_1010 -o r_1304; ; + _I453: $e_0540 -o r_1304; ; + _I454: $e_1028 -o r_1305; ; + _I455: $e_0138 -o r_1305; ; + _I456: $e_1019 -o r_1306; ; + _I457: $e_1019 -o r_1307; ; + _I458: $e_0253 -o r_1315; ; + _I459: $e_0254 -o r_1315; ; + _I460: $e_0774 -o r_1316; ; + _I461: $e_1014 -o r_1318; ; + _I462: $e_0869 -o r_1329; ; + _I463: $e_0870 -o r_1329; ; + _I464: $e_0872 -o r_1330; ; + _I465: $e_0873 -o r_1330; ; + _I466: $e_0979 -o r_1335; ; + _I467: $e_0177 -o r_1335; ; + _I468: $e_0330 -o r_1337; ; + _I469: $e_0076 -o r_1338; ; + _I470: $e_1253 -o r_1344; ; + _I471: $e_0146 -o r_1345; ; + _I472: $e_1374 -o r_1346; ; + _I473: $e_1250 -o r_1346; ; + _I474: $e_0805 -o r_1346; ; + _I475: $e_0151 -o r_1346; ; + _I476: $e_1252 -o r_1346; ; + _I477: $e_1172 -o r_1347; ; + _I478: $e_0822 -o r_1347; ; + _I479: $e_0318 -o r_1347; ; + _I480: $e_0313 -o r_1348; ; + _I481: $e_0813 -o r_1348; ; + _I482: $e_0003 -o r_1349; ; + _I483: $e_0894 -o r_1353; ; + _I484: $e_0770 -o r_1356; ; + _I485: $e_0005 -o r_1356; ; + _I486: $e_0771 -o r_1357; ; + _I487: $e_0928 -o r_1357; ; + _I488: $e_0771 -o r_1358; ; + _I489: $e_0928 -o r_1358; ; + _I490: $e_1226 -o r_1363; ; + _I491: $e_0425 -o r_1367; ; + _I492: $e_0426 -o r_1367; ; + _I493: $e_1141 -o r_1368; ; + _I494: $e_1251 -o r_1375; ; + _I495: $e_1276 -o r_1376; ; + _I496: $e_0332 -o r_1376; ; + _I497: $e_0081 -o r_1378; ; + _I498: $e_0044 -o r_1379; ; + _I499: $e_1248 -o r_1388; ; + _I500: $e_0991 -o r_1389; ; + _I501: $e_0375 -o r_1391; ; + _I502: $e_0083 -o r_1391; ; + _I503: $e_1150 -o r_1392; ; + _I504: $e_0041 -o r_1393; ; + _I505: $e_0042 -o r_1397; ; + _I506: $e_0040 -o r_1399; ; + _I507: $e_0037 -o r_1400; ; + _I508: $e_0038 -o r_1401; ; + _I509: $e_0186 -o r_1402; ; + _I510: $e_0328 -o r_1409; ; + _I511: $e_0077 -o r_1409; ; + _I512: $e_0079 -o r_1410; ; + _I513: $e_0962 -o r_1413; ; + _I514: $e_0433 -o r_1413; ; + _I515: $e_0300 -o r_1413; ; + _I516: $e_1256 -o r_1421; ; + _I517: $e_1184 -o r_1422; ; + _I518: $e_1019 -o r_1422; ; + _I519: $e_1185 -o r_1423; ; + _I520: $e_1167 -o r_1425; ; + _I521: $e_1086 -o r_1432; ; + // Species initializations: s_0003 = 0.1; s_0004 = 0.1; diff --git a/doc/examples/biomodels/BIOMD0000000471_url.txt b/doc/examples/biomodels/BIOMD0000000471/BIOMD0000000471_url.txt similarity index 84% rename from doc/examples/biomodels/BIOMD0000000471_url.txt rename to doc/examples/biomodels/BIOMD0000000471/BIOMD0000000471_url.txt index 0e9def0b7..33bf68ee9 100644 --- a/doc/examples/biomodels/BIOMD0000000471_url.txt +++ b/doc/examples/biomodels/BIOMD0000000471/BIOMD0000000471_url.txt @@ -1,4 +1,468 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 + +// Warnings from automatic translation: +// An interaction was declared that claims e_0682 modifies r_0005, but e_0682 does not appear in r_0005's kinetic law. +// An interaction was declared that claims e_0364 modifies r_0005, but e_0364 does not appear in r_0005's kinetic law. +// An interaction was declared that claims e_0973 modifies r_0006, but e_0973 does not appear in r_0006's kinetic law. +// An interaction was declared that claims e_0379 modifies r_0006, but e_0379 does not appear in r_0006's kinetic law. +// An interaction was declared that claims e_0465 modifies r_0007, but e_0465 does not appear in r_0007's kinetic law. +// An interaction was declared that claims e_0869 modifies r_0008, but e_0869 does not appear in r_0008's kinetic law. +// An interaction was declared that claims e_0133 modifies r_0008, but e_0133 does not appear in r_0008's kinetic law. +// An interaction was declared that claims e_0117 modifies r_0008, but e_0117 does not appear in r_0008's kinetic law. +// An interaction was declared that claims e_0431 modifies r_0012, but e_0431 does not appear in r_0012's kinetic law. +// An interaction was declared that claims e_0832 modifies r_0014, but e_0832 does not appear in r_0014's kinetic law. +// An interaction was declared that claims e_0071 modifies r_0015, but e_0071 does not appear in r_0015's kinetic law. +// An interaction was declared that claims e_0734 modifies r_0016, but e_0734 does not appear in r_0016's kinetic law. +// An interaction was declared that claims e_0100 modifies r_0016, but e_0100 does not appear in r_0016's kinetic law. +// An interaction was declared that claims e_0348 modifies r_0018, but e_0348 does not appear in r_0018's kinetic law. +// An interaction was declared that claims e_0496 modifies r_0018, but e_0496 does not appear in r_0018's kinetic law. +// An interaction was declared that claims e_0980 modifies r_0018, but e_0980 does not appear in r_0018's kinetic law. +// An interaction was declared that claims e_0169 modifies r_0020, but e_0169 does not appear in r_0020's kinetic law. +// An interaction was declared that claims e_0088 modifies r_0020, but e_0088 does not appear in r_0020's kinetic law. +// An interaction was declared that claims e_0328 modifies r_0023, but e_0328 does not appear in r_0023's kinetic law. +// An interaction was declared that claims e_0778 modifies r_0024, but e_0778 does not appear in r_0024's kinetic law. +// An interaction was declared that claims e_0855 modifies r_0024, but e_0855 does not appear in r_0024's kinetic law. +// An interaction was declared that claims e_0196 modifies r_0027, but e_0196 does not appear in r_0027's kinetic law. +// An interaction was declared that claims e_0550 modifies r_0029, but e_0550 does not appear in r_0029's kinetic law. +// An interaction was declared that claims e_0457 modifies r_0029, but e_0457 does not appear in r_0029's kinetic law. +// An interaction was declared that claims e_0830 modifies r_0032, but e_0830 does not appear in r_0032's kinetic law. +// An interaction was declared that claims e_0237 modifies r_0038, but e_0237 does not appear in r_0038's kinetic law. +// An interaction was declared that claims e_0182 modifies r_0039, but e_0182 does not appear in r_0039's kinetic law. +// An interaction was declared that claims e_0182 modifies r_0040, but e_0182 does not appear in r_0040's kinetic law. +// An interaction was declared that claims e_0092 modifies r_0041, but e_0092 does not appear in r_0041's kinetic law. +// An interaction was declared that claims e_0328 modifies r_0060, but e_0328 does not appear in r_0060's kinetic law. +// An interaction was declared that claims e_0101 modifies r_0061, but e_0101 does not appear in r_0061's kinetic law. +// An interaction was declared that claims e_0182 modifies r_0065, but e_0182 does not appear in r_0065's kinetic law. +// An interaction was declared that claims e_0368 modifies r_0079, but e_0368 does not appear in r_0079's kinetic law. +// An interaction was declared that claims e_0340 modifies r_0080, but e_0340 does not appear in r_0080's kinetic law. +// An interaction was declared that claims e_0903 modifies r_0080, but e_0903 does not appear in r_0080's kinetic law. +// An interaction was declared that claims e_0685 modifies r_0096, but e_0685 does not appear in r_0096's kinetic law. +// An interaction was declared that claims e_0734 modifies r_0097, but e_0734 does not appear in r_0097's kinetic law. +// An interaction was declared that claims e_0100 modifies r_0097, but e_0100 does not appear in r_0097's kinetic law. +// An interaction was declared that claims e_0904 modifies r_0103, but e_0904 does not appear in r_0103's kinetic law. +// An interaction was declared that claims e_0744 modifies r_0108, but e_0744 does not appear in r_0108's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0108, but e_0808 does not appear in r_0108's kinetic law. +// An interaction was declared that claims e_0022 modifies r_0110, but e_0022 does not appear in r_0110's kinetic law. +// An interaction was declared that claims e_0290 modifies r_0115, but e_0290 does not appear in r_0115's kinetic law. +// An interaction was declared that claims e_0840 modifies r_0118, but e_0840 does not appear in r_0118's kinetic law. +// An interaction was declared that claims e_0541 modifies r_0142, but e_0541 does not appear in r_0142's kinetic law. +// An interaction was declared that claims e_0280 modifies r_0144, but e_0280 does not appear in r_0144's kinetic law. +// An interaction was declared that claims e_0194 modifies r_0148, but e_0194 does not appear in r_0148's kinetic law. +// An interaction was declared that claims e_0303 modifies r_0148, but e_0303 does not appear in r_0148's kinetic law. +// An interaction was declared that claims e_0686 modifies r_0151, but e_0686 does not appear in r_0151's kinetic law. +// An interaction was declared that claims e_0686 modifies r_0152, but e_0686 does not appear in r_0152's kinetic law. +// An interaction was declared that claims e_0791 modifies r_0153, but e_0791 does not appear in r_0153's kinetic law. +// An interaction was declared that claims e_0556 modifies r_0154, but e_0556 does not appear in r_0154's kinetic law. +// An interaction was declared that claims e_0894 modifies r_0157, but e_0894 does not appear in r_0157's kinetic law. +// An interaction was declared that claims e_0711 modifies r_0195, but e_0711 does not appear in r_0195's kinetic law. +// An interaction was declared that claims e_0065 modifies r_0195, but e_0065 does not appear in r_0195's kinetic law. +// An interaction was declared that claims e_0179 modifies r_0195, but e_0179 does not appear in r_0195's kinetic law. +// An interaction was declared that claims e_0753 modifies r_0195, but e_0753 does not appear in r_0195's kinetic law. +// An interaction was declared that claims e_0219 modifies r_0202, but e_0219 does not appear in r_0202's kinetic law. +// An interaction was declared that claims e_0297 modifies r_0203, but e_0297 does not appear in r_0203's kinetic law. +// An interaction was declared that claims e_0591 modifies r_0203, but e_0591 does not appear in r_0203's kinetic law. +// An interaction was declared that claims e_0426 modifies r_0207, but e_0426 does not appear in r_0207's kinetic law. +// An interaction was declared that claims e_0826 modifies r_0208, but e_0826 does not appear in r_0208's kinetic law. +// An interaction was declared that claims e_0214 modifies r_0209, but e_0214 does not appear in r_0209's kinetic law. +// An interaction was declared that claims e_0970 modifies r_0211, but e_0970 does not appear in r_0211's kinetic law. +// An interaction was declared that claims e_0376 modifies r_0211, but e_0376 does not appear in r_0211's kinetic law. +// An interaction was declared that claims e_0427 modifies r_0212, but e_0427 does not appear in r_0212's kinetic law. +// An interaction was declared that claims e_0508 modifies r_0214, but e_0508 does not appear in r_0214's kinetic law. +// An interaction was declared that claims e_0281 modifies r_0215, but e_0281 does not appear in r_0215's kinetic law. +// An interaction was declared that claims e_0629 modifies r_0216, but e_0629 does not appear in r_0216's kinetic law. +// An interaction was declared that claims e_0574 modifies r_0216, but e_0574 does not appear in r_0216's kinetic law. +// An interaction was declared that claims e_0186 modifies r_0219, but e_0186 does not appear in r_0219's kinetic law. +// An interaction was declared that claims e_0615 modifies r_0220, but e_0615 does not appear in r_0220's kinetic law. +// An interaction was declared that claims e_0283 modifies r_0225, but e_0283 does not appear in r_0225's kinetic law. +// An interaction was declared that claims e_0800 modifies r_0231, but e_0800 does not appear in r_0231's kinetic law. +// An interaction was declared that claims e_0724 modifies r_0233, but e_0724 does not appear in r_0233's kinetic law. +// An interaction was declared that claims e_0326 modifies r_0234, but e_0326 does not appear in r_0234's kinetic law. +// An interaction was declared that claims e_0326 modifies r_0235, but e_0326 does not appear in r_0235's kinetic law. +// An interaction was declared that claims e_0644 modifies r_0236, but e_0644 does not appear in r_0236's kinetic law. +// An interaction was declared that claims e_0644 modifies r_0237, but e_0644 does not appear in r_0237's kinetic law. +// An interaction was declared that claims e_0367 modifies r_0238, but e_0367 does not appear in r_0238's kinetic law. +// An interaction was declared that claims e_0367 modifies r_0239, but e_0367 does not appear in r_0239's kinetic law. +// An interaction was declared that claims e_0367 modifies r_0240, but e_0367 does not appear in r_0240's kinetic law. +// An interaction was declared that claims e_0367 modifies r_0241, but e_0367 does not appear in r_0241's kinetic law. +// An interaction was declared that claims e_0637 modifies r_0242, but e_0637 does not appear in r_0242's kinetic law. +// An interaction was declared that claims e_0742 modifies r_0243, but e_0742 does not appear in r_0243's kinetic law. +// An interaction was declared that claims e_0329 modifies r_0244, but e_0329 does not appear in r_0244's kinetic law. +// An interaction was declared that claims e_0508 modifies r_0250, but e_0508 does not appear in r_0250's kinetic law. +// An interaction was declared that claims e_0542 modifies r_0250, but e_0542 does not appear in r_0250's kinetic law. +// An interaction was declared that claims e_0888 modifies r_0250, but e_0888 does not appear in r_0250's kinetic law. +// An interaction was declared that claims e_0045 modifies r_0257, but e_0045 does not appear in r_0257's kinetic law. +// An interaction was declared that claims e_0206 modifies r_0259, but e_0206 does not appear in r_0259's kinetic law. +// An interaction was declared that claims e_0756 modifies r_0267, but e_0756 does not appear in r_0267's kinetic law. +// An interaction was declared that claims e_0756 modifies r_0269, but e_0756 does not appear in r_0269's kinetic law. +// An interaction was declared that claims e_0959 modifies r_0278, but e_0959 does not appear in r_0278's kinetic law. +// An interaction was declared that claims e_0342 modifies r_0279, but e_0342 does not appear in r_0279's kinetic law. +// An interaction was declared that claims e_0675 modifies r_0280, but e_0675 does not appear in r_0280's kinetic law. +// An interaction was declared that claims e_0947 modifies r_0300, but e_0947 does not appear in r_0300's kinetic law. +// An interaction was declared that claims e_0805 modifies r_0300, but e_0805 does not appear in r_0300's kinetic law. +// An interaction was declared that claims e_0111 modifies r_0300, but e_0111 does not appear in r_0300's kinetic law. +// An interaction was declared that claims e_0675 modifies r_0302, but e_0675 does not appear in r_0302's kinetic law. +// An interaction was declared that claims e_0540 modifies r_0307, but e_0540 does not appear in r_0307's kinetic law. +// An interaction was declared that claims e_0026 modifies r_0307, but e_0026 does not appear in r_0307's kinetic law. +// An interaction was declared that claims e_0380 modifies r_0309, but e_0380 does not appear in r_0309's kinetic law. +// An interaction was declared that claims e_0008 modifies r_0310, but e_0008 does not appear in r_0310's kinetic law. +// An interaction was declared that claims e_0545 modifies r_0311, but e_0545 does not appear in r_0311's kinetic law. +// An interaction was declared that claims e_0793 modifies r_0313, but e_0793 does not appear in r_0313's kinetic law. +// An interaction was declared that claims e_0434 modifies r_0317, but e_0434 does not appear in r_0317's kinetic law. +// An interaction was declared that claims e_0424 modifies r_0317, but e_0424 does not appear in r_0317's kinetic law. +// An interaction was declared that claims e_0452 modifies r_0326, but e_0452 does not appear in r_0326's kinetic law. +// An interaction was declared that claims e_0234 modifies r_0330, but e_0234 does not appear in r_0330's kinetic law. +// An interaction was declared that claims e_0883 modifies r_0336, but e_0883 does not appear in r_0336's kinetic law. +// An interaction was declared that claims e_0203 modifies r_0337, but e_0203 does not appear in r_0337's kinetic law. +// An interaction was declared that claims e_0594 modifies r_0339, but e_0594 does not appear in r_0339's kinetic law. +// An interaction was declared that claims e_0914 modifies r_0340, but e_0914 does not appear in r_0340's kinetic law. +// An interaction was declared that claims e_0880 modifies r_0344, but e_0880 does not appear in r_0344's kinetic law. +// An interaction was declared that claims e_0692 modifies r_0349, but e_0692 does not appear in r_0349's kinetic law. +// An interaction was declared that claims e_0528 modifies r_0352, but e_0528 does not appear in r_0352's kinetic law. +// An interaction was declared that claims e_0528 modifies r_0353, but e_0528 does not appear in r_0353's kinetic law. +// An interaction was declared that claims e_0515 modifies r_0355, but e_0515 does not appear in r_0355's kinetic law. +// An interaction was declared that claims e_0976 modifies r_0361, but e_0976 does not appear in r_0361's kinetic law. +// An interaction was declared that claims e_0141 modifies r_0362, but e_0141 does not appear in r_0362's kinetic law. +// An interaction was declared that claims e_0549 modifies r_0362, but e_0549 does not appear in r_0362's kinetic law. +// An interaction was declared that claims e_0010 modifies r_0362, but e_0010 does not appear in r_0362's kinetic law. +// An interaction was declared that claims e_0890 modifies r_0362, but e_0890 does not appear in r_0362's kinetic law. +// An interaction was declared that claims e_0142 modifies r_0362, but e_0142 does not appear in r_0362's kinetic law. +// An interaction was declared that claims e_0089 modifies r_0364, but e_0089 does not appear in r_0364's kinetic law. +// An interaction was declared that claims e_0405 modifies r_0366, but e_0405 does not appear in r_0366's kinetic law. +// An interaction was declared that claims e_0454 modifies r_0366, but e_0454 does not appear in r_0366's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0386, but e_0808 does not appear in r_0386's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0386, but e_0365 does not appear in r_0386's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0386, but e_0586 does not appear in r_0386's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0386, but e_0934 does not appear in r_0386's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0387, but e_0808 does not appear in r_0387's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0387, but e_0365 does not appear in r_0387's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0387, but e_0586 does not appear in r_0387's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0387, but e_0934 does not appear in r_0387's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0389, but e_0808 does not appear in r_0389's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0389, but e_0365 does not appear in r_0389's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0389, but e_0586 does not appear in r_0389's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0389, but e_0934 does not appear in r_0389's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0391, but e_0808 does not appear in r_0391's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0391, but e_0365 does not appear in r_0391's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0391, but e_0586 does not appear in r_0391's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0391, but e_0934 does not appear in r_0391's kinetic law. +// An interaction was declared that claims e_0128 modifies r_0393, but e_0128 does not appear in r_0393's kinetic law. +// An interaction was declared that claims e_0117 modifies r_0393, but e_0117 does not appear in r_0393's kinetic law. +// An interaction was declared that claims e_0687 modifies r_0393, but e_0687 does not appear in r_0393's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0397, but e_0808 does not appear in r_0397's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0397, but e_0365 does not appear in r_0397's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0397, but e_0586 does not appear in r_0397's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0397, but e_0934 does not appear in r_0397's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0398, but e_0808 does not appear in r_0398's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0398, but e_0365 does not appear in r_0398's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0398, but e_0586 does not appear in r_0398's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0398, but e_0934 does not appear in r_0398's kinetic law. +// An interaction was declared that claims e_0273 modifies r_0399, but e_0273 does not appear in r_0399's kinetic law. +// An interaction was declared that claims e_0273 modifies r_0400, but e_0273 does not appear in r_0400's kinetic law. +// An interaction was declared that claims e_0750 modifies r_0407, but e_0750 does not appear in r_0407's kinetic law. +// An interaction was declared that claims e_0889 modifies r_0407, but e_0889 does not appear in r_0407's kinetic law. +// An interaction was declared that claims e_0462 modifies r_0407, but e_0462 does not appear in r_0407's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0432, but e_0808 does not appear in r_0432's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0432, but e_0365 does not appear in r_0432's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0432, but e_0586 does not appear in r_0432's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0432, but e_0934 does not appear in r_0432's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0433, but e_0808 does not appear in r_0433's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0433, but e_0365 does not appear in r_0433's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0433, but e_0586 does not appear in r_0433's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0433, but e_0934 does not appear in r_0433's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0434, but e_0808 does not appear in r_0434's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0434, but e_0365 does not appear in r_0434's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0434, but e_0586 does not appear in r_0434's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0434, but e_0934 does not appear in r_0434's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0435, but e_0808 does not appear in r_0435's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0435, but e_0365 does not appear in r_0435's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0435, but e_0586 does not appear in r_0435's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0435, but e_0934 does not appear in r_0435's kinetic law. +// An interaction was declared that claims e_0632 modifies r_0438, but e_0632 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0007 modifies r_0438, but e_0007 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0774 modifies r_0438, but e_0774 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0436 modifies r_0438, but e_0436 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0136 modifies r_0438, but e_0136 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0001 modifies r_0438, but e_0001 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0347 modifies r_0438, but e_0347 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0255 modifies r_0438, but e_0255 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0752 modifies r_0438, but e_0752 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0690 modifies r_0438, but e_0690 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0006 modifies r_0438, but e_0006 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0531 modifies r_0438, but e_0531 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0346 modifies r_0438, but e_0346 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0475 modifies r_0438, but e_0475 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0514 modifies r_0439, but e_0514 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0978 modifies r_0439, but e_0978 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0422 modifies r_0439, but e_0422 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0250 modifies r_0439, but e_0250 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0004 modifies r_0439, but e_0004 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0243 modifies r_0439, but e_0243 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0389 modifies r_0439, but e_0389 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0255 modifies r_0439, but e_0255 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0848 modifies r_0439, but e_0848 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0028 modifies r_0439, but e_0028 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0531 modifies r_0439, but e_0531 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0322 modifies r_0439, but e_0322 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0396 modifies r_0446, but e_0396 does not appear in r_0446's kinetic law. +// An interaction was declared that claims e_0057 modifies r_0446, but e_0057 does not appear in r_0446's kinetic law. +// An interaction was declared that claims e_0567 modifies r_0450, but e_0567 does not appear in r_0450's kinetic law. +// An interaction was declared that claims e_0940 modifies r_0451, but e_0940 does not appear in r_0451's kinetic law. +// An interaction was declared that claims e_0515 modifies r_0462, but e_0515 does not appear in r_0462's kinetic law. +// An interaction was declared that claims e_0079 modifies r_0467, but e_0079 does not appear in r_0467's kinetic law. +// An interaction was declared that claims e_0160 modifies r_0470, but e_0160 does not appear in r_0470's kinetic law. +// An interaction was declared that claims e_0016 modifies r_0471, but e_0016 does not appear in r_0471's kinetic law. +// An interaction was declared that claims e_0899 modifies r_0471, but e_0899 does not appear in r_0471's kinetic law. +// An interaction was declared that claims e_0955 modifies r_0476, but e_0955 does not appear in r_0476's kinetic law. +// An interaction was declared that claims e_0867 modifies r_0478, but e_0867 does not appear in r_0478's kinetic law. +// An interaction was declared that claims e_0353 modifies r_0479, but e_0353 does not appear in r_0479's kinetic law. +// An interaction was declared that claims e_0242 modifies r_0481, but e_0242 does not appear in r_0481's kinetic law. +// An interaction was declared that claims e_0104 modifies r_0481, but e_0104 does not appear in r_0481's kinetic law. +// An interaction was declared that claims e_0181 modifies r_0481, but e_0181 does not appear in r_0481's kinetic law. +// An interaction was declared that claims e_0304 modifies r_0481, but e_0304 does not appear in r_0481's kinetic law. +// An interaction was declared that claims e_0915 modifies r_0481, but e_0915 does not appear in r_0481's kinetic law. +// An interaction was declared that claims e_0910 modifies r_0481, but e_0910 does not appear in r_0481's kinetic law. +// An interaction was declared that claims e_0242 modifies r_0483, but e_0242 does not appear in r_0483's kinetic law. +// An interaction was declared that claims e_0563 modifies r_0483, but e_0563 does not appear in r_0483's kinetic law. +// An interaction was declared that claims e_0086 modifies r_0483, but e_0086 does not appear in r_0483's kinetic law. +// An interaction was declared that claims e_0104 modifies r_0483, but e_0104 does not appear in r_0483's kinetic law. +// An interaction was declared that claims e_0490 modifies r_0483, but e_0490 does not appear in r_0483's kinetic law. +// An interaction was declared that claims e_0910 modifies r_0483, but e_0910 does not appear in r_0483's kinetic law. +// An interaction was declared that claims e_0392 modifies r_0486, but e_0392 does not appear in r_0486's kinetic law. +// An interaction was declared that claims e_0495 modifies r_0486, but e_0495 does not appear in r_0486's kinetic law. +// An interaction was declared that claims e_0525 modifies r_0486, but e_0525 does not appear in r_0486's kinetic law. +// An interaction was declared that claims e_0129 modifies r_0491, but e_0129 does not appear in r_0491's kinetic law. +// An interaction was declared that claims e_0827 modifies r_0491, but e_0827 does not appear in r_0491's kinetic law. +// An interaction was declared that claims e_0020 modifies r_0495, but e_0020 does not appear in r_0495's kinetic law. +// An interaction was declared that claims e_0607 modifies r_0495, but e_0607 does not appear in r_0495's kinetic law. +// An interaction was declared that claims e_0231 modifies r_0499, but e_0231 does not appear in r_0499's kinetic law. +// An interaction was declared that claims e_0741 modifies r_0501, but e_0741 does not appear in r_0501's kinetic law. +// An interaction was declared that claims e_0012 modifies r_0501, but e_0012 does not appear in r_0501's kinetic law. +// An interaction was declared that claims e_0167 modifies r_0501, but e_0167 does not appear in r_0501's kinetic law. +// An interaction was declared that claims e_0311 modifies r_0501, but e_0311 does not appear in r_0501's kinetic law. +// An interaction was declared that claims e_0638 modifies r_0502, but e_0638 does not appear in r_0502's kinetic law. +// An interaction was declared that claims e_0091 modifies r_0502, but e_0091 does not appear in r_0502's kinetic law. +// An interaction was declared that claims e_0667 modifies r_0510, but e_0667 does not appear in r_0510's kinetic law. +// An interaction was declared that claims e_0510 modifies r_0510, but e_0510 does not appear in r_0510's kinetic law. +// An interaction was declared that claims e_0317 modifies r_0510, but e_0317 does not appear in r_0510's kinetic law. +// An interaction was declared that claims e_0603 modifies r_0510, but e_0603 does not appear in r_0510's kinetic law. +// An interaction was declared that claims e_0064 modifies r_0512, but e_0064 does not appear in r_0512's kinetic law. +// An interaction was declared that claims e_0963 modifies r_0512, but e_0963 does not appear in r_0512's kinetic law. +// An interaction was declared that claims e_0746 modifies r_0514, but e_0746 does not appear in r_0514's kinetic law. +// An interaction was declared that claims e_0025 modifies r_0525, but e_0025 does not appear in r_0525's kinetic law. +// An interaction was declared that claims e_0234 modifies r_0528, but e_0234 does not appear in r_0528's kinetic law. +// An interaction was declared that claims e_0234 modifies r_0529, but e_0234 does not appear in r_0529's kinetic law. +// An interaction was declared that claims e_0106 modifies r_0534, but e_0106 does not appear in r_0534's kinetic law. +// An interaction was declared that claims e_0325 modifies r_0534, but e_0325 does not appear in r_0534's kinetic law. +// An interaction was declared that claims e_0355 modifies r_0534, but e_0355 does not appear in r_0534's kinetic law. +// An interaction was declared that claims e_0103 modifies r_0536, but e_0103 does not appear in r_0536's kinetic law. +// An interaction was declared that claims e_0320 modifies r_0537, but e_0320 does not appear in r_0537's kinetic law. +// An interaction was declared that claims e_0476 modifies r_0538, but e_0476 does not appear in r_0538's kinetic law. +// An interaction was declared that claims e_0953 modifies r_0539, but e_0953 does not appear in r_0539's kinetic law. +// An interaction was declared that claims e_0196 modifies r_0542, but e_0196 does not appear in r_0542's kinetic law. +// An interaction was declared that claims e_0154 modifies r_0543, but e_0154 does not appear in r_0543's kinetic law. +// An interaction was declared that claims e_0146 modifies r_0543, but e_0146 does not appear in r_0543's kinetic law. +// An interaction was declared that claims e_0472 modifies r_0545, but e_0472 does not appear in r_0545's kinetic law. +// An interaction was declared that claims e_0548 modifies r_0547, but e_0548 does not appear in r_0547's kinetic law. +// An interaction was declared that claims e_0428 modifies r_0548, but e_0428 does not appear in r_0548's kinetic law. +// An interaction was declared that claims e_0799 modifies r_0549, but e_0799 does not appear in r_0549's kinetic law. +// An interaction was declared that claims e_0633 modifies r_0550, but e_0633 does not appear in r_0550's kinetic law. +// An interaction was declared that claims e_0398 modifies r_0550, but e_0398 does not appear in r_0550's kinetic law. +// An interaction was declared that claims e_0233 modifies r_0550, but e_0233 does not appear in r_0550's kinetic law. +// An interaction was declared that claims e_0463 modifies r_0550, but e_0463 does not appear in r_0550's kinetic law. +// An interaction was declared that claims e_0645 modifies r_0550, but e_0645 does not appear in r_0550's kinetic law. +// An interaction was declared that claims e_0029 modifies r_0550, but e_0029 does not appear in r_0550's kinetic law. +// An interaction was declared that claims e_0124 modifies r_0550, but e_0124 does not appear in r_0550's kinetic law. +// An interaction was declared that claims e_0697 modifies r_0558, but e_0697 does not appear in r_0558's kinetic law. +// An interaction was declared that claims e_0708 modifies r_0558, but e_0708 does not appear in r_0558's kinetic law. +// An interaction was declared that claims e_0716 modifies r_0559, but e_0716 does not appear in r_0559's kinetic law. +// An interaction was declared that claims e_0087 modifies r_0563, but e_0087 does not appear in r_0563's kinetic law. +// An interaction was declared that claims e_0875 modifies r_0564, but e_0875 does not appear in r_0564's kinetic law. +// An interaction was declared that claims e_0705 modifies r_0565, but e_0705 does not appear in r_0565's kinetic law. +// An interaction was declared that claims e_0458 modifies r_0565, but e_0458 does not appear in r_0565's kinetic law. +// An interaction was declared that claims e_0693 modifies r_0565, but e_0693 does not appear in r_0565's kinetic law. +// An interaction was declared that claims e_0591 modifies r_0566, but e_0591 does not appear in r_0566's kinetic law. +// An interaction was declared that claims e_0038 modifies r_0568, but e_0038 does not appear in r_0568's kinetic law. +// An interaction was declared that claims e_0754 modifies r_0568, but e_0754 does not appear in r_0568's kinetic law. +// An interaction was declared that claims e_0631 modifies r_0570, but e_0631 does not appear in r_0570's kinetic law. +// An interaction was declared that claims e_0736 modifies r_0570, but e_0736 does not appear in r_0570's kinetic law. +// An interaction was declared that claims e_0557 modifies r_0594, but e_0557 does not appear in r_0594's kinetic law. +// An interaction was declared that claims e_0220 modifies r_0594, but e_0220 does not appear in r_0594's kinetic law. +// An interaction was declared that claims e_0862 modifies r_0658, but e_0862 does not appear in r_0658's kinetic law. +// An interaction was declared that claims e_0771 modifies r_0658, but e_0771 does not appear in r_0658's kinetic law. +// An interaction was declared that claims e_0769 modifies r_0661, but e_0769 does not appear in r_0661's kinetic law. +// An interaction was declared that claims e_0135 modifies r_0661, but e_0135 does not appear in r_0661's kinetic law. +// An interaction was declared that claims e_0550 modifies r_0663, but e_0550 does not appear in r_0663's kinetic law. +// An interaction was declared that claims e_0457 modifies r_0663, but e_0457 does not appear in r_0663's kinetic law. +// An interaction was declared that claims e_0031 modifies r_0665, but e_0031 does not appear in r_0665's kinetic law. +// An interaction was declared that claims e_0922 modifies r_0667, but e_0922 does not appear in r_0667's kinetic law. +// An interaction was declared that claims e_0685 modifies r_0669, but e_0685 does not appear in r_0669's kinetic law. +// An interaction was declared that claims e_0642 modifies r_0674, but e_0642 does not appear in r_0674's kinetic law. +// An interaction was declared that claims e_0062 modifies r_0678, but e_0062 does not appear in r_0678's kinetic law. +// An interaction was declared that claims e_0343 modifies r_0678, but e_0343 does not appear in r_0678's kinetic law. +// An interaction was declared that claims e_0440 modifies r_0698, but e_0440 does not appear in r_0698's kinetic law. +// An interaction was declared that claims e_0550 modifies r_0699, but e_0550 does not appear in r_0699's kinetic law. +// An interaction was declared that claims e_0457 modifies r_0699, but e_0457 does not appear in r_0699's kinetic law. +// An interaction was declared that claims e_0926 modifies r_0701, but e_0926 does not appear in r_0701's kinetic law. +// An interaction was declared that claims e_0171 modifies r_0711, but e_0171 does not appear in r_0711's kinetic law. +// An interaction was declared that claims e_0571 modifies r_0713, but e_0571 does not appear in r_0713's kinetic law. +// An interaction was declared that claims e_0838 modifies r_0713, but e_0838 does not appear in r_0713's kinetic law. +// An interaction was declared that claims e_0137 modifies r_0713, but e_0137 does not appear in r_0713's kinetic law. +// An interaction was declared that claims e_0134 modifies r_0722, but e_0134 does not appear in r_0722's kinetic law. +// An interaction was declared that claims e_0269 modifies r_0723, but e_0269 does not appear in r_0723's kinetic law. +// An interaction was declared that claims e_0057 modifies r_0724, but e_0057 does not appear in r_0724's kinetic law. +// An interaction was declared that claims e_0396 modifies r_0724, but e_0396 does not appear in r_0724's kinetic law. +// An interaction was declared that claims e_0239 modifies r_0726, but e_0239 does not appear in r_0726's kinetic law. +// An interaction was declared that claims e_0658 modifies r_0726, but e_0658 does not appear in r_0726's kinetic law. +// An interaction was declared that claims e_0298 modifies r_0727, but e_0298 does not appear in r_0727's kinetic law. +// An interaction was declared that claims e_0409 modifies r_0729, but e_0409 does not appear in r_0729's kinetic law. +// An interaction was declared that claims e_0610 modifies r_0731, but e_0610 does not appear in r_0731's kinetic law. +// An interaction was declared that claims e_0396 modifies r_0732, but e_0396 does not appear in r_0732's kinetic law. +// An interaction was declared that claims e_0057 modifies r_0732, but e_0057 does not appear in r_0732's kinetic law. +// An interaction was declared that claims e_0745 modifies r_0736, but e_0745 does not appear in r_0736's kinetic law. +// An interaction was declared that claims e_0812 modifies r_0739, but e_0812 does not appear in r_0739's kinetic law. +// An interaction was declared that claims e_0204 modifies r_0757, but e_0204 does not appear in r_0757's kinetic law. +// An interaction was declared that claims e_0435 modifies r_0757, but e_0435 does not appear in r_0757's kinetic law. +// An interaction was declared that claims e_0512 modifies r_0758, but e_0512 does not appear in r_0758's kinetic law. +// An interaction was declared that claims e_0290 modifies r_0759, but e_0290 does not appear in r_0759's kinetic law. +// An interaction was declared that claims e_0139 modifies r_0770, but e_0139 does not appear in r_0770's kinetic law. +// An interaction was declared that claims e_0737 modifies r_0770, but e_0737 does not appear in r_0770's kinetic law. +// An interaction was declared that claims e_0714 modifies r_0770, but e_0714 does not appear in r_0770's kinetic law. +// An interaction was declared that claims e_0271 modifies r_0792, but e_0271 does not appear in r_0792's kinetic law. +// An interaction was declared that claims e_0568 modifies r_0800, but e_0568 does not appear in r_0800's kinetic law. +// An interaction was declared that claims e_0568 modifies r_0811, but e_0568 does not appear in r_0811's kinetic law. +// An interaction was declared that claims e_0674 modifies r_0813, but e_0674 does not appear in r_0813's kinetic law. +// An interaction was declared that claims e_0499 modifies r_0816, but e_0499 does not appear in r_0816's kinetic law. +// An interaction was declared that claims e_0729 modifies r_0818, but e_0729 does not appear in r_0818's kinetic law. +// An interaction was declared that claims e_0755 modifies r_0820, but e_0755 does not appear in r_0820's kinetic law. +// An interaction was declared that claims e_0712 modifies r_0820, but e_0712 does not appear in r_0820's kinetic law. +// An interaction was declared that claims e_0249 modifies r_0821, but e_0249 does not appear in r_0821's kinetic law. +// An interaction was declared that claims e_0348 modifies r_0851, but e_0348 does not appear in r_0851's kinetic law. +// An interaction was declared that claims e_0639 modifies r_0852, but e_0639 does not appear in r_0852's kinetic law. +// An interaction was declared that claims e_0312 modifies r_0852, but e_0312 does not appear in r_0852's kinetic law. +// An interaction was declared that claims e_0352 modifies r_0855, but e_0352 does not appear in r_0855's kinetic law. +// An interaction was declared that claims e_0536 modifies r_0858, but e_0536 does not appear in r_0858's kinetic law. +// An interaction was declared that claims e_0381 modifies r_0858, but e_0381 does not appear in r_0858's kinetic law. +// An interaction was declared that claims e_0964 modifies r_0874, but e_0964 does not appear in r_0874's kinetic law. +// An interaction was declared that claims e_0788 modifies r_0877, but e_0788 does not appear in r_0877's kinetic law. +// An interaction was declared that claims e_0382 modifies r_0877, but e_0382 does not appear in r_0877's kinetic law. +// An interaction was declared that claims e_0278 modifies r_0880, but e_0278 does not appear in r_0880's kinetic law. +// An interaction was declared that claims e_0633 modifies r_0883, but e_0633 does not appear in r_0883's kinetic law. +// An interaction was declared that claims e_0975 modifies r_0883, but e_0975 does not appear in r_0883's kinetic law. +// An interaction was declared that claims e_0398 modifies r_0883, but e_0398 does not appear in r_0883's kinetic law. +// An interaction was declared that claims e_0401 modifies r_0886, but e_0401 does not appear in r_0886's kinetic law. +// An interaction was declared that claims e_0743 modifies r_0886, but e_0743 does not appear in r_0886's kinetic law. +// An interaction was declared that claims e_0576 modifies r_0888, but e_0576 does not appear in r_0888's kinetic law. +// An interaction was declared that claims e_0757 modifies r_0888, but e_0757 does not appear in r_0888's kinetic law. +// An interaction was declared that claims e_0733 modifies r_0888, but e_0733 does not appear in r_0888's kinetic law. +// An interaction was declared that claims e_0294 modifies r_0891, but e_0294 does not appear in r_0891's kinetic law. +// An interaction was declared that claims e_0469 modifies r_0891, but e_0469 does not appear in r_0891's kinetic law. +// An interaction was declared that claims e_0113 modifies r_0892, but e_0113 does not appear in r_0892's kinetic law. +// An interaction was declared that claims e_0582 modifies r_0893, but e_0582 does not appear in r_0893's kinetic law. +// An interaction was declared that claims e_0536 modifies r_0900, but e_0536 does not appear in r_0900's kinetic law. +// An interaction was declared that claims e_0536 modifies r_0901, but e_0536 does not appear in r_0901's kinetic law. +// An interaction was declared that claims e_0314 modifies r_0902, but e_0314 does not appear in r_0902's kinetic law. +// An interaction was declared that claims e_0747 modifies r_0904, but e_0747 does not appear in r_0904's kinetic law. +// An interaction was declared that claims e_0017 modifies r_0908, but e_0017 does not appear in r_0908's kinetic law. +// An interaction was declared that claims e_0103 modifies r_0909, but e_0103 does not appear in r_0909's kinetic law. +// An interaction was declared that claims e_0103 modifies r_0910, but e_0103 does not appear in r_0910's kinetic law. +// An interaction was declared that claims e_0860 modifies r_0911, but e_0860 does not appear in r_0911's kinetic law. +// An interaction was declared that claims e_0631 modifies r_0912, but e_0631 does not appear in r_0912's kinetic law. +// An interaction was declared that claims e_0736 modifies r_0912, but e_0736 does not appear in r_0912's kinetic law. +// An interaction was declared that claims e_0165 modifies r_0913, but e_0165 does not appear in r_0913's kinetic law. +// An interaction was declared that claims e_0352 modifies r_0914, but e_0352 does not appear in r_0914's kinetic law. +// An interaction was declared that claims e_0763 modifies r_0915, but e_0763 does not appear in r_0915's kinetic law. +// An interaction was declared that claims e_0030 modifies r_0916, but e_0030 does not appear in r_0916's kinetic law. +// An interaction was declared that claims e_0299 modifies r_0916, but e_0299 does not appear in r_0916's kinetic law. +// An interaction was declared that claims e_0418 modifies r_0916, but e_0418 does not appear in r_0916's kinetic law. +// An interaction was declared that claims e_0585 modifies r_0916, but e_0585 does not appear in r_0916's kinetic law. +// An interaction was declared that claims e_0829 modifies r_0916, but e_0829 does not appear in r_0916's kinetic law. +// An interaction was declared that claims e_0397 modifies r_0917, but e_0397 does not appear in r_0917's kinetic law. +// An interaction was declared that claims e_0872 modifies r_0918, but e_0872 does not appear in r_0918's kinetic law. +// An interaction was declared that claims e_0077 modifies r_0919, but e_0077 does not appear in r_0919's kinetic law. +// An interaction was declared that claims e_0206 modifies r_0922, but e_0206 does not appear in r_0922's kinetic law. +// An interaction was declared that claims e_0802 modifies r_0938, but e_0802 does not appear in r_0938's kinetic law. +// An interaction was declared that claims e_0074 modifies r_0939, but e_0074 does not appear in r_0939's kinetic law. +// An interaction was declared that claims e_0296 modifies r_0941, but e_0296 does not appear in r_0941's kinetic law. +// An interaction was declared that claims e_0276 modifies r_0957, but e_0276 does not appear in r_0957's kinetic law. +// An interaction was declared that claims e_0334 modifies r_0958, but e_0334 does not appear in r_0958's kinetic law. +// An interaction was declared that claims e_0084 modifies r_0958, but e_0084 does not appear in r_0958's kinetic law. +// An interaction was declared that claims e_0085 modifies r_0961, but e_0085 does not appear in r_0961's kinetic law. +// An interaction was declared that claims e_0306 modifies r_0961, but e_0306 does not appear in r_0961's kinetic law. +// An interaction was declared that claims e_0393 modifies r_0961, but e_0393 does not appear in r_0961's kinetic law. +// An interaction was declared that claims e_0311 modifies r_0961, but e_0311 does not appear in r_0961's kinetic law. +// An interaction was declared that claims e_0775 modifies r_0961, but e_0775 does not appear in r_0961's kinetic law. +// An interaction was declared that claims e_0011 modifies r_0962, but e_0011 does not appear in r_0962's kinetic law. +// An interaction was declared that claims e_0895 modifies r_0962, but e_0895 does not appear in r_0962's kinetic law. +// An interaction was declared that claims e_0841 modifies r_0967, but e_0841 does not appear in r_0967's kinetic law. +// An interaction was declared that claims e_0090 modifies r_0968, but e_0090 does not appear in r_0968's kinetic law. +// An interaction was declared that claims e_0398 modifies r_0970, but e_0398 does not appear in r_0970's kinetic law. +// An interaction was declared that claims e_0398 modifies r_0973, but e_0398 does not appear in r_0973's kinetic law. +// An interaction was declared that claims e_0467 modifies r_0974, but e_0467 does not appear in r_0974's kinetic law. +// An interaction was declared that claims e_0492 modifies r_0974, but e_0492 does not appear in r_0974's kinetic law. +// An interaction was declared that claims e_0387 modifies r_0974, but e_0387 does not appear in r_0974's kinetic law. +// An interaction was declared that claims e_0291 modifies r_0974, but e_0291 does not appear in r_0974's kinetic law. +// An interaction was declared that claims e_0467 modifies r_0976, but e_0467 does not appear in r_0976's kinetic law. +// An interaction was declared that claims e_0492 modifies r_0976, but e_0492 does not appear in r_0976's kinetic law. +// An interaction was declared that claims e_0387 modifies r_0976, but e_0387 does not appear in r_0976's kinetic law. +// An interaction was declared that claims e_0291 modifies r_0976, but e_0291 does not appear in r_0976's kinetic law. +// An interaction was declared that claims e_0467 modifies r_0978, but e_0467 does not appear in r_0978's kinetic law. +// An interaction was declared that claims e_0492 modifies r_0978, but e_0492 does not appear in r_0978's kinetic law. +// An interaction was declared that claims e_0387 modifies r_0978, but e_0387 does not appear in r_0978's kinetic law. +// An interaction was declared that claims e_0291 modifies r_0978, but e_0291 does not appear in r_0978's kinetic law. +// An interaction was declared that claims e_0852 modifies r_0982, but e_0852 does not appear in r_0982's kinetic law. +// An interaction was declared that claims e_0506 modifies r_0984, but e_0506 does not appear in r_0984's kinetic law. +// An interaction was declared that claims e_0699 modifies r_0986, but e_0699 does not appear in r_0986's kinetic law. +// An interaction was declared that claims e_0489 modifies r_0988, but e_0489 does not appear in r_0988's kinetic law. +// An interaction was declared that claims e_0813 modifies r_0989, but e_0813 does not appear in r_0989's kinetic law. +// An interaction was declared that claims e_0054 modifies r_0993, but e_0054 does not appear in r_0993's kinetic law. +// An interaction was declared that claims e_0177 modifies r_0993, but e_0177 does not appear in r_0993's kinetic law. +// An interaction was declared that claims e_0761 modifies r_0993, but e_0761 does not appear in r_0993's kinetic law. +// An interaction was declared that claims e_0168 modifies r_0995, but e_0168 does not appear in r_0995's kinetic law. +// An interaction was declared that claims e_0425 modifies r_0995, but e_0425 does not appear in r_0995's kinetic law. +// An interaction was declared that claims e_0182 modifies r_0996, but e_0182 does not appear in r_0996's kinetic law. +// An interaction was declared that claims e_0182 modifies r_0997, but e_0182 does not appear in r_0997's kinetic law. +// An interaction was declared that claims e_0385 modifies r_1010, but e_0385 does not appear in r_1010's kinetic law. +// An interaction was declared that claims e_0385 modifies r_1011, but e_0385 does not appear in r_1011's kinetic law. +// An interaction was declared that claims e_0456 modifies r_1012, but e_0456 does not appear in r_1012's kinetic law. +// An interaction was declared that claims e_0578 modifies r_1014, but e_0578 does not appear in r_1014's kinetic law. +// An interaction was declared that claims e_0613 modifies r_1014, but e_0613 does not appear in r_1014's kinetic law. +// An interaction was declared that claims e_0107 modifies r_1026, but e_0107 does not appear in r_1026's kinetic law. +// An interaction was declared that claims e_0547 modifies r_1027, but e_0547 does not appear in r_1027's kinetic law. +// An interaction was declared that claims e_0321 modifies r_1027, but e_0321 does not appear in r_1027's kinetic law. +// An interaction was declared that claims e_0633 modifies r_1038, but e_0633 does not appear in r_1038's kinetic law. +// An interaction was declared that claims e_0218 modifies r_1038, but e_0218 does not appear in r_1038's kinetic law. +// An interaction was declared that claims e_0398 modifies r_1038, but e_0398 does not appear in r_1038's kinetic law. +// An interaction was declared that claims e_0448 modifies r_1038, but e_0448 does not appear in r_1038's kinetic law. +// An interaction was declared that claims e_0915 modifies r_1038, but e_0915 does not appear in r_1038's kinetic law. +// An interaction was declared that claims e_0124 modifies r_1038, but e_0124 does not appear in r_1038's kinetic law. +// An interaction was declared that claims e_0122 modifies r_1041, but e_0122 does not appear in r_1041's kinetic law. +// An interaction was declared that claims e_0470 modifies r_1042, but e_0470 does not appear in r_1042's kinetic law. +// An interaction was declared that claims e_0850 modifies r_1045, but e_0850 does not appear in r_1045's kinetic law. +// An interaction was declared that claims e_0684 modifies r_1048, but e_0684 does not appear in r_1048's kinetic law. +// An interaction was declared that claims e_0063 modifies r_1049, but e_0063 does not appear in r_1049's kinetic law. +// An interaction was declared that claims e_0962 modifies r_1049, but e_0962 does not appear in r_1049's kinetic law. +// An interaction was declared that claims e_0063 modifies r_1050, but e_0063 does not appear in r_1050's kinetic law. +// An interaction was declared that claims e_0962 modifies r_1050, but e_0962 does not appear in r_1050's kinetic law. +// An interaction was declared that claims e_0711 modifies r_1051, but e_0711 does not appear in r_1051's kinetic law. +// An interaction was declared that claims e_0065 modifies r_1051, but e_0065 does not appear in r_1051's kinetic law. +// An interaction was declared that claims e_0179 modifies r_1051, but e_0179 does not appear in r_1051's kinetic law. +// An interaction was declared that claims e_0753 modifies r_1051, but e_0753 does not appear in r_1051's kinetic law. +// An interaction was declared that claims e_0176 modifies r_1052, but e_0176 does not appear in r_1052's kinetic law. +// An interaction was declared that claims e_0611 modifies r_1052, but e_0611 does not appear in r_1052's kinetic law. +// An interaction was declared that claims e_0765 modifies r_1052, but e_0765 does not appear in r_1052's kinetic law. +// An interaction was declared that claims e_0851 modifies r_1052, but e_0851 does not appear in r_1052's kinetic law. +// An interaction was declared that claims e_0175 modifies r_1054, but e_0175 does not appear in r_1054's kinetic law. +// An interaction was declared that claims e_0330 modifies r_1055, but e_0330 does not appear in r_1055's kinetic law. +// An interaction was declared that claims e_0836 modifies r_1057, but e_0836 does not appear in r_1057's kinetic law. +// An interaction was declared that claims e_0348 modifies r_1063, but e_0348 does not appear in r_1063's kinetic law. +// An interaction was declared that claims e_0629 modifies r_1063, but e_0629 does not appear in r_1063's kinetic law. +// An interaction was declared that claims e_0390 modifies r_1066, but e_0390 does not appear in r_1066's kinetic law. +// An interaction was declared that claims e_0561 modifies r_1072, but e_0561 does not appear in r_1072's kinetic law. +// An interaction was declared that claims e_0565 modifies r_1084, but e_0565 does not appear in r_1084's kinetic law. +// An interaction was declared that claims e_0550 modifies r_1087, but e_0550 does not appear in r_1087's kinetic law. +// An interaction was declared that claims e_0457 modifies r_1087, but e_0457 does not appear in r_1087's kinetic law. +// An interaction was declared that claims e_0372 modifies r_1089, but e_0372 does not appear in r_1089's kinetic law. + model *MODEL1302140003() // Compartments and Species: @@ -453,6 +917,469 @@ model *MODEL1302140003() r_2030: s_0313 -> s_0314 + s_1322; cell*r_2030_v0*(1 + r_2030_ep0313*ln(s_0313/ic0313) + r_2030_ep0314*ln(s_0314/ic0314) + r_2030_ep1322*ln(s_1322/ic1322)); r_2111: 1.1348 s_0002 + 0.046 s_0423 + 59.276 s_0434 + 0.0447 s_0526 + 0.0036 s_0584 + 0.0024 s_0589 + 0.0024 s_0615 + 0.0036 s_0649 + 0.5185 s_0773 + 0.046 s_0782 + 0.8079 s_1107 + 0.00099 s_1405 + 0.02 s_1467 + 0.0234 s_1520 + 0.0599 s_1545 + 1.1348 s_0004 + 0.4588 s_0404 + 0.1607 s_0428 + 0.1017 s_0430 + 0.2975 s_0432 + 0.0066 s_0542 + 0.1054 s_0747 + 0.3018 s_0748 + 0.2904 s_0757 + 0.0663 s_0832 + 0.1927 s_0847 + 0.2964 s_1077 + 0.2862 s_1099 + 0.0507 s_1148 + 0.1339 s_1314 + 0.1647 s_1379 + 0.00039 s_1337 + 0.001583 s_0089 + 0.1854 s_1428 + 0.1914 s_1491 + 0.0284 s_1527 + 0.102 s_1533 + 0.2646 s_1561 + 5.6e-05 s_0122 + 0.000538625 s_0918 + 9.6e-05 s_0657 + 0.000125 s_0662 + 0.0056 s_0666 + 0.000812 s_0672 + 0.000892667 s_0056 + 0.000114 s_0700 + 3.2e-05 s_1059 + 0.00288 s_1346 + 0.000697 s_1351 + 0.000781 s_1524 + 1.5e-05 s_1569 => 59.276 s_0394 + 58.7 s_1322 + 0.4588 s_1582 + 0.1607 s_1583 + 0.1017 s_1585 + 0.2975 s_1587 + 0.0066 s_1589 + 0.1054 s_1590 + 0.3018 s_1591 + 0.2904 s_1593 + 0.0663 s_1594 + 0.1927 s_1596 + 0.2964 s_1598 + 0.2862 s_1600 + 0.0507 s_1602 + 0.1339 s_1604 + 0.1647 s_1606 + 0.1854 s_1607 + 0.1914 s_1608 + 0.0284 s_1610 + 0.102 s_1612 + 0.2646 s_1614; cell*((r_2111_v0*(1 + r_2111_ep0002*ln(s_0002/ic0002) + r_2111_ep0423*ln(s_0423/ic0423) + r_2111_ep0434*ln(s_0434/ic0434) + r_2111_ep0526*ln(s_0526/ic0526) + r_2111_ep0584*ln(s_0584/ic0584) + r_2111_ep0589*ln(s_0589/ic0589) + r_2111_ep0615*ln(s_0615/ic0615) + r_2111_ep0649*ln(s_0649/ic0649) + r_2111_ep0773*ln(s_0773/ic0773) + r_2111_ep0782*ln(s_0782/ic0782) + r_2111_ep1107*ln(s_1107/ic1107) + r_2111_ep1405*ln(s_1405/ic1405) + r_2111_ep1467*ln(s_1467/ic1467) + r_2111_ep1520*ln(s_1520/ic1520) + r_2111_ep1545*ln(s_1545/ic1545) + r_2111_ep0004*ln(s_0004/ic0004) + r_2111_ep0404*ln(s_0404/ic0404) + r_2111_ep0428*ln(s_0428/ic0428) + r_2111_ep0430*ln(s_0430/ic0430) + r_2111_ep0432*ln(s_0432/ic0432) + r_2111_ep0542*ln(s_0542/ic0542) + r_2111_ep0747*ln(s_0747/ic0747) + r_2111_ep0748*ln(s_0748/ic0748) + r_2111_ep0757*ln(s_0757/ic0757) + r_2111_ep0832*ln(s_0832/ic0832) + r_2111_ep0847*ln(s_0847/ic0847) + r_2111_ep1077*ln(s_1077/ic1077) + r_2111_ep1099*ln(s_1099/ic1099) + r_2111_ep1148*ln(s_1148/ic1148) + r_2111_ep1314*ln(s_1314/ic1314) + r_2111_ep1379*ln(s_1379/ic1379) + r_2111_ep1337*ln(s_1337/ic1337) + r_2111_ep0089*ln(s_0089/ic0089) + r_2111_ep1428*ln(s_1428/ic1428) + r_2111_ep1491*ln(s_1491/ic1491) + r_2111_ep1527*ln(s_1527/ic1527) + r_2111_ep1533*ln(s_1533/ic1533) + r_2111_ep1561*ln(s_1561/ic1561) + r_2111_ep0122*ln(s_0122/ic0122) + r_2111_ep0918*ln(s_0918/ic0918) + r_2111_ep0657*ln(s_0657/ic0657) + r_2111_ep0662*ln(s_0662/ic0662) + r_2111_ep0666*ln(s_0666/ic0666) + r_2111_ep0672*ln(s_0672/ic0672) + r_2111_ep0056*ln(s_0056/ic0056) + r_2111_ep0700*ln(s_0700/ic0700) + r_2111_ep1059*ln(s_1059/ic1059) + r_2111_ep1346*ln(s_1346/ic1346) + r_2111_ep1351*ln(s_1351/ic1351) + r_2111_ep1524*ln(s_1524/ic1524) + r_2111_ep1569*ln(s_1569/ic1569)) + zero_flux + abs(r_2111_v0*(1 + r_2111_ep0002*ln(s_0002/ic0002) + r_2111_ep0423*ln(s_0423/ic0423) + r_2111_ep0434*ln(s_0434/ic0434) + r_2111_ep0526*ln(s_0526/ic0526) + r_2111_ep0584*ln(s_0584/ic0584) + r_2111_ep0589*ln(s_0589/ic0589) + r_2111_ep0615*ln(s_0615/ic0615) + r_2111_ep0649*ln(s_0649/ic0649) + r_2111_ep0773*ln(s_0773/ic0773) + r_2111_ep0782*ln(s_0782/ic0782) + r_2111_ep1107*ln(s_1107/ic1107) + r_2111_ep1405*ln(s_1405/ic1405) + r_2111_ep1467*ln(s_1467/ic1467) + r_2111_ep1520*ln(s_1520/ic1520) + r_2111_ep1545*ln(s_1545/ic1545) + r_2111_ep0004*ln(s_0004/ic0004) + r_2111_ep0404*ln(s_0404/ic0404) + r_2111_ep0428*ln(s_0428/ic0428) + r_2111_ep0430*ln(s_0430/ic0430) + r_2111_ep0432*ln(s_0432/ic0432) + r_2111_ep0542*ln(s_0542/ic0542) + r_2111_ep0747*ln(s_0747/ic0747) + r_2111_ep0748*ln(s_0748/ic0748) + r_2111_ep0757*ln(s_0757/ic0757) + r_2111_ep0832*ln(s_0832/ic0832) + r_2111_ep0847*ln(s_0847/ic0847) + r_2111_ep1077*ln(s_1077/ic1077) + r_2111_ep1099*ln(s_1099/ic1099) + r_2111_ep1148*ln(s_1148/ic1148) + r_2111_ep1314*ln(s_1314/ic1314) + r_2111_ep1379*ln(s_1379/ic1379) + r_2111_ep1337*ln(s_1337/ic1337) + r_2111_ep0089*ln(s_0089/ic0089) + r_2111_ep1428*ln(s_1428/ic1428) + r_2111_ep1491*ln(s_1491/ic1491) + r_2111_ep1527*ln(s_1527/ic1527) + r_2111_ep1533*ln(s_1533/ic1533) + r_2111_ep1561*ln(s_1561/ic1561) + r_2111_ep0122*ln(s_0122/ic0122) + r_2111_ep0918*ln(s_0918/ic0918) + r_2111_ep0657*ln(s_0657/ic0657) + r_2111_ep0662*ln(s_0662/ic0662) + r_2111_ep0666*ln(s_0666/ic0666) + r_2111_ep0672*ln(s_0672/ic0672) + r_2111_ep0056*ln(s_0056/ic0056) + r_2111_ep0700*ln(s_0700/ic0700) + r_2111_ep1059*ln(s_1059/ic1059) + r_2111_ep1346*ln(s_1346/ic1346) + r_2111_ep1351*ln(s_1351/ic1351) + r_2111_ep1524*ln(s_1524/ic1524) + r_2111_ep1569*ln(s_1569/ic1569)) - zero_flux))/2); + // Interactions: + _I0: $e_0682 -o r_0005; ; + _I1: $e_0364 -o r_0005; ; + _I2: $e_0973 -o r_0006; ; + _I3: $e_0379 -o r_0006; ; + _I4: $e_0465 -o r_0007; ; + _I5: $e_0869 -o r_0008; ; + _I6: $e_0133 -o r_0008; ; + _I7: $e_0117 -o r_0008; ; + _I8: $e_0431 -o r_0012; ; + _I9: $e_0832 -o r_0014; ; + _I10: $e_0071 -o r_0015; ; + _I11: $e_0734 -o r_0016; ; + _I12: $e_0100 -o r_0016; ; + _I13: $e_0348 -o r_0018; ; + _I14: $e_0496 -o r_0018; ; + _I15: $e_0980 -o r_0018; ; + _I16: $e_0169 -o r_0020; ; + _I17: $e_0088 -o r_0020; ; + _I18: $e_0328 -o r_0023; ; + _I19: $e_0778 -o r_0024; ; + _I20: $e_0855 -o r_0024; ; + _I21: $e_0196 -o r_0027; ; + _I22: $e_0550 -o r_0029; ; + _I23: $e_0457 -o r_0029; ; + _I24: $e_0830 -o r_0032; ; + _I25: $e_0237 -o r_0038; ; + _I26: $e_0182 -o r_0039; ; + _I27: $e_0182 -o r_0040; ; + _I28: $e_0092 -o r_0041; ; + _I29: $e_0328 -o r_0060; ; + _I30: $e_0101 -o r_0061; ; + _I31: $e_0182 -o r_0065; ; + _I32: $e_0368 -o r_0079; ; + _I33: $e_0340 -o r_0080; ; + _I34: $e_0903 -o r_0080; ; + _I35: $e_0685 -o r_0096; ; + _I36: $e_0734 -o r_0097; ; + _I37: $e_0100 -o r_0097; ; + _I38: $e_0904 -o r_0103; ; + _I39: $e_0744 -o r_0108; ; + _I40: $e_0808 -o r_0108; ; + _I41: $e_0022 -o r_0110; ; + _I42: $e_0290 -o r_0115; ; + _I43: $e_0840 -o r_0118; ; + _I44: $e_0541 -o r_0142; ; + _I45: $e_0280 -o r_0144; ; + _I46: $e_0194 -o r_0148; ; + _I47: $e_0303 -o r_0148; ; + _I48: $e_0686 -o r_0151; ; + _I49: $e_0686 -o r_0152; ; + _I50: $e_0791 -o r_0153; ; + _I51: $e_0556 -o r_0154; ; + _I52: $e_0894 -o r_0157; ; + _I53: $e_0711 -o r_0195; ; + _I54: $e_0065 -o r_0195; ; + _I55: $e_0179 -o r_0195; ; + _I56: $e_0753 -o r_0195; ; + _I57: $e_0219 -o r_0202; ; + _I58: $e_0297 -o r_0203; ; + _I59: $e_0591 -o r_0203; ; + _I60: $e_0426 -o r_0207; ; + _I61: $e_0826 -o r_0208; ; + _I62: $e_0214 -o r_0209; ; + _I63: $e_0970 -o r_0211; ; + _I64: $e_0376 -o r_0211; ; + _I65: $e_0427 -o r_0212; ; + _I66: $e_0508 -o r_0214; ; + _I67: $e_0281 -o r_0215; ; + _I68: $e_0629 -o r_0216; ; + _I69: $e_0574 -o r_0216; ; + _I70: $e_0186 -o r_0219; ; + _I71: $e_0615 -o r_0220; ; + _I72: $e_0283 -o r_0225; ; + _I73: $e_0800 -o r_0231; ; + _I74: $e_0724 -o r_0233; ; + _I75: $e_0326 -o r_0234; ; + _I76: $e_0326 -o r_0235; ; + _I77: $e_0644 -o r_0236; ; + _I78: $e_0644 -o r_0237; ; + _I79: $e_0367 -o r_0238; ; + _I80: $e_0367 -o r_0239; ; + _I81: $e_0367 -o r_0240; ; + _I82: $e_0367 -o r_0241; ; + _I83: $e_0637 -o r_0242; ; + _I84: $e_0742 -o r_0243; ; + _I85: $e_0329 -o r_0244; ; + _I86: $e_0508 -o r_0250; ; + _I87: $e_0542 -o r_0250; ; + _I88: $e_0888 -o r_0250; ; + _I89: $e_0045 -o r_0257; ; + _I90: $e_0206 -o r_0259; ; + _I91: $e_0756 -o r_0267; ; + _I92: $e_0756 -o r_0269; ; + _I93: $e_0959 -o r_0278; ; + _I94: $e_0342 -o r_0279; ; + _I95: $e_0675 -o r_0280; ; + _I96: $e_0947 -o r_0300; ; + _I97: $e_0805 -o r_0300; ; + _I98: $e_0111 -o r_0300; ; + _I99: $e_0675 -o r_0302; ; + _I100: $e_0540 -o r_0307; ; + _I101: $e_0026 -o r_0307; ; + _I102: $e_0380 -o r_0309; ; + _I103: $e_0008 -o r_0310; ; + _I104: $e_0545 -o r_0311; ; + _I105: $e_0793 -o r_0313; ; + _I106: $e_0434 -o r_0317; ; + _I107: $e_0424 -o r_0317; ; + _I108: $e_0452 -o r_0326; ; + _I109: $e_0234 -o r_0330; ; + _I110: $e_0883 -o r_0336; ; + _I111: $e_0203 -o r_0337; ; + _I112: $e_0594 -o r_0339; ; + _I113: $e_0914 -o r_0340; ; + _I114: $e_0880 -o r_0344; ; + _I115: $e_0692 -o r_0349; ; + _I116: $e_0528 -o r_0352; ; + _I117: $e_0528 -o r_0353; ; + _I118: $e_0515 -o r_0355; ; + _I119: $e_0976 -o r_0361; ; + _I120: $e_0141 -o r_0362; ; + _I121: $e_0549 -o r_0362; ; + _I122: $e_0010 -o r_0362; ; + _I123: $e_0890 -o r_0362; ; + _I124: $e_0142 -o r_0362; ; + _I125: $e_0089 -o r_0364; ; + _I126: $e_0405 -o r_0366; ; + _I127: $e_0454 -o r_0366; ; + _I128: $e_0808 -o r_0386; ; + _I129: $e_0365 -o r_0386; ; + _I130: $e_0586 -o r_0386; ; + _I131: $e_0934 -o r_0386; ; + _I132: $e_0808 -o r_0387; ; + _I133: $e_0365 -o r_0387; ; + _I134: $e_0586 -o r_0387; ; + _I135: $e_0934 -o r_0387; ; + _I136: $e_0808 -o r_0389; ; + _I137: $e_0365 -o r_0389; ; + _I138: $e_0586 -o r_0389; ; + _I139: $e_0934 -o r_0389; ; + _I140: $e_0808 -o r_0391; ; + _I141: $e_0365 -o r_0391; ; + _I142: $e_0586 -o r_0391; ; + _I143: $e_0934 -o r_0391; ; + _I144: $e_0128 -o r_0393; ; + _I145: $e_0117 -o r_0393; ; + _I146: $e_0687 -o r_0393; ; + _I147: $e_0808 -o r_0397; ; + _I148: $e_0365 -o r_0397; ; + _I149: $e_0586 -o r_0397; ; + _I150: $e_0934 -o r_0397; ; + _I151: $e_0808 -o r_0398; ; + _I152: $e_0365 -o r_0398; ; + _I153: $e_0586 -o r_0398; ; + _I154: $e_0934 -o r_0398; ; + _I155: $e_0273 -o r_0399; ; + _I156: $e_0273 -o r_0400; ; + _I157: $e_0750 -o r_0407; ; + _I158: $e_0889 -o r_0407; ; + _I159: $e_0462 -o r_0407; ; + _I160: $e_0808 -o r_0432; ; + _I161: $e_0365 -o r_0432; ; + _I162: $e_0586 -o r_0432; ; + _I163: $e_0934 -o r_0432; ; + _I164: $e_0808 -o r_0433; ; + _I165: $e_0365 -o r_0433; ; + _I166: $e_0586 -o r_0433; ; + _I167: $e_0934 -o r_0433; ; + _I168: $e_0808 -o r_0434; ; + _I169: $e_0365 -o r_0434; ; + _I170: $e_0586 -o r_0434; ; + _I171: $e_0934 -o r_0434; ; + _I172: $e_0808 -o r_0435; ; + _I173: $e_0365 -o r_0435; ; + _I174: $e_0586 -o r_0435; ; + _I175: $e_0934 -o r_0435; ; + _I176: $e_0632 -o r_0438; ; + _I177: $e_0007 -o r_0438; ; + _I178: $e_0774 -o r_0438; ; + _I179: $e_0436 -o r_0438; ; + _I180: $e_0136 -o r_0438; ; + _I181: $e_0001 -o r_0438; ; + _I182: $e_0347 -o r_0438; ; + _I183: $e_0255 -o r_0438; ; + _I184: $e_0752 -o r_0438; ; + _I185: $e_0690 -o r_0438; ; + _I186: $e_0006 -o r_0438; ; + _I187: $e_0531 -o r_0438; ; + _I188: $e_0346 -o r_0438; ; + _I189: $e_0475 -o r_0438; ; + _I190: $e_0514 -o r_0439; ; + _I191: $e_0978 -o r_0439; ; + _I192: $e_0422 -o r_0439; ; + _I193: $e_0250 -o r_0439; ; + _I194: $e_0004 -o r_0439; ; + _I195: $e_0243 -o r_0439; ; + _I196: $e_0389 -o r_0439; ; + _I197: $e_0255 -o r_0439; ; + _I198: $e_0848 -o r_0439; ; + _I199: $e_0028 -o r_0439; ; + _I200: $e_0531 -o r_0439; ; + _I201: $e_0322 -o r_0439; ; + _I202: $e_0396 -o r_0446; ; + _I203: $e_0057 -o r_0446; ; + _I204: $e_0567 -o r_0450; ; + _I205: $e_0940 -o r_0451; ; + _I206: $e_0515 -o r_0462; ; + _I207: $e_0079 -o r_0467; ; + _I208: $e_0160 -o r_0470; ; + _I209: $e_0016 -o r_0471; ; + _I210: $e_0899 -o r_0471; ; + _I211: $e_0955 -o r_0476; ; + _I212: $e_0867 -o r_0478; ; + _I213: $e_0353 -o r_0479; ; + _I214: $e_0242 -o r_0481; ; + _I215: $e_0104 -o r_0481; ; + _I216: $e_0181 -o r_0481; ; + _I217: $e_0304 -o r_0481; ; + _I218: $e_0915 -o r_0481; ; + _I219: $e_0910 -o r_0481; ; + _I220: $e_0242 -o r_0483; ; + _I221: $e_0563 -o r_0483; ; + _I222: $e_0086 -o r_0483; ; + _I223: $e_0104 -o r_0483; ; + _I224: $e_0490 -o r_0483; ; + _I225: $e_0910 -o r_0483; ; + _I226: $e_0392 -o r_0486; ; + _I227: $e_0495 -o r_0486; ; + _I228: $e_0525 -o r_0486; ; + _I229: $e_0129 -o r_0491; ; + _I230: $e_0827 -o r_0491; ; + _I231: $e_0020 -o r_0495; ; + _I232: $e_0607 -o r_0495; ; + _I233: $e_0231 -o r_0499; ; + _I234: $e_0741 -o r_0501; ; + _I235: $e_0012 -o r_0501; ; + _I236: $e_0167 -o r_0501; ; + _I237: $e_0311 -o r_0501; ; + _I238: $e_0638 -o r_0502; ; + _I239: $e_0091 -o r_0502; ; + _I240: $e_0667 -o r_0510; ; + _I241: $e_0510 -o r_0510; ; + _I242: $e_0317 -o r_0510; ; + _I243: $e_0603 -o r_0510; ; + _I244: $e_0064 -o r_0512; ; + _I245: $e_0963 -o r_0512; ; + _I246: $e_0746 -o r_0514; ; + _I247: $e_0025 -o r_0525; ; + _I248: $e_0234 -o r_0528; ; + _I249: $e_0234 -o r_0529; ; + _I250: $e_0106 -o r_0534; ; + _I251: $e_0325 -o r_0534; ; + _I252: $e_0355 -o r_0534; ; + _I253: $e_0103 -o r_0536; ; + _I254: $e_0320 -o r_0537; ; + _I255: $e_0476 -o r_0538; ; + _I256: $e_0953 -o r_0539; ; + _I257: $e_0196 -o r_0542; ; + _I258: $e_0154 -o r_0543; ; + _I259: $e_0146 -o r_0543; ; + _I260: $e_0472 -o r_0545; ; + _I261: $e_0548 -o r_0547; ; + _I262: $e_0428 -o r_0548; ; + _I263: $e_0799 -o r_0549; ; + _I264: $e_0633 -o r_0550; ; + _I265: $e_0398 -o r_0550; ; + _I266: $e_0233 -o r_0550; ; + _I267: $e_0463 -o r_0550; ; + _I268: $e_0645 -o r_0550; ; + _I269: $e_0029 -o r_0550; ; + _I270: $e_0124 -o r_0550; ; + _I271: $e_0697 -o r_0558; ; + _I272: $e_0708 -o r_0558; ; + _I273: $e_0716 -o r_0559; ; + _I274: $e_0087 -o r_0563; ; + _I275: $e_0875 -o r_0564; ; + _I276: $e_0705 -o r_0565; ; + _I277: $e_0458 -o r_0565; ; + _I278: $e_0693 -o r_0565; ; + _I279: $e_0591 -o r_0566; ; + _I280: $e_0038 -o r_0568; ; + _I281: $e_0754 -o r_0568; ; + _I282: $e_0631 -o r_0570; ; + _I283: $e_0736 -o r_0570; ; + _I284: $e_0557 -o r_0594; ; + _I285: $e_0220 -o r_0594; ; + _I286: $e_0862 -o r_0658; ; + _I287: $e_0771 -o r_0658; ; + _I288: $e_0769 -o r_0661; ; + _I289: $e_0135 -o r_0661; ; + _I290: $e_0550 -o r_0663; ; + _I291: $e_0457 -o r_0663; ; + _I292: $e_0031 -o r_0665; ; + _I293: $e_0922 -o r_0667; ; + _I294: $e_0685 -o r_0669; ; + _I295: $e_0642 -o r_0674; ; + _I296: $e_0062 -o r_0678; ; + _I297: $e_0343 -o r_0678; ; + _I298: $e_0440 -o r_0698; ; + _I299: $e_0550 -o r_0699; ; + _I300: $e_0457 -o r_0699; ; + _I301: $e_0926 -o r_0701; ; + _I302: $e_0171 -o r_0711; ; + _I303: $e_0571 -o r_0713; ; + _I304: $e_0838 -o r_0713; ; + _I305: $e_0137 -o r_0713; ; + _I306: $e_0134 -o r_0722; ; + _I307: $e_0269 -o r_0723; ; + _I308: $e_0057 -o r_0724; ; + _I309: $e_0396 -o r_0724; ; + _I310: $e_0239 -o r_0726; ; + _I311: $e_0658 -o r_0726; ; + _I312: $e_0298 -o r_0727; ; + _I313: $e_0409 -o r_0729; ; + _I314: $e_0610 -o r_0731; ; + _I315: $e_0396 -o r_0732; ; + _I316: $e_0057 -o r_0732; ; + _I317: $e_0745 -o r_0736; ; + _I318: $e_0812 -o r_0739; ; + _I319: $e_0204 -o r_0757; ; + _I320: $e_0435 -o r_0757; ; + _I321: $e_0512 -o r_0758; ; + _I322: $e_0290 -o r_0759; ; + _I323: $e_0139 -o r_0770; ; + _I324: $e_0737 -o r_0770; ; + _I325: $e_0714 -o r_0770; ; + _I326: $e_0271 -o r_0792; ; + _I327: $e_0568 -o r_0800; ; + _I328: $e_0568 -o r_0811; ; + _I329: $e_0674 -o r_0813; ; + _I330: $e_0499 -o r_0816; ; + _I331: $e_0729 -o r_0818; ; + _I332: $e_0755 -o r_0820; ; + _I333: $e_0712 -o r_0820; ; + _I334: $e_0249 -o r_0821; ; + _I335: $e_0348 -o r_0851; ; + _I336: $e_0639 -o r_0852; ; + _I337: $e_0312 -o r_0852; ; + _I338: $e_0352 -o r_0855; ; + _I339: $e_0536 -o r_0858; ; + _I340: $e_0381 -o r_0858; ; + _I341: $e_0964 -o r_0874; ; + _I342: $e_0788 -o r_0877; ; + _I343: $e_0382 -o r_0877; ; + _I344: $e_0278 -o r_0880; ; + _I345: $e_0633 -o r_0883; ; + _I346: $e_0975 -o r_0883; ; + _I347: $e_0398 -o r_0883; ; + _I348: $e_0401 -o r_0886; ; + _I349: $e_0743 -o r_0886; ; + _I350: $e_0576 -o r_0888; ; + _I351: $e_0757 -o r_0888; ; + _I352: $e_0733 -o r_0888; ; + _I353: $e_0294 -o r_0891; ; + _I354: $e_0469 -o r_0891; ; + _I355: $e_0113 -o r_0892; ; + _I356: $e_0582 -o r_0893; ; + _I357: $e_0536 -o r_0900; ; + _I358: $e_0536 -o r_0901; ; + _I359: $e_0314 -o r_0902; ; + _I360: $e_0747 -o r_0904; ; + _I361: $e_0017 -o r_0908; ; + _I362: $e_0103 -o r_0909; ; + _I363: $e_0103 -o r_0910; ; + _I364: $e_0860 -o r_0911; ; + _I365: $e_0631 -o r_0912; ; + _I366: $e_0736 -o r_0912; ; + _I367: $e_0165 -o r_0913; ; + _I368: $e_0352 -o r_0914; ; + _I369: $e_0763 -o r_0915; ; + _I370: $e_0030 -o r_0916; ; + _I371: $e_0299 -o r_0916; ; + _I372: $e_0418 -o r_0916; ; + _I373: $e_0585 -o r_0916; ; + _I374: $e_0829 -o r_0916; ; + _I375: $e_0397 -o r_0917; ; + _I376: $e_0872 -o r_0918; ; + _I377: $e_0077 -o r_0919; ; + _I378: $e_0206 -o r_0922; ; + _I379: $e_0802 -o r_0938; ; + _I380: $e_0074 -o r_0939; ; + _I381: $e_0296 -o r_0941; ; + _I382: $e_0276 -o r_0957; ; + _I383: $e_0334 -o r_0958; ; + _I384: $e_0084 -o r_0958; ; + _I385: $e_0085 -o r_0961; ; + _I386: $e_0306 -o r_0961; ; + _I387: $e_0393 -o r_0961; ; + _I388: $e_0311 -o r_0961; ; + _I389: $e_0775 -o r_0961; ; + _I390: $e_0011 -o r_0962; ; + _I391: $e_0895 -o r_0962; ; + _I392: $e_0841 -o r_0967; ; + _I393: $e_0090 -o r_0968; ; + _I394: $e_0398 -o r_0970; ; + _I395: $e_0398 -o r_0973; ; + _I396: $e_0467 -o r_0974; ; + _I397: $e_0492 -o r_0974; ; + _I398: $e_0387 -o r_0974; ; + _I399: $e_0291 -o r_0974; ; + _I400: $e_0467 -o r_0976; ; + _I401: $e_0492 -o r_0976; ; + _I402: $e_0387 -o r_0976; ; + _I403: $e_0291 -o r_0976; ; + _I404: $e_0467 -o r_0978; ; + _I405: $e_0492 -o r_0978; ; + _I406: $e_0387 -o r_0978; ; + _I407: $e_0291 -o r_0978; ; + _I408: $e_0852 -o r_0982; ; + _I409: $e_0506 -o r_0984; ; + _I410: $e_0699 -o r_0986; ; + _I411: $e_0489 -o r_0988; ; + _I412: $e_0813 -o r_0989; ; + _I413: $e_0054 -o r_0993; ; + _I414: $e_0177 -o r_0993; ; + _I415: $e_0761 -o r_0993; ; + _I416: $e_0168 -o r_0995; ; + _I417: $e_0425 -o r_0995; ; + _I418: $e_0182 -o r_0996; ; + _I419: $e_0182 -o r_0997; ; + _I420: $e_0385 -o r_1010; ; + _I421: $e_0385 -o r_1011; ; + _I422: $e_0456 -o r_1012; ; + _I423: $e_0578 -o r_1014; ; + _I424: $e_0613 -o r_1014; ; + _I425: $e_0107 -o r_1026; ; + _I426: $e_0547 -o r_1027; ; + _I427: $e_0321 -o r_1027; ; + _I428: $e_0633 -o r_1038; ; + _I429: $e_0218 -o r_1038; ; + _I430: $e_0398 -o r_1038; ; + _I431: $e_0448 -o r_1038; ; + _I432: $e_0915 -o r_1038; ; + _I433: $e_0124 -o r_1038; ; + _I434: $e_0122 -o r_1041; ; + _I435: $e_0470 -o r_1042; ; + _I436: $e_0850 -o r_1045; ; + _I437: $e_0684 -o r_1048; ; + _I438: $e_0063 -o r_1049; ; + _I439: $e_0962 -o r_1049; ; + _I440: $e_0063 -o r_1050; ; + _I441: $e_0962 -o r_1050; ; + _I442: $e_0711 -o r_1051; ; + _I443: $e_0065 -o r_1051; ; + _I444: $e_0179 -o r_1051; ; + _I445: $e_0753 -o r_1051; ; + _I446: $e_0176 -o r_1052; ; + _I447: $e_0611 -o r_1052; ; + _I448: $e_0765 -o r_1052; ; + _I449: $e_0851 -o r_1052; ; + _I450: $e_0175 -o r_1054; ; + _I451: $e_0330 -o r_1055; ; + _I452: $e_0836 -o r_1057; ; + _I453: $e_0348 -o r_1063; ; + _I454: $e_0629 -o r_1063; ; + _I455: $e_0390 -o r_1066; ; + _I456: $e_0561 -o r_1072; ; + _I457: $e_0565 -o r_1084; ; + _I458: $e_0550 -o r_1087; ; + _I459: $e_0457 -o r_1087; ; + _I460: $e_0372 -o r_1089; ; + // Species initializations: s_0002 = 0.1; s_0004 = 0.1; diff --git a/doc/examples/biomodels/BIOMD0000000472_url.txt b/doc/examples/biomodels/BIOMD0000000472/BIOMD0000000472_url.txt similarity index 86% rename from doc/examples/biomodels/BIOMD0000000472_url.txt rename to doc/examples/biomodels/BIOMD0000000472/BIOMD0000000472_url.txt index 0a1d561df..b1b0dd100 100644 --- a/doc/examples/biomodels/BIOMD0000000472_url.txt +++ b/doc/examples/biomodels/BIOMD0000000472/BIOMD0000000472_url.txt @@ -1,4 +1,468 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 + +// Warnings from automatic translation: +// An interaction was declared that claims e_0682 modifies r_0005, but e_0682 does not appear in r_0005's kinetic law. +// An interaction was declared that claims e_0364 modifies r_0005, but e_0364 does not appear in r_0005's kinetic law. +// An interaction was declared that claims e_0973 modifies r_0006, but e_0973 does not appear in r_0006's kinetic law. +// An interaction was declared that claims e_0379 modifies r_0006, but e_0379 does not appear in r_0006's kinetic law. +// An interaction was declared that claims e_0465 modifies r_0007, but e_0465 does not appear in r_0007's kinetic law. +// An interaction was declared that claims e_0869 modifies r_0008, but e_0869 does not appear in r_0008's kinetic law. +// An interaction was declared that claims e_0133 modifies r_0008, but e_0133 does not appear in r_0008's kinetic law. +// An interaction was declared that claims e_0117 modifies r_0008, but e_0117 does not appear in r_0008's kinetic law. +// An interaction was declared that claims e_0431 modifies r_0012, but e_0431 does not appear in r_0012's kinetic law. +// An interaction was declared that claims e_0832 modifies r_0014, but e_0832 does not appear in r_0014's kinetic law. +// An interaction was declared that claims e_0071 modifies r_0015, but e_0071 does not appear in r_0015's kinetic law. +// An interaction was declared that claims e_0734 modifies r_0016, but e_0734 does not appear in r_0016's kinetic law. +// An interaction was declared that claims e_0100 modifies r_0016, but e_0100 does not appear in r_0016's kinetic law. +// An interaction was declared that claims e_0348 modifies r_0018, but e_0348 does not appear in r_0018's kinetic law. +// An interaction was declared that claims e_0496 modifies r_0018, but e_0496 does not appear in r_0018's kinetic law. +// An interaction was declared that claims e_0980 modifies r_0018, but e_0980 does not appear in r_0018's kinetic law. +// An interaction was declared that claims e_0169 modifies r_0020, but e_0169 does not appear in r_0020's kinetic law. +// An interaction was declared that claims e_0088 modifies r_0020, but e_0088 does not appear in r_0020's kinetic law. +// An interaction was declared that claims e_0328 modifies r_0023, but e_0328 does not appear in r_0023's kinetic law. +// An interaction was declared that claims e_0778 modifies r_0024, but e_0778 does not appear in r_0024's kinetic law. +// An interaction was declared that claims e_0855 modifies r_0024, but e_0855 does not appear in r_0024's kinetic law. +// An interaction was declared that claims e_0196 modifies r_0027, but e_0196 does not appear in r_0027's kinetic law. +// An interaction was declared that claims e_0550 modifies r_0029, but e_0550 does not appear in r_0029's kinetic law. +// An interaction was declared that claims e_0457 modifies r_0029, but e_0457 does not appear in r_0029's kinetic law. +// An interaction was declared that claims e_0830 modifies r_0032, but e_0830 does not appear in r_0032's kinetic law. +// An interaction was declared that claims e_0237 modifies r_0038, but e_0237 does not appear in r_0038's kinetic law. +// An interaction was declared that claims e_0182 modifies r_0039, but e_0182 does not appear in r_0039's kinetic law. +// An interaction was declared that claims e_0182 modifies r_0040, but e_0182 does not appear in r_0040's kinetic law. +// An interaction was declared that claims e_0092 modifies r_0041, but e_0092 does not appear in r_0041's kinetic law. +// An interaction was declared that claims e_0328 modifies r_0060, but e_0328 does not appear in r_0060's kinetic law. +// An interaction was declared that claims e_0101 modifies r_0061, but e_0101 does not appear in r_0061's kinetic law. +// An interaction was declared that claims e_0182 modifies r_0065, but e_0182 does not appear in r_0065's kinetic law. +// An interaction was declared that claims e_0368 modifies r_0079, but e_0368 does not appear in r_0079's kinetic law. +// An interaction was declared that claims e_0340 modifies r_0080, but e_0340 does not appear in r_0080's kinetic law. +// An interaction was declared that claims e_0903 modifies r_0080, but e_0903 does not appear in r_0080's kinetic law. +// An interaction was declared that claims e_0685 modifies r_0096, but e_0685 does not appear in r_0096's kinetic law. +// An interaction was declared that claims e_0734 modifies r_0097, but e_0734 does not appear in r_0097's kinetic law. +// An interaction was declared that claims e_0100 modifies r_0097, but e_0100 does not appear in r_0097's kinetic law. +// An interaction was declared that claims e_0904 modifies r_0103, but e_0904 does not appear in r_0103's kinetic law. +// An interaction was declared that claims e_0744 modifies r_0108, but e_0744 does not appear in r_0108's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0108, but e_0808 does not appear in r_0108's kinetic law. +// An interaction was declared that claims e_0022 modifies r_0110, but e_0022 does not appear in r_0110's kinetic law. +// An interaction was declared that claims e_0290 modifies r_0115, but e_0290 does not appear in r_0115's kinetic law. +// An interaction was declared that claims e_0840 modifies r_0118, but e_0840 does not appear in r_0118's kinetic law. +// An interaction was declared that claims e_0541 modifies r_0142, but e_0541 does not appear in r_0142's kinetic law. +// An interaction was declared that claims e_0280 modifies r_0144, but e_0280 does not appear in r_0144's kinetic law. +// An interaction was declared that claims e_0194 modifies r_0148, but e_0194 does not appear in r_0148's kinetic law. +// An interaction was declared that claims e_0303 modifies r_0148, but e_0303 does not appear in r_0148's kinetic law. +// An interaction was declared that claims e_0686 modifies r_0151, but e_0686 does not appear in r_0151's kinetic law. +// An interaction was declared that claims e_0686 modifies r_0152, but e_0686 does not appear in r_0152's kinetic law. +// An interaction was declared that claims e_0791 modifies r_0153, but e_0791 does not appear in r_0153's kinetic law. +// An interaction was declared that claims e_0556 modifies r_0154, but e_0556 does not appear in r_0154's kinetic law. +// An interaction was declared that claims e_0894 modifies r_0157, but e_0894 does not appear in r_0157's kinetic law. +// An interaction was declared that claims e_0711 modifies r_0195, but e_0711 does not appear in r_0195's kinetic law. +// An interaction was declared that claims e_0065 modifies r_0195, but e_0065 does not appear in r_0195's kinetic law. +// An interaction was declared that claims e_0179 modifies r_0195, but e_0179 does not appear in r_0195's kinetic law. +// An interaction was declared that claims e_0753 modifies r_0195, but e_0753 does not appear in r_0195's kinetic law. +// An interaction was declared that claims e_0219 modifies r_0202, but e_0219 does not appear in r_0202's kinetic law. +// An interaction was declared that claims e_0297 modifies r_0203, but e_0297 does not appear in r_0203's kinetic law. +// An interaction was declared that claims e_0591 modifies r_0203, but e_0591 does not appear in r_0203's kinetic law. +// An interaction was declared that claims e_0426 modifies r_0207, but e_0426 does not appear in r_0207's kinetic law. +// An interaction was declared that claims e_0826 modifies r_0208, but e_0826 does not appear in r_0208's kinetic law. +// An interaction was declared that claims e_0214 modifies r_0209, but e_0214 does not appear in r_0209's kinetic law. +// An interaction was declared that claims e_0970 modifies r_0211, but e_0970 does not appear in r_0211's kinetic law. +// An interaction was declared that claims e_0376 modifies r_0211, but e_0376 does not appear in r_0211's kinetic law. +// An interaction was declared that claims e_0427 modifies r_0212, but e_0427 does not appear in r_0212's kinetic law. +// An interaction was declared that claims e_0508 modifies r_0214, but e_0508 does not appear in r_0214's kinetic law. +// An interaction was declared that claims e_0281 modifies r_0215, but e_0281 does not appear in r_0215's kinetic law. +// An interaction was declared that claims e_0629 modifies r_0216, but e_0629 does not appear in r_0216's kinetic law. +// An interaction was declared that claims e_0574 modifies r_0216, but e_0574 does not appear in r_0216's kinetic law. +// An interaction was declared that claims e_0186 modifies r_0219, but e_0186 does not appear in r_0219's kinetic law. +// An interaction was declared that claims e_0615 modifies r_0220, but e_0615 does not appear in r_0220's kinetic law. +// An interaction was declared that claims e_0283 modifies r_0225, but e_0283 does not appear in r_0225's kinetic law. +// An interaction was declared that claims e_0800 modifies r_0231, but e_0800 does not appear in r_0231's kinetic law. +// An interaction was declared that claims e_0724 modifies r_0233, but e_0724 does not appear in r_0233's kinetic law. +// An interaction was declared that claims e_0326 modifies r_0234, but e_0326 does not appear in r_0234's kinetic law. +// An interaction was declared that claims e_0326 modifies r_0235, but e_0326 does not appear in r_0235's kinetic law. +// An interaction was declared that claims e_0644 modifies r_0236, but e_0644 does not appear in r_0236's kinetic law. +// An interaction was declared that claims e_0644 modifies r_0237, but e_0644 does not appear in r_0237's kinetic law. +// An interaction was declared that claims e_0367 modifies r_0238, but e_0367 does not appear in r_0238's kinetic law. +// An interaction was declared that claims e_0367 modifies r_0239, but e_0367 does not appear in r_0239's kinetic law. +// An interaction was declared that claims e_0367 modifies r_0240, but e_0367 does not appear in r_0240's kinetic law. +// An interaction was declared that claims e_0367 modifies r_0241, but e_0367 does not appear in r_0241's kinetic law. +// An interaction was declared that claims e_0637 modifies r_0242, but e_0637 does not appear in r_0242's kinetic law. +// An interaction was declared that claims e_0742 modifies r_0243, but e_0742 does not appear in r_0243's kinetic law. +// An interaction was declared that claims e_0329 modifies r_0244, but e_0329 does not appear in r_0244's kinetic law. +// An interaction was declared that claims e_0508 modifies r_0250, but e_0508 does not appear in r_0250's kinetic law. +// An interaction was declared that claims e_0542 modifies r_0250, but e_0542 does not appear in r_0250's kinetic law. +// An interaction was declared that claims e_0888 modifies r_0250, but e_0888 does not appear in r_0250's kinetic law. +// An interaction was declared that claims e_0045 modifies r_0257, but e_0045 does not appear in r_0257's kinetic law. +// An interaction was declared that claims e_0206 modifies r_0259, but e_0206 does not appear in r_0259's kinetic law. +// An interaction was declared that claims e_0756 modifies r_0267, but e_0756 does not appear in r_0267's kinetic law. +// An interaction was declared that claims e_0756 modifies r_0269, but e_0756 does not appear in r_0269's kinetic law. +// An interaction was declared that claims e_0959 modifies r_0278, but e_0959 does not appear in r_0278's kinetic law. +// An interaction was declared that claims e_0342 modifies r_0279, but e_0342 does not appear in r_0279's kinetic law. +// An interaction was declared that claims e_0675 modifies r_0280, but e_0675 does not appear in r_0280's kinetic law. +// An interaction was declared that claims e_0947 modifies r_0300, but e_0947 does not appear in r_0300's kinetic law. +// An interaction was declared that claims e_0805 modifies r_0300, but e_0805 does not appear in r_0300's kinetic law. +// An interaction was declared that claims e_0111 modifies r_0300, but e_0111 does not appear in r_0300's kinetic law. +// An interaction was declared that claims e_0675 modifies r_0302, but e_0675 does not appear in r_0302's kinetic law. +// An interaction was declared that claims e_0540 modifies r_0307, but e_0540 does not appear in r_0307's kinetic law. +// An interaction was declared that claims e_0026 modifies r_0307, but e_0026 does not appear in r_0307's kinetic law. +// An interaction was declared that claims e_0380 modifies r_0309, but e_0380 does not appear in r_0309's kinetic law. +// An interaction was declared that claims e_0008 modifies r_0310, but e_0008 does not appear in r_0310's kinetic law. +// An interaction was declared that claims e_0545 modifies r_0311, but e_0545 does not appear in r_0311's kinetic law. +// An interaction was declared that claims e_0793 modifies r_0313, but e_0793 does not appear in r_0313's kinetic law. +// An interaction was declared that claims e_0434 modifies r_0317, but e_0434 does not appear in r_0317's kinetic law. +// An interaction was declared that claims e_0424 modifies r_0317, but e_0424 does not appear in r_0317's kinetic law. +// An interaction was declared that claims e_0452 modifies r_0326, but e_0452 does not appear in r_0326's kinetic law. +// An interaction was declared that claims e_0234 modifies r_0330, but e_0234 does not appear in r_0330's kinetic law. +// An interaction was declared that claims e_0883 modifies r_0336, but e_0883 does not appear in r_0336's kinetic law. +// An interaction was declared that claims e_0203 modifies r_0337, but e_0203 does not appear in r_0337's kinetic law. +// An interaction was declared that claims e_0594 modifies r_0339, but e_0594 does not appear in r_0339's kinetic law. +// An interaction was declared that claims e_0914 modifies r_0340, but e_0914 does not appear in r_0340's kinetic law. +// An interaction was declared that claims e_0880 modifies r_0344, but e_0880 does not appear in r_0344's kinetic law. +// An interaction was declared that claims e_0692 modifies r_0349, but e_0692 does not appear in r_0349's kinetic law. +// An interaction was declared that claims e_0528 modifies r_0352, but e_0528 does not appear in r_0352's kinetic law. +// An interaction was declared that claims e_0528 modifies r_0353, but e_0528 does not appear in r_0353's kinetic law. +// An interaction was declared that claims e_0515 modifies r_0355, but e_0515 does not appear in r_0355's kinetic law. +// An interaction was declared that claims e_0976 modifies r_0361, but e_0976 does not appear in r_0361's kinetic law. +// An interaction was declared that claims e_0141 modifies r_0362, but e_0141 does not appear in r_0362's kinetic law. +// An interaction was declared that claims e_0549 modifies r_0362, but e_0549 does not appear in r_0362's kinetic law. +// An interaction was declared that claims e_0010 modifies r_0362, but e_0010 does not appear in r_0362's kinetic law. +// An interaction was declared that claims e_0890 modifies r_0362, but e_0890 does not appear in r_0362's kinetic law. +// An interaction was declared that claims e_0142 modifies r_0362, but e_0142 does not appear in r_0362's kinetic law. +// An interaction was declared that claims e_0089 modifies r_0364, but e_0089 does not appear in r_0364's kinetic law. +// An interaction was declared that claims e_0405 modifies r_0366, but e_0405 does not appear in r_0366's kinetic law. +// An interaction was declared that claims e_0454 modifies r_0366, but e_0454 does not appear in r_0366's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0386, but e_0808 does not appear in r_0386's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0386, but e_0365 does not appear in r_0386's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0386, but e_0586 does not appear in r_0386's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0386, but e_0934 does not appear in r_0386's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0387, but e_0808 does not appear in r_0387's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0387, but e_0365 does not appear in r_0387's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0387, but e_0586 does not appear in r_0387's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0387, but e_0934 does not appear in r_0387's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0389, but e_0808 does not appear in r_0389's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0389, but e_0365 does not appear in r_0389's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0389, but e_0586 does not appear in r_0389's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0389, but e_0934 does not appear in r_0389's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0391, but e_0808 does not appear in r_0391's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0391, but e_0365 does not appear in r_0391's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0391, but e_0586 does not appear in r_0391's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0391, but e_0934 does not appear in r_0391's kinetic law. +// An interaction was declared that claims e_0128 modifies r_0393, but e_0128 does not appear in r_0393's kinetic law. +// An interaction was declared that claims e_0117 modifies r_0393, but e_0117 does not appear in r_0393's kinetic law. +// An interaction was declared that claims e_0687 modifies r_0393, but e_0687 does not appear in r_0393's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0397, but e_0808 does not appear in r_0397's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0397, but e_0365 does not appear in r_0397's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0397, but e_0586 does not appear in r_0397's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0397, but e_0934 does not appear in r_0397's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0398, but e_0808 does not appear in r_0398's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0398, but e_0365 does not appear in r_0398's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0398, but e_0586 does not appear in r_0398's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0398, but e_0934 does not appear in r_0398's kinetic law. +// An interaction was declared that claims e_0273 modifies r_0399, but e_0273 does not appear in r_0399's kinetic law. +// An interaction was declared that claims e_0273 modifies r_0400, but e_0273 does not appear in r_0400's kinetic law. +// An interaction was declared that claims e_0750 modifies r_0407, but e_0750 does not appear in r_0407's kinetic law. +// An interaction was declared that claims e_0889 modifies r_0407, but e_0889 does not appear in r_0407's kinetic law. +// An interaction was declared that claims e_0462 modifies r_0407, but e_0462 does not appear in r_0407's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0432, but e_0808 does not appear in r_0432's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0432, but e_0365 does not appear in r_0432's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0432, but e_0586 does not appear in r_0432's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0432, but e_0934 does not appear in r_0432's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0433, but e_0808 does not appear in r_0433's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0433, but e_0365 does not appear in r_0433's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0433, but e_0586 does not appear in r_0433's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0433, but e_0934 does not appear in r_0433's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0434, but e_0808 does not appear in r_0434's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0434, but e_0365 does not appear in r_0434's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0434, but e_0586 does not appear in r_0434's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0434, but e_0934 does not appear in r_0434's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0435, but e_0808 does not appear in r_0435's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0435, but e_0365 does not appear in r_0435's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0435, but e_0586 does not appear in r_0435's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0435, but e_0934 does not appear in r_0435's kinetic law. +// An interaction was declared that claims e_0632 modifies r_0438, but e_0632 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0007 modifies r_0438, but e_0007 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0774 modifies r_0438, but e_0774 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0436 modifies r_0438, but e_0436 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0136 modifies r_0438, but e_0136 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0001 modifies r_0438, but e_0001 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0347 modifies r_0438, but e_0347 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0255 modifies r_0438, but e_0255 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0752 modifies r_0438, but e_0752 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0690 modifies r_0438, but e_0690 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0006 modifies r_0438, but e_0006 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0531 modifies r_0438, but e_0531 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0346 modifies r_0438, but e_0346 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0475 modifies r_0438, but e_0475 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0514 modifies r_0439, but e_0514 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0978 modifies r_0439, but e_0978 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0422 modifies r_0439, but e_0422 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0250 modifies r_0439, but e_0250 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0004 modifies r_0439, but e_0004 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0243 modifies r_0439, but e_0243 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0389 modifies r_0439, but e_0389 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0255 modifies r_0439, but e_0255 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0848 modifies r_0439, but e_0848 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0028 modifies r_0439, but e_0028 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0531 modifies r_0439, but e_0531 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0322 modifies r_0439, but e_0322 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0396 modifies r_0446, but e_0396 does not appear in r_0446's kinetic law. +// An interaction was declared that claims e_0057 modifies r_0446, but e_0057 does not appear in r_0446's kinetic law. +// An interaction was declared that claims e_0567 modifies r_0450, but e_0567 does not appear in r_0450's kinetic law. +// An interaction was declared that claims e_0940 modifies r_0451, but e_0940 does not appear in r_0451's kinetic law. +// An interaction was declared that claims e_0515 modifies r_0462, but e_0515 does not appear in r_0462's kinetic law. +// An interaction was declared that claims e_0079 modifies r_0467, but e_0079 does not appear in r_0467's kinetic law. +// An interaction was declared that claims e_0160 modifies r_0470, but e_0160 does not appear in r_0470's kinetic law. +// An interaction was declared that claims e_0016 modifies r_0471, but e_0016 does not appear in r_0471's kinetic law. +// An interaction was declared that claims e_0899 modifies r_0471, but e_0899 does not appear in r_0471's kinetic law. +// An interaction was declared that claims e_0955 modifies r_0476, but e_0955 does not appear in r_0476's kinetic law. +// An interaction was declared that claims e_0867 modifies r_0478, but e_0867 does not appear in r_0478's kinetic law. +// An interaction was declared that claims e_0353 modifies r_0479, but e_0353 does not appear in r_0479's kinetic law. +// An interaction was declared that claims e_0242 modifies r_0481, but e_0242 does not appear in r_0481's kinetic law. +// An interaction was declared that claims e_0104 modifies r_0481, but e_0104 does not appear in r_0481's kinetic law. +// An interaction was declared that claims e_0181 modifies r_0481, but e_0181 does not appear in r_0481's kinetic law. +// An interaction was declared that claims e_0304 modifies r_0481, but e_0304 does not appear in r_0481's kinetic law. +// An interaction was declared that claims e_0915 modifies r_0481, but e_0915 does not appear in r_0481's kinetic law. +// An interaction was declared that claims e_0910 modifies r_0481, but e_0910 does not appear in r_0481's kinetic law. +// An interaction was declared that claims e_0242 modifies r_0483, but e_0242 does not appear in r_0483's kinetic law. +// An interaction was declared that claims e_0563 modifies r_0483, but e_0563 does not appear in r_0483's kinetic law. +// An interaction was declared that claims e_0086 modifies r_0483, but e_0086 does not appear in r_0483's kinetic law. +// An interaction was declared that claims e_0104 modifies r_0483, but e_0104 does not appear in r_0483's kinetic law. +// An interaction was declared that claims e_0490 modifies r_0483, but e_0490 does not appear in r_0483's kinetic law. +// An interaction was declared that claims e_0910 modifies r_0483, but e_0910 does not appear in r_0483's kinetic law. +// An interaction was declared that claims e_0392 modifies r_0486, but e_0392 does not appear in r_0486's kinetic law. +// An interaction was declared that claims e_0495 modifies r_0486, but e_0495 does not appear in r_0486's kinetic law. +// An interaction was declared that claims e_0525 modifies r_0486, but e_0525 does not appear in r_0486's kinetic law. +// An interaction was declared that claims e_0129 modifies r_0491, but e_0129 does not appear in r_0491's kinetic law. +// An interaction was declared that claims e_0827 modifies r_0491, but e_0827 does not appear in r_0491's kinetic law. +// An interaction was declared that claims e_0020 modifies r_0495, but e_0020 does not appear in r_0495's kinetic law. +// An interaction was declared that claims e_0607 modifies r_0495, but e_0607 does not appear in r_0495's kinetic law. +// An interaction was declared that claims e_0231 modifies r_0499, but e_0231 does not appear in r_0499's kinetic law. +// An interaction was declared that claims e_0741 modifies r_0501, but e_0741 does not appear in r_0501's kinetic law. +// An interaction was declared that claims e_0012 modifies r_0501, but e_0012 does not appear in r_0501's kinetic law. +// An interaction was declared that claims e_0167 modifies r_0501, but e_0167 does not appear in r_0501's kinetic law. +// An interaction was declared that claims e_0311 modifies r_0501, but e_0311 does not appear in r_0501's kinetic law. +// An interaction was declared that claims e_0638 modifies r_0502, but e_0638 does not appear in r_0502's kinetic law. +// An interaction was declared that claims e_0091 modifies r_0502, but e_0091 does not appear in r_0502's kinetic law. +// An interaction was declared that claims e_0667 modifies r_0510, but e_0667 does not appear in r_0510's kinetic law. +// An interaction was declared that claims e_0510 modifies r_0510, but e_0510 does not appear in r_0510's kinetic law. +// An interaction was declared that claims e_0317 modifies r_0510, but e_0317 does not appear in r_0510's kinetic law. +// An interaction was declared that claims e_0603 modifies r_0510, but e_0603 does not appear in r_0510's kinetic law. +// An interaction was declared that claims e_0064 modifies r_0512, but e_0064 does not appear in r_0512's kinetic law. +// An interaction was declared that claims e_0963 modifies r_0512, but e_0963 does not appear in r_0512's kinetic law. +// An interaction was declared that claims e_0746 modifies r_0514, but e_0746 does not appear in r_0514's kinetic law. +// An interaction was declared that claims e_0025 modifies r_0525, but e_0025 does not appear in r_0525's kinetic law. +// An interaction was declared that claims e_0234 modifies r_0528, but e_0234 does not appear in r_0528's kinetic law. +// An interaction was declared that claims e_0234 modifies r_0529, but e_0234 does not appear in r_0529's kinetic law. +// An interaction was declared that claims e_0106 modifies r_0534, but e_0106 does not appear in r_0534's kinetic law. +// An interaction was declared that claims e_0325 modifies r_0534, but e_0325 does not appear in r_0534's kinetic law. +// An interaction was declared that claims e_0355 modifies r_0534, but e_0355 does not appear in r_0534's kinetic law. +// An interaction was declared that claims e_0103 modifies r_0536, but e_0103 does not appear in r_0536's kinetic law. +// An interaction was declared that claims e_0320 modifies r_0537, but e_0320 does not appear in r_0537's kinetic law. +// An interaction was declared that claims e_0476 modifies r_0538, but e_0476 does not appear in r_0538's kinetic law. +// An interaction was declared that claims e_0953 modifies r_0539, but e_0953 does not appear in r_0539's kinetic law. +// An interaction was declared that claims e_0196 modifies r_0542, but e_0196 does not appear in r_0542's kinetic law. +// An interaction was declared that claims e_0154 modifies r_0543, but e_0154 does not appear in r_0543's kinetic law. +// An interaction was declared that claims e_0146 modifies r_0543, but e_0146 does not appear in r_0543's kinetic law. +// An interaction was declared that claims e_0472 modifies r_0545, but e_0472 does not appear in r_0545's kinetic law. +// An interaction was declared that claims e_0548 modifies r_0547, but e_0548 does not appear in r_0547's kinetic law. +// An interaction was declared that claims e_0428 modifies r_0548, but e_0428 does not appear in r_0548's kinetic law. +// An interaction was declared that claims e_0799 modifies r_0549, but e_0799 does not appear in r_0549's kinetic law. +// An interaction was declared that claims e_0633 modifies r_0550, but e_0633 does not appear in r_0550's kinetic law. +// An interaction was declared that claims e_0398 modifies r_0550, but e_0398 does not appear in r_0550's kinetic law. +// An interaction was declared that claims e_0233 modifies r_0550, but e_0233 does not appear in r_0550's kinetic law. +// An interaction was declared that claims e_0463 modifies r_0550, but e_0463 does not appear in r_0550's kinetic law. +// An interaction was declared that claims e_0645 modifies r_0550, but e_0645 does not appear in r_0550's kinetic law. +// An interaction was declared that claims e_0029 modifies r_0550, but e_0029 does not appear in r_0550's kinetic law. +// An interaction was declared that claims e_0124 modifies r_0550, but e_0124 does not appear in r_0550's kinetic law. +// An interaction was declared that claims e_0697 modifies r_0558, but e_0697 does not appear in r_0558's kinetic law. +// An interaction was declared that claims e_0708 modifies r_0558, but e_0708 does not appear in r_0558's kinetic law. +// An interaction was declared that claims e_0716 modifies r_0559, but e_0716 does not appear in r_0559's kinetic law. +// An interaction was declared that claims e_0087 modifies r_0563, but e_0087 does not appear in r_0563's kinetic law. +// An interaction was declared that claims e_0875 modifies r_0564, but e_0875 does not appear in r_0564's kinetic law. +// An interaction was declared that claims e_0705 modifies r_0565, but e_0705 does not appear in r_0565's kinetic law. +// An interaction was declared that claims e_0458 modifies r_0565, but e_0458 does not appear in r_0565's kinetic law. +// An interaction was declared that claims e_0693 modifies r_0565, but e_0693 does not appear in r_0565's kinetic law. +// An interaction was declared that claims e_0591 modifies r_0566, but e_0591 does not appear in r_0566's kinetic law. +// An interaction was declared that claims e_0038 modifies r_0568, but e_0038 does not appear in r_0568's kinetic law. +// An interaction was declared that claims e_0754 modifies r_0568, but e_0754 does not appear in r_0568's kinetic law. +// An interaction was declared that claims e_0631 modifies r_0570, but e_0631 does not appear in r_0570's kinetic law. +// An interaction was declared that claims e_0736 modifies r_0570, but e_0736 does not appear in r_0570's kinetic law. +// An interaction was declared that claims e_0557 modifies r_0594, but e_0557 does not appear in r_0594's kinetic law. +// An interaction was declared that claims e_0220 modifies r_0594, but e_0220 does not appear in r_0594's kinetic law. +// An interaction was declared that claims e_0862 modifies r_0658, but e_0862 does not appear in r_0658's kinetic law. +// An interaction was declared that claims e_0771 modifies r_0658, but e_0771 does not appear in r_0658's kinetic law. +// An interaction was declared that claims e_0769 modifies r_0661, but e_0769 does not appear in r_0661's kinetic law. +// An interaction was declared that claims e_0135 modifies r_0661, but e_0135 does not appear in r_0661's kinetic law. +// An interaction was declared that claims e_0550 modifies r_0663, but e_0550 does not appear in r_0663's kinetic law. +// An interaction was declared that claims e_0457 modifies r_0663, but e_0457 does not appear in r_0663's kinetic law. +// An interaction was declared that claims e_0031 modifies r_0665, but e_0031 does not appear in r_0665's kinetic law. +// An interaction was declared that claims e_0922 modifies r_0667, but e_0922 does not appear in r_0667's kinetic law. +// An interaction was declared that claims e_0685 modifies r_0669, but e_0685 does not appear in r_0669's kinetic law. +// An interaction was declared that claims e_0642 modifies r_0674, but e_0642 does not appear in r_0674's kinetic law. +// An interaction was declared that claims e_0062 modifies r_0678, but e_0062 does not appear in r_0678's kinetic law. +// An interaction was declared that claims e_0343 modifies r_0678, but e_0343 does not appear in r_0678's kinetic law. +// An interaction was declared that claims e_0440 modifies r_0698, but e_0440 does not appear in r_0698's kinetic law. +// An interaction was declared that claims e_0550 modifies r_0699, but e_0550 does not appear in r_0699's kinetic law. +// An interaction was declared that claims e_0457 modifies r_0699, but e_0457 does not appear in r_0699's kinetic law. +// An interaction was declared that claims e_0926 modifies r_0701, but e_0926 does not appear in r_0701's kinetic law. +// An interaction was declared that claims e_0171 modifies r_0711, but e_0171 does not appear in r_0711's kinetic law. +// An interaction was declared that claims e_0571 modifies r_0713, but e_0571 does not appear in r_0713's kinetic law. +// An interaction was declared that claims e_0838 modifies r_0713, but e_0838 does not appear in r_0713's kinetic law. +// An interaction was declared that claims e_0137 modifies r_0713, but e_0137 does not appear in r_0713's kinetic law. +// An interaction was declared that claims e_0134 modifies r_0722, but e_0134 does not appear in r_0722's kinetic law. +// An interaction was declared that claims e_0269 modifies r_0723, but e_0269 does not appear in r_0723's kinetic law. +// An interaction was declared that claims e_0057 modifies r_0724, but e_0057 does not appear in r_0724's kinetic law. +// An interaction was declared that claims e_0396 modifies r_0724, but e_0396 does not appear in r_0724's kinetic law. +// An interaction was declared that claims e_0239 modifies r_0726, but e_0239 does not appear in r_0726's kinetic law. +// An interaction was declared that claims e_0658 modifies r_0726, but e_0658 does not appear in r_0726's kinetic law. +// An interaction was declared that claims e_0298 modifies r_0727, but e_0298 does not appear in r_0727's kinetic law. +// An interaction was declared that claims e_0409 modifies r_0729, but e_0409 does not appear in r_0729's kinetic law. +// An interaction was declared that claims e_0610 modifies r_0731, but e_0610 does not appear in r_0731's kinetic law. +// An interaction was declared that claims e_0396 modifies r_0732, but e_0396 does not appear in r_0732's kinetic law. +// An interaction was declared that claims e_0057 modifies r_0732, but e_0057 does not appear in r_0732's kinetic law. +// An interaction was declared that claims e_0745 modifies r_0736, but e_0745 does not appear in r_0736's kinetic law. +// An interaction was declared that claims e_0812 modifies r_0739, but e_0812 does not appear in r_0739's kinetic law. +// An interaction was declared that claims e_0204 modifies r_0757, but e_0204 does not appear in r_0757's kinetic law. +// An interaction was declared that claims e_0435 modifies r_0757, but e_0435 does not appear in r_0757's kinetic law. +// An interaction was declared that claims e_0512 modifies r_0758, but e_0512 does not appear in r_0758's kinetic law. +// An interaction was declared that claims e_0290 modifies r_0759, but e_0290 does not appear in r_0759's kinetic law. +// An interaction was declared that claims e_0139 modifies r_0770, but e_0139 does not appear in r_0770's kinetic law. +// An interaction was declared that claims e_0737 modifies r_0770, but e_0737 does not appear in r_0770's kinetic law. +// An interaction was declared that claims e_0714 modifies r_0770, but e_0714 does not appear in r_0770's kinetic law. +// An interaction was declared that claims e_0271 modifies r_0792, but e_0271 does not appear in r_0792's kinetic law. +// An interaction was declared that claims e_0568 modifies r_0800, but e_0568 does not appear in r_0800's kinetic law. +// An interaction was declared that claims e_0568 modifies r_0811, but e_0568 does not appear in r_0811's kinetic law. +// An interaction was declared that claims e_0674 modifies r_0813, but e_0674 does not appear in r_0813's kinetic law. +// An interaction was declared that claims e_0499 modifies r_0816, but e_0499 does not appear in r_0816's kinetic law. +// An interaction was declared that claims e_0729 modifies r_0818, but e_0729 does not appear in r_0818's kinetic law. +// An interaction was declared that claims e_0755 modifies r_0820, but e_0755 does not appear in r_0820's kinetic law. +// An interaction was declared that claims e_0712 modifies r_0820, but e_0712 does not appear in r_0820's kinetic law. +// An interaction was declared that claims e_0249 modifies r_0821, but e_0249 does not appear in r_0821's kinetic law. +// An interaction was declared that claims e_0348 modifies r_0851, but e_0348 does not appear in r_0851's kinetic law. +// An interaction was declared that claims e_0639 modifies r_0852, but e_0639 does not appear in r_0852's kinetic law. +// An interaction was declared that claims e_0312 modifies r_0852, but e_0312 does not appear in r_0852's kinetic law. +// An interaction was declared that claims e_0352 modifies r_0855, but e_0352 does not appear in r_0855's kinetic law. +// An interaction was declared that claims e_0536 modifies r_0858, but e_0536 does not appear in r_0858's kinetic law. +// An interaction was declared that claims e_0381 modifies r_0858, but e_0381 does not appear in r_0858's kinetic law. +// An interaction was declared that claims e_0964 modifies r_0874, but e_0964 does not appear in r_0874's kinetic law. +// An interaction was declared that claims e_0788 modifies r_0877, but e_0788 does not appear in r_0877's kinetic law. +// An interaction was declared that claims e_0382 modifies r_0877, but e_0382 does not appear in r_0877's kinetic law. +// An interaction was declared that claims e_0278 modifies r_0880, but e_0278 does not appear in r_0880's kinetic law. +// An interaction was declared that claims e_0633 modifies r_0883, but e_0633 does not appear in r_0883's kinetic law. +// An interaction was declared that claims e_0975 modifies r_0883, but e_0975 does not appear in r_0883's kinetic law. +// An interaction was declared that claims e_0398 modifies r_0883, but e_0398 does not appear in r_0883's kinetic law. +// An interaction was declared that claims e_0401 modifies r_0886, but e_0401 does not appear in r_0886's kinetic law. +// An interaction was declared that claims e_0743 modifies r_0886, but e_0743 does not appear in r_0886's kinetic law. +// An interaction was declared that claims e_0576 modifies r_0888, but e_0576 does not appear in r_0888's kinetic law. +// An interaction was declared that claims e_0757 modifies r_0888, but e_0757 does not appear in r_0888's kinetic law. +// An interaction was declared that claims e_0733 modifies r_0888, but e_0733 does not appear in r_0888's kinetic law. +// An interaction was declared that claims e_0294 modifies r_0891, but e_0294 does not appear in r_0891's kinetic law. +// An interaction was declared that claims e_0469 modifies r_0891, but e_0469 does not appear in r_0891's kinetic law. +// An interaction was declared that claims e_0113 modifies r_0892, but e_0113 does not appear in r_0892's kinetic law. +// An interaction was declared that claims e_0582 modifies r_0893, but e_0582 does not appear in r_0893's kinetic law. +// An interaction was declared that claims e_0536 modifies r_0900, but e_0536 does not appear in r_0900's kinetic law. +// An interaction was declared that claims e_0536 modifies r_0901, but e_0536 does not appear in r_0901's kinetic law. +// An interaction was declared that claims e_0314 modifies r_0902, but e_0314 does not appear in r_0902's kinetic law. +// An interaction was declared that claims e_0747 modifies r_0904, but e_0747 does not appear in r_0904's kinetic law. +// An interaction was declared that claims e_0017 modifies r_0908, but e_0017 does not appear in r_0908's kinetic law. +// An interaction was declared that claims e_0103 modifies r_0909, but e_0103 does not appear in r_0909's kinetic law. +// An interaction was declared that claims e_0103 modifies r_0910, but e_0103 does not appear in r_0910's kinetic law. +// An interaction was declared that claims e_0860 modifies r_0911, but e_0860 does not appear in r_0911's kinetic law. +// An interaction was declared that claims e_0631 modifies r_0912, but e_0631 does not appear in r_0912's kinetic law. +// An interaction was declared that claims e_0736 modifies r_0912, but e_0736 does not appear in r_0912's kinetic law. +// An interaction was declared that claims e_0165 modifies r_0913, but e_0165 does not appear in r_0913's kinetic law. +// An interaction was declared that claims e_0352 modifies r_0914, but e_0352 does not appear in r_0914's kinetic law. +// An interaction was declared that claims e_0763 modifies r_0915, but e_0763 does not appear in r_0915's kinetic law. +// An interaction was declared that claims e_0030 modifies r_0916, but e_0030 does not appear in r_0916's kinetic law. +// An interaction was declared that claims e_0299 modifies r_0916, but e_0299 does not appear in r_0916's kinetic law. +// An interaction was declared that claims e_0418 modifies r_0916, but e_0418 does not appear in r_0916's kinetic law. +// An interaction was declared that claims e_0585 modifies r_0916, but e_0585 does not appear in r_0916's kinetic law. +// An interaction was declared that claims e_0829 modifies r_0916, but e_0829 does not appear in r_0916's kinetic law. +// An interaction was declared that claims e_0397 modifies r_0917, but e_0397 does not appear in r_0917's kinetic law. +// An interaction was declared that claims e_0872 modifies r_0918, but e_0872 does not appear in r_0918's kinetic law. +// An interaction was declared that claims e_0077 modifies r_0919, but e_0077 does not appear in r_0919's kinetic law. +// An interaction was declared that claims e_0206 modifies r_0922, but e_0206 does not appear in r_0922's kinetic law. +// An interaction was declared that claims e_0802 modifies r_0938, but e_0802 does not appear in r_0938's kinetic law. +// An interaction was declared that claims e_0074 modifies r_0939, but e_0074 does not appear in r_0939's kinetic law. +// An interaction was declared that claims e_0296 modifies r_0941, but e_0296 does not appear in r_0941's kinetic law. +// An interaction was declared that claims e_0276 modifies r_0957, but e_0276 does not appear in r_0957's kinetic law. +// An interaction was declared that claims e_0334 modifies r_0958, but e_0334 does not appear in r_0958's kinetic law. +// An interaction was declared that claims e_0084 modifies r_0958, but e_0084 does not appear in r_0958's kinetic law. +// An interaction was declared that claims e_0085 modifies r_0961, but e_0085 does not appear in r_0961's kinetic law. +// An interaction was declared that claims e_0306 modifies r_0961, but e_0306 does not appear in r_0961's kinetic law. +// An interaction was declared that claims e_0393 modifies r_0961, but e_0393 does not appear in r_0961's kinetic law. +// An interaction was declared that claims e_0311 modifies r_0961, but e_0311 does not appear in r_0961's kinetic law. +// An interaction was declared that claims e_0775 modifies r_0961, but e_0775 does not appear in r_0961's kinetic law. +// An interaction was declared that claims e_0011 modifies r_0962, but e_0011 does not appear in r_0962's kinetic law. +// An interaction was declared that claims e_0895 modifies r_0962, but e_0895 does not appear in r_0962's kinetic law. +// An interaction was declared that claims e_0841 modifies r_0967, but e_0841 does not appear in r_0967's kinetic law. +// An interaction was declared that claims e_0090 modifies r_0968, but e_0090 does not appear in r_0968's kinetic law. +// An interaction was declared that claims e_0398 modifies r_0970, but e_0398 does not appear in r_0970's kinetic law. +// An interaction was declared that claims e_0398 modifies r_0973, but e_0398 does not appear in r_0973's kinetic law. +// An interaction was declared that claims e_0467 modifies r_0974, but e_0467 does not appear in r_0974's kinetic law. +// An interaction was declared that claims e_0492 modifies r_0974, but e_0492 does not appear in r_0974's kinetic law. +// An interaction was declared that claims e_0387 modifies r_0974, but e_0387 does not appear in r_0974's kinetic law. +// An interaction was declared that claims e_0291 modifies r_0974, but e_0291 does not appear in r_0974's kinetic law. +// An interaction was declared that claims e_0467 modifies r_0976, but e_0467 does not appear in r_0976's kinetic law. +// An interaction was declared that claims e_0492 modifies r_0976, but e_0492 does not appear in r_0976's kinetic law. +// An interaction was declared that claims e_0387 modifies r_0976, but e_0387 does not appear in r_0976's kinetic law. +// An interaction was declared that claims e_0291 modifies r_0976, but e_0291 does not appear in r_0976's kinetic law. +// An interaction was declared that claims e_0467 modifies r_0978, but e_0467 does not appear in r_0978's kinetic law. +// An interaction was declared that claims e_0492 modifies r_0978, but e_0492 does not appear in r_0978's kinetic law. +// An interaction was declared that claims e_0387 modifies r_0978, but e_0387 does not appear in r_0978's kinetic law. +// An interaction was declared that claims e_0291 modifies r_0978, but e_0291 does not appear in r_0978's kinetic law. +// An interaction was declared that claims e_0852 modifies r_0982, but e_0852 does not appear in r_0982's kinetic law. +// An interaction was declared that claims e_0506 modifies r_0984, but e_0506 does not appear in r_0984's kinetic law. +// An interaction was declared that claims e_0699 modifies r_0986, but e_0699 does not appear in r_0986's kinetic law. +// An interaction was declared that claims e_0489 modifies r_0988, but e_0489 does not appear in r_0988's kinetic law. +// An interaction was declared that claims e_0813 modifies r_0989, but e_0813 does not appear in r_0989's kinetic law. +// An interaction was declared that claims e_0054 modifies r_0993, but e_0054 does not appear in r_0993's kinetic law. +// An interaction was declared that claims e_0177 modifies r_0993, but e_0177 does not appear in r_0993's kinetic law. +// An interaction was declared that claims e_0761 modifies r_0993, but e_0761 does not appear in r_0993's kinetic law. +// An interaction was declared that claims e_0168 modifies r_0995, but e_0168 does not appear in r_0995's kinetic law. +// An interaction was declared that claims e_0425 modifies r_0995, but e_0425 does not appear in r_0995's kinetic law. +// An interaction was declared that claims e_0182 modifies r_0996, but e_0182 does not appear in r_0996's kinetic law. +// An interaction was declared that claims e_0182 modifies r_0997, but e_0182 does not appear in r_0997's kinetic law. +// An interaction was declared that claims e_0385 modifies r_1010, but e_0385 does not appear in r_1010's kinetic law. +// An interaction was declared that claims e_0385 modifies r_1011, but e_0385 does not appear in r_1011's kinetic law. +// An interaction was declared that claims e_0456 modifies r_1012, but e_0456 does not appear in r_1012's kinetic law. +// An interaction was declared that claims e_0578 modifies r_1014, but e_0578 does not appear in r_1014's kinetic law. +// An interaction was declared that claims e_0613 modifies r_1014, but e_0613 does not appear in r_1014's kinetic law. +// An interaction was declared that claims e_0107 modifies r_1026, but e_0107 does not appear in r_1026's kinetic law. +// An interaction was declared that claims e_0547 modifies r_1027, but e_0547 does not appear in r_1027's kinetic law. +// An interaction was declared that claims e_0321 modifies r_1027, but e_0321 does not appear in r_1027's kinetic law. +// An interaction was declared that claims e_0633 modifies r_1038, but e_0633 does not appear in r_1038's kinetic law. +// An interaction was declared that claims e_0218 modifies r_1038, but e_0218 does not appear in r_1038's kinetic law. +// An interaction was declared that claims e_0398 modifies r_1038, but e_0398 does not appear in r_1038's kinetic law. +// An interaction was declared that claims e_0448 modifies r_1038, but e_0448 does not appear in r_1038's kinetic law. +// An interaction was declared that claims e_0915 modifies r_1038, but e_0915 does not appear in r_1038's kinetic law. +// An interaction was declared that claims e_0124 modifies r_1038, but e_0124 does not appear in r_1038's kinetic law. +// An interaction was declared that claims e_0122 modifies r_1041, but e_0122 does not appear in r_1041's kinetic law. +// An interaction was declared that claims e_0470 modifies r_1042, but e_0470 does not appear in r_1042's kinetic law. +// An interaction was declared that claims e_0850 modifies r_1045, but e_0850 does not appear in r_1045's kinetic law. +// An interaction was declared that claims e_0684 modifies r_1048, but e_0684 does not appear in r_1048's kinetic law. +// An interaction was declared that claims e_0063 modifies r_1049, but e_0063 does not appear in r_1049's kinetic law. +// An interaction was declared that claims e_0962 modifies r_1049, but e_0962 does not appear in r_1049's kinetic law. +// An interaction was declared that claims e_0063 modifies r_1050, but e_0063 does not appear in r_1050's kinetic law. +// An interaction was declared that claims e_0962 modifies r_1050, but e_0962 does not appear in r_1050's kinetic law. +// An interaction was declared that claims e_0711 modifies r_1051, but e_0711 does not appear in r_1051's kinetic law. +// An interaction was declared that claims e_0065 modifies r_1051, but e_0065 does not appear in r_1051's kinetic law. +// An interaction was declared that claims e_0179 modifies r_1051, but e_0179 does not appear in r_1051's kinetic law. +// An interaction was declared that claims e_0753 modifies r_1051, but e_0753 does not appear in r_1051's kinetic law. +// An interaction was declared that claims e_0176 modifies r_1052, but e_0176 does not appear in r_1052's kinetic law. +// An interaction was declared that claims e_0611 modifies r_1052, but e_0611 does not appear in r_1052's kinetic law. +// An interaction was declared that claims e_0765 modifies r_1052, but e_0765 does not appear in r_1052's kinetic law. +// An interaction was declared that claims e_0851 modifies r_1052, but e_0851 does not appear in r_1052's kinetic law. +// An interaction was declared that claims e_0175 modifies r_1054, but e_0175 does not appear in r_1054's kinetic law. +// An interaction was declared that claims e_0330 modifies r_1055, but e_0330 does not appear in r_1055's kinetic law. +// An interaction was declared that claims e_0836 modifies r_1057, but e_0836 does not appear in r_1057's kinetic law. +// An interaction was declared that claims e_0348 modifies r_1063, but e_0348 does not appear in r_1063's kinetic law. +// An interaction was declared that claims e_0629 modifies r_1063, but e_0629 does not appear in r_1063's kinetic law. +// An interaction was declared that claims e_0390 modifies r_1066, but e_0390 does not appear in r_1066's kinetic law. +// An interaction was declared that claims e_0561 modifies r_1072, but e_0561 does not appear in r_1072's kinetic law. +// An interaction was declared that claims e_0565 modifies r_1084, but e_0565 does not appear in r_1084's kinetic law. +// An interaction was declared that claims e_0550 modifies r_1087, but e_0550 does not appear in r_1087's kinetic law. +// An interaction was declared that claims e_0457 modifies r_1087, but e_0457 does not appear in r_1087's kinetic law. +// An interaction was declared that claims e_0372 modifies r_1089, but e_0372 does not appear in r_1089's kinetic law. + model *MODEL1302140004() // Compartments and Species: @@ -453,6 +917,469 @@ model *MODEL1302140004() r_2030: s_0313 -> s_0314 + s_1322; cell*r_2030_Vmax*(s_0313 - s_0314*s_1322/r_2030_Keq)/r_2030_Km0313/(1 + s_0313/r_2030_Km0313 + (1 + s_0314/r_2030_Km0314)*(1 + s_1322/r_2030_Km1322) - 1); r_2111: 1.1348 s_0002 + 0.046 s_0423 + 59.276 s_0434 + 0.0447 s_0526 + 0.0036 s_0584 + 0.0024 s_0589 + 0.0024 s_0615 + 0.0036 s_0649 + 0.5185 s_0773 + 0.046 s_0782 + 0.8079 s_1107 + 0.00099 s_1405 + 0.02 s_1467 + 0.0234 s_1520 + 0.0599 s_1545 + 1.1348 s_0004 + 0.4588 s_0404 + 0.1607 s_0428 + 0.1017 s_0430 + 0.2975 s_0432 + 0.0066 s_0542 + 0.1054 s_0747 + 0.3018 s_0748 + 0.2904 s_0757 + 0.0663 s_0832 + 0.1927 s_0847 + 0.2964 s_1077 + 0.2862 s_1099 + 0.0507 s_1148 + 0.1339 s_1314 + 0.1647 s_1379 + 0.00039 s_1337 + 0.001583 s_0089 + 0.1854 s_1428 + 0.1914 s_1491 + 0.0284 s_1527 + 0.102 s_1533 + 0.2646 s_1561 + 5.6e-05 s_0122 + 0.000538625 s_0918 + 9.6e-05 s_0657 + 0.000125 s_0662 + 0.0056 s_0666 + 0.000812 s_0672 + 0.000892667 s_0056 + 0.000114 s_0700 + 3.2e-05 s_1059 + 0.00288 s_1346 + 0.000697 s_1351 + 0.000781 s_1524 + 1.5e-05 s_1569 => 59.276 s_0394 + 58.7 s_1322 + 0.4588 s_1582 + 0.1607 s_1583 + 0.1017 s_1585 + 0.2975 s_1587 + 0.0066 s_1589 + 0.1054 s_1590 + 0.3018 s_1591 + 0.2904 s_1593 + 0.0663 s_1594 + 0.1927 s_1596 + 0.2964 s_1598 + 0.2862 s_1600 + 0.0507 s_1602 + 0.1339 s_1604 + 0.1647 s_1606 + 0.1854 s_1607 + 0.1914 s_1608 + 0.0284 s_1610 + 0.102 s_1612 + 0.2646 s_1614; cell*((r_2111_V0*(1 + r_2111_ep0002*ln(s_0002/r_2111_ic0002) + r_2111_ep0423*ln(s_0423/r_2111_ic0423) + r_2111_ep0434*ln(s_0434/r_2111_ic0434) + r_2111_ep0526*ln(s_0526/r_2111_ic0526) + r_2111_ep0584*ln(s_0584/r_2111_ic0584) + r_2111_ep0589*ln(s_0589/r_2111_ic0589) + r_2111_ep0615*ln(s_0615/r_2111_ic0615) + r_2111_ep0649*ln(s_0649/r_2111_ic0649) + r_2111_ep0773*ln(s_0773/r_2111_ic0773) + r_2111_ep0782*ln(s_0782/r_2111_ic0782) + r_2111_ep1107*ln(s_1107/r_2111_ic1107) + r_2111_ep1405*ln(s_1405/r_2111_ic1405) + r_2111_ep1467*ln(s_1467/r_2111_ic1467) + r_2111_ep1520*ln(s_1520/r_2111_ic1520) + r_2111_ep1545*ln(s_1545/r_2111_ic1545) + r_2111_ep0004*ln(s_0004/r_2111_ic0004) + r_2111_ep0404*ln(s_0404/r_2111_ic0404) + r_2111_ep0428*ln(s_0428/r_2111_ic0428) + r_2111_ep0430*ln(s_0430/r_2111_ic0430) + r_2111_ep0432*ln(s_0432/r_2111_ic0432) + r_2111_ep0542*ln(s_0542/r_2111_ic0542) + r_2111_ep0747*ln(s_0747/r_2111_ic0747) + r_2111_ep0748*ln(s_0748/r_2111_ic0748) + r_2111_ep0757*ln(s_0757/r_2111_ic0757) + r_2111_ep0832*ln(s_0832/r_2111_ic0832) + r_2111_ep0847*ln(s_0847/r_2111_ic0847) + r_2111_ep1077*ln(s_1077/r_2111_ic1077) + r_2111_ep1099*ln(s_1099/r_2111_ic1099) + r_2111_ep1148*ln(s_1148/r_2111_ic1148) + r_2111_ep1314*ln(s_1314/r_2111_ic1314) + r_2111_ep1379*ln(s_1379/r_2111_ic1379) + r_2111_ep1337*ln(s_1337/r_2111_ic1337) + r_2111_ep0089*ln(s_0089/r_2111_ic0089) + r_2111_ep1428*ln(s_1428/r_2111_ic1428) + r_2111_ep1491*ln(s_1491/r_2111_ic1491) + r_2111_ep1527*ln(s_1527/r_2111_ic1527) + r_2111_ep1533*ln(s_1533/r_2111_ic1533) + r_2111_ep1561*ln(s_1561/r_2111_ic1561) + r_2111_ep0122*ln(s_0122/r_2111_ic0122) + r_2111_ep0918*ln(s_0918/r_2111_ic0918) + r_2111_ep0657*ln(s_0657/r_2111_ic0657) + r_2111_ep0662*ln(s_0662/r_2111_ic0662) + r_2111_ep0666*ln(s_0666/r_2111_ic0666) + r_2111_ep0672*ln(s_0672/r_2111_ic0672) + r_2111_ep0056*ln(s_0056/r_2111_ic0056) + r_2111_ep0700*ln(s_0700/r_2111_ic0700) + r_2111_ep1059*ln(s_1059/r_2111_ic1059) + r_2111_ep1346*ln(s_1346/r_2111_ic1346) + r_2111_ep1351*ln(s_1351/r_2111_ic1351) + r_2111_ep1524*ln(s_1524/r_2111_ic1524) + r_2111_ep1569*ln(s_1569/r_2111_ic1569)) + r_2111_zero_flux + abs(r_2111_V0*(1 + r_2111_ep0002*ln(s_0002/r_2111_ic0002) + r_2111_ep0423*ln(s_0423/r_2111_ic0423) + r_2111_ep0434*ln(s_0434/r_2111_ic0434) + r_2111_ep0526*ln(s_0526/r_2111_ic0526) + r_2111_ep0584*ln(s_0584/r_2111_ic0584) + r_2111_ep0589*ln(s_0589/r_2111_ic0589) + r_2111_ep0615*ln(s_0615/r_2111_ic0615) + r_2111_ep0649*ln(s_0649/r_2111_ic0649) + r_2111_ep0773*ln(s_0773/r_2111_ic0773) + r_2111_ep0782*ln(s_0782/r_2111_ic0782) + r_2111_ep1107*ln(s_1107/r_2111_ic1107) + r_2111_ep1405*ln(s_1405/r_2111_ic1405) + r_2111_ep1467*ln(s_1467/r_2111_ic1467) + r_2111_ep1520*ln(s_1520/r_2111_ic1520) + r_2111_ep1545*ln(s_1545/r_2111_ic1545) + r_2111_ep0004*ln(s_0004/r_2111_ic0004) + r_2111_ep0404*ln(s_0404/r_2111_ic0404) + r_2111_ep0428*ln(s_0428/r_2111_ic0428) + r_2111_ep0430*ln(s_0430/r_2111_ic0430) + r_2111_ep0432*ln(s_0432/r_2111_ic0432) + r_2111_ep0542*ln(s_0542/r_2111_ic0542) + r_2111_ep0747*ln(s_0747/r_2111_ic0747) + r_2111_ep0748*ln(s_0748/r_2111_ic0748) + r_2111_ep0757*ln(s_0757/r_2111_ic0757) + r_2111_ep0832*ln(s_0832/r_2111_ic0832) + r_2111_ep0847*ln(s_0847/r_2111_ic0847) + r_2111_ep1077*ln(s_1077/r_2111_ic1077) + r_2111_ep1099*ln(s_1099/r_2111_ic1099) + r_2111_ep1148*ln(s_1148/r_2111_ic1148) + r_2111_ep1314*ln(s_1314/r_2111_ic1314) + r_2111_ep1379*ln(s_1379/r_2111_ic1379) + r_2111_ep1337*ln(s_1337/r_2111_ic1337) + r_2111_ep0089*ln(s_0089/r_2111_ic0089) + r_2111_ep1428*ln(s_1428/r_2111_ic1428) + r_2111_ep1491*ln(s_1491/r_2111_ic1491) + r_2111_ep1527*ln(s_1527/r_2111_ic1527) + r_2111_ep1533*ln(s_1533/r_2111_ic1533) + r_2111_ep1561*ln(s_1561/r_2111_ic1561) + r_2111_ep0122*ln(s_0122/r_2111_ic0122) + r_2111_ep0918*ln(s_0918/r_2111_ic0918) + r_2111_ep0657*ln(s_0657/r_2111_ic0657) + r_2111_ep0662*ln(s_0662/r_2111_ic0662) + r_2111_ep0666*ln(s_0666/r_2111_ic0666) + r_2111_ep0672*ln(s_0672/r_2111_ic0672) + r_2111_ep0056*ln(s_0056/r_2111_ic0056) + r_2111_ep0700*ln(s_0700/r_2111_ic0700) + r_2111_ep1059*ln(s_1059/r_2111_ic1059) + r_2111_ep1346*ln(s_1346/r_2111_ic1346) + r_2111_ep1351*ln(s_1351/r_2111_ic1351) + r_2111_ep1524*ln(s_1524/r_2111_ic1524) + r_2111_ep1569*ln(s_1569/r_2111_ic1569)) - r_2111_zero_flux))/2); + // Interactions: + _I0: $e_0682 -o r_0005; ; + _I1: $e_0364 -o r_0005; ; + _I2: $e_0973 -o r_0006; ; + _I3: $e_0379 -o r_0006; ; + _I4: $e_0465 -o r_0007; ; + _I5: $e_0869 -o r_0008; ; + _I6: $e_0133 -o r_0008; ; + _I7: $e_0117 -o r_0008; ; + _I8: $e_0431 -o r_0012; ; + _I9: $e_0832 -o r_0014; ; + _I10: $e_0071 -o r_0015; ; + _I11: $e_0734 -o r_0016; ; + _I12: $e_0100 -o r_0016; ; + _I13: $e_0348 -o r_0018; ; + _I14: $e_0496 -o r_0018; ; + _I15: $e_0980 -o r_0018; ; + _I16: $e_0169 -o r_0020; ; + _I17: $e_0088 -o r_0020; ; + _I18: $e_0328 -o r_0023; ; + _I19: $e_0778 -o r_0024; ; + _I20: $e_0855 -o r_0024; ; + _I21: $e_0196 -o r_0027; ; + _I22: $e_0550 -o r_0029; ; + _I23: $e_0457 -o r_0029; ; + _I24: $e_0830 -o r_0032; ; + _I25: $e_0237 -o r_0038; ; + _I26: $e_0182 -o r_0039; ; + _I27: $e_0182 -o r_0040; ; + _I28: $e_0092 -o r_0041; ; + _I29: $e_0328 -o r_0060; ; + _I30: $e_0101 -o r_0061; ; + _I31: $e_0182 -o r_0065; ; + _I32: $e_0368 -o r_0079; ; + _I33: $e_0340 -o r_0080; ; + _I34: $e_0903 -o r_0080; ; + _I35: $e_0685 -o r_0096; ; + _I36: $e_0734 -o r_0097; ; + _I37: $e_0100 -o r_0097; ; + _I38: $e_0904 -o r_0103; ; + _I39: $e_0744 -o r_0108; ; + _I40: $e_0808 -o r_0108; ; + _I41: $e_0022 -o r_0110; ; + _I42: $e_0290 -o r_0115; ; + _I43: $e_0840 -o r_0118; ; + _I44: $e_0541 -o r_0142; ; + _I45: $e_0280 -o r_0144; ; + _I46: $e_0194 -o r_0148; ; + _I47: $e_0303 -o r_0148; ; + _I48: $e_0686 -o r_0151; ; + _I49: $e_0686 -o r_0152; ; + _I50: $e_0791 -o r_0153; ; + _I51: $e_0556 -o r_0154; ; + _I52: $e_0894 -o r_0157; ; + _I53: $e_0711 -o r_0195; ; + _I54: $e_0065 -o r_0195; ; + _I55: $e_0179 -o r_0195; ; + _I56: $e_0753 -o r_0195; ; + _I57: $e_0219 -o r_0202; ; + _I58: $e_0297 -o r_0203; ; + _I59: $e_0591 -o r_0203; ; + _I60: $e_0426 -o r_0207; ; + _I61: $e_0826 -o r_0208; ; + _I62: $e_0214 -o r_0209; ; + _I63: $e_0970 -o r_0211; ; + _I64: $e_0376 -o r_0211; ; + _I65: $e_0427 -o r_0212; ; + _I66: $e_0508 -o r_0214; ; + _I67: $e_0281 -o r_0215; ; + _I68: $e_0629 -o r_0216; ; + _I69: $e_0574 -o r_0216; ; + _I70: $e_0186 -o r_0219; ; + _I71: $e_0615 -o r_0220; ; + _I72: $e_0283 -o r_0225; ; + _I73: $e_0800 -o r_0231; ; + _I74: $e_0724 -o r_0233; ; + _I75: $e_0326 -o r_0234; ; + _I76: $e_0326 -o r_0235; ; + _I77: $e_0644 -o r_0236; ; + _I78: $e_0644 -o r_0237; ; + _I79: $e_0367 -o r_0238; ; + _I80: $e_0367 -o r_0239; ; + _I81: $e_0367 -o r_0240; ; + _I82: $e_0367 -o r_0241; ; + _I83: $e_0637 -o r_0242; ; + _I84: $e_0742 -o r_0243; ; + _I85: $e_0329 -o r_0244; ; + _I86: $e_0508 -o r_0250; ; + _I87: $e_0542 -o r_0250; ; + _I88: $e_0888 -o r_0250; ; + _I89: $e_0045 -o r_0257; ; + _I90: $e_0206 -o r_0259; ; + _I91: $e_0756 -o r_0267; ; + _I92: $e_0756 -o r_0269; ; + _I93: $e_0959 -o r_0278; ; + _I94: $e_0342 -o r_0279; ; + _I95: $e_0675 -o r_0280; ; + _I96: $e_0947 -o r_0300; ; + _I97: $e_0805 -o r_0300; ; + _I98: $e_0111 -o r_0300; ; + _I99: $e_0675 -o r_0302; ; + _I100: $e_0540 -o r_0307; ; + _I101: $e_0026 -o r_0307; ; + _I102: $e_0380 -o r_0309; ; + _I103: $e_0008 -o r_0310; ; + _I104: $e_0545 -o r_0311; ; + _I105: $e_0793 -o r_0313; ; + _I106: $e_0434 -o r_0317; ; + _I107: $e_0424 -o r_0317; ; + _I108: $e_0452 -o r_0326; ; + _I109: $e_0234 -o r_0330; ; + _I110: $e_0883 -o r_0336; ; + _I111: $e_0203 -o r_0337; ; + _I112: $e_0594 -o r_0339; ; + _I113: $e_0914 -o r_0340; ; + _I114: $e_0880 -o r_0344; ; + _I115: $e_0692 -o r_0349; ; + _I116: $e_0528 -o r_0352; ; + _I117: $e_0528 -o r_0353; ; + _I118: $e_0515 -o r_0355; ; + _I119: $e_0976 -o r_0361; ; + _I120: $e_0141 -o r_0362; ; + _I121: $e_0549 -o r_0362; ; + _I122: $e_0010 -o r_0362; ; + _I123: $e_0890 -o r_0362; ; + _I124: $e_0142 -o r_0362; ; + _I125: $e_0089 -o r_0364; ; + _I126: $e_0405 -o r_0366; ; + _I127: $e_0454 -o r_0366; ; + _I128: $e_0808 -o r_0386; ; + _I129: $e_0365 -o r_0386; ; + _I130: $e_0586 -o r_0386; ; + _I131: $e_0934 -o r_0386; ; + _I132: $e_0808 -o r_0387; ; + _I133: $e_0365 -o r_0387; ; + _I134: $e_0586 -o r_0387; ; + _I135: $e_0934 -o r_0387; ; + _I136: $e_0808 -o r_0389; ; + _I137: $e_0365 -o r_0389; ; + _I138: $e_0586 -o r_0389; ; + _I139: $e_0934 -o r_0389; ; + _I140: $e_0808 -o r_0391; ; + _I141: $e_0365 -o r_0391; ; + _I142: $e_0586 -o r_0391; ; + _I143: $e_0934 -o r_0391; ; + _I144: $e_0128 -o r_0393; ; + _I145: $e_0117 -o r_0393; ; + _I146: $e_0687 -o r_0393; ; + _I147: $e_0808 -o r_0397; ; + _I148: $e_0365 -o r_0397; ; + _I149: $e_0586 -o r_0397; ; + _I150: $e_0934 -o r_0397; ; + _I151: $e_0808 -o r_0398; ; + _I152: $e_0365 -o r_0398; ; + _I153: $e_0586 -o r_0398; ; + _I154: $e_0934 -o r_0398; ; + _I155: $e_0273 -o r_0399; ; + _I156: $e_0273 -o r_0400; ; + _I157: $e_0750 -o r_0407; ; + _I158: $e_0889 -o r_0407; ; + _I159: $e_0462 -o r_0407; ; + _I160: $e_0808 -o r_0432; ; + _I161: $e_0365 -o r_0432; ; + _I162: $e_0586 -o r_0432; ; + _I163: $e_0934 -o r_0432; ; + _I164: $e_0808 -o r_0433; ; + _I165: $e_0365 -o r_0433; ; + _I166: $e_0586 -o r_0433; ; + _I167: $e_0934 -o r_0433; ; + _I168: $e_0808 -o r_0434; ; + _I169: $e_0365 -o r_0434; ; + _I170: $e_0586 -o r_0434; ; + _I171: $e_0934 -o r_0434; ; + _I172: $e_0808 -o r_0435; ; + _I173: $e_0365 -o r_0435; ; + _I174: $e_0586 -o r_0435; ; + _I175: $e_0934 -o r_0435; ; + _I176: $e_0632 -o r_0438; ; + _I177: $e_0007 -o r_0438; ; + _I178: $e_0774 -o r_0438; ; + _I179: $e_0436 -o r_0438; ; + _I180: $e_0136 -o r_0438; ; + _I181: $e_0001 -o r_0438; ; + _I182: $e_0347 -o r_0438; ; + _I183: $e_0255 -o r_0438; ; + _I184: $e_0752 -o r_0438; ; + _I185: $e_0690 -o r_0438; ; + _I186: $e_0006 -o r_0438; ; + _I187: $e_0531 -o r_0438; ; + _I188: $e_0346 -o r_0438; ; + _I189: $e_0475 -o r_0438; ; + _I190: $e_0514 -o r_0439; ; + _I191: $e_0978 -o r_0439; ; + _I192: $e_0422 -o r_0439; ; + _I193: $e_0250 -o r_0439; ; + _I194: $e_0004 -o r_0439; ; + _I195: $e_0243 -o r_0439; ; + _I196: $e_0389 -o r_0439; ; + _I197: $e_0255 -o r_0439; ; + _I198: $e_0848 -o r_0439; ; + _I199: $e_0028 -o r_0439; ; + _I200: $e_0531 -o r_0439; ; + _I201: $e_0322 -o r_0439; ; + _I202: $e_0396 -o r_0446; ; + _I203: $e_0057 -o r_0446; ; + _I204: $e_0567 -o r_0450; ; + _I205: $e_0940 -o r_0451; ; + _I206: $e_0515 -o r_0462; ; + _I207: $e_0079 -o r_0467; ; + _I208: $e_0160 -o r_0470; ; + _I209: $e_0016 -o r_0471; ; + _I210: $e_0899 -o r_0471; ; + _I211: $e_0955 -o r_0476; ; + _I212: $e_0867 -o r_0478; ; + _I213: $e_0353 -o r_0479; ; + _I214: $e_0242 -o r_0481; ; + _I215: $e_0104 -o r_0481; ; + _I216: $e_0181 -o r_0481; ; + _I217: $e_0304 -o r_0481; ; + _I218: $e_0915 -o r_0481; ; + _I219: $e_0910 -o r_0481; ; + _I220: $e_0242 -o r_0483; ; + _I221: $e_0563 -o r_0483; ; + _I222: $e_0086 -o r_0483; ; + _I223: $e_0104 -o r_0483; ; + _I224: $e_0490 -o r_0483; ; + _I225: $e_0910 -o r_0483; ; + _I226: $e_0392 -o r_0486; ; + _I227: $e_0495 -o r_0486; ; + _I228: $e_0525 -o r_0486; ; + _I229: $e_0129 -o r_0491; ; + _I230: $e_0827 -o r_0491; ; + _I231: $e_0020 -o r_0495; ; + _I232: $e_0607 -o r_0495; ; + _I233: $e_0231 -o r_0499; ; + _I234: $e_0741 -o r_0501; ; + _I235: $e_0012 -o r_0501; ; + _I236: $e_0167 -o r_0501; ; + _I237: $e_0311 -o r_0501; ; + _I238: $e_0638 -o r_0502; ; + _I239: $e_0091 -o r_0502; ; + _I240: $e_0667 -o r_0510; ; + _I241: $e_0510 -o r_0510; ; + _I242: $e_0317 -o r_0510; ; + _I243: $e_0603 -o r_0510; ; + _I244: $e_0064 -o r_0512; ; + _I245: $e_0963 -o r_0512; ; + _I246: $e_0746 -o r_0514; ; + _I247: $e_0025 -o r_0525; ; + _I248: $e_0234 -o r_0528; ; + _I249: $e_0234 -o r_0529; ; + _I250: $e_0106 -o r_0534; ; + _I251: $e_0325 -o r_0534; ; + _I252: $e_0355 -o r_0534; ; + _I253: $e_0103 -o r_0536; ; + _I254: $e_0320 -o r_0537; ; + _I255: $e_0476 -o r_0538; ; + _I256: $e_0953 -o r_0539; ; + _I257: $e_0196 -o r_0542; ; + _I258: $e_0154 -o r_0543; ; + _I259: $e_0146 -o r_0543; ; + _I260: $e_0472 -o r_0545; ; + _I261: $e_0548 -o r_0547; ; + _I262: $e_0428 -o r_0548; ; + _I263: $e_0799 -o r_0549; ; + _I264: $e_0633 -o r_0550; ; + _I265: $e_0398 -o r_0550; ; + _I266: $e_0233 -o r_0550; ; + _I267: $e_0463 -o r_0550; ; + _I268: $e_0645 -o r_0550; ; + _I269: $e_0029 -o r_0550; ; + _I270: $e_0124 -o r_0550; ; + _I271: $e_0697 -o r_0558; ; + _I272: $e_0708 -o r_0558; ; + _I273: $e_0716 -o r_0559; ; + _I274: $e_0087 -o r_0563; ; + _I275: $e_0875 -o r_0564; ; + _I276: $e_0705 -o r_0565; ; + _I277: $e_0458 -o r_0565; ; + _I278: $e_0693 -o r_0565; ; + _I279: $e_0591 -o r_0566; ; + _I280: $e_0038 -o r_0568; ; + _I281: $e_0754 -o r_0568; ; + _I282: $e_0631 -o r_0570; ; + _I283: $e_0736 -o r_0570; ; + _I284: $e_0557 -o r_0594; ; + _I285: $e_0220 -o r_0594; ; + _I286: $e_0862 -o r_0658; ; + _I287: $e_0771 -o r_0658; ; + _I288: $e_0769 -o r_0661; ; + _I289: $e_0135 -o r_0661; ; + _I290: $e_0550 -o r_0663; ; + _I291: $e_0457 -o r_0663; ; + _I292: $e_0031 -o r_0665; ; + _I293: $e_0922 -o r_0667; ; + _I294: $e_0685 -o r_0669; ; + _I295: $e_0642 -o r_0674; ; + _I296: $e_0062 -o r_0678; ; + _I297: $e_0343 -o r_0678; ; + _I298: $e_0440 -o r_0698; ; + _I299: $e_0550 -o r_0699; ; + _I300: $e_0457 -o r_0699; ; + _I301: $e_0926 -o r_0701; ; + _I302: $e_0171 -o r_0711; ; + _I303: $e_0571 -o r_0713; ; + _I304: $e_0838 -o r_0713; ; + _I305: $e_0137 -o r_0713; ; + _I306: $e_0134 -o r_0722; ; + _I307: $e_0269 -o r_0723; ; + _I308: $e_0057 -o r_0724; ; + _I309: $e_0396 -o r_0724; ; + _I310: $e_0239 -o r_0726; ; + _I311: $e_0658 -o r_0726; ; + _I312: $e_0298 -o r_0727; ; + _I313: $e_0409 -o r_0729; ; + _I314: $e_0610 -o r_0731; ; + _I315: $e_0396 -o r_0732; ; + _I316: $e_0057 -o r_0732; ; + _I317: $e_0745 -o r_0736; ; + _I318: $e_0812 -o r_0739; ; + _I319: $e_0204 -o r_0757; ; + _I320: $e_0435 -o r_0757; ; + _I321: $e_0512 -o r_0758; ; + _I322: $e_0290 -o r_0759; ; + _I323: $e_0139 -o r_0770; ; + _I324: $e_0737 -o r_0770; ; + _I325: $e_0714 -o r_0770; ; + _I326: $e_0271 -o r_0792; ; + _I327: $e_0568 -o r_0800; ; + _I328: $e_0568 -o r_0811; ; + _I329: $e_0674 -o r_0813; ; + _I330: $e_0499 -o r_0816; ; + _I331: $e_0729 -o r_0818; ; + _I332: $e_0755 -o r_0820; ; + _I333: $e_0712 -o r_0820; ; + _I334: $e_0249 -o r_0821; ; + _I335: $e_0348 -o r_0851; ; + _I336: $e_0639 -o r_0852; ; + _I337: $e_0312 -o r_0852; ; + _I338: $e_0352 -o r_0855; ; + _I339: $e_0536 -o r_0858; ; + _I340: $e_0381 -o r_0858; ; + _I341: $e_0964 -o r_0874; ; + _I342: $e_0788 -o r_0877; ; + _I343: $e_0382 -o r_0877; ; + _I344: $e_0278 -o r_0880; ; + _I345: $e_0633 -o r_0883; ; + _I346: $e_0975 -o r_0883; ; + _I347: $e_0398 -o r_0883; ; + _I348: $e_0401 -o r_0886; ; + _I349: $e_0743 -o r_0886; ; + _I350: $e_0576 -o r_0888; ; + _I351: $e_0757 -o r_0888; ; + _I352: $e_0733 -o r_0888; ; + _I353: $e_0294 -o r_0891; ; + _I354: $e_0469 -o r_0891; ; + _I355: $e_0113 -o r_0892; ; + _I356: $e_0582 -o r_0893; ; + _I357: $e_0536 -o r_0900; ; + _I358: $e_0536 -o r_0901; ; + _I359: $e_0314 -o r_0902; ; + _I360: $e_0747 -o r_0904; ; + _I361: $e_0017 -o r_0908; ; + _I362: $e_0103 -o r_0909; ; + _I363: $e_0103 -o r_0910; ; + _I364: $e_0860 -o r_0911; ; + _I365: $e_0631 -o r_0912; ; + _I366: $e_0736 -o r_0912; ; + _I367: $e_0165 -o r_0913; ; + _I368: $e_0352 -o r_0914; ; + _I369: $e_0763 -o r_0915; ; + _I370: $e_0030 -o r_0916; ; + _I371: $e_0299 -o r_0916; ; + _I372: $e_0418 -o r_0916; ; + _I373: $e_0585 -o r_0916; ; + _I374: $e_0829 -o r_0916; ; + _I375: $e_0397 -o r_0917; ; + _I376: $e_0872 -o r_0918; ; + _I377: $e_0077 -o r_0919; ; + _I378: $e_0206 -o r_0922; ; + _I379: $e_0802 -o r_0938; ; + _I380: $e_0074 -o r_0939; ; + _I381: $e_0296 -o r_0941; ; + _I382: $e_0276 -o r_0957; ; + _I383: $e_0334 -o r_0958; ; + _I384: $e_0084 -o r_0958; ; + _I385: $e_0085 -o r_0961; ; + _I386: $e_0306 -o r_0961; ; + _I387: $e_0393 -o r_0961; ; + _I388: $e_0311 -o r_0961; ; + _I389: $e_0775 -o r_0961; ; + _I390: $e_0011 -o r_0962; ; + _I391: $e_0895 -o r_0962; ; + _I392: $e_0841 -o r_0967; ; + _I393: $e_0090 -o r_0968; ; + _I394: $e_0398 -o r_0970; ; + _I395: $e_0398 -o r_0973; ; + _I396: $e_0467 -o r_0974; ; + _I397: $e_0492 -o r_0974; ; + _I398: $e_0387 -o r_0974; ; + _I399: $e_0291 -o r_0974; ; + _I400: $e_0467 -o r_0976; ; + _I401: $e_0492 -o r_0976; ; + _I402: $e_0387 -o r_0976; ; + _I403: $e_0291 -o r_0976; ; + _I404: $e_0467 -o r_0978; ; + _I405: $e_0492 -o r_0978; ; + _I406: $e_0387 -o r_0978; ; + _I407: $e_0291 -o r_0978; ; + _I408: $e_0852 -o r_0982; ; + _I409: $e_0506 -o r_0984; ; + _I410: $e_0699 -o r_0986; ; + _I411: $e_0489 -o r_0988; ; + _I412: $e_0813 -o r_0989; ; + _I413: $e_0054 -o r_0993; ; + _I414: $e_0177 -o r_0993; ; + _I415: $e_0761 -o r_0993; ; + _I416: $e_0168 -o r_0995; ; + _I417: $e_0425 -o r_0995; ; + _I418: $e_0182 -o r_0996; ; + _I419: $e_0182 -o r_0997; ; + _I420: $e_0385 -o r_1010; ; + _I421: $e_0385 -o r_1011; ; + _I422: $e_0456 -o r_1012; ; + _I423: $e_0578 -o r_1014; ; + _I424: $e_0613 -o r_1014; ; + _I425: $e_0107 -o r_1026; ; + _I426: $e_0547 -o r_1027; ; + _I427: $e_0321 -o r_1027; ; + _I428: $e_0633 -o r_1038; ; + _I429: $e_0218 -o r_1038; ; + _I430: $e_0398 -o r_1038; ; + _I431: $e_0448 -o r_1038; ; + _I432: $e_0915 -o r_1038; ; + _I433: $e_0124 -o r_1038; ; + _I434: $e_0122 -o r_1041; ; + _I435: $e_0470 -o r_1042; ; + _I436: $e_0850 -o r_1045; ; + _I437: $e_0684 -o r_1048; ; + _I438: $e_0063 -o r_1049; ; + _I439: $e_0962 -o r_1049; ; + _I440: $e_0063 -o r_1050; ; + _I441: $e_0962 -o r_1050; ; + _I442: $e_0711 -o r_1051; ; + _I443: $e_0065 -o r_1051; ; + _I444: $e_0179 -o r_1051; ; + _I445: $e_0753 -o r_1051; ; + _I446: $e_0176 -o r_1052; ; + _I447: $e_0611 -o r_1052; ; + _I448: $e_0765 -o r_1052; ; + _I449: $e_0851 -o r_1052; ; + _I450: $e_0175 -o r_1054; ; + _I451: $e_0330 -o r_1055; ; + _I452: $e_0836 -o r_1057; ; + _I453: $e_0348 -o r_1063; ; + _I454: $e_0629 -o r_1063; ; + _I455: $e_0390 -o r_1066; ; + _I456: $e_0561 -o r_1072; ; + _I457: $e_0565 -o r_1084; ; + _I458: $e_0550 -o r_1087; ; + _I459: $e_0457 -o r_1087; ; + _I460: $e_0372 -o r_1089; ; + // Species initializations: s_0002 = 0.1; s_0004 = 0.1; @@ -6493,7 +7420,7 @@ model *MODEL1302140004() s_1192.sboTerm = 247 s_1194.sboTerm = 247 s_1198.sboTerm = 247 - s_1203.sboTerm = 247 + s_1203.sboTerm = 247 s_1207.sboTerm = 247 s_1212.sboTerm = 247 s_1233.sboTerm = 247 @@ -6991,7 +7918,7 @@ model *MODEL1302140004() r_0020_Km0551.sboTerm = 322 r_0020_Km1360.sboTerm = 322 r_0020_Km0349.sboTerm = 323 - r_0020_Km1322.sboTerm = 323 + r_0020_Km1322.sboTerm = 323 r_0023.sboTerm = 176 r_0023_Vmax.sboTerm = 324 r_0023_Keq.sboTerm = 281 @@ -8527,7 +9454,7 @@ model *MODEL1302140004() r_0922_Km1366.sboTerm = 323 r_0938.sboTerm = 176 r_0938_Vmax.sboTerm = 324 - r_0938_Keq.sboTerm = 281 + r_0938_Keq.sboTerm = 281 r_0938_Km1377.sboTerm = 322 r_0938_Km0456.sboTerm = 323 r_0938_Km0951.sboTerm = 323 diff --git a/doc/examples/biomodels/BIOMD0000000473_url.txt b/doc/examples/biomodels/BIOMD0000000473/BIOMD0000000473_url.txt similarity index 85% rename from doc/examples/biomodels/BIOMD0000000473_url.txt rename to doc/examples/biomodels/BIOMD0000000473/BIOMD0000000473_url.txt index f651b3d23..7a0b3f1ba 100644 --- a/doc/examples/biomodels/BIOMD0000000473_url.txt +++ b/doc/examples/biomodels/BIOMD0000000473/BIOMD0000000473_url.txt @@ -1,4 +1,514 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 + +// Warnings from automatic translation: +// An interaction was declared that claims e_0151 modifies r_0001, but e_0151 does not appear in r_0001's kinetic law. +// An interaction was declared that claims e_0268 modifies r_0001, but e_0268 does not appear in r_0001's kinetic law. +// An interaction was declared that claims e_0255 modifies r_0001, but e_0255 does not appear in r_0001's kinetic law. +// An interaction was declared that claims e_0531 modifies r_0001, but e_0531 does not appear in r_0001's kinetic law. +// An interaction was declared that claims e_0152 modifies r_0001, but e_0152 does not appear in r_0001's kinetic law. +// An interaction was declared that claims e_0704 modifies r_0004, but e_0704 does not appear in r_0004's kinetic law. +// An interaction was declared that claims e_0531 modifies r_0004, but e_0531 does not appear in r_0004's kinetic law. +// An interaction was declared that claims e_0255 modifies r_0004, but e_0255 does not appear in r_0004's kinetic law. +// An interaction was declared that claims e_0682 modifies r_0005, but e_0682 does not appear in r_0005's kinetic law. +// An interaction was declared that claims e_0364 modifies r_0005, but e_0364 does not appear in r_0005's kinetic law. +// An interaction was declared that claims e_0973 modifies r_0006, but e_0973 does not appear in r_0006's kinetic law. +// An interaction was declared that claims e_0379 modifies r_0006, but e_0379 does not appear in r_0006's kinetic law. +// An interaction was declared that claims e_0465 modifies r_0007, but e_0465 does not appear in r_0007's kinetic law. +// An interaction was declared that claims e_0869 modifies r_0008, but e_0869 does not appear in r_0008's kinetic law. +// An interaction was declared that claims e_0133 modifies r_0008, but e_0133 does not appear in r_0008's kinetic law. +// An interaction was declared that claims e_0117 modifies r_0008, but e_0117 does not appear in r_0008's kinetic law. +// An interaction was declared that claims e_0431 modifies r_0012, but e_0431 does not appear in r_0012's kinetic law. +// An interaction was declared that claims e_0832 modifies r_0014, but e_0832 does not appear in r_0014's kinetic law. +// An interaction was declared that claims e_0071 modifies r_0015, but e_0071 does not appear in r_0015's kinetic law. +// An interaction was declared that claims e_0734 modifies r_0016, but e_0734 does not appear in r_0016's kinetic law. +// An interaction was declared that claims e_0100 modifies r_0016, but e_0100 does not appear in r_0016's kinetic law. +// An interaction was declared that claims e_0348 modifies r_0018, but e_0348 does not appear in r_0018's kinetic law. +// An interaction was declared that claims e_0496 modifies r_0018, but e_0496 does not appear in r_0018's kinetic law. +// An interaction was declared that claims e_0980 modifies r_0018, but e_0980 does not appear in r_0018's kinetic law. +// An interaction was declared that claims e_0169 modifies r_0020, but e_0169 does not appear in r_0020's kinetic law. +// An interaction was declared that claims e_0088 modifies r_0020, but e_0088 does not appear in r_0020's kinetic law. +// An interaction was declared that claims e_0328 modifies r_0023, but e_0328 does not appear in r_0023's kinetic law. +// An interaction was declared that claims e_0778 modifies r_0024, but e_0778 does not appear in r_0024's kinetic law. +// An interaction was declared that claims e_0855 modifies r_0024, but e_0855 does not appear in r_0024's kinetic law. +// An interaction was declared that claims e_0196 modifies r_0027, but e_0196 does not appear in r_0027's kinetic law. +// An interaction was declared that claims e_0550 modifies r_0029, but e_0550 does not appear in r_0029's kinetic law. +// An interaction was declared that claims e_0457 modifies r_0029, but e_0457 does not appear in r_0029's kinetic law. +// An interaction was declared that claims e_0830 modifies r_0032, but e_0830 does not appear in r_0032's kinetic law. +// An interaction was declared that claims e_0237 modifies r_0038, but e_0237 does not appear in r_0038's kinetic law. +// An interaction was declared that claims e_0182 modifies r_0039, but e_0182 does not appear in r_0039's kinetic law. +// An interaction was declared that claims e_0182 modifies r_0040, but e_0182 does not appear in r_0040's kinetic law. +// An interaction was declared that claims e_0092 modifies r_0041, but e_0092 does not appear in r_0041's kinetic law. +// An interaction was declared that claims e_0328 modifies r_0060, but e_0328 does not appear in r_0060's kinetic law. +// An interaction was declared that claims e_0101 modifies r_0061, but e_0101 does not appear in r_0061's kinetic law. +// An interaction was declared that claims e_0182 modifies r_0065, but e_0182 does not appear in r_0065's kinetic law. +// An interaction was declared that claims e_0368 modifies r_0079, but e_0368 does not appear in r_0079's kinetic law. +// An interaction was declared that claims e_0340 modifies r_0080, but e_0340 does not appear in r_0080's kinetic law. +// An interaction was declared that claims e_0903 modifies r_0080, but e_0903 does not appear in r_0080's kinetic law. +// An interaction was declared that claims e_0453 modifies r_0091, but e_0453 does not appear in r_0091's kinetic law. +// An interaction was declared that claims e_0404 modifies r_0091, but e_0404 does not appear in r_0091's kinetic law. +// An interaction was declared that claims e_0685 modifies r_0096, but e_0685 does not appear in r_0096's kinetic law. +// An interaction was declared that claims e_0734 modifies r_0097, but e_0734 does not appear in r_0097's kinetic law. +// An interaction was declared that claims e_0100 modifies r_0097, but e_0100 does not appear in r_0097's kinetic law. +// An interaction was declared that claims e_0904 modifies r_0103, but e_0904 does not appear in r_0103's kinetic law. +// An interaction was declared that claims e_0744 modifies r_0108, but e_0744 does not appear in r_0108's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0108, but e_0808 does not appear in r_0108's kinetic law. +// An interaction was declared that claims e_0022 modifies r_0110, but e_0022 does not appear in r_0110's kinetic law. +// An interaction was declared that claims e_0290 modifies r_0115, but e_0290 does not appear in r_0115's kinetic law. +// An interaction was declared that claims e_0840 modifies r_0118, but e_0840 does not appear in r_0118's kinetic law. +// An interaction was declared that claims e_0541 modifies r_0142, but e_0541 does not appear in r_0142's kinetic law. +// An interaction was declared that claims e_0280 modifies r_0144, but e_0280 does not appear in r_0144's kinetic law. +// An interaction was declared that claims e_0194 modifies AK, but e_0194 does not appear in AK's kinetic law. +// An interaction was declared that claims e_0303 modifies AK, but e_0303 does not appear in AK's kinetic law. +// An interaction was declared that claims e_0303 modifies r_0150, but e_0303 does not appear in r_0150's kinetic law. +// An interaction was declared that claims e_0686 modifies r_0151, but e_0686 does not appear in r_0151's kinetic law. +// An interaction was declared that claims e_0686 modifies r_0152, but e_0686 does not appear in r_0152's kinetic law. +// An interaction was declared that claims e_0791 modifies r_0153, but e_0791 does not appear in r_0153's kinetic law. +// An interaction was declared that claims e_0556 modifies r_0154, but e_0556 does not appear in r_0154's kinetic law. +// An interaction was declared that claims e_0313 modifies r_0156, but e_0313 does not appear in r_0156's kinetic law. +// An interaction was declared that claims e_0894 modifies r_0157, but e_0894 does not appear in r_0157's kinetic law. +// An interaction was declared that claims e_0730 modifies ADH, but e_0730 does not appear in ADH's kinetic law. +// An interaction was declared that claims e_0356 modifies ADH, but e_0356 does not appear in ADH's kinetic law. +// An interaction was declared that claims e_0069 modifies ADH, but e_0069 does not appear in ADH's kinetic law. +// An interaction was declared that claims e_0834 modifies ADH, but e_0834 does not appear in ADH's kinetic law. +// An interaction was declared that claims e_0911 modifies r_0173, but e_0911 does not appear in r_0173's kinetic law. +// An interaction was declared that claims e_0898 modifies r_0173, but e_0898 does not appear in r_0173's kinetic law. +// An interaction was declared that claims e_0293 modifies r_0173, but e_0293 does not appear in r_0173's kinetic law. +// An interaction was declared that claims e_0898 modifies r_0174, but e_0898 does not appear in r_0174's kinetic law. +// An interaction was declared that claims e_0740 modifies r_0174, but e_0740 does not appear in r_0174's kinetic law. +// An interaction was declared that claims e_0711 modifies r_0195, but e_0711 does not appear in r_0195's kinetic law. +// An interaction was declared that claims e_0065 modifies r_0195, but e_0065 does not appear in r_0195's kinetic law. +// An interaction was declared that claims e_0179 modifies r_0195, but e_0179 does not appear in r_0195's kinetic law. +// An interaction was declared that claims e_0753 modifies r_0195, but e_0753 does not appear in r_0195's kinetic law. +// An interaction was declared that claims e_0219 modifies r_0202, but e_0219 does not appear in r_0202's kinetic law. +// An interaction was declared that claims e_0297 modifies r_0203, but e_0297 does not appear in r_0203's kinetic law. +// An interaction was declared that claims e_0591 modifies r_0203, but e_0591 does not appear in r_0203's kinetic law. +// An interaction was declared that claims e_0426 modifies r_0207, but e_0426 does not appear in r_0207's kinetic law. +// An interaction was declared that claims e_0826 modifies r_0208, but e_0826 does not appear in r_0208's kinetic law. +// An interaction was declared that claims e_0214 modifies r_0209, but e_0214 does not appear in r_0209's kinetic law. +// An interaction was declared that claims e_0970 modifies r_0211, but e_0970 does not appear in r_0211's kinetic law. +// An interaction was declared that claims e_0376 modifies r_0211, but e_0376 does not appear in r_0211's kinetic law. +// An interaction was declared that claims e_0427 modifies r_0212, but e_0427 does not appear in r_0212's kinetic law. +// An interaction was declared that claims e_0508 modifies r_0214, but e_0508 does not appear in r_0214's kinetic law. +// An interaction was declared that claims e_0281 modifies r_0215, but e_0281 does not appear in r_0215's kinetic law. +// An interaction was declared that claims e_0629 modifies r_0216, but e_0629 does not appear in r_0216's kinetic law. +// An interaction was declared that claims e_0574 modifies r_0216, but e_0574 does not appear in r_0216's kinetic law. +// An interaction was declared that claims e_0186 modifies r_0219, but e_0186 does not appear in r_0219's kinetic law. +// An interaction was declared that claims e_0615 modifies r_0220, but e_0615 does not appear in r_0220's kinetic law. +// An interaction was declared that claims e_0283 modifies r_0225, but e_0283 does not appear in r_0225's kinetic law. +// An interaction was declared that claims e_0950 modifies r_0226, but e_0950 does not appear in r_0226's kinetic law. +// An interaction was declared that claims e_0944 modifies r_0226, but e_0944 does not appear in r_0226's kinetic law. +// An interaction was declared that claims e_0005 modifies r_0226, but e_0005 does not appear in r_0226's kinetic law. +// An interaction was declared that claims e_0033 modifies r_0226, but e_0033 does not appear in r_0226's kinetic law. +// An interaction was declared that claims e_0207 modifies r_0226, but e_0207 does not appear in r_0226's kinetic law. +// An interaction was declared that claims e_0003 modifies r_0226, but e_0003 does not appear in r_0226's kinetic law. +// An interaction was declared that claims e_0671 modifies r_0226, but e_0671 does not appear in r_0226's kinetic law. +// An interaction was declared that claims e_0002 modifies r_0226, but e_0002 does not appear in r_0226's kinetic law. +// An interaction was declared that claims e_0051 modifies r_0226, but e_0051 does not appear in r_0226's kinetic law. +// An interaction was declared that claims e_0223 modifies r_0226, but e_0223 does not appear in r_0226's kinetic law. +// An interaction was declared that claims e_0709 modifies r_0226, but e_0709 does not appear in r_0226's kinetic law. +// An interaction was declared that claims e_0213 modifies r_0226, but e_0213 does not appear in r_0226's kinetic law. +// An interaction was declared that claims e_0544 modifies r_0226, but e_0544 does not appear in r_0226's kinetic law. +// An interaction was declared that claims e_0559 modifies r_0226, but e_0559 does not appear in r_0226's kinetic law. +// An interaction was declared that claims e_0127 modifies r_0226, but e_0127 does not appear in r_0226's kinetic law. +// An interaction was declared that claims e_0913 modifies r_0226, but e_0913 does not appear in r_0226's kinetic law. +// An interaction was declared that claims e_0727 modifies ATPase, but e_0727 does not appear in ATPase's kinetic law. +// An interaction was declared that claims e_0569 modifies ATPase, but e_0569 does not appear in ATPase's kinetic law. +// An interaction was declared that claims e_0432 modifies ATPase, but e_0432 does not appear in ATPase's kinetic law. +// An interaction was declared that claims e_0263 modifies ATPase, but e_0263 does not appear in ATPase's kinetic law. +// An interaction was declared that claims e_0956 modifies ATPase, but e_0956 does not appear in ATPase's kinetic law. +// An interaction was declared that claims e_0155 modifies ATPase, but e_0155 does not appear in ATPase's kinetic law. +// An interaction was declared that claims e_0892 modifies ATPase, but e_0892 does not appear in ATPase's kinetic law. +// An interaction was declared that claims e_0362 modifies ATPase, but e_0362 does not appear in ATPase's kinetic law. +// An interaction was declared that claims e_0251 modifies ATPase, but e_0251 does not appear in ATPase's kinetic law. +// An interaction was declared that claims e_0695 modifies ATPase, but e_0695 does not appear in ATPase's kinetic law. +// An interaction was declared that claims e_0935 modifies ATPase, but e_0935 does not appear in ATPase's kinetic law. +// An interaction was declared that claims e_0066 modifies ATPase, but e_0066 does not appear in ATPase's kinetic law. +// An interaction was declared that claims e_0429 modifies ATPase, but e_0429 does not appear in ATPase's kinetic law. +// An interaction was declared that claims e_0183 modifies ATPase, but e_0183 does not appear in ATPase's kinetic law. +// An interaction was declared that claims e_0621 modifies ATPase, but e_0621 does not appear in ATPase's kinetic law. +// An interaction was declared that claims e_0884 modifies ATPase, but e_0884 does not appear in ATPase's kinetic law. +// An interaction was declared that claims e_0588 modifies ATPase, but e_0588 does not appear in ATPase's kinetic law. +// An interaction was declared that claims e_0924 modifies ATPase, but e_0924 does not appear in ATPase's kinetic law. +// An interaction was declared that claims e_0800 modifies r_0231, but e_0800 does not appear in r_0231's kinetic law. +// An interaction was declared that claims e_0326 modifies r_0234, but e_0326 does not appear in r_0234's kinetic law. +// An interaction was declared that claims e_0326 modifies r_0235, but e_0326 does not appear in r_0235's kinetic law. +// An interaction was declared that claims e_0644 modifies r_0236, but e_0644 does not appear in r_0236's kinetic law. +// An interaction was declared that claims e_0644 modifies r_0237, but e_0644 does not appear in r_0237's kinetic law. +// An interaction was declared that claims e_0367 modifies r_0238, but e_0367 does not appear in r_0238's kinetic law. +// An interaction was declared that claims e_0367 modifies r_0239, but e_0367 does not appear in r_0239's kinetic law. +// An interaction was declared that claims e_0367 modifies r_0240, but e_0367 does not appear in r_0240's kinetic law. +// An interaction was declared that claims e_0367 modifies r_0241, but e_0367 does not appear in r_0241's kinetic law. +// An interaction was declared that claims e_0742 modifies r_0243, but e_0742 does not appear in r_0243's kinetic law. +// An interaction was declared that claims e_0329 modifies r_0244, but e_0329 does not appear in r_0244's kinetic law. +// An interaction was declared that claims e_0508 modifies r_0250, but e_0508 does not appear in r_0250's kinetic law. +// An interaction was declared that claims e_0542 modifies r_0250, but e_0542 does not appear in r_0250's kinetic law. +// An interaction was declared that claims e_0888 modifies r_0250, but e_0888 does not appear in r_0250's kinetic law. +// An interaction was declared that claims e_0045 modifies r_0257, but e_0045 does not appear in r_0257's kinetic law. +// An interaction was declared that claims e_0558 modifies r_0264, but e_0558 does not appear in r_0264's kinetic law. +// An interaction was declared that claims e_0417 modifies r_0264, but e_0417 does not appear in r_0264's kinetic law. +// An interaction was declared that claims e_0762 modifies r_0264, but e_0762 does not appear in r_0264's kinetic law. +// An interaction was declared that claims e_0959 modifies r_0278, but e_0959 does not appear in r_0278's kinetic law. +// An interaction was declared that claims e_0342 modifies r_0279, but e_0342 does not appear in r_0279's kinetic law. +// An interaction was declared that claims e_0675 modifies r_0280, but e_0675 does not appear in r_0280's kinetic law. +// An interaction was declared that claims e_0947 modifies r_0300, but e_0947 does not appear in r_0300's kinetic law. +// An interaction was declared that claims e_0805 modifies r_0300, but e_0805 does not appear in r_0300's kinetic law. +// An interaction was declared that claims e_0111 modifies r_0300, but e_0111 does not appear in r_0300's kinetic law. +// An interaction was declared that claims e_0675 modifies r_0302, but e_0675 does not appear in r_0302's kinetic law. +// An interaction was declared that claims e_0540 modifies r_0307, but e_0540 does not appear in r_0307's kinetic law. +// An interaction was declared that claims e_0026 modifies r_0307, but e_0026 does not appear in r_0307's kinetic law. +// An interaction was declared that claims e_0380 modifies r_0309, but e_0380 does not appear in r_0309's kinetic law. +// An interaction was declared that claims e_0008 modifies r_0310, but e_0008 does not appear in r_0310's kinetic law. +// An interaction was declared that claims e_0545 modifies r_0311, but e_0545 does not appear in r_0311's kinetic law. +// An interaction was declared that claims e_0793 modifies r_0313, but e_0793 does not appear in r_0313's kinetic law. +// An interaction was declared that claims e_0434 modifies r_0317, but e_0434 does not appear in r_0317's kinetic law. +// An interaction was declared that claims e_0424 modifies r_0317, but e_0424 does not appear in r_0317's kinetic law. +// An interaction was declared that claims e_0452 modifies r_0326, but e_0452 does not appear in r_0326's kinetic law. +// An interaction was declared that claims e_0234 modifies r_0330, but e_0234 does not appear in r_0330's kinetic law. +// An interaction was declared that claims e_0883 modifies r_0336, but e_0883 does not appear in r_0336's kinetic law. +// An interaction was declared that claims e_0203 modifies r_0337, but e_0203 does not appear in r_0337's kinetic law. +// An interaction was declared that claims e_0880 modifies r_0344, but e_0880 does not appear in r_0344's kinetic law. +// An interaction was declared that claims e_0692 modifies r_0349, but e_0692 does not appear in r_0349's kinetic law. +// An interaction was declared that claims e_0528 modifies r_0352, but e_0528 does not appear in r_0352's kinetic law. +// An interaction was declared that claims e_0528 modifies r_0353, but e_0528 does not appear in r_0353's kinetic law. +// An interaction was declared that claims e_0515 modifies r_0355, but e_0515 does not appear in r_0355's kinetic law. +// An interaction was declared that claims e_0976 modifies r_0361, but e_0976 does not appear in r_0361's kinetic law. +// An interaction was declared that claims e_0141 modifies r_0362, but e_0141 does not appear in r_0362's kinetic law. +// An interaction was declared that claims e_0549 modifies r_0362, but e_0549 does not appear in r_0362's kinetic law. +// An interaction was declared that claims e_0010 modifies r_0362, but e_0010 does not appear in r_0362's kinetic law. +// An interaction was declared that claims e_0890 modifies r_0362, but e_0890 does not appear in r_0362's kinetic law. +// An interaction was declared that claims e_0142 modifies r_0362, but e_0142 does not appear in r_0362's kinetic law. +// An interaction was declared that claims e_0089 modifies r_0364, but e_0089 does not appear in r_0364's kinetic law. +// An interaction was declared that claims e_0405 modifies ENO, but e_0405 does not appear in ENO's kinetic law. +// An interaction was declared that claims e_0454 modifies ENO, but e_0454 does not appear in ENO's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0386, but e_0808 does not appear in r_0386's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0386, but e_0365 does not appear in r_0386's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0386, but e_0586 does not appear in r_0386's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0386, but e_0934 does not appear in r_0386's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0387, but e_0808 does not appear in r_0387's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0387, but e_0365 does not appear in r_0387's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0387, but e_0586 does not appear in r_0387's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0387, but e_0934 does not appear in r_0387's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0389, but e_0808 does not appear in r_0389's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0389, but e_0365 does not appear in r_0389's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0389, but e_0586 does not appear in r_0389's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0389, but e_0934 does not appear in r_0389's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0391, but e_0808 does not appear in r_0391's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0391, but e_0365 does not appear in r_0391's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0391, but e_0586 does not appear in r_0391's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0391, but e_0934 does not appear in r_0391's kinetic law. +// An interaction was declared that claims e_0128 modifies r_0393, but e_0128 does not appear in r_0393's kinetic law. +// An interaction was declared that claims e_0117 modifies r_0393, but e_0117 does not appear in r_0393's kinetic law. +// An interaction was declared that claims e_0687 modifies r_0393, but e_0687 does not appear in r_0393's kinetic law. +// An interaction was declared that claims e_0128 modifies r_0394, but e_0128 does not appear in r_0394's kinetic law. +// An interaction was declared that claims e_0117 modifies r_0394, but e_0117 does not appear in r_0394's kinetic law. +// An interaction was declared that claims e_0687 modifies r_0394, but e_0687 does not appear in r_0394's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0397, but e_0808 does not appear in r_0397's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0397, but e_0365 does not appear in r_0397's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0397, but e_0586 does not appear in r_0397's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0397, but e_0934 does not appear in r_0397's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0398, but e_0808 does not appear in r_0398's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0398, but e_0365 does not appear in r_0398's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0398, but e_0586 does not appear in r_0398's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0398, but e_0934 does not appear in r_0398's kinetic law. +// An interaction was declared that claims e_0273 modifies r_0399, but e_0273 does not appear in r_0399's kinetic law. +// An interaction was declared that claims e_0273 modifies r_0400, but e_0273 does not appear in r_0400's kinetic law. +// An interaction was declared that claims e_0053 modifies r_0406, but e_0053 does not appear in r_0406's kinetic law. +// An interaction was declared that claims e_0750 modifies r_0407, but e_0750 does not appear in r_0407's kinetic law. +// An interaction was declared that claims e_0889 modifies r_0407, but e_0889 does not appear in r_0407's kinetic law. +// An interaction was declared that claims e_0462 modifies r_0407, but e_0462 does not appear in r_0407's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0432, but e_0808 does not appear in r_0432's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0432, but e_0365 does not appear in r_0432's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0432, but e_0586 does not appear in r_0432's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0432, but e_0934 does not appear in r_0432's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0433, but e_0808 does not appear in r_0433's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0433, but e_0365 does not appear in r_0433's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0433, but e_0586 does not appear in r_0433's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0433, but e_0934 does not appear in r_0433's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0434, but e_0808 does not appear in r_0434's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0434, but e_0365 does not appear in r_0434's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0434, but e_0586 does not appear in r_0434's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0434, but e_0934 does not appear in r_0434's kinetic law. +// An interaction was declared that claims e_0808 modifies r_0435, but e_0808 does not appear in r_0435's kinetic law. +// An interaction was declared that claims e_0365 modifies r_0435, but e_0365 does not appear in r_0435's kinetic law. +// An interaction was declared that claims e_0586 modifies r_0435, but e_0586 does not appear in r_0435's kinetic law. +// An interaction was declared that claims e_0934 modifies r_0435, but e_0934 does not appear in r_0435's kinetic law. +// An interaction was declared that claims e_0632 modifies r_0438, but e_0632 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0007 modifies r_0438, but e_0007 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0774 modifies r_0438, but e_0774 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0436 modifies r_0438, but e_0436 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0136 modifies r_0438, but e_0136 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0001 modifies r_0438, but e_0001 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0347 modifies r_0438, but e_0347 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0255 modifies r_0438, but e_0255 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0752 modifies r_0438, but e_0752 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0690 modifies r_0438, but e_0690 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0006 modifies r_0438, but e_0006 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0531 modifies r_0438, but e_0531 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0346 modifies r_0438, but e_0346 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0475 modifies r_0438, but e_0475 does not appear in r_0438's kinetic law. +// An interaction was declared that claims e_0514 modifies r_0439, but e_0514 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0978 modifies r_0439, but e_0978 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0422 modifies r_0439, but e_0422 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0250 modifies r_0439, but e_0250 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0004 modifies r_0439, but e_0004 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0243 modifies r_0439, but e_0243 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0389 modifies r_0439, but e_0389 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0255 modifies r_0439, but e_0255 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0848 modifies r_0439, but e_0848 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0028 modifies r_0439, but e_0028 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0531 modifies r_0439, but e_0531 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0322 modifies r_0439, but e_0322 does not appear in r_0439's kinetic law. +// An interaction was declared that claims e_0396 modifies r_0446, but e_0396 does not appear in r_0446's kinetic law. +// An interaction was declared that claims e_0057 modifies r_0446, but e_0057 does not appear in r_0446's kinetic law. +// An interaction was declared that claims e_0567 modifies FBA, but e_0567 does not appear in FBA's kinetic law. +// An interaction was declared that claims e_0940 modifies r_0451, but e_0940 does not appear in r_0451's kinetic law. +// An interaction was declared that claims e_0515 modifies r_0462, but e_0515 does not appear in r_0462's kinetic law. +// An interaction was declared that claims e_0792 modifies r_0466, but e_0792 does not appear in r_0466's kinetic law. +// An interaction was declared that claims e_0079 modifies PGI, but e_0079 does not appear in PGI's kinetic law. +// An interaction was declared that claims e_0160 modifies r_0470, but e_0160 does not appear in r_0470's kinetic law. +// An interaction was declared that claims e_0955 modifies r_0476, but e_0955 does not appear in r_0476's kinetic law. +// An interaction was declared that claims e_0867 modifies r_0478, but e_0867 does not appear in r_0478's kinetic law. +// An interaction was declared that claims e_0353 modifies r_0479, but e_0353 does not appear in r_0479's kinetic law. +// An interaction was declared that claims e_0392 modifies TDH, but e_0392 does not appear in TDH's kinetic law. +// An interaction was declared that claims e_0495 modifies TDH, but e_0495 does not appear in TDH's kinetic law. +// An interaction was declared that claims e_0525 modifies TDH, but e_0525 does not appear in TDH's kinetic law. +// An interaction was declared that claims e_0466 modifies r_0489, but e_0466 does not appear in r_0489's kinetic law. +// An interaction was declared that claims e_0288 modifies r_0489, but e_0288 does not appear in r_0489's kinetic law. +// An interaction was declared that claims e_0129 modifies r_0491, but e_0129 does not appear in r_0491's kinetic law. +// An interaction was declared that claims e_0827 modifies r_0491, but e_0827 does not appear in r_0491's kinetic law. +// An interaction was declared that claims e_0020 modifies r_0495, but e_0020 does not appear in r_0495's kinetic law. +// An interaction was declared that claims e_0607 modifies r_0495, but e_0607 does not appear in r_0495's kinetic law. +// An interaction was declared that claims e_0231 modifies r_0499, but e_0231 does not appear in r_0499's kinetic law. +// An interaction was declared that claims e_0741 modifies r_0501, but e_0741 does not appear in r_0501's kinetic law. +// An interaction was declared that claims e_0012 modifies r_0501, but e_0012 does not appear in r_0501's kinetic law. +// An interaction was declared that claims e_0167 modifies r_0501, but e_0167 does not appear in r_0501's kinetic law. +// An interaction was declared that claims e_0311 modifies r_0501, but e_0311 does not appear in r_0501's kinetic law. +// An interaction was declared that claims e_0638 modifies r_0502, but e_0638 does not appear in r_0502's kinetic law. +// An interaction was declared that claims e_0091 modifies r_0502, but e_0091 does not appear in r_0502's kinetic law. +// An interaction was declared that claims e_0667 modifies r_0510, but e_0667 does not appear in r_0510's kinetic law. +// An interaction was declared that claims e_0510 modifies r_0510, but e_0510 does not appear in r_0510's kinetic law. +// An interaction was declared that claims e_0317 modifies r_0510, but e_0317 does not appear in r_0510's kinetic law. +// An interaction was declared that claims e_0603 modifies r_0510, but e_0603 does not appear in r_0510's kinetic law. +// An interaction was declared that claims e_0064 modifies r_0512, but e_0064 does not appear in r_0512's kinetic law. +// An interaction was declared that claims e_0963 modifies r_0512, but e_0963 does not appear in r_0512's kinetic law. +// An interaction was declared that claims e_0746 modifies r_0514, but e_0746 does not appear in r_0514's kinetic law. +// An interaction was declared that claims e_0025 modifies r_0525, but e_0025 does not appear in r_0525's kinetic law. +// An interaction was declared that claims e_0234 modifies r_0528, but e_0234 does not appear in r_0528's kinetic law. +// An interaction was declared that claims e_0234 modifies r_0529, but e_0234 does not appear in r_0529's kinetic law. +// An interaction was declared that claims e_0106 modifies HXK, but e_0106 does not appear in HXK's kinetic law. +// An interaction was declared that claims e_0325 modifies HXK, but e_0325 does not appear in HXK's kinetic law. +// An interaction was declared that claims e_0355 modifies HXK, but e_0355 does not appear in HXK's kinetic law. +// An interaction was declared that claims e_0103 modifies r_0536, but e_0103 does not appear in r_0536's kinetic law. +// An interaction was declared that claims e_0320 modifies r_0537, but e_0320 does not appear in r_0537's kinetic law. +// An interaction was declared that claims e_0476 modifies r_0538, but e_0476 does not appear in r_0538's kinetic law. +// An interaction was declared that claims e_0953 modifies r_0539, but e_0953 does not appear in r_0539's kinetic law. +// An interaction was declared that claims e_0196 modifies r_0542, but e_0196 does not appear in r_0542's kinetic law. +// An interaction was declared that claims e_0154 modifies r_0543, but e_0154 does not appear in r_0543's kinetic law. +// An interaction was declared that claims e_0146 modifies r_0543, but e_0146 does not appear in r_0543's kinetic law. +// An interaction was declared that claims e_0472 modifies r_0545, but e_0472 does not appear in r_0545's kinetic law. +// An interaction was declared that claims e_0548 modifies r_0547, but e_0548 does not appear in r_0547's kinetic law. +// An interaction was declared that claims e_0428 modifies r_0548, but e_0428 does not appear in r_0548's kinetic law. +// An interaction was declared that claims e_0799 modifies r_0549, but e_0799 does not appear in r_0549's kinetic law. +// An interaction was declared that claims e_0202 modifies r_0553, but e_0202 does not appear in r_0553's kinetic law. +// An interaction was declared that claims e_0846 modifies r_0553, but e_0846 does not appear in r_0553's kinetic law. +// An interaction was declared that claims e_0697 modifies r_0558, but e_0697 does not appear in r_0558's kinetic law. +// An interaction was declared that claims e_0708 modifies r_0558, but e_0708 does not appear in r_0558's kinetic law. +// An interaction was declared that claims e_0716 modifies r_0559, but e_0716 does not appear in r_0559's kinetic law. +// An interaction was declared that claims e_0087 modifies r_0563, but e_0087 does not appear in r_0563's kinetic law. +// An interaction was declared that claims e_0875 modifies r_0564, but e_0875 does not appear in r_0564's kinetic law. +// An interaction was declared that claims e_0705 modifies r_0565, but e_0705 does not appear in r_0565's kinetic law. +// An interaction was declared that claims e_0458 modifies r_0565, but e_0458 does not appear in r_0565's kinetic law. +// An interaction was declared that claims e_0693 modifies r_0565, but e_0693 does not appear in r_0565's kinetic law. +// An interaction was declared that claims e_0591 modifies r_0566, but e_0591 does not appear in r_0566's kinetic law. +// An interaction was declared that claims e_0038 modifies r_0568, but e_0038 does not appear in r_0568's kinetic law. +// An interaction was declared that claims e_0754 modifies r_0568, but e_0754 does not appear in r_0568's kinetic law. +// An interaction was declared that claims e_0631 modifies r_0570, but e_0631 does not appear in r_0570's kinetic law. +// An interaction was declared that claims e_0736 modifies r_0570, but e_0736 does not appear in r_0570's kinetic law. +// An interaction was declared that claims e_0557 modifies r_0591, but e_0557 does not appear in r_0591's kinetic law. +// An interaction was declared that claims e_0220 modifies r_0591, but e_0220 does not appear in r_0591's kinetic law. +// An interaction was declared that claims e_0862 modifies r_0658, but e_0862 does not appear in r_0658's kinetic law. +// An interaction was declared that claims e_0771 modifies r_0658, but e_0771 does not appear in r_0658's kinetic law. +// An interaction was declared that claims e_0769 modifies r_0661, but e_0769 does not appear in r_0661's kinetic law. +// An interaction was declared that claims e_0135 modifies r_0661, but e_0135 does not appear in r_0661's kinetic law. +// An interaction was declared that claims e_0289 modifies r_0662, but e_0289 does not appear in r_0662's kinetic law. +// An interaction was declared that claims e_0550 modifies r_0663, but e_0550 does not appear in r_0663's kinetic law. +// An interaction was declared that claims e_0457 modifies r_0663, but e_0457 does not appear in r_0663's kinetic law. +// An interaction was declared that claims e_0031 modifies r_0665, but e_0031 does not appear in r_0665's kinetic law. +// An interaction was declared that claims e_0922 modifies r_0667, but e_0922 does not appear in r_0667's kinetic law. +// An interaction was declared that claims e_0685 modifies r_0669, but e_0685 does not appear in r_0669's kinetic law. +// An interaction was declared that claims e_0642 modifies r_0674, but e_0642 does not appear in r_0674's kinetic law. +// An interaction was declared that claims e_0062 modifies r_0678, but e_0062 does not appear in r_0678's kinetic law. +// An interaction was declared that claims e_0343 modifies r_0678, but e_0343 does not appear in r_0678's kinetic law. +// An interaction was declared that claims e_0842 modifies r_0688, but e_0842 does not appear in r_0688's kinetic law. +// An interaction was declared that claims e_0447 modifies r_0688, but e_0447 does not appear in r_0688's kinetic law. +// An interaction was declared that claims e_0109 modifies r_0692, but e_0109 does not appear in r_0692's kinetic law. +// An interaction was declared that claims e_0295 modifies r_0692, but e_0295 does not appear in r_0692's kinetic law. +// An interaction was declared that claims e_0698 modifies r_0697, but e_0698 does not appear in r_0697's kinetic law. +// An interaction was declared that claims e_0440 modifies r_0698, but e_0440 does not appear in r_0698's kinetic law. +// An interaction was declared that claims e_0550 modifies r_0699, but e_0550 does not appear in r_0699's kinetic law. +// An interaction was declared that claims e_0457 modifies r_0699, but e_0457 does not appear in r_0699's kinetic law. +// An interaction was declared that claims e_0926 modifies r_0701, but e_0926 does not appear in r_0701's kinetic law. +// An interaction was declared that claims e_0171 modifies r_0711, but e_0171 does not appear in r_0711's kinetic law. +// An interaction was declared that claims e_0571 modifies r_0713, but e_0571 does not appear in r_0713's kinetic law. +// An interaction was declared that claims e_0838 modifies r_0713, but e_0838 does not appear in r_0713's kinetic law. +// An interaction was declared that claims e_0137 modifies r_0713, but e_0137 does not appear in r_0713's kinetic law. +// An interaction was declared that claims e_0134 modifies r_0722, but e_0134 does not appear in r_0722's kinetic law. +// An interaction was declared that claims e_0269 modifies r_0723, but e_0269 does not appear in r_0723's kinetic law. +// An interaction was declared that claims e_0057 modifies r_0724, but e_0057 does not appear in r_0724's kinetic law. +// An interaction was declared that claims e_0396 modifies r_0724, but e_0396 does not appear in r_0724's kinetic law. +// An interaction was declared that claims e_0239 modifies r_0726, but e_0239 does not appear in r_0726's kinetic law. +// An interaction was declared that claims e_0658 modifies r_0726, but e_0658 does not appear in r_0726's kinetic law. +// An interaction was declared that claims e_0298 modifies r_0727, but e_0298 does not appear in r_0727's kinetic law. +// An interaction was declared that claims e_0409 modifies r_0729, but e_0409 does not appear in r_0729's kinetic law. +// An interaction was declared that claims e_0610 modifies r_0731, but e_0610 does not appear in r_0731's kinetic law. +// An interaction was declared that claims e_0396 modifies r_0732, but e_0396 does not appear in r_0732's kinetic law. +// An interaction was declared that claims e_0057 modifies r_0732, but e_0057 does not appear in r_0732's kinetic law. +// An interaction was declared that claims e_0745 modifies r_0735, but e_0745 does not appear in r_0735's kinetic law. +// An interaction was declared that claims e_0745 modifies r_0736, but e_0745 does not appear in r_0736's kinetic law. +// An interaction was declared that claims e_0812 modifies r_0739, but e_0812 does not appear in r_0739's kinetic law. +// An interaction was declared that claims e_0204 modifies r_0757, but e_0204 does not appear in r_0757's kinetic law. +// An interaction was declared that claims e_0435 modifies r_0757, but e_0435 does not appear in r_0757's kinetic law. +// An interaction was declared that claims e_0512 modifies r_0758, but e_0512 does not appear in r_0758's kinetic law. +// An interaction was declared that claims e_0290 modifies r_0759, but e_0290 does not appear in r_0759's kinetic law. +// An interaction was declared that claims e_0271 modifies r_0792, but e_0271 does not appear in r_0792's kinetic law. +// An interaction was declared that claims e_0568 modifies r_0800, but e_0568 does not appear in r_0800's kinetic law. +// An interaction was declared that claims e_0568 modifies r_0811, but e_0568 does not appear in r_0811's kinetic law. +// An interaction was declared that claims e_0674 modifies r_0813, but e_0674 does not appear in r_0813's kinetic law. +// An interaction was declared that claims e_0499 modifies r_0816, but e_0499 does not appear in r_0816's kinetic law. +// An interaction was declared that claims e_0729 modifies r_0818, but e_0729 does not appear in r_0818's kinetic law. +// An interaction was declared that claims e_0755 modifies r_0820, but e_0755 does not appear in r_0820's kinetic law. +// An interaction was declared that claims e_0712 modifies r_0820, but e_0712 does not appear in r_0820's kinetic law. +// An interaction was declared that claims e_0249 modifies r_0821, but e_0249 does not appear in r_0821's kinetic law. +// An interaction was declared that claims e_0348 modifies r_0851, but e_0348 does not appear in r_0851's kinetic law. +// An interaction was declared that claims e_0639 modifies r_0852, but e_0639 does not appear in r_0852's kinetic law. +// An interaction was declared that claims e_0312 modifies r_0852, but e_0312 does not appear in r_0852's kinetic law. +// An interaction was declared that claims e_0352 modifies r_0855, but e_0352 does not appear in r_0855's kinetic law. +// An interaction was declared that claims e_0536 modifies r_0858, but e_0536 does not appear in r_0858's kinetic law. +// An interaction was declared that claims e_0381 modifies r_0858, but e_0381 does not appear in r_0858's kinetic law. +// An interaction was declared that claims e_0964 modifies r_0874, but e_0964 does not appear in r_0874's kinetic law. +// An interaction was declared that claims e_0788 modifies r_0877, but e_0788 does not appear in r_0877's kinetic law. +// An interaction was declared that claims e_0382 modifies r_0877, but e_0382 does not appear in r_0877's kinetic law. +// An interaction was declared that claims e_0278 modifies r_0880, but e_0278 does not appear in r_0880's kinetic law. +// An interaction was declared that claims e_0633 modifies r_0883, but e_0633 does not appear in r_0883's kinetic law. +// An interaction was declared that claims e_0975 modifies r_0883, but e_0975 does not appear in r_0883's kinetic law. +// An interaction was declared that claims e_0398 modifies r_0883, but e_0398 does not appear in r_0883's kinetic law. +// An interaction was declared that claims e_0612 modifies r_0884, but e_0612 does not appear in r_0884's kinetic law. +// An interaction was declared that claims e_0401 modifies PFK, but e_0401 does not appear in PFK's kinetic law. +// An interaction was declared that claims e_0743 modifies PFK, but e_0743 does not appear in PFK's kinetic law. +// An interaction was declared that claims e_0576 modifies r_0888, but e_0576 does not appear in r_0888's kinetic law. +// An interaction was declared that claims e_0757 modifies r_0888, but e_0757 does not appear in r_0888's kinetic law. +// An interaction was declared that claims e_0733 modifies r_0888, but e_0733 does not appear in r_0888's kinetic law. +// An interaction was declared that claims e_0455 modifies r_0889, but e_0455 does not appear in r_0889's kinetic law. +// An interaction was declared that claims e_0407 modifies r_0889, but e_0407 does not appear in r_0889's kinetic law. +// An interaction was declared that claims e_0113 modifies PGK, but e_0113 does not appear in PGK's kinetic law. +// An interaction was declared that claims e_0582 modifies GPM, but e_0582 does not appear in GPM's kinetic law. +// An interaction was declared that claims e_0536 modifies r_0900, but e_0536 does not appear in r_0900's kinetic law. +// An interaction was declared that claims e_0536 modifies r_0901, but e_0536 does not appear in r_0901's kinetic law. +// An interaction was declared that claims e_0314 modifies r_0902, but e_0314 does not appear in r_0902's kinetic law. +// An interaction was declared that claims e_0747 modifies r_0904, but e_0747 does not appear in r_0904's kinetic law. +// An interaction was declared that claims e_0017 modifies r_0908, but e_0017 does not appear in r_0908's kinetic law. +// An interaction was declared that claims e_0103 modifies r_0909, but e_0103 does not appear in r_0909's kinetic law. +// An interaction was declared that claims e_0103 modifies r_0910, but e_0103 does not appear in r_0910's kinetic law. +// An interaction was declared that claims e_0860 modifies r_0911, but e_0860 does not appear in r_0911's kinetic law. +// An interaction was declared that claims e_0631 modifies r_0912, but e_0631 does not appear in r_0912's kinetic law. +// An interaction was declared that claims e_0736 modifies r_0912, but e_0736 does not appear in r_0912's kinetic law. +// An interaction was declared that claims e_0165 modifies r_0913, but e_0165 does not appear in r_0913's kinetic law. +// An interaction was declared that claims e_0352 modifies r_0914, but e_0352 does not appear in r_0914's kinetic law. +// An interaction was declared that claims e_0763 modifies r_0915, but e_0763 does not appear in r_0915's kinetic law. +// An interaction was declared that claims e_0030 modifies r_0916, but e_0030 does not appear in r_0916's kinetic law. +// An interaction was declared that claims e_0299 modifies r_0916, but e_0299 does not appear in r_0916's kinetic law. +// An interaction was declared that claims e_0418 modifies r_0916, but e_0418 does not appear in r_0916's kinetic law. +// An interaction was declared that claims e_0585 modifies r_0916, but e_0585 does not appear in r_0916's kinetic law. +// An interaction was declared that claims e_0829 modifies r_0916, but e_0829 does not appear in r_0916's kinetic law. +// An interaction was declared that claims e_0802 modifies r_0938, but e_0802 does not appear in r_0938's kinetic law. +// An interaction was declared that claims e_0074 modifies r_0939, but e_0074 does not appear in r_0939's kinetic law. +// An interaction was declared that claims e_0296 modifies r_0941, but e_0296 does not appear in r_0941's kinetic law. +// An interaction was declared that claims e_0276 modifies r_0957, but e_0276 does not appear in r_0957's kinetic law. +// An interaction was declared that claims e_0334 modifies r_0958, but e_0334 does not appear in r_0958's kinetic law. +// An interaction was declared that claims e_0084 modifies r_0958, but e_0084 does not appear in r_0958's kinetic law. +// An interaction was declared that claims e_0370 modifies PDC, but e_0370 does not appear in PDC's kinetic law. +// An interaction was declared that claims e_0636 modifies PDC, but e_0636 does not appear in PDC's kinetic law. +// An interaction was declared that claims e_0647 modifies PDC, but e_0647 does not appear in PDC's kinetic law. +// An interaction was declared that claims e_0011 modifies PYK, but e_0011 does not appear in PYK's kinetic law. +// An interaction was declared that claims e_0895 modifies PYK, but e_0895 does not appear in PYK's kinetic law. +// An interaction was declared that claims e_0841 modifies r_0967, but e_0841 does not appear in r_0967's kinetic law. +// An interaction was declared that claims e_0090 modifies r_0968, but e_0090 does not appear in r_0968's kinetic law. +// An interaction was declared that claims e_0398 modifies r_0970, but e_0398 does not appear in r_0970's kinetic law. +// An interaction was declared that claims e_0398 modifies r_0973, but e_0398 does not appear in r_0973's kinetic law. +// An interaction was declared that claims e_0467 modifies r_0974, but e_0467 does not appear in r_0974's kinetic law. +// An interaction was declared that claims e_0492 modifies r_0974, but e_0492 does not appear in r_0974's kinetic law. +// An interaction was declared that claims e_0387 modifies r_0974, but e_0387 does not appear in r_0974's kinetic law. +// An interaction was declared that claims e_0291 modifies r_0974, but e_0291 does not appear in r_0974's kinetic law. +// An interaction was declared that claims e_0467 modifies r_0976, but e_0467 does not appear in r_0976's kinetic law. +// An interaction was declared that claims e_0492 modifies r_0976, but e_0492 does not appear in r_0976's kinetic law. +// An interaction was declared that claims e_0387 modifies r_0976, but e_0387 does not appear in r_0976's kinetic law. +// An interaction was declared that claims e_0291 modifies r_0976, but e_0291 does not appear in r_0976's kinetic law. +// An interaction was declared that claims e_0467 modifies r_0978, but e_0467 does not appear in r_0978's kinetic law. +// An interaction was declared that claims e_0492 modifies r_0978, but e_0492 does not appear in r_0978's kinetic law. +// An interaction was declared that claims e_0387 modifies r_0978, but e_0387 does not appear in r_0978's kinetic law. +// An interaction was declared that claims e_0291 modifies r_0978, but e_0291 does not appear in r_0978's kinetic law. +// An interaction was declared that claims e_0852 modifies r_0982, but e_0852 does not appear in r_0982's kinetic law. +// An interaction was declared that claims e_0506 modifies r_0984, but e_0506 does not appear in r_0984's kinetic law. +// An interaction was declared that claims e_0699 modifies r_0986, but e_0699 does not appear in r_0986's kinetic law. +// An interaction was declared that claims e_0489 modifies r_0988, but e_0489 does not appear in r_0988's kinetic law. +// An interaction was declared that claims e_0813 modifies r_0989, but e_0813 does not appear in r_0989's kinetic law. +// An interaction was declared that claims e_0567 modifies r_0990, but e_0567 does not appear in r_0990's kinetic law. +// An interaction was declared that claims e_0054 modifies r_0993, but e_0054 does not appear in r_0993's kinetic law. +// An interaction was declared that claims e_0177 modifies r_0993, but e_0177 does not appear in r_0993's kinetic law. +// An interaction was declared that claims e_0761 modifies r_0993, but e_0761 does not appear in r_0993's kinetic law. +// An interaction was declared that claims e_0168 modifies r_0995, but e_0168 does not appear in r_0995's kinetic law. +// An interaction was declared that claims e_0425 modifies r_0995, but e_0425 does not appear in r_0995's kinetic law. +// An interaction was declared that claims e_0182 modifies r_0996, but e_0182 does not appear in r_0996's kinetic law. +// An interaction was declared that claims e_0182 modifies r_0997, but e_0182 does not appear in r_0997's kinetic law. +// An interaction was declared that claims e_0385 modifies r_1010, but e_0385 does not appear in r_1010's kinetic law. +// An interaction was declared that claims e_0456 modifies r_1012, but e_0456 does not appear in r_1012's kinetic law. +// An interaction was declared that claims e_0578 modifies r_1014, but e_0578 does not appear in r_1014's kinetic law. +// An interaction was declared that claims e_0613 modifies r_1014, but e_0613 does not appear in r_1014's kinetic law. +// An interaction was declared that claims e_0579 modifies r_1021, but e_0579 does not appear in r_1021's kinetic law. +// An interaction was declared that claims e_0188 modifies r_1021, but e_0188 does not appear in r_1021's kinetic law. +// An interaction was declared that claims e_0494 modifies r_1021, but e_0494 does not appear in r_1021's kinetic law. +// An interaction was declared that claims e_0619 modifies r_1021, but e_0619 does not appear in r_1021's kinetic law. +// An interaction was declared that claims e_0581 modifies r_1021, but e_0581 does not appear in r_1021's kinetic law. +// An interaction was declared that claims e_0107 modifies r_1026, but e_0107 does not appear in r_1026's kinetic law. +// An interaction was declared that claims e_0547 modifies r_1027, but e_0547 does not appear in r_1027's kinetic law. +// An interaction was declared that claims e_0321 modifies r_1027, but e_0321 does not appear in r_1027's kinetic law. +// An interaction was declared that claims e_0633 modifies r_1038, but e_0633 does not appear in r_1038's kinetic law. +// An interaction was declared that claims e_0218 modifies r_1038, but e_0218 does not appear in r_1038's kinetic law. +// An interaction was declared that claims e_0398 modifies r_1038, but e_0398 does not appear in r_1038's kinetic law. +// An interaction was declared that claims e_0448 modifies r_1038, but e_0448 does not appear in r_1038's kinetic law. +// An interaction was declared that claims e_0915 modifies r_1038, but e_0915 does not appear in r_1038's kinetic law. +// An interaction was declared that claims e_0124 modifies r_1038, but e_0124 does not appear in r_1038's kinetic law. +// An interaction was declared that claims e_0260 modifies r_1040, but e_0260 does not appear in r_1040's kinetic law. +// An interaction was declared that claims e_0122 modifies r_1041, but e_0122 does not appear in r_1041's kinetic law. +// An interaction was declared that claims e_0470 modifies r_1042, but e_0470 does not appear in r_1042's kinetic law. +// An interaction was declared that claims e_0850 modifies r_1045, but e_0850 does not appear in r_1045's kinetic law. +// An interaction was declared that claims e_0684 modifies r_1048, but e_0684 does not appear in r_1048's kinetic law. +// An interaction was declared that claims e_0063 modifies r_1049, but e_0063 does not appear in r_1049's kinetic law. +// An interaction was declared that claims e_0962 modifies r_1049, but e_0962 does not appear in r_1049's kinetic law. +// An interaction was declared that claims e_0063 modifies r_1050, but e_0063 does not appear in r_1050's kinetic law. +// An interaction was declared that claims e_0962 modifies r_1050, but e_0962 does not appear in r_1050's kinetic law. +// An interaction was declared that claims e_0711 modifies r_1051, but e_0711 does not appear in r_1051's kinetic law. +// An interaction was declared that claims e_0065 modifies r_1051, but e_0065 does not appear in r_1051's kinetic law. +// An interaction was declared that claims e_0179 modifies r_1051, but e_0179 does not appear in r_1051's kinetic law. +// An interaction was declared that claims e_0753 modifies r_1051, but e_0753 does not appear in r_1051's kinetic law. +// An interaction was declared that claims e_0176 modifies r_1052, but e_0176 does not appear in r_1052's kinetic law. +// An interaction was declared that claims e_0611 modifies r_1052, but e_0611 does not appear in r_1052's kinetic law. +// An interaction was declared that claims e_0765 modifies r_1052, but e_0765 does not appear in r_1052's kinetic law. +// An interaction was declared that claims e_0851 modifies r_1052, but e_0851 does not appear in r_1052's kinetic law. +// An interaction was declared that claims e_0175 modifies TPI, but e_0175 does not appear in TPI's kinetic law. +// An interaction was declared that claims e_0330 modifies r_1055, but e_0330 does not appear in r_1055's kinetic law. +// An interaction was declared that claims e_0836 modifies r_1057, but e_0836 does not appear in r_1057's kinetic law. +// An interaction was declared that claims e_0348 modifies r_1063, but e_0348 does not appear in r_1063's kinetic law. +// An interaction was declared that claims e_0629 modifies r_1063, but e_0629 does not appear in r_1063's kinetic law. +// An interaction was declared that claims e_0390 modifies r_1066, but e_0390 does not appear in r_1066's kinetic law. +// An interaction was declared that claims e_0561 modifies r_1072, but e_0561 does not appear in r_1072's kinetic law. +// An interaction was declared that claims e_0565 modifies r_1084, but e_0565 does not appear in r_1084's kinetic law. +// An interaction was declared that claims e_0550 modifies r_1087, but e_0550 does not appear in r_1087's kinetic law. +// An interaction was declared that claims e_0457 modifies r_1087, but e_0457 does not appear in r_1087's kinetic law. +// An interaction was declared that claims e_0372 modifies r_1089, but e_0372 does not appear in r_1089's kinetic law. +// An interaction was declared that claims e_0601 modifies r_2126, but e_0601 does not appear in r_2126's kinetic law. +// An interaction was declared that claims e_0594 modifies r_2127, but e_0594 does not appear in r_2127's kinetic law. + model *MODEL1302140005() // Compartments and Species: @@ -479,6 +989,527 @@ model *MODEL1302140005() r_2126: s_1426 -> s_1427 + PHO; cell*r_2126_Vmax*(s_1426 - s_1427*PHO/r_2126_Keq)/r_2126_Km1426/(1 + s_1426/r_2126_Km1426 + (1 + s_1427/r_2126_Km1427)*(1 + PHO/r_2126_KmPHO) - 1); r_2127: s_0061 + NAD -> s_1269 + NADH; cell*r_2127_Vmax*(s_0061*NAD - s_1269*NADH/r_2127_Keq)/(r_2127_Km0061*r_2127_KmNAD)/((1 + s_0061/r_2127_Km0061)*(1 + NAD/r_2127_KmNAD) + (1 + s_1269/r_2127_Km1269)*(1 + NADH/r_2127_KmNADH) - 1); + // Interactions: + _I0: $e_0151 -o r_0001; ; + _I1: $e_0268 -o r_0001; ; + _I2: $e_0255 -o r_0001; ; + _I3: $e_0531 -o r_0001; ; + _I4: $e_0152 -o r_0001; ; + _I5: $e_0704 -o r_0004; ; + _I6: $e_0531 -o r_0004; ; + _I7: $e_0255 -o r_0004; ; + _I8: $e_0682 -o r_0005; ; + _I9: $e_0364 -o r_0005; ; + _I10: $e_0973 -o r_0006; ; + _I11: $e_0379 -o r_0006; ; + _I12: $e_0465 -o r_0007; ; + _I13: $e_0869 -o r_0008; ; + _I14: $e_0133 -o r_0008; ; + _I15: $e_0117 -o r_0008; ; + _I16: $e_0431 -o r_0012; ; + _I17: $e_0832 -o r_0014; ; + _I18: $e_0071 -o r_0015; ; + _I19: $e_0734 -o r_0016; ; + _I20: $e_0100 -o r_0016; ; + _I21: $e_0348 -o r_0018; ; + _I22: $e_0496 -o r_0018; ; + _I23: $e_0980 -o r_0018; ; + _I24: $e_0169 -o r_0020; ; + _I25: $e_0088 -o r_0020; ; + _I26: $e_0328 -o r_0023; ; + _I27: $e_0778 -o r_0024; ; + _I28: $e_0855 -o r_0024; ; + _I29: $e_0196 -o r_0027; ; + _I30: $e_0550 -o r_0029; ; + _I31: $e_0457 -o r_0029; ; + _I32: $e_0830 -o r_0032; ; + _I33: $e_0237 -o r_0038; ; + _I34: $e_0182 -o r_0039; ; + _I35: $e_0182 -o r_0040; ; + _I36: $e_0092 -o r_0041; ; + _I37: $e_0328 -o r_0060; ; + _I38: $e_0101 -o r_0061; ; + _I39: $e_0182 -o r_0065; ; + _I40: $e_0368 -o r_0079; ; + _I41: $e_0340 -o r_0080; ; + _I42: $e_0903 -o r_0080; ; + _I43: $e_0453 -o r_0091; ; + _I44: $e_0404 -o r_0091; ; + _I45: $e_0685 -o r_0096; ; + _I46: $e_0734 -o r_0097; ; + _I47: $e_0100 -o r_0097; ; + _I48: $e_0904 -o r_0103; ; + _I49: $e_0744 -o r_0108; ; + _I50: $e_0808 -o r_0108; ; + _I51: $e_0022 -o r_0110; ; + _I52: $e_0290 -o r_0115; ; + _I53: $e_0840 -o r_0118; ; + _I54: $e_0541 -o r_0142; ; + _I55: $e_0280 -o r_0144; ; + _I56: $e_0194 -o AK; ; + _I57: $e_0303 -o AK; ; + _I58: $e_0303 -o r_0150; ; + _I59: $e_0686 -o r_0151; ; + _I60: $e_0686 -o r_0152; ; + _I61: $e_0791 -o r_0153; ; + _I62: $e_0556 -o r_0154; ; + _I63: $e_0313 -o r_0156; ; + _I64: $e_0894 -o r_0157; ; + _I65: $e_0730 -o ADH; ; + _I66: $e_0356 -o ADH; ; + _I67: $e_0069 -o ADH; ; + _I68: $e_0834 -o ADH; ; + _I69: $e_0911 -o r_0173; ; + _I70: $e_0898 -o r_0173; ; + _I71: $e_0293 -o r_0173; ; + _I72: $e_0898 -o r_0174; ; + _I73: $e_0740 -o r_0174; ; + _I74: $e_0711 -o r_0195; ; + _I75: $e_0065 -o r_0195; ; + _I76: $e_0179 -o r_0195; ; + _I77: $e_0753 -o r_0195; ; + _I78: $e_0219 -o r_0202; ; + _I79: $e_0297 -o r_0203; ; + _I80: $e_0591 -o r_0203; ; + _I81: $e_0426 -o r_0207; ; + _I82: $e_0826 -o r_0208; ; + _I83: $e_0214 -o r_0209; ; + _I84: $e_0970 -o r_0211; ; + _I85: $e_0376 -o r_0211; ; + _I86: $e_0427 -o r_0212; ; + _I87: $e_0508 -o r_0214; ; + _I88: $e_0281 -o r_0215; ; + _I89: $e_0629 -o r_0216; ; + _I90: $e_0574 -o r_0216; ; + _I91: $e_0186 -o r_0219; ; + _I92: $e_0615 -o r_0220; ; + _I93: $e_0283 -o r_0225; ; + _I94: $e_0950 -o r_0226; ; + _I95: $e_0944 -o r_0226; ; + _I96: $e_0005 -o r_0226; ; + _I97: $e_0033 -o r_0226; ; + _I98: $e_0207 -o r_0226; ; + _I99: $e_0003 -o r_0226; ; + _I100: $e_0671 -o r_0226; ; + _I101: $e_0002 -o r_0226; ; + _I102: $e_0051 -o r_0226; ; + _I103: $e_0223 -o r_0226; ; + _I104: $e_0709 -o r_0226; ; + _I105: $e_0213 -o r_0226; ; + _I106: $e_0544 -o r_0226; ; + _I107: $e_0559 -o r_0226; ; + _I108: $e_0127 -o r_0226; ; + _I109: $e_0913 -o r_0226; ; + _I110: $e_0727 -o ATPase; ; + _I111: $e_0569 -o ATPase; ; + _I112: $e_0432 -o ATPase; ; + _I113: $e_0263 -o ATPase; ; + _I114: $e_0956 -o ATPase; ; + _I115: $e_0155 -o ATPase; ; + _I116: $e_0892 -o ATPase; ; + _I117: $e_0362 -o ATPase; ; + _I118: $e_0251 -o ATPase; ; + _I119: $e_0695 -o ATPase; ; + _I120: $e_0935 -o ATPase; ; + _I121: $e_0066 -o ATPase; ; + _I122: $e_0429 -o ATPase; ; + _I123: $e_0183 -o ATPase; ; + _I124: $e_0621 -o ATPase; ; + _I125: $e_0569 -o ATPase; ; + _I126: $e_0432 -o ATPase; ; + _I127: $e_0263 -o ATPase; ; + _I128: $e_0956 -o ATPase; ; + _I129: $e_0155 -o ATPase; ; + _I130: $e_0892 -o ATPase; ; + _I131: $e_0362 -o ATPase; ; + _I132: $e_0251 -o ATPase; ; + _I133: $e_0695 -o ATPase; ; + _I134: $e_0884 -o ATPase; ; + _I135: $e_0935 -o ATPase; ; + _I136: $e_0066 -o ATPase; ; + _I137: $e_0429 -o ATPase; ; + _I138: $e_0588 -o ATPase; ; + _I139: $e_0924 -o ATPase; ; + _I140: $e_0800 -o r_0231; ; + _I141: $e_0326 -o r_0234; ; + _I142: $e_0326 -o r_0235; ; + _I143: $e_0644 -o r_0236; ; + _I144: $e_0644 -o r_0237; ; + _I145: $e_0367 -o r_0238; ; + _I146: $e_0367 -o r_0239; ; + _I147: $e_0367 -o r_0240; ; + _I148: $e_0367 -o r_0241; ; + _I149: $e_0742 -o r_0243; ; + _I150: $e_0329 -o r_0244; ; + _I151: $e_0508 -o r_0250; ; + _I152: $e_0542 -o r_0250; ; + _I153: $e_0888 -o r_0250; ; + _I154: $e_0045 -o r_0257; ; + _I155: $e_0558 -o r_0264; ; + _I156: $e_0417 -o r_0264; ; + _I157: $e_0762 -o r_0264; ; + _I158: $e_0959 -o r_0278; ; + _I159: $e_0342 -o r_0279; ; + _I160: $e_0675 -o r_0280; ; + _I161: $e_0947 -o r_0300; ; + _I162: $e_0805 -o r_0300; ; + _I163: $e_0111 -o r_0300; ; + _I164: $e_0675 -o r_0302; ; + _I165: $e_0540 -o r_0307; ; + _I166: $e_0026 -o r_0307; ; + _I167: $e_0380 -o r_0309; ; + _I168: $e_0008 -o r_0310; ; + _I169: $e_0545 -o r_0311; ; + _I170: $e_0793 -o r_0313; ; + _I171: $e_0434 -o r_0317; ; + _I172: $e_0424 -o r_0317; ; + _I173: $e_0452 -o r_0326; ; + _I174: $e_0234 -o r_0330; ; + _I175: $e_0883 -o r_0336; ; + _I176: $e_0203 -o r_0337; ; + _I177: $e_0880 -o r_0344; ; + _I178: $e_0692 -o r_0349; ; + _I179: $e_0528 -o r_0352; ; + _I180: $e_0528 -o r_0353; ; + _I181: $e_0515 -o r_0355; ; + _I182: $e_0976 -o r_0361; ; + _I183: $e_0141 -o r_0362; ; + _I184: $e_0549 -o r_0362; ; + _I185: $e_0010 -o r_0362; ; + _I186: $e_0890 -o r_0362; ; + _I187: $e_0142 -o r_0362; ; + _I188: $e_0089 -o r_0364; ; + _I189: $e_0405 -o ENO; ; + _I190: $e_0454 -o ENO; ; + _I191: $e_0808 -o r_0386; ; + _I192: $e_0365 -o r_0386; ; + _I193: $e_0586 -o r_0386; ; + _I194: $e_0934 -o r_0386; ; + _I195: $e_0808 -o r_0387; ; + _I196: $e_0365 -o r_0387; ; + _I197: $e_0586 -o r_0387; ; + _I198: $e_0934 -o r_0387; ; + _I199: $e_0808 -o r_0389; ; + _I200: $e_0365 -o r_0389; ; + _I201: $e_0586 -o r_0389; ; + _I202: $e_0934 -o r_0389; ; + _I203: $e_0808 -o r_0391; ; + _I204: $e_0365 -o r_0391; ; + _I205: $e_0586 -o r_0391; ; + _I206: $e_0934 -o r_0391; ; + _I207: $e_0128 -o r_0393; ; + _I208: $e_0117 -o r_0393; ; + _I209: $e_0687 -o r_0393; ; + _I210: $e_0128 -o r_0394; ; + _I211: $e_0117 -o r_0394; ; + _I212: $e_0687 -o r_0394; ; + _I213: $e_0808 -o r_0397; ; + _I214: $e_0365 -o r_0397; ; + _I215: $e_0586 -o r_0397; ; + _I216: $e_0934 -o r_0397; ; + _I217: $e_0808 -o r_0398; ; + _I218: $e_0365 -o r_0398; ; + _I219: $e_0586 -o r_0398; ; + _I220: $e_0934 -o r_0398; ; + _I221: $e_0273 -o r_0399; ; + _I222: $e_0273 -o r_0400; ; + _I223: $e_0053 -o r_0406; ; + _I224: $e_0750 -o r_0407; ; + _I225: $e_0889 -o r_0407; ; + _I226: $e_0462 -o r_0407; ; + _I227: $e_0808 -o r_0432; ; + _I228: $e_0365 -o r_0432; ; + _I229: $e_0586 -o r_0432; ; + _I230: $e_0934 -o r_0432; ; + _I231: $e_0808 -o r_0433; ; + _I232: $e_0365 -o r_0433; ; + _I233: $e_0586 -o r_0433; ; + _I234: $e_0934 -o r_0433; ; + _I235: $e_0808 -o r_0434; ; + _I236: $e_0365 -o r_0434; ; + _I237: $e_0586 -o r_0434; ; + _I238: $e_0934 -o r_0434; ; + _I239: $e_0808 -o r_0435; ; + _I240: $e_0365 -o r_0435; ; + _I241: $e_0586 -o r_0435; ; + _I242: $e_0934 -o r_0435; ; + _I243: $e_0632 -o r_0438; ; + _I244: $e_0007 -o r_0438; ; + _I245: $e_0774 -o r_0438; ; + _I246: $e_0436 -o r_0438; ; + _I247: $e_0136 -o r_0438; ; + _I248: $e_0001 -o r_0438; ; + _I249: $e_0347 -o r_0438; ; + _I250: $e_0255 -o r_0438; ; + _I251: $e_0752 -o r_0438; ; + _I252: $e_0690 -o r_0438; ; + _I253: $e_0006 -o r_0438; ; + _I254: $e_0531 -o r_0438; ; + _I255: $e_0346 -o r_0438; ; + _I256: $e_0475 -o r_0438; ; + _I257: $e_0514 -o r_0439; ; + _I258: $e_0978 -o r_0439; ; + _I259: $e_0422 -o r_0439; ; + _I260: $e_0250 -o r_0439; ; + _I261: $e_0004 -o r_0439; ; + _I262: $e_0243 -o r_0439; ; + _I263: $e_0389 -o r_0439; ; + _I264: $e_0255 -o r_0439; ; + _I265: $e_0848 -o r_0439; ; + _I266: $e_0028 -o r_0439; ; + _I267: $e_0531 -o r_0439; ; + _I268: $e_0322 -o r_0439; ; + _I269: $e_0396 -o r_0446; ; + _I270: $e_0057 -o r_0446; ; + _I271: $e_0567 -o FBA; ; + _I272: $e_0940 -o r_0451; ; + _I273: $e_0515 -o r_0462; ; + _I274: $e_0792 -o r_0466; ; + _I275: $e_0079 -o PGI; ; + _I276: $e_0160 -o r_0470; ; + _I277: $e_0955 -o r_0476; ; + _I278: $e_0867 -o r_0478; ; + _I279: $e_0353 -o r_0479; ; + _I280: $e_0392 -o TDH; ; + _I281: $e_0495 -o TDH; ; + _I282: $e_0525 -o TDH; ; + _I283: $e_0466 -o r_0489; ; + _I284: $e_0288 -o r_0489; ; + _I285: $e_0129 -o r_0491; ; + _I286: $e_0827 -o r_0491; ; + _I287: $e_0020 -o r_0495; ; + _I288: $e_0607 -o r_0495; ; + _I289: $e_0231 -o r_0499; ; + _I290: $e_0741 -o r_0501; ; + _I291: $e_0012 -o r_0501; ; + _I292: $e_0167 -o r_0501; ; + _I293: $e_0311 -o r_0501; ; + _I294: $e_0638 -o r_0502; ; + _I295: $e_0091 -o r_0502; ; + _I296: $e_0667 -o r_0510; ; + _I297: $e_0510 -o r_0510; ; + _I298: $e_0317 -o r_0510; ; + _I299: $e_0603 -o r_0510; ; + _I300: $e_0064 -o r_0512; ; + _I301: $e_0963 -o r_0512; ; + _I302: $e_0746 -o r_0514; ; + _I303: $e_0025 -o r_0525; ; + _I304: $e_0234 -o r_0528; ; + _I305: $e_0234 -o r_0529; ; + _I306: $e_0106 -o HXK; ; + _I307: $e_0325 -o HXK; ; + _I308: $e_0355 -o HXK; ; + _I309: $e_0103 -o r_0536; ; + _I310: $e_0320 -o r_0537; ; + _I311: $e_0476 -o r_0538; ; + _I312: $e_0953 -o r_0539; ; + _I313: $e_0196 -o r_0542; ; + _I314: $e_0154 -o r_0543; ; + _I315: $e_0146 -o r_0543; ; + _I316: $e_0472 -o r_0545; ; + _I317: $e_0548 -o r_0547; ; + _I318: $e_0428 -o r_0548; ; + _I319: $e_0799 -o r_0549; ; + _I320: $e_0202 -o r_0553; ; + _I321: $e_0846 -o r_0553; ; + _I322: $e_0697 -o r_0558; ; + _I323: $e_0708 -o r_0558; ; + _I324: $e_0716 -o r_0559; ; + _I325: $e_0087 -o r_0563; ; + _I326: $e_0875 -o r_0564; ; + _I327: $e_0705 -o r_0565; ; + _I328: $e_0458 -o r_0565; ; + _I329: $e_0693 -o r_0565; ; + _I330: $e_0591 -o r_0566; ; + _I331: $e_0038 -o r_0568; ; + _I332: $e_0754 -o r_0568; ; + _I333: $e_0631 -o r_0570; ; + _I334: $e_0736 -o r_0570; ; + _I335: $e_0557 -o r_0591; ; + _I336: $e_0220 -o r_0591; ; + _I337: $e_0862 -o r_0658; ; + _I338: $e_0771 -o r_0658; ; + _I339: $e_0769 -o r_0661; ; + _I340: $e_0135 -o r_0661; ; + _I341: $e_0289 -o r_0662; ; + _I342: $e_0550 -o r_0663; ; + _I343: $e_0457 -o r_0663; ; + _I344: $e_0031 -o r_0665; ; + _I345: $e_0922 -o r_0667; ; + _I346: $e_0685 -o r_0669; ; + _I347: $e_0642 -o r_0674; ; + _I348: $e_0062 -o r_0678; ; + _I349: $e_0343 -o r_0678; ; + _I350: $e_0842 -o r_0688; ; + _I351: $e_0447 -o r_0688; ; + _I352: $e_0109 -o r_0692; ; + _I353: $e_0295 -o r_0692; ; + _I354: $e_0698 -o r_0697; ; + _I355: $e_0440 -o r_0698; ; + _I356: $e_0550 -o r_0699; ; + _I357: $e_0457 -o r_0699; ; + _I358: $e_0926 -o r_0701; ; + _I359: $e_0171 -o r_0711; ; + _I360: $e_0571 -o r_0713; ; + _I361: $e_0838 -o r_0713; ; + _I362: $e_0137 -o r_0713; ; + _I363: $e_0134 -o r_0722; ; + _I364: $e_0269 -o r_0723; ; + _I365: $e_0057 -o r_0724; ; + _I366: $e_0396 -o r_0724; ; + _I367: $e_0239 -o r_0726; ; + _I368: $e_0658 -o r_0726; ; + _I369: $e_0298 -o r_0727; ; + _I370: $e_0409 -o r_0729; ; + _I371: $e_0610 -o r_0731; ; + _I372: $e_0396 -o r_0732; ; + _I373: $e_0057 -o r_0732; ; + _I374: $e_0745 -o r_0735; ; + _I375: $e_0745 -o r_0736; ; + _I376: $e_0812 -o r_0739; ; + _I377: $e_0204 -o r_0757; ; + _I378: $e_0435 -o r_0757; ; + _I379: $e_0512 -o r_0758; ; + _I380: $e_0290 -o r_0759; ; + _I381: $e_0271 -o r_0792; ; + _I382: $e_0568 -o r_0800; ; + _I383: $e_0568 -o r_0811; ; + _I384: $e_0674 -o r_0813; ; + _I385: $e_0499 -o r_0816; ; + _I386: $e_0729 -o r_0818; ; + _I387: $e_0755 -o r_0820; ; + _I388: $e_0712 -o r_0820; ; + _I389: $e_0249 -o r_0821; ; + _I390: $e_0348 -o r_0851; ; + _I391: $e_0639 -o r_0852; ; + _I392: $e_0312 -o r_0852; ; + _I393: $e_0352 -o r_0855; ; + _I394: $e_0536 -o r_0858; ; + _I395: $e_0381 -o r_0858; ; + _I396: $e_0964 -o r_0874; ; + _I397: $e_0788 -o r_0877; ; + _I398: $e_0382 -o r_0877; ; + _I399: $e_0278 -o r_0880; ; + _I400: $e_0633 -o r_0883; ; + _I401: $e_0975 -o r_0883; ; + _I402: $e_0398 -o r_0883; ; + _I403: $e_0612 -o r_0884; ; + _I404: $e_0401 -o PFK; ; + _I405: $e_0743 -o PFK; ; + _I406: $e_0576 -o r_0888; ; + _I407: $e_0757 -o r_0888; ; + _I408: $e_0733 -o r_0888; ; + _I409: $e_0455 -o r_0889; ; + _I410: $e_0407 -o r_0889; ; + _I411: $e_0113 -o PGK; ; + _I412: $e_0582 -o GPM; ; + _I413: $e_0536 -o r_0900; ; + _I414: $e_0536 -o r_0901; ; + _I415: $e_0314 -o r_0902; ; + _I416: $e_0747 -o r_0904; ; + _I417: $e_0017 -o r_0908; ; + _I418: $e_0103 -o r_0909; ; + _I419: $e_0103 -o r_0910; ; + _I420: $e_0860 -o r_0911; ; + _I421: $e_0631 -o r_0912; ; + _I422: $e_0736 -o r_0912; ; + _I423: $e_0165 -o r_0913; ; + _I424: $e_0352 -o r_0914; ; + _I425: $e_0763 -o r_0915; ; + _I426: $e_0030 -o r_0916; ; + _I427: $e_0299 -o r_0916; ; + _I428: $e_0418 -o r_0916; ; + _I429: $e_0585 -o r_0916; ; + _I430: $e_0829 -o r_0916; ; + _I431: $e_0802 -o r_0938; ; + _I432: $e_0074 -o r_0939; ; + _I433: $e_0296 -o r_0941; ; + _I434: $e_0276 -o r_0957; ; + _I435: $e_0334 -o r_0958; ; + _I436: $e_0084 -o r_0958; ; + _I437: $e_0370 -o PDC; ; + _I438: $e_0636 -o PDC; ; + _I439: $e_0647 -o PDC; ; + _I440: $e_0011 -o PYK; ; + _I441: $e_0895 -o PYK; ; + _I442: $e_0841 -o r_0967; ; + _I443: $e_0090 -o r_0968; ; + _I444: $e_0398 -o r_0970; ; + _I445: $e_0398 -o r_0973; ; + _I446: $e_0467 -o r_0974; ; + _I447: $e_0492 -o r_0974; ; + _I448: $e_0387 -o r_0974; ; + _I449: $e_0291 -o r_0974; ; + _I450: $e_0467 -o r_0976; ; + _I451: $e_0492 -o r_0976; ; + _I452: $e_0387 -o r_0976; ; + _I453: $e_0291 -o r_0976; ; + _I454: $e_0467 -o r_0978; ; + _I455: $e_0492 -o r_0978; ; + _I456: $e_0387 -o r_0978; ; + _I457: $e_0291 -o r_0978; ; + _I458: $e_0852 -o r_0982; ; + _I459: $e_0506 -o r_0984; ; + _I460: $e_0699 -o r_0986; ; + _I461: $e_0489 -o r_0988; ; + _I462: $e_0813 -o r_0989; ; + _I463: $e_0567 -o r_0990; ; + _I464: $e_0054 -o r_0993; ; + _I465: $e_0177 -o r_0993; ; + _I466: $e_0761 -o r_0993; ; + _I467: $e_0168 -o r_0995; ; + _I468: $e_0425 -o r_0995; ; + _I469: $e_0182 -o r_0996; ; + _I470: $e_0182 -o r_0997; ; + _I471: $e_0385 -o r_1010; ; + _I472: $e_0456 -o r_1012; ; + _I473: $e_0578 -o r_1014; ; + _I474: $e_0613 -o r_1014; ; + _I475: $e_0579 -o r_1021; ; + _I476: $e_0188 -o r_1021; ; + _I477: $e_0494 -o r_1021; ; + _I478: $e_0619 -o r_1021; ; + _I479: $e_0581 -o r_1021; ; + _I480: $e_0107 -o r_1026; ; + _I481: $e_0547 -o r_1027; ; + _I482: $e_0321 -o r_1027; ; + _I483: $e_0633 -o r_1038; ; + _I484: $e_0218 -o r_1038; ; + _I485: $e_0398 -o r_1038; ; + _I486: $e_0448 -o r_1038; ; + _I487: $e_0915 -o r_1038; ; + _I488: $e_0124 -o r_1038; ; + _I489: $e_0260 -o r_1040; ; + _I490: $e_0122 -o r_1041; ; + _I491: $e_0470 -o r_1042; ; + _I492: $e_0850 -o r_1045; ; + _I493: $e_0684 -o r_1048; ; + _I494: $e_0063 -o r_1049; ; + _I495: $e_0962 -o r_1049; ; + _I496: $e_0063 -o r_1050; ; + _I497: $e_0962 -o r_1050; ; + _I498: $e_0711 -o r_1051; ; + _I499: $e_0065 -o r_1051; ; + _I500: $e_0179 -o r_1051; ; + _I501: $e_0753 -o r_1051; ; + _I502: $e_0176 -o r_1052; ; + _I503: $e_0611 -o r_1052; ; + _I504: $e_0765 -o r_1052; ; + _I505: $e_0851 -o r_1052; ; + _I506: $e_0175 -o TPI; ; + _I507: $e_0330 -o r_1055; ; + _I508: $e_0836 -o r_1057; ; + _I509: $e_0348 -o r_1063; ; + _I510: $e_0629 -o r_1063; ; + _I511: $e_0390 -o r_1066; ; + _I512: $e_0561 -o r_1072; ; + _I513: $e_0565 -o r_1084; ; + _I514: $e_0550 -o r_1087; ; + _I515: $e_0457 -o r_1087; ; + _I516: $e_0372 -o r_1089; ; + _I517: $e_0601 -o r_2126; ; + _I518: $e_0594 -o r_2127; ; + // Species initializations: s_0002 = 0.1; s_0004 = 0.1; diff --git a/doc/examples/biomodels/BIOMD0000000474_url.txt b/doc/examples/biomodels/BIOMD0000000474/BIOMD0000000474_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000474_url.txt rename to doc/examples/biomodels/BIOMD0000000474/BIOMD0000000474_url.txt index deb0d6600..eedbfd038 100644 --- a/doc/examples/biomodels/BIOMD0000000474_url.txt +++ b/doc/examples/biomodels/BIOMD0000000474/BIOMD0000000474_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1212210000() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1212210000_eventsForFigure3A.txt b/doc/examples/biomodels/BIOMD0000000474/MODEL1212210000_eventsForFigure3A.txt similarity index 99% rename from doc/examples/biomodels/MODEL1212210000_eventsForFigure3A.txt rename to doc/examples/biomodels/BIOMD0000000474/MODEL1212210000_eventsForFigure3A.txt index 3a7f1d99f..0db519577 100644 --- a/doc/examples/biomodels/MODEL1212210000_eventsForFigure3A.txt +++ b/doc/examples/biomodels/BIOMD0000000474/MODEL1212210000_eventsForFigure3A.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1212210000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000475_url.txt b/doc/examples/biomodels/BIOMD0000000475/BIOMD0000000475_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000475_url.txt rename to doc/examples/biomodels/BIOMD0000000475/BIOMD0000000475_url.txt index e338bbe7e..0f0586cd8 100644 --- a/doc/examples/biomodels/BIOMD0000000475_url.txt +++ b/doc/examples/biomodels/BIOMD0000000475/BIOMD0000000475_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *PRR_model() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000476_url.txt b/doc/examples/biomodels/BIOMD0000000476/BIOMD0000000476_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000476_url.txt rename to doc/examples/biomodels/BIOMD0000000476/BIOMD0000000476_url.txt index e379ec0eb..a3f5fb0a4 100644 --- a/doc/examples/biomodels/BIOMD0000000476_url.txt +++ b/doc/examples/biomodels/BIOMD0000000476/BIOMD0000000476_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1001130000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000477_url.txt b/doc/examples/biomodels/BIOMD0000000477/BIOMD0000000477_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000477_url.txt rename to doc/examples/biomodels/BIOMD0000000477/BIOMD0000000477_url.txt index 3f214d15c..daff626e3 100644 --- a/doc/examples/biomodels/BIOMD0000000477_url.txt +++ b/doc/examples/biomodels/BIOMD0000000477/BIOMD0000000477_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1308080000() // Compartments and Species: @@ -100,91 +100,91 @@ model *MODEL1308080000() // Species initializations: mw4d2e70a7_f499_461d_ae18_bc53b365b091 = 1.5; - mw4d2e70a7_f499_461d_ae18_bc53b365b091 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw4d2e70a7_f499_461d_ae18_bc53b365b091 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw8cc67de0_64e6_428f_ab09_4c2825cc172c = 1.3; - mw8cc67de0_64e6_428f_ab09_4c2825cc172c has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw8cc67de0_64e6_428f_ab09_4c2825cc172c has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw6ee00a71_ab68_454b_b1cd_60c1ebd19cfa = 1.3; - mw6ee00a71_ab68_454b_b1cd_60c1ebd19cfa has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw6ee00a71_ab68_454b_b1cd_60c1ebd19cfa has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw2dc73059_a841_48d5_b4bd_3ac24d94c42e = 0.8; - mw2dc73059_a841_48d5_b4bd_3ac24d94c42e has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw2dc73059_a841_48d5_b4bd_3ac24d94c42e has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw136c8391_14f4_4a28_83a3_35cc74a2e040 = 1.5; - mw136c8391_14f4_4a28_83a3_35cc74a2e040 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw136c8391_14f4_4a28_83a3_35cc74a2e040 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw7204ab72_2ee5_4b92_b420_2583dacc4343 = 1.4; - mw7204ab72_2ee5_4b92_b420_2583dacc4343 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw7204ab72_2ee5_4b92_b420_2583dacc4343 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw6939cefe_e7ff_4a3f_b45b_a9234d1b5573 = 1.2; - mw6939cefe_e7ff_4a3f_b45b_a9234d1b5573 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw6939cefe_e7ff_4a3f_b45b_a9234d1b5573 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mwf8cfed1b_6fcf_4cba_bc30_b44490814a7a = 1.4; - mwf8cfed1b_6fcf_4cba_bc30_b44490814a7a has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mwf8cfed1b_6fcf_4cba_bc30_b44490814a7a has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw702be69a_eb4f_425e_87c7_ef7d85254536 = 1.2; - mw702be69a_eb4f_425e_87c7_ef7d85254536 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw702be69a_eb4f_425e_87c7_ef7d85254536 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mwbee11634_55df_4a3f_998a_634dfaf46fd7 = 1.2; - mwbee11634_55df_4a3f_998a_634dfaf46fd7 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mwbee11634_55df_4a3f_998a_634dfaf46fd7 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw805b55df_cc91_4227_bb52_930e961b682c = 1.5; - mw805b55df_cc91_4227_bb52_930e961b682c has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw805b55df_cc91_4227_bb52_930e961b682c has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mwb71eb539_dca6_47ab_8df5_430d84af0bfb = 0.9; - mwb71eb539_dca6_47ab_8df5_430d84af0bfb has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mwb71eb539_dca6_47ab_8df5_430d84af0bfb has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mwa5d6f7e4_dc4d_4931_91ce_1e78e7b2f195 = 1.5; - mwa5d6f7e4_dc4d_4931_91ce_1e78e7b2f195 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mwa5d6f7e4_dc4d_4931_91ce_1e78e7b2f195 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw4079e13c_446e_4aa2_9ec4_233583833d02 = 1.5; - mw4079e13c_446e_4aa2_9ec4_233583833d02 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw4079e13c_446e_4aa2_9ec4_233583833d02 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mwe5fade7d_1715_4bb1_843f_923da8ecddf1 = 0.85; - mwe5fade7d_1715_4bb1_843f_923da8ecddf1 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mwe5fade7d_1715_4bb1_843f_923da8ecddf1 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw262497ec_3d54_4367_bfe3_76a9c57497cb = 1; - mw262497ec_3d54_4367_bfe3_76a9c57497cb has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw262497ec_3d54_4367_bfe3_76a9c57497cb has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw8bffd47e_34de_4738_81bf_7a39a40b3ae8 = 1.1; - mw8bffd47e_34de_4738_81bf_7a39a40b3ae8 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw8bffd47e_34de_4738_81bf_7a39a40b3ae8 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw308b75ec_28b7_4d97_92e2_51a8ce04116a = 1.3; - mw308b75ec_28b7_4d97_92e2_51a8ce04116a has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw308b75ec_28b7_4d97_92e2_51a8ce04116a has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw75377e12_e23d_44b3_9823_5fac9b23edc8 = 1.1; - mw75377e12_e23d_44b3_9823_5fac9b23edc8 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw75377e12_e23d_44b3_9823_5fac9b23edc8 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw67d0cf04_d6a7_4725_a869_098a96a3350d = 0.8; - mw67d0cf04_d6a7_4725_a869_098a96a3350d has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw67d0cf04_d6a7_4725_a869_098a96a3350d has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw46ee629a_dd6b_4163_9da1_2614bb1d74bc = 1.5; - mw46ee629a_dd6b_4163_9da1_2614bb1d74bc has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw46ee629a_dd6b_4163_9da1_2614bb1d74bc has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw0be0d193_fd6b_4824_8928_dbade8b5c99c = 1.6; - mw0be0d193_fd6b_4824_8928_dbade8b5c99c has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw0be0d193_fd6b_4824_8928_dbade8b5c99c has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw280197c8_98de_43f0_bf01_0f332a1ab689 = 1.3; - mw280197c8_98de_43f0_bf01_0f332a1ab689 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw280197c8_98de_43f0_bf01_0f332a1ab689 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw9a5baf6d_0285_4ad3_9499_059c553d9cf6 = 1.6; - mw9a5baf6d_0285_4ad3_9499_059c553d9cf6 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw9a5baf6d_0285_4ad3_9499_059c553d9cf6 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw05469f51_73f7_4ba1_9f1a_bce5fea143c2 = 1.45; - mw05469f51_73f7_4ba1_9f1a_bce5fea143c2 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw05469f51_73f7_4ba1_9f1a_bce5fea143c2 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mwf20834c8_a115_460b_859c_4e3ca1ffd953 = 0.9; - mwf20834c8_a115_460b_859c_4e3ca1ffd953 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mwf20834c8_a115_460b_859c_4e3ca1ffd953 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mwb4633da9_f9d6_4ad8_a7e5_da075c830e17 = 1.5; - mwb4633da9_f9d6_4ad8_a7e5_da075c830e17 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mwb4633da9_f9d6_4ad8_a7e5_da075c830e17 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw9bb804c9_3e4e_4684_9f6b_4e6f6706a58e = 1.6; - mw9bb804c9_3e4e_4684_9f6b_4e6f6706a58e has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw9bb804c9_3e4e_4684_9f6b_4e6f6706a58e has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw64453fc5_a275_4bba_84f0_2af249b31514 = 1.2; - mw64453fc5_a275_4bba_84f0_2af249b31514 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw64453fc5_a275_4bba_84f0_2af249b31514 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw323a57b4_8e59_4116_9ad1_fe547b89c858 = 0.3; - mw323a57b4_8e59_4116_9ad1_fe547b89c858 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw323a57b4_8e59_4116_9ad1_fe547b89c858 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw173d8585_5817_4b4c_932a_cf7d673680ac = 1.2; - mw173d8585_5817_4b4c_932a_cf7d673680ac has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw173d8585_5817_4b4c_932a_cf7d673680ac has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw32c21c39_237b_4d4c_bb5d_117cb30ce68a = 1.2; - mw32c21c39_237b_4d4c_bb5d_117cb30ce68a has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw32c21c39_237b_4d4c_bb5d_117cb30ce68a has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw3832f277_aef2_4f1d_87af_abc2a3c1a7d5 = 1.6; - mw3832f277_aef2_4f1d_87af_abc2a3c1a7d5 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw3832f277_aef2_4f1d_87af_abc2a3c1a7d5 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw13651143_feb5_49a5_adab_9105c2647446 = 1.1; - mw13651143_feb5_49a5_adab_9105c2647446 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw13651143_feb5_49a5_adab_9105c2647446 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw8a358487_b18b_42df_a646_cd75eb5bfcc2 = 0.2; - mw8a358487_b18b_42df_a646_cd75eb5bfcc2 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw8a358487_b18b_42df_a646_cd75eb5bfcc2 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mwd9e7a9b9_6f1b_4bbc_afa5_6cb192b62ce8 = 0.6; - mwd9e7a9b9_6f1b_4bbc_afa5_6cb192b62ce8 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mwd9e7a9b9_6f1b_4bbc_afa5_6cb192b62ce8 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mwfed5a135_c91b_4d20_91b2_3a61723544dd = 0.91; - mwfed5a135_c91b_4d20_91b2_3a61723544dd has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mwfed5a135_c91b_4d20_91b2_3a61723544dd has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw97345a67_a8e8_42aa_8e62_69e9d2b6cf45 = 0.8; - mw97345a67_a8e8_42aa_8e62_69e9d2b6cf45 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw97345a67_a8e8_42aa_8e62_69e9d2b6cf45 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw5c67812a_17f5_43cf_8acb_9bde272c1911 = 0.5; - mw5c67812a_17f5_43cf_8acb_9bde272c1911 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw5c67812a_17f5_43cf_8acb_9bde272c1911 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw1f12e5bc_ebbc_4347_b6b7_5cd1740ac69a = 0; - mw1f12e5bc_ebbc_4347_b6b7_5cd1740ac69a has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw1f12e5bc_ebbc_4347_b6b7_5cd1740ac69a has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mwda4716f1_ae00_4149_aec3_12531380425a = 0; - mwda4716f1_ae00_4149_aec3_12531380425a has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mwda4716f1_ae00_4149_aec3_12531380425a has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mw17ae9adc_54ab_407b_a34d_8413a3a10cc6 = 0; - mw17ae9adc_54ab_407b_a34d_8413a3a10cc6 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mw17ae9adc_54ab_407b_a34d_8413a3a10cc6 has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; mwc844b7c0_98f5_4d0d_8f0c_00dfe8b54e6d = 0; - mwc844b7c0_98f5_4d0d_8f0c_00dfe8b54e6d has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume; + mwc844b7c0_98f5_4d0d_8f0c_00dfe8b54e6d has MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole; // Compartment initializations: mw0cba5a10_f303_4c95_aaf1_b6f942374d31 = 1; @@ -362,7 +362,6 @@ model *MODEL1308080000() unit MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole = 1e-09 mole; unit MWDERIVEDUNIT_1__second = dimensionless / second; unit MWDERIVEDUNIT_nanomole__second = mole * 1e-09 dimensionless / second; - unit MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole_per_volume = 1e-09 mole / litre; // Display Names: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole is "nanomole"; diff --git a/doc/examples/biomodels/BIOMD0000000478_url.txt b/doc/examples/biomodels/BIOMD0000000478/BIOMD0000000478_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000478_url.txt rename to doc/examples/biomodels/BIOMD0000000478/BIOMD0000000478_url.txt index 9299a3c50..ed9dadd42 100644 --- a/doc/examples/biomodels/BIOMD0000000478_url.txt +++ b/doc/examples/biomodels/BIOMD0000000478/BIOMD0000000478_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1309060000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000479_url.txt b/doc/examples/biomodels/BIOMD0000000479/BIOMD0000000479_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000479_url.txt rename to doc/examples/biomodels/BIOMD0000000479/BIOMD0000000479_url.txt index 650c265e1..34d1d501a 100644 --- a/doc/examples/biomodels/BIOMD0000000479_url.txt +++ b/doc/examples/biomodels/BIOMD0000000479/BIOMD0000000479_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1305280000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000480_url.txt b/doc/examples/biomodels/BIOMD0000000480/BIOMD0000000480_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000480_url.txt rename to doc/examples/biomodels/BIOMD0000000480/BIOMD0000000480_url.txt index b9f03aa01..126326d22 100644 --- a/doc/examples/biomodels/BIOMD0000000480_url.txt +++ b/doc/examples/biomodels/BIOMD0000000480/BIOMD0000000480_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1307130000() // Compartments and Species: @@ -160,8 +160,8 @@ model *MODEL1307130000() reaction_58: species_15 => species_17; c1*reaction_58_k1*species_15; // Events: - event_1: at time >= 2: species_10 = species_10 + species_11, s1 = s1 + species_7*parameter_6; - event_2: at time >= 4: species_10 = species_10 + species_11, s1 = s1 + species_7*parameter_6; + event_1: at time >= 2: s1 = s1 + species_7*parameter_6, species_10 = species_10 + species_11; + event_2: at time >= 4: s1 = s1 + species_7*parameter_6, species_10 = species_10 + species_11; // Species initializations: s1 = parameter_6*species_7; diff --git a/doc/examples/biomodels/BIOMD0000000481_url.txt b/doc/examples/biomodels/BIOMD0000000481/BIOMD0000000481_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000481_url.txt rename to doc/examples/biomodels/BIOMD0000000481/BIOMD0000000481_url.txt index b32974d91..7e66ca99d 100644 --- a/doc/examples/biomodels/BIOMD0000000481_url.txt +++ b/doc/examples/biomodels/BIOMD0000000481/BIOMD0000000481_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1308100000() // Compartments and Species: @@ -324,7 +324,7 @@ model *MODEL1308100000() src_P4.sboTerm = 291 src_Inh.sboTerm = 291 src_OT.sboTerm = 291 - src_Enz.sboTerm = 291 + src_Enz.sboTerm = 291 src_PGF.sboTerm = 291 src_LH.sboTerm = 291 src_FSH.sboTerm = 291 diff --git a/doc/examples/biomodels/BIOMD0000000482_url.txt b/doc/examples/biomodels/BIOMD0000000482/BIOMD0000000482_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000482_url.txt rename to doc/examples/biomodels/BIOMD0000000482/BIOMD0000000482_url.txt index cdbfba236..83991f85b 100644 --- a/doc/examples/biomodels/BIOMD0000000482_url.txt +++ b/doc/examples/biomodels/BIOMD0000000482/BIOMD0000000482_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1301020001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000483_url.txt b/doc/examples/biomodels/BIOMD0000000483/BIOMD0000000483_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000483_url.txt rename to doc/examples/biomodels/BIOMD0000000483/BIOMD0000000483_url.txt index e4d57b3c7..4470e93e9 100644 --- a/doc/examples/biomodels/BIOMD0000000483_url.txt +++ b/doc/examples/biomodels/BIOMD0000000483/BIOMD0000000483_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1308080008() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000484_url.txt b/doc/examples/biomodels/BIOMD0000000484/BIOMD0000000484_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000484_url.txt rename to doc/examples/biomodels/BIOMD0000000484/BIOMD0000000484_url.txt index 17a5f28ee..be37f5d26 100644 --- a/doc/examples/biomodels/BIOMD0000000484_url.txt +++ b/doc/examples/biomodels/BIOMD0000000484/BIOMD0000000484_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1308080004() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000485_url.txt b/doc/examples/biomodels/BIOMD0000000485/BIOMD0000000485_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000485_url.txt rename to doc/examples/biomodels/BIOMD0000000485/BIOMD0000000485_url.txt index dd6d87929..698a7c359 100644 --- a/doc/examples/biomodels/BIOMD0000000485_url.txt +++ b/doc/examples/biomodels/BIOMD0000000485/BIOMD0000000485_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1308080005() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000486_url.txt b/doc/examples/biomodels/BIOMD0000000486/BIOMD0000000486_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000486_url.txt rename to doc/examples/biomodels/BIOMD0000000486/BIOMD0000000486_url.txt index 2bc23002d..9740475d6 100644 --- a/doc/examples/biomodels/BIOMD0000000486_url.txt +++ b/doc/examples/biomodels/BIOMD0000000486/BIOMD0000000486_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1308080006() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000487_url.txt b/doc/examples/biomodels/BIOMD0000000487/BIOMD0000000487_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000487_url.txt rename to doc/examples/biomodels/BIOMD0000000487/BIOMD0000000487_url.txt index 145f0610b..22088e3a2 100644 --- a/doc/examples/biomodels/BIOMD0000000487_url.txt +++ b/doc/examples/biomodels/BIOMD0000000487/BIOMD0000000487_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1308080007() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000488_url.txt b/doc/examples/biomodels/BIOMD0000000488/BIOMD0000000488_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000488_url.txt rename to doc/examples/biomodels/BIOMD0000000488/BIOMD0000000488_url.txt index 5617b396e..d4f3c3c4b 100644 --- a/doc/examples/biomodels/BIOMD0000000488_url.txt +++ b/doc/examples/biomodels/BIOMD0000000488/BIOMD0000000488_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1212030000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000489_url.txt b/doc/examples/biomodels/BIOMD0000000489/BIOMD0000000489_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000489_url.txt rename to doc/examples/biomodels/BIOMD0000000489/BIOMD0000000489_url.txt index 234ad9a9e..978bef1e8 100644 --- a/doc/examples/biomodels/BIOMD0000000489_url.txt +++ b/doc/examples/biomodels/BIOMD0000000489/BIOMD0000000489_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1303230000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000490_url.txt b/doc/examples/biomodels/BIOMD0000000490/BIOMD0000000490_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000490_url.txt rename to doc/examples/biomodels/BIOMD0000000490/BIOMD0000000490_url.txt index 73a0cc447..b6a1c4f24 100644 --- a/doc/examples/biomodels/BIOMD0000000490_url.txt +++ b/doc/examples/biomodels/BIOMD0000000490/BIOMD0000000490_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1309160000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000491_url.txt b/doc/examples/biomodels/BIOMD0000000491/BIOMD0000000491_url.txt similarity index 95% rename from doc/examples/biomodels/BIOMD0000000491_url.txt rename to doc/examples/biomodels/BIOMD0000000491/BIOMD0000000491_url.txt index 237841bc8..31f58b043 100644 --- a/doc/examples/biomodels/BIOMD0000000491_url.txt +++ b/doc/examples/biomodels/BIOMD0000000491/BIOMD0000000491_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1308220001() // Compartments and Species: @@ -106,119 +106,119 @@ model *MODEL1308220001() // Species initializations: s1 = 0.5; - s1 has substance_per_volume; + s1 has substance; s2 = 0.5; - s2 has substance_per_volume; + s2 has substance; s3 = 0.5; - s3 has substance_per_volume; + s3 has substance; s4 = 0.5; - s4 has substance_per_volume; + s4 has substance; s5 = 0.5; - s5 has substance_per_volume; + s5 has substance; s6 = 0.5; - s6 has substance_per_volume; + s6 has substance; s7 = 0.8; - s7 has substance_per_volume; + s7 has substance; s8 = 0.8; - s8 has substance_per_volume; + s8 has substance; s9 = 0.8; - s9 has substance_per_volume; + s9 has substance; s10 = 0.8; - s10 has substance_per_volume; + s10 has substance; s11 = 0.8; - s11 has substance_per_volume; + s11 has substance; s12 = 0.8; - s12 has substance_per_volume; + s12 has substance; s13 = 1; - s13 has substance_per_volume; + s13 has substance; s14 = 1; - s14 has substance_per_volume; + s14 has substance; s15 = 1; - s15 has substance_per_volume; + s15 has substance; s16 = 1; - s16 has substance_per_volume; + s16 has substance; s17 = 1; - s17 has substance_per_volume; + s17 has substance; s18 = 1; - s18 has substance_per_volume; + s18 has substance; s27 = 1; - s27 has substance_per_volume; + s27 has substance; s28 = 1; - s28 has substance_per_volume; + s28 has substance; s19 = 1; - s19 has substance_per_volume; + s19 has substance; s20 = 1; - s20 has substance_per_volume; + s20 has substance; s21 = 1; - s21 has substance_per_volume; + s21 has substance; s22 = 1; - s22 has substance_per_volume; + s22 has substance; s23 = 1; - s23 has substance_per_volume; + s23 has substance; s24 = 1; - s24 has substance_per_volume; + s24 has substance; s25 = 1; - s25 has substance_per_volume; + s25 has substance; s26 = 1; - s26 has substance_per_volume; + s26 has substance; s29 = 1; - s29 has substance_per_volume; + s29 has substance; s30 = 1; - s30 has substance_per_volume; + s30 has substance; s31 = 1; - s31 has substance_per_volume; + s31 has substance; s32 = 1; - s32 has substance_per_volume; + s32 has substance; s33 = 1.2; - s33 has substance_per_volume; + s33 has substance; s34 = 1.2; - s34 has substance_per_volume; + s34 has substance; s35 = 1.2; - s35 has substance_per_volume; + s35 has substance; s36 = 1.2; - s36 has substance_per_volume; + s36 has substance; s37 = 1.2; - s37 has substance_per_volume; + s37 has substance; s38 = 1.2; - s38 has substance_per_volume; + s38 has substance; s39 = 1.2; - s39 has substance_per_volume; + s39 has substance; s40 = 1.2; - s40 has substance_per_volume; + s40 has substance; s41 = 1.2; - s41 has substance_per_volume; + s41 has substance; s42 = 1.2; - s42 has substance_per_volume; + s42 has substance; s43 = 1.2; - s43 has substance_per_volume; + s43 has substance; s44 = 1.2; - s44 has substance_per_volume; + s44 has substance; s45 = 1.2; - s45 has substance_per_volume; + s45 has substance; s46 = 1.2; - s46 has substance_per_volume; + s46 has substance; s47 = 1.2; - s47 has substance_per_volume; + s47 has substance; s48 = 1.2; - s48 has substance_per_volume; + s48 has substance; s49 = 1.5; - s49 has substance_per_volume; + s49 has substance; s50 = 1.5; - s50 has substance_per_volume; + s50 has substance; s51 = 1.5; - s51 has substance_per_volume; + s51 has substance; s52 = 1.5; - s52 has substance_per_volume; + s52 has substance; s53 = 1.5; - s53 has substance_per_volume; + s53 has substance; s54 = 1.8; - s54 has substance_per_volume; + s54 has substance; s55 = 2; - s55 has substance_per_volume; + s55 has substance; s56 = 2.2; - s56 has substance_per_volume; + s56 has substance; s57 = 2.5; - s57 has substance_per_volume; + s57 has substance; // Compartment initializations: default = 1; @@ -612,7 +612,7 @@ model *MODEL1308220001() unit length = metre; unit time_unit = second; unit per_second = 1 / second; - unit substance_per_volume = 1e-3 mole / 1e-3 litre; + unit substance_volume = 1e-3 mole * 1e-3 litre; // Display Names: time_unit is "time"; diff --git a/doc/examples/biomodels/BIOMD0000000492_url.txt b/doc/examples/biomodels/BIOMD0000000492/BIOMD0000000492_url.txt similarity index 95% rename from doc/examples/biomodels/BIOMD0000000492_url.txt rename to doc/examples/biomodels/BIOMD0000000492/BIOMD0000000492_url.txt index e132d7977..894188717 100644 --- a/doc/examples/biomodels/BIOMD0000000492_url.txt +++ b/doc/examples/biomodels/BIOMD0000000492/BIOMD0000000492_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1308220000() // Compartments and Species: @@ -107,109 +107,109 @@ model *MODEL1308220000() // Species initializations: s1 = 0.5; - s1 has substance_per_volume; + s1 has substance; s2 = 0.5; - s2 has substance_per_volume; + s2 has substance; s3 = 0.8; - s3 has substance_per_volume; + s3 has substance; s4 = 0.8; - s4 has substance_per_volume; + s4 has substance; s5 = 0.8; - s5 has substance_per_volume; + s5 has substance; s6 = 0.8; - s6 has substance_per_volume; + s6 has substance; s7 = 1; - s7 has substance_per_volume; + s7 has substance; s8 = 1; - s8 has substance_per_volume; + s8 has substance; s9 = 1; - s9 has substance_per_volume; + s9 has substance; s10 = 1; - s10 has substance_per_volume; + s10 has substance; s11 = 1; - s11 has substance_per_volume; + s11 has substance; s12 = 1; - s12 has substance_per_volume; + s12 has substance; s13 = 1; - s13 has substance_per_volume; + s13 has substance; s14 = 1; - s14 has substance_per_volume; + s14 has substance; s15 = 1; - s15 has substance_per_volume; + s15 has substance; s16 = 1; - s16 has substance_per_volume; + s16 has substance; s17 = 1; - s17 has substance_per_volume; + s17 has substance; s18 = 1; - s18 has substance_per_volume; + s18 has substance; s19 = 1; - s19 has substance_per_volume; + s19 has substance; s20 = 1; - s20 has substance_per_volume; + s20 has substance; s21 = 1; - s21 has substance_per_volume; + s21 has substance; s22 = 1; - s22 has substance_per_volume; + s22 has substance; s23 = 1; - s23 has substance_per_volume; + s23 has substance; s24 = 1; - s24 has substance_per_volume; + s24 has substance; s25 = 1; - s25 has substance_per_volume; + s25 has substance; s28 = 1.2; - s28 has substance_per_volume; + s28 has substance; s29 = 1.2; - s29 has substance_per_volume; + s29 has substance; s30 = 1.5; - s30 has substance_per_volume; + s30 has substance; s31 = 1.5; - s31 has substance_per_volume; + s31 has substance; s32 = 1.2; - s32 has substance_per_volume; + s32 has substance; s33 = 1.2; - s33 has substance_per_volume; + s33 has substance; s34 = 1.2; - s34 has substance_per_volume; + s34 has substance; s35 = 1.2; - s35 has substance_per_volume; + s35 has substance; s36 = 1.5; - s36 has substance_per_volume; + s36 has substance; s37 = 1.5; - s37 has substance_per_volume; + s37 has substance; s38 = 1.2; - s38 has substance_per_volume; + s38 has substance; s39 = 1.2; - s39 has substance_per_volume; + s39 has substance; s40 = 1.2; - s40 has substance_per_volume; + s40 has substance; s41 = 1.2; - s41 has substance_per_volume; + s41 has substance; s42 = 1.2; - s42 has substance_per_volume; + s42 has substance; s43 = 1.2; - s43 has substance_per_volume; + s43 has substance; s44 = 1.2; - s44 has substance_per_volume; + s44 has substance; s45 = 1.2; - s45 has substance_per_volume; + s45 has substance; s46 = 1.2; - s46 has substance_per_volume; + s46 has substance; s47 = 1.2; - s47 has substance_per_volume; + s47 has substance; s48 = 1.5; - s48 has substance_per_volume; + s48 has substance; s49 = 1.8; - s49 has substance_per_volume; + s49 has substance; s50 = 2; - s50 has substance_per_volume; + s50 has substance; s51 = 2.2; - s51 has substance_per_volume; + s51 has substance; s52 = 2.5; - s52 has substance_per_volume; + s52 has substance; s26 = 1; - s26 has substance_per_volume; + s26 has substance; s27 = 1; - s27 has substance_per_volume; + s27 has substance; // Compartment initializations: default = 1; @@ -612,7 +612,7 @@ model *MODEL1308220000() unit length = metre; unit time_unit = second; unit per_second = 1 / second; - unit substance_per_volume = 1e-3 mole / 1e-3 litre; + unit substance_volume = 1e-3 mole * 1e-3 litre; // Display Names: time_unit is "time"; diff --git a/doc/examples/biomodels/BIOMD0000000493_url.txt b/doc/examples/biomodels/BIOMD0000000493/BIOMD0000000493_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000493_url.txt rename to doc/examples/biomodels/BIOMD0000000493/BIOMD0000000493_url.txt index 8f97b60a5..01502da02 100644 --- a/doc/examples/biomodels/BIOMD0000000493_url.txt +++ b/doc/examples/biomodels/BIOMD0000000493/BIOMD0000000493_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1310150000() // Compartments and Species: @@ -13,8 +13,8 @@ model *MODEL1310150000() a6: C -> ; kC*C; // Events: - _E0: at 100 after P > 12.03: zD = 0.8, zO = 1; - _E1: at 800 after P > 12.03: zD = 0, zO = 0; + _E0: at 100 after P > 12.03: zO = 1, zD = 0.8; + _E1: at 800 after P > 12.03: zO = 0, zD = 0; // Species initializations: P = 12.03; diff --git a/doc/examples/biomodels/Schittler2010_Osteochondroswitch_Figure5b.txt b/doc/examples/biomodels/BIOMD0000000493/Schittler2010_Osteochondroswitch_Figure5b.txt similarity index 92% rename from doc/examples/biomodels/Schittler2010_Osteochondroswitch_Figure5b.txt rename to doc/examples/biomodels/BIOMD0000000493/Schittler2010_Osteochondroswitch_Figure5b.txt index ea0070d4c..dc32e1fe7 100644 --- a/doc/examples/biomodels/Schittler2010_Osteochondroswitch_Figure5b.txt +++ b/doc/examples/biomodels/BIOMD0000000493/Schittler2010_Osteochondroswitch_Figure5b.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Schittler2010_Osteochondroswitch() // Compartments and Species: @@ -15,7 +15,7 @@ model *Schittler2010_Osteochondroswitch() // Events: _E0: at 100 after P > 12.03: zD = 0.8; _E2: at 500 after P > 12.03: zO = 1; - _E1: at 800 after P > 12.03: zD = 0, zO = 0; + _E1: at 800 after P > 12.03: zO = 0, zD = 0; // Species initializations: P = 12.03; diff --git a/doc/examples/biomodels/Schittler2010_Osteochondroswitch_Figure5c.txt b/doc/examples/biomodels/BIOMD0000000493/Schittler2010_Osteochondroswitch_Figure5c.txt similarity index 92% rename from doc/examples/biomodels/Schittler2010_Osteochondroswitch_Figure5c.txt rename to doc/examples/biomodels/BIOMD0000000493/Schittler2010_Osteochondroswitch_Figure5c.txt index 0a3729517..1d8fe747c 100644 --- a/doc/examples/biomodels/Schittler2010_Osteochondroswitch_Figure5c.txt +++ b/doc/examples/biomodels/BIOMD0000000493/Schittler2010_Osteochondroswitch_Figure5c.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Schittler2010_Osteochondroswitch() // Compartments and Species: @@ -15,7 +15,7 @@ model *Schittler2010_Osteochondroswitch() // Events: _E0: at 500 after P > 12.03: zD = 0.8; _E2: at 100 after P > 12.03: zO = 1; - _E1: at 800 after P > 12.03: zD = 0, zO = 0; + _E1: at 800 after P > 12.03: zO = 0, zD = 0; // Species initializations: P = 12.03; diff --git a/doc/examples/biomodels/Schittler2010_Osteochondroswitch_Figure5d.txt b/doc/examples/biomodels/BIOMD0000000493/Schittler2010_Osteochondroswitch_Figure5d.txt similarity index 92% rename from doc/examples/biomodels/Schittler2010_Osteochondroswitch_Figure5d.txt rename to doc/examples/biomodels/BIOMD0000000493/Schittler2010_Osteochondroswitch_Figure5d.txt index cec12b679..4baea7a6b 100644 --- a/doc/examples/biomodels/Schittler2010_Osteochondroswitch_Figure5d.txt +++ b/doc/examples/biomodels/BIOMD0000000493/Schittler2010_Osteochondroswitch_Figure5d.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Schittler2010_Osteochondroswitch() // Compartments and Species: @@ -15,7 +15,7 @@ model *Schittler2010_Osteochondroswitch() // Events: _E0: at 100 after P > 12.03: zD = 0.8; _E2: at 500 after P > 12.03: zO = 1; - _E1: at 800 after P > 12.03: zD = 0, zO = 0; + _E1: at 800 after P > 12.03: zO = 0, zD = 0; // Species initializations: P = 12.03; diff --git a/doc/examples/biomodels/BIOMD0000000494_url.txt b/doc/examples/biomodels/BIOMD0000000494/BIOMD0000000494_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000494_url.txt rename to doc/examples/biomodels/BIOMD0000000494/BIOMD0000000494_url.txt index ccdd57bc6..5168a5f73 100644 --- a/doc/examples/biomodels/BIOMD0000000494_url.txt +++ b/doc/examples/biomodels/BIOMD0000000494/BIOMD0000000494_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1311220000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000495_url.txt b/doc/examples/biomodels/BIOMD0000000495/BIOMD0000000495_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000495_url.txt rename to doc/examples/biomodels/BIOMD0000000495/BIOMD0000000495_url.txt index 60458f437..999811ebf 100644 --- a/doc/examples/biomodels/BIOMD0000000495_url.txt +++ b/doc/examples/biomodels/BIOMD0000000495/BIOMD0000000495_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1310130000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000496_url.txt b/doc/examples/biomodels/BIOMD0000000496/BIOMD0000000496_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000496_url.txt rename to doc/examples/biomodels/BIOMD0000000496/BIOMD0000000496_url.txt index c5618d0cb..2419a086b 100644 --- a/doc/examples/biomodels/BIOMD0000000496_url.txt +++ b/doc/examples/biomodels/BIOMD0000000496/BIOMD0000000496_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1204270000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000497_url.txt b/doc/examples/biomodels/BIOMD0000000497/BIOMD0000000497_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000497_url.txt rename to doc/examples/biomodels/BIOMD0000000497/BIOMD0000000497_url.txt index cc90162b4..2f4939b4d 100644 --- a/doc/examples/biomodels/BIOMD0000000497_url.txt +++ b/doc/examples/biomodels/BIOMD0000000497/BIOMD0000000497_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1307040000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000498_url.txt b/doc/examples/biomodels/BIOMD0000000498/BIOMD0000000498_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000498_url.txt rename to doc/examples/biomodels/BIOMD0000000498/BIOMD0000000498_url.txt index a951b5e12..f13cc124c 100644 --- a/doc/examples/biomodels/BIOMD0000000498_url.txt +++ b/doc/examples/biomodels/BIOMD0000000498/BIOMD0000000498_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1302260000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000499_url.txt b/doc/examples/biomodels/BIOMD0000000499/BIOMD0000000499_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000499_url.txt rename to doc/examples/biomodels/BIOMD0000000499/BIOMD0000000499_url.txt index 7eb06cdac..4badf7bf0 100644 --- a/doc/examples/biomodels/BIOMD0000000499_url.txt +++ b/doc/examples/biomodels/BIOMD0000000499/BIOMD0000000499_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000500_url.txt b/doc/examples/biomodels/BIOMD0000000500/BIOMD0000000500_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000500_url.txt rename to doc/examples/biomodels/BIOMD0000000500/BIOMD0000000500_url.txt index e2562776a..eb7cf5af7 100644 --- a/doc/examples/biomodels/BIOMD0000000500_url.txt +++ b/doc/examples/biomodels/BIOMD0000000500/BIOMD0000000500_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1311130001() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1311130001_lowcoop.txt b/doc/examples/biomodels/BIOMD0000000500/MODEL1311130001_lowcoop.txt similarity index 98% rename from doc/examples/biomodels/MODEL1311130001_lowcoop.txt rename to doc/examples/biomodels/BIOMD0000000500/MODEL1311130001_lowcoop.txt index fe1d2c84d..2c2054c8a 100644 --- a/doc/examples/biomodels/MODEL1311130001_lowcoop.txt +++ b/doc/examples/biomodels/BIOMD0000000500/MODEL1311130001_lowcoop.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000501_url.txt b/doc/examples/biomodels/BIOMD0000000501/BIOMD0000000501_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000501_url.txt rename to doc/examples/biomodels/BIOMD0000000501/BIOMD0000000501_url.txt index 6c9422b58..ebe4e7e85 100644 --- a/doc/examples/biomodels/BIOMD0000000501_url.txt +++ b/doc/examples/biomodels/BIOMD0000000501/BIOMD0000000501_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1311130000() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1311130000_lowcoop.txt b/doc/examples/biomodels/BIOMD0000000501/MODEL1311130000_lowcoop.txt similarity index 99% rename from doc/examples/biomodels/MODEL1311130000_lowcoop.txt rename to doc/examples/biomodels/BIOMD0000000501/MODEL1311130000_lowcoop.txt index 662cd7140..6266b2298 100644 --- a/doc/examples/biomodels/MODEL1311130000_lowcoop.txt +++ b/doc/examples/biomodels/BIOMD0000000501/MODEL1311130000_lowcoop.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1311130000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000502_url.txt b/doc/examples/biomodels/BIOMD0000000502/BIOMD0000000502_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000502_url.txt rename to doc/examples/biomodels/BIOMD0000000502/BIOMD0000000502_url.txt index 4f2cb9f53..3df2536ba 100644 --- a/doc/examples/biomodels/BIOMD0000000502_url.txt +++ b/doc/examples/biomodels/BIOMD0000000502/BIOMD0000000502_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1311290000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000503_url.txt b/doc/examples/biomodels/BIOMD0000000503/BIOMD0000000503_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000503_url.txt rename to doc/examples/biomodels/BIOMD0000000503/BIOMD0000000503_url.txt index 5769d58f3..7bfbba715 100644 --- a/doc/examples/biomodels/BIOMD0000000503_url.txt +++ b/doc/examples/biomodels/BIOMD0000000503/BIOMD0000000503_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1311290001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000504_url.txt b/doc/examples/biomodels/BIOMD0000000504/BIOMD0000000504_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000504_url.txt rename to doc/examples/biomodels/BIOMD0000000504/BIOMD0000000504_url.txt index eac6b0747..976165216 100644 --- a/doc/examples/biomodels/BIOMD0000000504_url.txt +++ b/doc/examples/biomodels/BIOMD0000000504/BIOMD0000000504_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1305280001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000505_url.txt b/doc/examples/biomodels/BIOMD0000000505/BIOMD0000000505_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000505_url.txt rename to doc/examples/biomodels/BIOMD0000000505/BIOMD0000000505_url.txt index 01be48116..a7a686297 100644 --- a/doc/examples/biomodels/BIOMD0000000505_url.txt +++ b/doc/examples/biomodels/BIOMD0000000505/BIOMD0000000505_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1312040000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000506_url.txt b/doc/examples/biomodels/BIOMD0000000506/BIOMD0000000506_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000506_url.txt rename to doc/examples/biomodels/BIOMD0000000506/BIOMD0000000506_url.txt index 7dc0d4e9a..42ab5d1ca 100644 --- a/doc/examples/biomodels/BIOMD0000000506_url.txt +++ b/doc/examples/biomodels/BIOMD0000000506/BIOMD0000000506_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1312040001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000507_url.txt b/doc/examples/biomodels/BIOMD0000000507/BIOMD0000000507_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000507_url.txt rename to doc/examples/biomodels/BIOMD0000000507/BIOMD0000000507_url.txt index 0a7c81a88..046e5582c 100644 --- a/doc/examples/biomodels/BIOMD0000000507_url.txt +++ b/doc/examples/biomodels/BIOMD0000000507/BIOMD0000000507_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1401190000() // Compartments and Species: @@ -47,7 +47,7 @@ model *MODEL1401190000() unit length = metre; unit area = metre^2; unit volume = litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = mole; unit extent = substance; unit mole_per_litre = mole / litre; diff --git a/doc/examples/biomodels/BIOMD0000000508_url.txt b/doc/examples/biomodels/BIOMD0000000508/BIOMD0000000508_url.txt similarity index 96% rename from doc/examples/biomodels/BIOMD0000000508_url.txt rename to doc/examples/biomodels/BIOMD0000000508/BIOMD0000000508_url.txt index 54f50c44c..d4b44be57 100644 --- a/doc/examples/biomodels/BIOMD0000000508_url.txt +++ b/doc/examples/biomodels/BIOMD0000000508/BIOMD0000000508_url.txt @@ -1,11 +1,11 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1401200000() // Compartments and Species: compartment cell; - species $d in cell, $ad in cell, $e in cell, $ca in cell, $rs in cell, $x in cell; - species $r in cell, $ip3 in cell, $gstar in cell, $kg in cell, $ro in cell; - species $delta in cell, $atp in cell, $ip3con in cell, $dcon in cell, $y in cell; + species d in cell, ad in cell, e in cell, ca in cell, rs in cell, x in cell; + species r in cell, ip3 in cell, gstar in cell, kg in cell, ro in cell, delta in cell; + species atp in cell, ip3con in cell, dcon in cell, y in cell; // Assignment Rules: ad := addash + gamma_*(ca - p1); diff --git a/doc/examples/biomodels/BIOMD0000000509_url.txt b/doc/examples/biomodels/BIOMD0000000509/BIOMD0000000509_url.txt similarity index 96% rename from doc/examples/biomodels/BIOMD0000000509_url.txt rename to doc/examples/biomodels/BIOMD0000000509/BIOMD0000000509_url.txt index 773ddd996..6b9128dc2 100644 --- a/doc/examples/biomodels/BIOMD0000000509_url.txt +++ b/doc/examples/biomodels/BIOMD0000000509/BIOMD0000000509_url.txt @@ -1,11 +1,11 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1401200001() // Compartments and Species: compartment cell; - species $d in cell, $ad in cell, $e in cell, $ca in cell, $rs in cell, $x in cell; - species $r in cell, $ip3 in cell, $gstar in cell, $kg in cell, $ro in cell; - species $delta in cell, $atp in cell, $ip3con in cell, $rscon in cell, $y in cell; + species d in cell, ad in cell, e in cell, ca in cell, rs in cell, x in cell; + species r in cell, ip3 in cell, gstar in cell, kg in cell, ro in cell, delta in cell; + species atp in cell, ip3con in cell, rscon in cell, y in cell; // Assignment Rules: ad := addash + gamma_*(ca - p1); diff --git a/doc/examples/biomodels/BIOMD0000000510_url.txt b/doc/examples/biomodels/BIOMD0000000510/BIOMD0000000510_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000510_url.txt rename to doc/examples/biomodels/BIOMD0000000510/BIOMD0000000510_url.txt index f814e8519..0e534a321 100644 --- a/doc/examples/biomodels/BIOMD0000000510_url.txt +++ b/doc/examples/biomodels/BIOMD0000000510/BIOMD0000000510_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1401070000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000511_url.txt b/doc/examples/biomodels/BIOMD0000000511/BIOMD0000000511_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000511_url.txt rename to doc/examples/biomodels/BIOMD0000000511/BIOMD0000000511_url.txt index f61239097..9c6414888 100644 --- a/doc/examples/biomodels/BIOMD0000000511_url.txt +++ b/doc/examples/biomodels/BIOMD0000000511/BIOMD0000000511_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1401070001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000512_url.txt b/doc/examples/biomodels/BIOMD0000000512/BIOMD0000000512_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000512_url.txt rename to doc/examples/biomodels/BIOMD0000000512/BIOMD0000000512_url.txt index d7f185194..5d191dd5a 100644 --- a/doc/examples/biomodels/BIOMD0000000512_url.txt +++ b/doc/examples/biomodels/BIOMD0000000512/BIOMD0000000512_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1402030000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000513_url.txt b/doc/examples/biomodels/BIOMD0000000513/BIOMD0000000513_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000513_url.txt rename to doc/examples/biomodels/BIOMD0000000513/BIOMD0000000513_url.txt index 2dcfc4768..e30da80ba 100644 --- a/doc/examples/biomodels/BIOMD0000000513_url.txt +++ b/doc/examples/biomodels/BIOMD0000000513/BIOMD0000000513_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1401310000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000514_url.txt b/doc/examples/biomodels/BIOMD0000000514/BIOMD0000000514_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000514_url.txt rename to doc/examples/biomodels/BIOMD0000000514/BIOMD0000000514_url.txt index 2a722033a..78ce0cba2 100644 --- a/doc/examples/biomodels/BIOMD0000000514_url.txt +++ b/doc/examples/biomodels/BIOMD0000000514/BIOMD0000000514_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1401310001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000515_url.txt b/doc/examples/biomodels/BIOMD0000000515/BIOMD0000000515_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000515_url.txt rename to doc/examples/biomodels/BIOMD0000000515/BIOMD0000000515_url.txt index b6d835011..505124ab5 100644 --- a/doc/examples/biomodels/BIOMD0000000515_url.txt +++ b/doc/examples/biomodels/BIOMD0000000515/BIOMD0000000515_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1401310002() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000516_url.txt b/doc/examples/biomodels/BIOMD0000000516/BIOMD0000000516_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000516_url.txt rename to doc/examples/biomodels/BIOMD0000000516/BIOMD0000000516_url.txt index 4783ccf9e..d67e8c011 100644 --- a/doc/examples/biomodels/BIOMD0000000516_url.txt +++ b/doc/examples/biomodels/BIOMD0000000516/BIOMD0000000516_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1401310003() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000517_url.txt b/doc/examples/biomodels/BIOMD0000000517/BIOMD0000000517_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000517_url.txt rename to doc/examples/biomodels/BIOMD0000000517/BIOMD0000000517_url.txt index b76f08d8a..f0d52905e 100644 --- a/doc/examples/biomodels/BIOMD0000000517_url.txt +++ b/doc/examples/biomodels/BIOMD0000000517/BIOMD0000000517_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1306190003() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000518_url.txt b/doc/examples/biomodels/BIOMD0000000518/BIOMD0000000518_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000518_url.txt rename to doc/examples/biomodels/BIOMD0000000518/BIOMD0000000518_url.txt index 267f70c4a..304652043 100644 --- a/doc/examples/biomodels/BIOMD0000000518_url.txt +++ b/doc/examples/biomodels/BIOMD0000000518/BIOMD0000000518_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1306190002() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000519_url.txt b/doc/examples/biomodels/BIOMD0000000519/BIOMD0000000519_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000519_url.txt rename to doc/examples/biomodels/BIOMD0000000519/BIOMD0000000519_url.txt index 128408411..6741f5e95 100644 --- a/doc/examples/biomodels/BIOMD0000000519_url.txt +++ b/doc/examples/biomodels/BIOMD0000000519/BIOMD0000000519_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1306190001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000520_url.txt b/doc/examples/biomodels/BIOMD0000000520/BIOMD0000000520_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000520_url.txt rename to doc/examples/biomodels/BIOMD0000000520/BIOMD0000000520_url.txt index 0eee2afda..fa285db54 100644 --- a/doc/examples/biomodels/BIOMD0000000520_url.txt +++ b/doc/examples/biomodels/BIOMD0000000520/BIOMD0000000520_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1306190000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000521_url.txt b/doc/examples/biomodels/BIOMD0000000521/BIOMD0000000521_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000521_url.txt rename to doc/examples/biomodels/BIOMD0000000521/BIOMD0000000521_url.txt index 1fd925455..507887f67 100644 --- a/doc/examples/biomodels/BIOMD0000000521_url.txt +++ b/doc/examples/biomodels/BIOMD0000000521/BIOMD0000000521_url.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1402250000() // Compartments and Species: compartment plama, tissue; - species $C in plama, $P in tissue, $Qp in tissue, $Q in tissue; + species C in plama, P in tissue, Qp in tissue, Q in tissue; // Assignment Rules: Pstar := P + Q + Qp; diff --git a/doc/examples/biomodels/BIOMD0000000522_url.txt b/doc/examples/biomodels/BIOMD0000000522/BIOMD0000000522_url.txt similarity index 94% rename from doc/examples/biomodels/BIOMD0000000522_url.txt rename to doc/examples/biomodels/BIOMD0000000522/BIOMD0000000522_url.txt index bf6b0da93..a58a0fbaa 100644 --- a/doc/examples/biomodels/BIOMD0000000522_url.txt +++ b/doc/examples/biomodels/BIOMD0000000522/BIOMD0000000522_url.txt @@ -1,14 +1,14 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1403110000() // Compartments and Species: compartment compartment_; - species $Auxin in compartment_, $Cytokinin in compartment_, $AHP6m in compartment_; - species $AHP6p in compartment_, $IAA2m in compartment_, $IAA2p in compartment_; - species $ARR5m in compartment_, $ARR5p in compartment_, $PHBm in compartment_; - species $miRNA in compartment_, $PHBp in compartment_, CKX3m in compartment_; - species $CKX3p in compartment_, $PIN3m in compartment_, $PIN1m in compartment_; - species $PIN7m in compartment_; + species Auxin in compartment_, Cytokinin in compartment_, AHP6m in compartment_; + species AHP6p in compartment_, IAA2m in compartment_, IAA2p in compartment_; + species ARR5m in compartment_, ARR5p in compartment_, PHBm in compartment_; + species miRNA in compartment_, PHBp in compartment_, CKX3m in compartment_; + species CKX3p in compartment_, PIN3m in compartment_, PIN1m in compartment_; + species PIN7m in compartment_; // Assignment Rules: F_CK := 1/(1 + (CKX3p/theta_CKX3)^hill_ckx3); diff --git a/doc/examples/biomodels/BIOMD0000000523_url.txt b/doc/examples/biomodels/BIOMD0000000523/BIOMD0000000523_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000523_url.txt rename to doc/examples/biomodels/BIOMD0000000523/BIOMD0000000523_url.txt index f0351d19e..2ff99e16b 100644 --- a/doc/examples/biomodels/BIOMD0000000523_url.txt +++ b/doc/examples/biomodels/BIOMD0000000523/BIOMD0000000523_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1403050000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000524_url.txt b/doc/examples/biomodels/BIOMD0000000524/BIOMD0000000524_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000524_url.txt rename to doc/examples/biomodels/BIOMD0000000524/BIOMD0000000524_url.txt index d3a847015..1183ad6b8 100644 --- a/doc/examples/biomodels/BIOMD0000000524_url.txt +++ b/doc/examples/biomodels/BIOMD0000000524/BIOMD0000000524_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1403050001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000525_url.txt b/doc/examples/biomodels/BIOMD0000000525/BIOMD0000000525_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000525_url.txt rename to doc/examples/biomodels/BIOMD0000000525/BIOMD0000000525_url.txt index 6b489e5ff..a75c7deb9 100644 --- a/doc/examples/biomodels/BIOMD0000000525_url.txt +++ b/doc/examples/biomodels/BIOMD0000000525/BIOMD0000000525_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1403050002() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000526_url.txt b/doc/examples/biomodels/BIOMD0000000526/BIOMD0000000526_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000526_url.txt rename to doc/examples/biomodels/BIOMD0000000526/BIOMD0000000526_url.txt index f7c3057da..f69ef76c0 100644 --- a/doc/examples/biomodels/BIOMD0000000526_url.txt +++ b/doc/examples/biomodels/BIOMD0000000526/BIOMD0000000526_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1403050003() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000527_url.txt b/doc/examples/biomodels/BIOMD0000000527/BIOMD0000000527_url.txt similarity index 96% rename from doc/examples/biomodels/BIOMD0000000527_url.txt rename to doc/examples/biomodels/BIOMD0000000527/BIOMD0000000527_url.txt index 9b9ff0394..5c4398f3b 100644 --- a/doc/examples/biomodels/BIOMD0000000527_url.txt +++ b/doc/examples/biomodels/BIOMD0000000527/BIOMD0000000527_url.txt @@ -1,16 +1,16 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1312170001() // Compartments and Species: compartment LN; - substanceOnly species $L in LN; + substanceOnly species L in LN; // Rate Rules: L' = piecewise(mu1 + (r1 - c1)*L, (time >= 0) && (time <= t1), mu3 + (r3 - c3)*L, (time > t1) && (time <= t3), mu5 + (r5 - c5)*L, (time > t3) && (time <= t5), mu10 + (r10 - c10)*L, (time > t5) && (time <= t10)); // Species initializations: L = 0; - L has dimensionless_per_dimensionles; + L has dimensionless; // Compartment initializations: LN = 1; @@ -57,7 +57,6 @@ model *MODEL1312170001() // Unit definitions: unit day = 86400e1 second; unit per_day = 1 / 86400e1 second; - unit dimensionless_per_dimensionles = dimensionless / dimensionless; // Display Names: LN is "Lymph node"; diff --git a/doc/examples/biomodels/BIOMD0000000528_url.txt b/doc/examples/biomodels/BIOMD0000000528/BIOMD0000000528_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000528_url.txt rename to doc/examples/biomodels/BIOMD0000000528/BIOMD0000000528_url.txt index a636c327d..c4e0b315d 100644 --- a/doc/examples/biomodels/BIOMD0000000528_url.txt +++ b/doc/examples/biomodels/BIOMD0000000528/BIOMD0000000528_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1403310002() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000529_url.txt b/doc/examples/biomodels/BIOMD0000000529/BIOMD0000000529_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000529_url.txt rename to doc/examples/biomodels/BIOMD0000000529/BIOMD0000000529_url.txt index d506e8083..db805d5bd 100644 --- a/doc/examples/biomodels/BIOMD0000000529_url.txt +++ b/doc/examples/biomodels/BIOMD0000000529/BIOMD0000000529_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1403310001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000530_url.txt b/doc/examples/biomodels/BIOMD0000000530/BIOMD0000000530_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000530_url.txt rename to doc/examples/biomodels/BIOMD0000000530/BIOMD0000000530_url.txt index 026ec8e66..71ad51e46 100644 --- a/doc/examples/biomodels/BIOMD0000000530_url.txt +++ b/doc/examples/biomodels/BIOMD0000000530/BIOMD0000000530_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000531_url.txt b/doc/examples/biomodels/BIOMD0000000531/BIOMD0000000531_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000531_url.txt rename to doc/examples/biomodels/BIOMD0000000531/BIOMD0000000531_url.txt index adbec4b28..ba589afbd 100644 --- a/doc/examples/biomodels/BIOMD0000000531_url.txt +++ b/doc/examples/biomodels/BIOMD0000000531/BIOMD0000000531_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1407170000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000532_url.txt b/doc/examples/biomodels/BIOMD0000000532/BIOMD0000000532_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000532_url.txt rename to doc/examples/biomodels/BIOMD0000000532/BIOMD0000000532_url.txt index 133dd6a6f..d3ca13694 100644 --- a/doc/examples/biomodels/BIOMD0000000532_url.txt +++ b/doc/examples/biomodels/BIOMD0000000532/BIOMD0000000532_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1407300000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000533_url.txt b/doc/examples/biomodels/BIOMD0000000533/BIOMD0000000533_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000533_url.txt rename to doc/examples/biomodels/BIOMD0000000533/BIOMD0000000533_url.txt index a8d48d72d..91eaf171c 100644 --- a/doc/examples/biomodels/BIOMD0000000533_url.txt +++ b/doc/examples/biomodels/BIOMD0000000533/BIOMD0000000533_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1407300001() // Compartments and Species: diff --git a/doc/examples/biomodels/Steckmann2012 (F4).txt b/doc/examples/biomodels/BIOMD0000000533/Steckmann2012 (F4).txt similarity index 97% rename from doc/examples/biomodels/Steckmann2012 (F4).txt rename to doc/examples/biomodels/BIOMD0000000533/Steckmann2012 (F4).txt index e1b6e494e..64dfbde3a 100644 --- a/doc/examples/biomodels/Steckmann2012 (F4).txt +++ b/doc/examples/biomodels/BIOMD0000000533/Steckmann2012 (F4).txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000534_url.txt b/doc/examples/biomodels/BIOMD0000000534/BIOMD0000000534_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000534_url.txt rename to doc/examples/biomodels/BIOMD0000000534/BIOMD0000000534_url.txt index dcada03cc..171fb86d6 100644 --- a/doc/examples/biomodels/BIOMD0000000534_url.txt +++ b/doc/examples/biomodels/BIOMD0000000534/BIOMD0000000534_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1408050000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000535_url.txt b/doc/examples/biomodels/BIOMD0000000535/BIOMD0000000535_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000535_url.txt rename to doc/examples/biomodels/BIOMD0000000535/BIOMD0000000535_url.txt index e69c8f2c7..13d22b7a6 100644 --- a/doc/examples/biomodels/BIOMD0000000535_url.txt +++ b/doc/examples/biomodels/BIOMD0000000535/BIOMD0000000535_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1408050001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000536_url.txt b/doc/examples/biomodels/BIOMD0000000536/BIOMD0000000536_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000536_url.txt rename to doc/examples/biomodels/BIOMD0000000536/BIOMD0000000536_url.txt index 3f37e78b6..182467f40 100644 --- a/doc/examples/biomodels/BIOMD0000000536_url.txt +++ b/doc/examples/biomodels/BIOMD0000000536/BIOMD0000000536_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1408050003() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000537_url.txt b/doc/examples/biomodels/BIOMD0000000537/BIOMD0000000537_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000537_url.txt rename to doc/examples/biomodels/BIOMD0000000537/BIOMD0000000537_url.txt index 4f1f57254..5ad68c79f 100644 --- a/doc/examples/biomodels/BIOMD0000000537_url.txt +++ b/doc/examples/biomodels/BIOMD0000000537/BIOMD0000000537_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1408050002() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000538_url.txt b/doc/examples/biomodels/BIOMD0000000538/BIOMD0000000538_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000538_url.txt rename to doc/examples/biomodels/BIOMD0000000538/BIOMD0000000538_url.txt index 6ff851f7b..35874c150 100644 --- a/doc/examples/biomodels/BIOMD0000000538_url.txt +++ b/doc/examples/biomodels/BIOMD0000000538/BIOMD0000000538_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1408070000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000539_url.txt b/doc/examples/biomodels/BIOMD0000000539/BIOMD0000000539_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000539_url.txt rename to doc/examples/biomodels/BIOMD0000000539/BIOMD0000000539_url.txt index ede363e08..580ce7528 100644 --- a/doc/examples/biomodels/BIOMD0000000539_url.txt +++ b/doc/examples/biomodels/BIOMD0000000539/BIOMD0000000539_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1408130000() // Compartments and Species: @@ -57,7 +57,7 @@ model *MODEL1408130000() unit length = metre; unit area = metre^2; unit volume = 1e-12 litre; - unit time_unit = time_unit; + unit time_unit = 60 second; unit substance = item; unit extent = substance; unit mole_per_litre = mole / litre; diff --git a/doc/examples/biomodels/BIOMD0000000540_url.txt b/doc/examples/biomodels/BIOMD0000000540/BIOMD0000000540_url.txt similarity index 85% rename from doc/examples/biomodels/BIOMD0000000540_url.txt rename to doc/examples/biomodels/BIOMD0000000540/BIOMD0000000540_url.txt index 34c7bb0e7..2ecb88991 100644 --- a/doc/examples/biomodels/BIOMD0000000540_url.txt +++ b/doc/examples/biomodels/BIOMD0000000540/BIOMD0000000540_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1406130000() // Compartments and Species: @@ -28,13 +28,13 @@ model *MODEL1406130000() re11: s3 => s21; -k_f6p; // Events: - ev2min: at time > 2: k_pfkl_s775 = -0.011384308, k_pep = 7.54147813, k_mal = -1.508295626, k_f26bp = 0.028924455, k_icit = -0.038210156, k_f6p = 1.357466063, k_cit = 0.351935646, k_akg = -1.357466063; - ev5min: at time > 5: k_pfkl_s775 = 0.057596439, k_pep = -6.334841629, k_mal = -0.904977376, k_f26bp = 0.119075279, k_icit = -0.038210156, k_f6p = 0.271493213, k_cit = -0.211161388, k_akg = 0; - ev10min: at time > 10: k_pfkl_s775 = 0.006730598, k_pep = 9.049773756, k_mal = 3.921568627, k_f26bp = -0.050207413, k_icit = -0.038210156, k_f6p = -1.055806938, k_cit = 1.085972851, k_akg = 0.36199095; - ev15min: at time > 15: k_pfkl_s775 = 0.006730598, k_pep = -4.826546003, k_mal = 1.809954751, k_f26bp = 0.100115778, k_icit = -0.018099548, k_f6p = -0.12066365, k_cit = 0.452488688, k_akg = 1.085972851; - ev20min: at time > 20: k_pfkl_s775 = 0.006730598, k_pep = -3.619909502, k_mal = 1.206636501, k_f26bp = -0.032601514, k_icit = 0.031674208, k_f6p = -0.165912519, k_cit = 0.377073906, k_akg = 0.226244344; - ev30min: at time > 30: k_pfkl_s775 = 0.006730598, k_pep = -0.301659125, k_mal = 0.502765209, k_f26bp = -0.003055632, k_icit = 0.031674208, k_f6p = 0.070387129, k_cit = 0.306686777, k_akg = 0.369532428; - ev45min: at time > 45: k_pfkl_s775 = 0.00673059831429, k_pep = -0.301659125, k_mal = 0.502765209, k_f26bp = -0.003055632, k_icit = 0.031674208, k_f6p = 0.070387129, k_cit = 0.306686777, k_akg = 0.369532428; + ev2min: at time > 2: k_akg = -1.357466063, k_cit = 0.351935646, k_f6p = 1.357466063, k_icit = -0.038210156, k_f26bp = 0.028924455, k_mal = -1.508295626, k_pep = 7.54147813, k_pfkl_s775 = -0.011384308; + ev5min: at time > 5: k_akg = 0, k_cit = -0.211161388, k_f6p = 0.271493213, k_icit = -0.038210156, k_f26bp = 0.119075279, k_mal = -0.904977376, k_pep = -6.334841629, k_pfkl_s775 = 0.057596439; + ev10min: at time > 10: k_akg = 0.36199095, k_cit = 1.085972851, k_f6p = -1.055806938, k_icit = -0.038210156, k_f26bp = -0.050207413, k_mal = 3.921568627, k_pep = 9.049773756, k_pfkl_s775 = 0.006730598; + ev15min: at time > 15: k_akg = 1.085972851, k_cit = 0.452488688, k_f6p = -0.12066365, k_icit = -0.018099548, k_f26bp = 0.100115778, k_mal = 1.809954751, k_pep = -4.826546003, k_pfkl_s775 = 0.006730598; + ev20min: at time > 20: k_akg = 0.226244344, k_cit = 0.377073906, k_f6p = -0.165912519, k_icit = 0.031674208, k_f26bp = -0.032601514, k_mal = 1.206636501, k_pep = -3.619909502, k_pfkl_s775 = 0.006730598; + ev30min: at time > 30: k_akg = 0.369532428, k_cit = 0.306686777, k_f6p = 0.070387129, k_icit = 0.031674208, k_f26bp = -0.003055632, k_mal = 0.502765209, k_pep = -0.301659125, k_pfkl_s775 = 0.006730598; + ev45min: at time > 45: k_akg = 0.369532428, k_cit = 0.306686777, k_f6p = 0.070387129, k_icit = 0.031674208, k_f26bp = -0.003055632, k_mal = 0.502765209, k_pep = -0.301659125, k_pfkl_s775 = 0.00673059831429; // Species initializations: s1 = 1; @@ -58,7 +58,7 @@ model *MODEL1406130000() s20 = 0; s21 = 0; s19 = 0; - s22 has substance_per_volume; + s22 has substance; // Compartment initializations: default = 1; @@ -122,7 +122,7 @@ model *MODEL1406130000() unit area = metre^2; unit length = metre; unit time_unit = second; - unit substance_per_volume = mole / litre; + unit substance_volume = mole * litre; // Display Names: time_unit is "time"; diff --git a/doc/examples/biomodels/PFKL_ins001.txt b/doc/examples/biomodels/BIOMD0000000540/PFKL_ins001.txt similarity index 67% rename from doc/examples/biomodels/PFKL_ins001.txt rename to doc/examples/biomodels/BIOMD0000000540/PFKL_ins001.txt index 6fa38779d..32981da74 100644 --- a/doc/examples/biomodels/PFKL_ins001.txt +++ b/doc/examples/biomodels/BIOMD0000000540/PFKL_ins001.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *PFKL() // Compartments and Species: @@ -28,40 +28,40 @@ model *PFKL() re11: s3 => s21; -k_f6p; // Events: - ev2min: at time > 2: k_pfkl_s775 = 0, k_pep = 1.50829562594, k_mal = -6.03318250377, k_f26bp = 0.010962773, k_icit = 0, k_f6p = 2.36299648065, k_cit = 0.150829562594, k_akg = -1.43288084467; - ev5min: at time > 5: k_pfkl_s775 = 0, k_pep = -4.52488687783, k_mal = 0, k_f26bp = 0.034852204, k_icit = 0.0113122171946, k_f6p = 1.62895927602, k_cit = -0.27149321267, k_akg = -0.27149321267; - ev10min: at time > 10: k_pfkl_s775 = 0, k_pep = 0.904977376, k_mal = 2.714932127, k_f26bp = -0.031487108, k_icit = -0.011312217, k_f6p = -1.900452489, k_cit = 0.060331825, k_akg = 0; - ev15min: at time > 15: k_pfkl_s775 = 0, k_pep = -2.413273002, k_mal = 0, k_f26bp = 0.083691707, k_icit = -0.002262443, k_f6p = 0.693815988, k_cit = 0.2413273, k_akg = 0.090497738; - ev20min: at time > 20: k_pfkl_s775 = 0, k_pep = -2.865761689, k_mal = 0.60331825, k_f26bp = -0.010719796, k_icit = -0.033936652, k_f6p = -0.090497738, k_cit = 0.090497738, k_akg = 0.113122172; - ev30min: at time > 30: k_pfkl_s775 = 0, k_pep = -0.301659125, k_mal = 0.351935646, k_f26bp = -0.003477353, k_icit = 0.011689291, k_f6p = -0.09552539, k_cit = 0.135746606, k_akg = 0.263951735; - ev45min: at time > 45: k_pfkl_s775 = 0, k_pep = -0.301659125, k_mal = 0.351935646, k_f26bp = -0.003477353, k_icit = 0.011689291, k_f6p = -0.09552539, k_cit = 0.135746606, k_akg = 0.263951735; + ev2min: at time > 2: k_akg = -1.43288084467, k_cit = 0.150829562594, k_f6p = 2.36299648065, k_icit = 0, k_f26bp = 0.010962773, k_mal = -6.03318250377, k_pep = 1.50829562594, k_pfkl_s775 = 0; + ev5min: at time > 5: k_akg = -0.27149321267, k_cit = -0.27149321267, k_f6p = 1.62895927602, k_icit = 0.0113122171946, k_f26bp = 0.034852204, k_mal = 0, k_pep = -4.52488687783, k_pfkl_s775 = 0; + ev10min: at time > 10: k_akg = 0, k_cit = 0.060331825, k_f6p = -1.900452489, k_icit = -0.011312217, k_f26bp = -0.031487108, k_mal = 2.714932127, k_pep = 0.904977376, k_pfkl_s775 = 0; + ev15min: at time > 15: k_akg = 0.090497738, k_cit = 0.2413273, k_f6p = 0.693815988, k_icit = -0.002262443, k_f26bp = 0.083691707, k_mal = 0, k_pep = -2.413273002, k_pfkl_s775 = 0; + ev20min: at time > 20: k_akg = 0.113122172, k_cit = 0.090497738, k_f6p = -0.090497738, k_icit = -0.033936652, k_f26bp = -0.010719796, k_mal = 0.60331825, k_pep = -2.865761689, k_pfkl_s775 = 0; + ev30min: at time > 30: k_akg = 0.263951735, k_cit = 0.135746606, k_f6p = -0.09552539, k_icit = 0.011689291, k_f26bp = -0.003477353, k_mal = 0.351935646, k_pep = -0.301659125, k_pfkl_s775 = 0; + ev45min: at time > 45: k_akg = 0.263951735, k_cit = 0.135746606, k_f6p = -0.09552539, k_icit = 0.011689291, k_f26bp = -0.003477353, k_mal = 0.351935646, k_pep = -0.301659125, k_pfkl_s775 = 0; // Species initializations: s1 = 1; - s1 has dimensionless_per_volume; + s1 has dimensionless; s2 = 1; - s2 has dimensionless_per_volume; + s2 has dimensionless; s3 = 14.0774258421; - s3 has substance_per_volume; + s3 has substance; s4 = 104.07239819; - s4 has substance_per_volume; + s4 has substance; s5 = 108.094519859; - s5 has substance_per_volume; + s5 has substance; s6 = 1.79487179487; - s6 has substance_per_volume; + s6 has substance; s7 = 25.1885369533; - s7 has substance_per_volume; + s7 has substance; s8 = 68.8788335846; - s8 has substance_per_volume; + s8 has substance; s9 = 1; - s9 has substance_per_volume; + s9 has substance; s10 = 17.7476118652; - s10 has substance_per_volume; + s10 has substance; s11 = 0; s12 = 1; - s12 has dimensionless_per_volume; + s12 has dimensionless; s13 = 0.768939345; - s13 has dimensionless_per_volume; + s13 has dimensionless; s14 = 0; s15 = 0; s16 = 0; @@ -70,7 +70,7 @@ model *PFKL() s20 = 0; s21 = 0; s19 = 0; - s22 has substance_per_volume; + s22 has substance; // Compartment initializations: default = 1; @@ -135,8 +135,8 @@ model *PFKL() unit length = metre; unit time_unit = second; unit rate = 1 / 60 second; - unit dimensionless_per_volume = dimensionless / litre; - unit substance_per_volume = mole / litre; + unit dimensionless_volume = dimensionless * litre; + unit substance_volume = mole * litre; // Display Names: time_unit is "time"; diff --git a/doc/examples/biomodels/BIOMD0000000541_url.txt b/doc/examples/biomodels/BIOMD0000000541/BIOMD0000000541_url.txt similarity index 90% rename from doc/examples/biomodels/BIOMD0000000541_url.txt rename to doc/examples/biomodels/BIOMD0000000541/BIOMD0000000541_url.txt index e6361b587..c568e91ee 100644 --- a/doc/examples/biomodels/BIOMD0000000541_url.txt +++ b/doc/examples/biomodels/BIOMD0000000541/BIOMD0000000541_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1406130001() // Compartments and Species: @@ -50,17 +50,17 @@ model *MODEL1406130001() re59: s13 => $s1; re59_k1*s13; // Events: - ev2min: at time > 2: k_pep = 7.54147813, k_mal = -1.508295626, k_f26bp = 0.028924455, k_icit = -0.038210156, k_f6p = 1.357466063, k_cit = 0.351935646, k_akg = -1.357466063; - ev5min: at time > 5: k_pep = -6.334841629, k_mal = -0.904977376, k_f26bp = 0.119075279, k_icit = -0.038210156, k_f6p = 0.271493213, k_cit = -0.211161388, k_akg = 0; - ev10min: at time > 10: k_pep = 9.049773756, k_mal = 3.921568627, k_f26bp = -0.050207413, k_icit = -0.038210156, k_f6p = -1.055806938, k_cit = 1.085972851, k_akg = 0.36199095; - ev15min: at time > 15: k_pep = -4.826546003, k_mal = 1.809954751, k_f26bp = 0.100115778, k_icit = -0.018099548, k_f6p = -0.12066365, k_cit = 0.452488688, k_akg = 1.085972851; - ev20min: at time > 20: k_pep = -3.619909502, k_mal = 1.206636501, k_f26bp = -0.032601514, k_icit = 0.031674208, k_f6p = -0.165912519, k_cit = 0.377073906, k_akg = 0.226244344; - ev30min: at time > 30: k_pep = -0.301659125, k_mal = 0.502765209, k_f26bp = -0.003055632, k_icit = 0.031674208, k_f6p = 0.070387129, k_cit = 0.306686777, k_akg = 0.369532428; - ev45min: at time > 45: k_pep = -0.301659125, k_mal = 0.502765209, k_f26bp = -0.003055632, k_icit = 0.031674208, k_f6p = 0.070387129, k_cit = 0.306686777, k_akg = 0.369532428; + ev2min: at time > 2: k_akg = -1.357466063, k_cit = 0.351935646, k_f6p = 1.357466063, k_icit = -0.038210156, k_f26bp = 0.028924455, k_mal = -1.508295626, k_pep = 7.54147813; + ev5min: at time > 5: k_akg = 0, k_cit = -0.211161388, k_f6p = 0.271493213, k_icit = -0.038210156, k_f26bp = 0.119075279, k_mal = -0.904977376, k_pep = -6.334841629; + ev10min: at time > 10: k_akg = 0.36199095, k_cit = 1.085972851, k_f6p = -1.055806938, k_icit = -0.038210156, k_f26bp = -0.050207413, k_mal = 3.921568627, k_pep = 9.049773756; + ev15min: at time > 15: k_akg = 1.085972851, k_cit = 0.452488688, k_f6p = -0.12066365, k_icit = -0.018099548, k_f26bp = 0.100115778, k_mal = 1.809954751, k_pep = -4.826546003; + ev20min: at time > 20: k_akg = 0.226244344, k_cit = 0.377073906, k_f6p = -0.165912519, k_icit = 0.031674208, k_f26bp = -0.032601514, k_mal = 1.206636501, k_pep = -3.619909502; + ev30min: at time > 30: k_akg = 0.369532428, k_cit = 0.306686777, k_f6p = 0.070387129, k_icit = 0.031674208, k_f26bp = -0.003055632, k_mal = 0.502765209, k_pep = -0.301659125; + ev45min: at time > 45: k_akg = 0.369532428, k_cit = 0.306686777, k_f6p = 0.070387129, k_icit = 0.031674208, k_f26bp = -0.003055632, k_mal = 0.502765209, k_pep = -0.301659125; // Species initializations: s1 = 1.235570941; - s1 has substance_per_volume; + s1 has substance; s2 = 1; s3 = 14.0774258421; s4 = 104.07239819; @@ -73,7 +73,7 @@ model *MODEL1406130001() s11 = 0; s12 = 1; s13 = 0.759332005; - s13 has substance_per_volume; + s13 has substance; s14 = 0; s15 = 0; s16 = 0; @@ -97,7 +97,7 @@ model *MODEL1406130001() s36 = 0; s37 = 0; s38 = 0; - s22 has substance_per_volume; + s22 has substance; // Compartment initializations: default = 1; @@ -205,7 +205,7 @@ model *MODEL1406130001() unit area = metre^2; unit length = metre; unit time_unit = second; - unit substance_per_volume = mole / litre; + unit substance_volume = mole * litre; // Display Names: time_unit is "time"; diff --git a/doc/examples/biomodels/PFKL_signal_ins001.txt b/doc/examples/biomodels/BIOMD0000000541/PFKL_signal_ins001.txt similarity index 83% rename from doc/examples/biomodels/PFKL_signal_ins001.txt rename to doc/examples/biomodels/BIOMD0000000541/PFKL_signal_ins001.txt index 2fee9a2ff..73777dbf8 100644 --- a/doc/examples/biomodels/PFKL_signal_ins001.txt +++ b/doc/examples/biomodels/BIOMD0000000541/PFKL_signal_ins001.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *PFKL() // Compartments and Species: @@ -50,20 +50,20 @@ model *PFKL() re32: s13 => $s1; re32_k1*s13; // Events: - ev2min: at time > 2: k_pep = 1.50829562594, k_mal = -6.03318250377, k_f26bp = 0.010962773, k_icit = 0, k_f6p = 2.36299648065, k_cit = 0.150829562594, k_akg = -1.43288084467; - ev5min: at time > 5: k_pep = -4.52488687783, k_mal = 0, k_f26bp = 0.034852204, k_icit = 0.0113122171946, k_f6p = 1.62895927602, k_cit = -0.27149321267, k_akg = -0.27149321267; - ev10min: at time > 10: k_pep = 0.904977376, k_mal = 2.714932127, k_f26bp = -0.031487108, k_icit = -0.011312217, k_f6p = -1.900452489, k_cit = 0.060331825, k_akg = 0; - ev15min: at time > 15: k_pep = -2.413273002, k_mal = 0, k_f26bp = 0.083691707, k_icit = -0.002262443, k_f6p = 0.693815988, k_cit = 0.2413273, k_akg = 0.090497738; - ev20min: at time > 20: k_pep = -2.865761689, k_mal = 0.60331825, k_f26bp = -0.010719796, k_icit = -0.033936652, k_f6p = -0.090497738, k_cit = 0.090497738, k_akg = 0.113122172; - ev30min: at time > 30: k_pep = -0.301659125, k_mal = 0.351935646, k_f26bp = -0.003477353, k_icit = 0.011689291, k_f6p = -0.09552539, k_cit = 0.135746606, k_akg = 0.263951735; - ev45min: at time > 45: k_pep = -0.301659125, k_mal = 0.351935646, k_f26bp = -0.003477353, k_icit = 0.011689291, k_f6p = -0.09552539, k_cit = 0.135746606, k_akg = 0.263951735; + ev2min: at time > 2: k_akg = -1.43288084467, k_cit = 0.150829562594, k_f6p = 2.36299648065, k_icit = 0, k_f26bp = 0.010962773, k_mal = -6.03318250377, k_pep = 1.50829562594; + ev5min: at time > 5: k_akg = -0.27149321267, k_cit = -0.27149321267, k_f6p = 1.62895927602, k_icit = 0.0113122171946, k_f26bp = 0.034852204, k_mal = 0, k_pep = -4.52488687783; + ev10min: at time > 10: k_akg = 0, k_cit = 0.060331825, k_f6p = -1.900452489, k_icit = -0.011312217, k_f26bp = -0.031487108, k_mal = 2.714932127, k_pep = 0.904977376; + ev15min: at time > 15: k_akg = 0.090497738, k_cit = 0.2413273, k_f6p = 0.693815988, k_icit = -0.002262443, k_f26bp = 0.083691707, k_mal = 0, k_pep = -2.413273002; + ev20min: at time > 20: k_akg = 0.113122172, k_cit = 0.090497738, k_f6p = -0.090497738, k_icit = -0.033936652, k_f26bp = -0.010719796, k_mal = 0.60331825, k_pep = -2.865761689; + ev30min: at time > 30: k_akg = 0.263951735, k_cit = 0.135746606, k_f6p = -0.09552539, k_icit = 0.011689291, k_f26bp = -0.003477353, k_mal = 0.351935646, k_pep = -0.301659125; + ev45min: at time > 45: k_akg = 0.263951735, k_cit = 0.135746606, k_f6p = -0.09552539, k_icit = 0.011689291, k_f26bp = -0.003477353, k_mal = 0.351935646, k_pep = -0.301659125; // Species initializations: s1 = 1.235570941; s2 = 1; s3 = 14.0774258421; s4 = 104.07239819; - s4 has substance_per_volume; + s4 has substance; s5 = 108.094519859; s6 = 1.79487179487; s7 = 25.1885369533; @@ -96,7 +96,7 @@ model *PFKL() s37 = 0; s38 = 0; s13 = 0.759332005; - s22 has substance_per_volume; + s22 has substance; // Compartment initializations: default = 1; @@ -204,7 +204,7 @@ model *PFKL() unit area = metre^2; unit length = metre; unit time_unit = 60 second; - unit substance_per_volume = 1e-06 mole / litre; + unit substance_volume = 1e-06 mole * litre; // Display Names: time_unit is "time"; diff --git a/doc/examples/biomodels/PFKL_signal_ins100.txt b/doc/examples/biomodels/BIOMD0000000541/PFKL_signal_ins100.txt similarity index 82% rename from doc/examples/biomodels/PFKL_signal_ins100.txt rename to doc/examples/biomodels/BIOMD0000000541/PFKL_signal_ins100.txt index 3f45eae37..8d4782d6a 100644 --- a/doc/examples/biomodels/PFKL_signal_ins100.txt +++ b/doc/examples/biomodels/BIOMD0000000541/PFKL_signal_ins100.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *PFKL() // Compartments and Species: @@ -50,22 +50,22 @@ model *PFKL() re59: s13 => $s1; re59_k1*s13; // Events: - ev2min: at time > 2: k_pep = 18.09954751, k_mal = -3.016591252, k_f26bp = 0.124220778, k_icit = -0.01256913, k_f6p = -0.703871292, k_cit = 1.860231272, k_akg = -1.131221719; - ev5min: at time > 5: k_pep = -6.636500754, k_mal = 0.904977376, k_f26bp = 0.095229112, k_icit = -0.01256913, k_f6p = 0.301659125, k_cit = -0.301659125, k_akg = 0.316742081; - ev10min: at time > 10: k_pep = 12.36802413, k_mal = 3.016591252, k_f26bp = -0.052409266, k_icit = -0.01256913, k_f6p = -0.4826546, k_cit = 0.814479638, k_akg = 0.090497738; - ev15min: at time > 15: k_pep = -1.809954751, k_mal = -0.60331825, k_f26bp = 0.062662112, k_icit = -0.01256913, k_f6p = 0.090497738, k_cit = 0.814479638, k_akg = 0.452488688; - ev20min: at time > 20: k_pep = -3.921568627, k_mal = 2.564102564, k_f26bp = 0.003116153, k_icit = 0.012443439, k_f6p = -0.331825038, k_cit = 0.618401207, k_akg = 0.339366516; - ev30min: at time > 30: k_pep = -0.854700855, k_mal = 0.301659125, k_f26bp = -0.014023035, k_icit = 0.012443439, k_f6p = 0.191050779, k_cit = 0.2413273, k_akg = 0.716440422; - ev45min: at time > 45: k_pep = -0.854700855, k_mal = 0.301659125, k_f26bp = -0.014023035, k_icit = 0.012443439, k_f6p = 0.191050779, k_cit = 0.2413273, k_akg = 0.716440422; + ev2min: at time > 2: k_akg = -1.131221719, k_cit = 1.860231272, k_f6p = -0.703871292, k_icit = -0.01256913, k_f26bp = 0.124220778, k_mal = -3.016591252, k_pep = 18.09954751; + ev5min: at time > 5: k_akg = 0.316742081, k_cit = -0.301659125, k_f6p = 0.301659125, k_icit = -0.01256913, k_f26bp = 0.095229112, k_mal = 0.904977376, k_pep = -6.636500754; + ev10min: at time > 10: k_akg = 0.090497738, k_cit = 0.814479638, k_f6p = -0.4826546, k_icit = -0.01256913, k_f26bp = -0.052409266, k_mal = 3.016591252, k_pep = 12.36802413; + ev15min: at time > 15: k_akg = 0.452488688, k_cit = 0.814479638, k_f6p = 0.090497738, k_icit = -0.01256913, k_f26bp = 0.062662112, k_mal = -0.60331825, k_pep = -1.809954751; + ev20min: at time > 20: k_akg = 0.339366516, k_cit = 0.618401207, k_f6p = -0.331825038, k_icit = 0.012443439, k_f26bp = 0.003116153, k_mal = 2.564102564, k_pep = -3.921568627; + ev30min: at time > 30: k_akg = 0.716440422, k_cit = 0.2413273, k_f6p = 0.191050779, k_icit = 0.012443439, k_f26bp = -0.014023035, k_mal = 0.301659125, k_pep = -0.854700855; + ev45min: at time > 45: k_akg = 0.716440422, k_cit = 0.2413273, k_f6p = 0.191050779, k_icit = 0.012443439, k_f26bp = -0.014023035, k_mal = 0.301659125, k_pep = -0.854700855; // Species initializations: s1 = 1.235570941; - s1 has substance_per_volume; + s1 has substance; s2 = 1; s3 = 14.0774258421; - s3 has substance_per_volume; + s3 has substance; s4 = 104.07239819; - s4 has substance_per_volume; + s4 has substance; s5 = 108.094519859; s6 = 1.79487179487; s7 = 25.1885369533; @@ -75,7 +75,7 @@ model *PFKL() s11 = 0; s12 = 1; s13 = 0.759332005; - s13 has substance_per_volume; + s13 has substance; s14 = 0; s15 = 0; s16 = 0; @@ -99,7 +99,7 @@ model *PFKL() s36 = 0; s37 = 0; s38 = 0; - s22 has substance_per_volume; + s22 has substance; // Compartment initializations: default = 1; @@ -207,7 +207,7 @@ model *PFKL() unit area = metre^2; unit length = metre; unit time_unit = second; - unit substance_per_volume = mole / litre; + unit substance_volume = mole * litre; // Display Names: time_unit is "time"; diff --git a/doc/examples/biomodels/BIOMD0000000542_url.txt b/doc/examples/biomodels/BIOMD0000000542/BIOMD0000000542_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000542_url.txt rename to doc/examples/biomodels/BIOMD0000000542/BIOMD0000000542_url.txt index 7933c8168..cf26af463 100644 --- a/doc/examples/biomodels/BIOMD0000000542_url.txt +++ b/doc/examples/biomodels/BIOMD0000000542/BIOMD0000000542_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1408150000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000543_url.txt b/doc/examples/biomodels/BIOMD0000000543/BIOMD0000000543_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000543_url.txt rename to doc/examples/biomodels/BIOMD0000000543/BIOMD0000000543_url.txt index 09b6010e4..749b407db 100644 --- a/doc/examples/biomodels/BIOMD0000000543_url.txt +++ b/doc/examples/biomodels/BIOMD0000000543/BIOMD0000000543_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1408190003() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000544_url.txt b/doc/examples/biomodels/BIOMD0000000544/BIOMD0000000544_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000544_url.txt rename to doc/examples/biomodels/BIOMD0000000544/BIOMD0000000544_url.txt index c1f68ecaa..f6bad9f9c 100644 --- a/doc/examples/biomodels/BIOMD0000000544_url.txt +++ b/doc/examples/biomodels/BIOMD0000000544/BIOMD0000000544_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1408190002() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000545_url.txt b/doc/examples/biomodels/BIOMD0000000545/BIOMD0000000545_url.txt similarity index 95% rename from doc/examples/biomodels/BIOMD0000000545_url.txt rename to doc/examples/biomodels/BIOMD0000000545/BIOMD0000000545_url.txt index 543ba3882..695684a55 100644 --- a/doc/examples/biomodels/BIOMD0000000545_url.txt +++ b/doc/examples/biomodels/BIOMD0000000545/BIOMD0000000545_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1407230000() // Compartments and Species: @@ -27,23 +27,23 @@ model *MODEL1407230000() // Species initializations: CS = 0.2; - CS has mole_per_volume; + CS has mole; CD = 10; - CD has mole_per_volume; + CD has mole; CDCS = 2; - CDCS has mole_per_volume; + CDCS has mole; UVR8M = 0; - UVR8M has mole_per_volume; + UVR8M has mole; UCS = 0; - UCS has mole_per_volume; + UCS has mole; UVR8D = 20; - UVR8D has mole_per_volume; + UVR8D has mole; RUP = 0; - RUP has mole_per_volume; + RUP has mole; UR = 0; - UR has mole_per_volume; + UR has mole; UVR8_M = 0; - UVR8_M has mole_per_volume; + UVR8_M has mole; COP1 = 4.2/Hypctol; HY5 = 0.25/Hypctol; FHY3 = 5/Hypctol; @@ -83,9 +83,6 @@ model *MODEL1407230000() const Hypctol, ks1, ks2, kdr1, kdr2, k1, k2, ka1, ka2, ka3, kd1, kd2, kd3; const ks3, kdr3, UV, ka4, kd4, n1, n2, n3, kdr3a, kdr3b, ksr; - // Unit definitions: - unit mole_per_volume = mole / litre; - // CV terms: Hypctol isVersionOf "http://identifiers.org/bto/BTO:0000613" CS hasPart "http://identifiers.org/uniprot/Q9SYX2", diff --git a/doc/examples/biomodels/BIOMD0000000546.txt b/doc/examples/biomodels/BIOMD0000000546/BIOMD0000000546.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000546.txt rename to doc/examples/biomodels/BIOMD0000000546/BIOMD0000000546.txt index 6fbe671b5..7f97508fc 100644 --- a/doc/examples/biomodels/BIOMD0000000546.txt +++ b/doc/examples/biomodels/BIOMD0000000546/BIOMD0000000546.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Miao2010___Innate_and_adaptive_immune_responses_to_primary_Influenza_A_Virus_infection() // Compartments and Species: @@ -49,7 +49,7 @@ model *Miao2010___Innate_and_adaptive_immune_responses_to_primary_Influenza_A_Vi unit length = metre; unit area = metre^2; unit volume = litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = mole; unit unit_0 = mole; unit extent = substance; @@ -67,7 +67,7 @@ model *Miao2010___Innate_and_adaptive_immune_responses_to_primary_Influenza_A_Vi re6 is "re6 Viral Clearance"; re7 is "re7 Production of virus from infected epithelial cells"; - # General layout options + // General layout options model.layout = on model.layout.size = {352.62, 388.85} model.layout.background = "#FFFFFFFF" diff --git a/doc/examples/biomodels/BIOMD0000000546_url model1.txt b/doc/examples/biomodels/BIOMD0000000546/BIOMD0000000546_url model1.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000546_url model1.txt rename to doc/examples/biomodels/BIOMD0000000546/BIOMD0000000546_url model1.txt index 5f1872b86..359786a91 100644 --- a/doc/examples/biomodels/BIOMD0000000546_url model1.txt +++ b/doc/examples/biomodels/BIOMD0000000546/BIOMD0000000546_url model1.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Miao2010___Innate_and_adaptive_immune_responses_to_primary_Influenza_A_Virus_infection_1() // Compartments and Species: @@ -53,7 +53,7 @@ model *Miao2010___Innate_and_adaptive_immune_responses_to_primary_Influenza_A_Vi unit length = metre; unit area = metre^2; unit volume = litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = mole; unit unit_0 = mole; unit extent = substance; @@ -77,7 +77,7 @@ model *Miao2010___Innate_and_adaptive_immune_responses_to_primary_Influenza_A_Vi re8_Neutralization_of_virus_by_IgG is "re8 Neutralization of virus by IgG"; re9_Neutralization_of_virus_by_IgM is "re9 Neutralization of virus by IgM"; - # General layout options + // General layout options model.layout = on model.layout.size = {352.62, 388.85} model.layout.background = "#FFFFFFFF" diff --git a/doc/examples/biomodels/BIOMD0000000547_url.txt b/doc/examples/biomodels/BIOMD0000000547/BIOMD0000000547_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000547_url.txt rename to doc/examples/biomodels/BIOMD0000000547/BIOMD0000000547_url.txt index d79dfd269..6585bb3dc 100644 --- a/doc/examples/biomodels/BIOMD0000000547_url.txt +++ b/doc/examples/biomodels/BIOMD0000000547/BIOMD0000000547_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1403280000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000548_url.txt b/doc/examples/biomodels/BIOMD0000000548/BIOMD0000000548_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000548_url.txt rename to doc/examples/biomodels/BIOMD0000000548/BIOMD0000000548_url.txt index 9135045ef..c510d3e83 100644 --- a/doc/examples/biomodels/BIOMD0000000548_url.txt +++ b/doc/examples/biomodels/BIOMD0000000548/BIOMD0000000548_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1409100000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000549_url.txt b/doc/examples/biomodels/BIOMD0000000549/BIOMD0000000549_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000549_url.txt rename to doc/examples/biomodels/BIOMD0000000549/BIOMD0000000549_url.txt index 33f239eaa..0d76b0a18 100644 --- a/doc/examples/biomodels/BIOMD0000000549_url.txt +++ b/doc/examples/biomodels/BIOMD0000000549/BIOMD0000000549_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1409250001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000550_url.txt b/doc/examples/biomodels/BIOMD0000000550/BIOMD0000000550_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000550_url.txt rename to doc/examples/biomodels/BIOMD0000000550/BIOMD0000000550_url.txt index 7f3e2ca75..de0be99f6 100644 --- a/doc/examples/biomodels/BIOMD0000000550_url.txt +++ b/doc/examples/biomodels/BIOMD0000000550/BIOMD0000000550_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1409250000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000551_url.txt b/doc/examples/biomodels/BIOMD0000000551/BIOMD0000000551_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000551_url.txt rename to doc/examples/biomodels/BIOMD0000000551/BIOMD0000000551_url.txt index 405ee3c2d..2fe1e247b 100644 --- a/doc/examples/biomodels/BIOMD0000000551_url.txt +++ b/doc/examples/biomodels/BIOMD0000000551/BIOMD0000000551_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Das2010___Effect_of_a_gamma_secretase_inhibitor_on_Amyloid_beta_dynamics() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000552_url.txt b/doc/examples/biomodels/BIOMD0000000552/BIOMD0000000552_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000552_url.txt rename to doc/examples/biomodels/BIOMD0000000552/BIOMD0000000552_url.txt index 96fed1fba..0e3db0879 100644 --- a/doc/examples/biomodels/BIOMD0000000552_url.txt +++ b/doc/examples/biomodels/BIOMD0000000552/BIOMD0000000552_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1410200001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000553_url.txt b/doc/examples/biomodels/BIOMD0000000553/BIOMD0000000553_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000553_url.txt rename to doc/examples/biomodels/BIOMD0000000553/BIOMD0000000553_url.txt index 2126ed9c8..209b00530 100644 --- a/doc/examples/biomodels/BIOMD0000000553_url.txt +++ b/doc/examples/biomodels/BIOMD0000000553/BIOMD0000000553_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1410200000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000554_url.txt b/doc/examples/biomodels/BIOMD0000000554/BIOMD0000000554_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000554_url.txt rename to doc/examples/biomodels/BIOMD0000000554/BIOMD0000000554_url.txt index cc82039f4..48cce1ad9 100644 --- a/doc/examples/biomodels/BIOMD0000000554_url.txt +++ b/doc/examples/biomodels/BIOMD0000000554/BIOMD0000000554_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Cloutier2009_BrainEnergyMetabolism() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000555_url.txt b/doc/examples/biomodels/BIOMD0000000555/BIOMD0000000555_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000555_url.txt rename to doc/examples/biomodels/BIOMD0000000555/BIOMD0000000555_url.txt index 997840c63..1c31ef40a 100644 --- a/doc/examples/biomodels/BIOMD0000000555_url.txt +++ b/doc/examples/biomodels/BIOMD0000000555/BIOMD0000000555_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1411100000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000556_url.txt b/doc/examples/biomodels/BIOMD0000000556/BIOMD0000000556_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000556_url.txt rename to doc/examples/biomodels/BIOMD0000000556/BIOMD0000000556_url.txt index 992c2178e..cb9b77871 100644 --- a/doc/examples/biomodels/BIOMD0000000556_url.txt +++ b/doc/examples/biomodels/BIOMD0000000556/BIOMD0000000556_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ortega2013() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000557_url.txt b/doc/examples/biomodels/BIOMD0000000557/BIOMD0000000557_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000557_url.txt rename to doc/examples/biomodels/BIOMD0000000557/BIOMD0000000557_url.txt index 0573b6f7e..70440136f 100644 --- a/doc/examples/biomodels/BIOMD0000000557_url.txt +++ b/doc/examples/biomodels/BIOMD0000000557/BIOMD0000000557_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1410300001() // Compartments and Species: @@ -8,9 +8,9 @@ model *MODEL1410300001() species ppERK_DUSPc in cytosol, ERKn in nucleus, pERKn in nucleus, ppERKn in nucleus; species pERK_DUSPn in nucleus, ppERK_DUSPn in nucleus, STYXn in nucleus; species ERK_STYXn in nucleus, pERK_STYXn in nucleus, ppERK_STYXn in nucleus; - species duspn in nucleus, DUSPn in nucleus, $u_ppMEKc_tot in cytosol, $ppMEKc_tot in cytosol; - species $ERKc_obs in cytosol, $pERKc_obs in cytosol, $ppERKc_obs in cytosol; - species $ERK_ppMEKc_obs in cytosol; + species duspn in nucleus, DUSPn in nucleus, u_ppMEKc_tot in cytosol, ppMEKc_tot in cytosol; + species ERKc_obs in cytosol, pERKc_obs in cytosol, ppERKc_obs in cytosol; + species ERK_ppMEKc_obs in cytosol; // Assignment Rules: u_ppMEKc_tot := piecewise(0, time < -1, 0, time < 0, 1, time < 120, 1); diff --git a/doc/examples/biomodels/BIOMD0000000558_url.txt b/doc/examples/biomodels/BIOMD0000000558/BIOMD0000000558_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000558_url.txt rename to doc/examples/biomodels/BIOMD0000000558/BIOMD0000000558_url.txt index e727337c6..19c5451bd 100644 --- a/doc/examples/biomodels/BIOMD0000000558_url.txt +++ b/doc/examples/biomodels/BIOMD0000000558/BIOMD0000000558_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Cloutier2012() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000559_url.txt b/doc/examples/biomodels/BIOMD0000000559/BIOMD0000000559_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000559_url.txt rename to doc/examples/biomodels/BIOMD0000000559/BIOMD0000000559_url.txt index 65a11cafa..a4064ece3 100644 --- a/doc/examples/biomodels/BIOMD0000000559_url.txt +++ b/doc/examples/biomodels/BIOMD0000000559/BIOMD0000000559_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1412010000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000560_url.txt b/doc/examples/biomodels/BIOMD0000000560/BIOMD0000000560_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000560_url.txt rename to doc/examples/biomodels/BIOMD0000000560/BIOMD0000000560_url.txt index 8d360d4b0..273ef1196 100644 --- a/doc/examples/biomodels/BIOMD0000000560_url.txt +++ b/doc/examples/biomodels/BIOMD0000000560/BIOMD0000000560_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1402200004() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000561_url.txt b/doc/examples/biomodels/BIOMD0000000561/BIOMD0000000561_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000561_url.txt rename to doc/examples/biomodels/BIOMD0000000561/BIOMD0000000561_url.txt index 19fc4d19f..93ac21c00 100644 --- a/doc/examples/biomodels/BIOMD0000000561_url.txt +++ b/doc/examples/biomodels/BIOMD0000000561/BIOMD0000000561_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1412110000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000562_url.txt b/doc/examples/biomodels/BIOMD0000000562/BIOMD0000000562_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000562_url.txt rename to doc/examples/biomodels/BIOMD0000000562/BIOMD0000000562_url.txt index aaa3740b3..cd9bc0b2c 100644 --- a/doc/examples/biomodels/BIOMD0000000562_url.txt +++ b/doc/examples/biomodels/BIOMD0000000562/BIOMD0000000562_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1411240000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000563_url.txt b/doc/examples/biomodels/BIOMD0000000563/BIOMD0000000563_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000563_url.txt rename to doc/examples/biomodels/BIOMD0000000563/BIOMD0000000563_url.txt index 8eafb5c5a..6ede38e75 100644 --- a/doc/examples/biomodels/BIOMD0000000563_url.txt +++ b/doc/examples/biomodels/BIOMD0000000563/BIOMD0000000563_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Pritchart2014() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000564_url.txt b/doc/examples/biomodels/BIOMD0000000564/BIOMD0000000564_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000564_url.txt rename to doc/examples/biomodels/BIOMD0000000564/BIOMD0000000564_url.txt index ee45f841b..2cd535bcf 100644 --- a/doc/examples/biomodels/BIOMD0000000564_url.txt +++ b/doc/examples/biomodels/BIOMD0000000564/BIOMD0000000564_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1410030000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000565_url.txt b/doc/examples/biomodels/BIOMD0000000565/BIOMD0000000565_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000565_url.txt rename to doc/examples/biomodels/BIOMD0000000565/BIOMD0000000565_url.txt index f8c292b12..8c01e01ee 100644 --- a/doc/examples/biomodels/BIOMD0000000565_url.txt +++ b/doc/examples/biomodels/BIOMD0000000565/BIOMD0000000565_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1406060000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000566_url.txt b/doc/examples/biomodels/BIOMD0000000566/BIOMD0000000566_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000566_url.txt rename to doc/examples/biomodels/BIOMD0000000566/BIOMD0000000566_url.txt index a5e5f012b..6c76b0701 100644 --- a/doc/examples/biomodels/BIOMD0000000566_url.txt +++ b/doc/examples/biomodels/BIOMD0000000566/BIOMD0000000566_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1501160000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000567_url.txt b/doc/examples/biomodels/BIOMD0000000567/BIOMD0000000567_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000567_url.txt rename to doc/examples/biomodels/BIOMD0000000567/BIOMD0000000567_url.txt index 9b2ab680f..4edfdc324 100644 --- a/doc/examples/biomodels/BIOMD0000000567_url.txt +++ b/doc/examples/biomodels/BIOMD0000000567/BIOMD0000000567_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1501160001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000568_url.txt b/doc/examples/biomodels/BIOMD0000000568/BIOMD0000000568_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000568_url.txt rename to doc/examples/biomodels/BIOMD0000000568/BIOMD0000000568_url.txt index e7351ae49..c19072066 100644 --- a/doc/examples/biomodels/BIOMD0000000568_url.txt +++ b/doc/examples/biomodels/BIOMD0000000568/BIOMD0000000568_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Mueller2015() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000569_url.txt b/doc/examples/biomodels/BIOMD0000000569/BIOMD0000000569_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000569_url.txt rename to doc/examples/biomodels/BIOMD0000000569/BIOMD0000000569_url.txt index 57fe2ab56..7916c6203 100644 --- a/doc/examples/biomodels/BIOMD0000000569_url.txt +++ b/doc/examples/biomodels/BIOMD0000000569/BIOMD0000000569_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1407160000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000570_url.txt b/doc/examples/biomodels/BIOMD0000000570/BIOMD0000000570_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000570_url.txt rename to doc/examples/biomodels/BIOMD0000000570/BIOMD0000000570_url.txt index a095fa11f..dc2f2c54c 100644 --- a/doc/examples/biomodels/BIOMD0000000570_url.txt +++ b/doc/examples/biomodels/BIOMD0000000570/BIOMD0000000570_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Aubert2002() // Compartments and Species: @@ -60,8 +60,8 @@ model *Aubert2002() outflow_of_dHb: dHb => ; compartment_3*(F_out*(dHb/compartment_3)/compartment_4); // Events: - from_increase_to_stable: at time == ModelValue_52: is_rising = 0, is_maximum = 1; - from_stable_to_decrease__end_of_stimulation: at time == ModelValue_53: v_stim_constant = 0, is_falling = 1, is_maximum = 0; + from_increase_to_stable: at time == ModelValue_52: is_maximum = 1, is_rising = 0; + from_stable_to_decrease__end_of_stimulation: at time == ModelValue_53: is_maximum = 0, is_falling = 1, v_stim_constant = 0; from_decrease_to_at_rest: at time == (ModelValue_53 + ModelValue_52): is_falling = 0; // Species initializations: diff --git a/doc/examples/biomodels/BIOMD0000000571_url.txt b/doc/examples/biomodels/BIOMD0000000571/BIOMD0000000571_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000571_url.txt rename to doc/examples/biomodels/BIOMD0000000571/BIOMD0000000571_url.txt index b39368f77..af9d019c5 100644 --- a/doc/examples/biomodels/BIOMD0000000571_url.txt +++ b/doc/examples/biomodels/BIOMD0000000571/BIOMD0000000571_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1501300000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000572_url.txt b/doc/examples/biomodels/BIOMD0000000572/BIOMD0000000572_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000572_url.txt rename to doc/examples/biomodels/BIOMD0000000572/BIOMD0000000572_url.txt index 4059a7972..a65e3fd7d 100644 --- a/doc/examples/biomodels/BIOMD0000000572_url.txt +++ b/doc/examples/biomodels/BIOMD0000000572/BIOMD0000000572_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1503180000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000573_url.txt b/doc/examples/biomodels/BIOMD0000000573/BIOMD0000000573_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000573_url.txt rename to doc/examples/biomodels/BIOMD0000000573/BIOMD0000000573_url.txt index 2baaf333d..561586a4f 100644 --- a/doc/examples/biomodels/BIOMD0000000573_url.txt +++ b/doc/examples/biomodels/BIOMD0000000573/BIOMD0000000573_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1503180001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000574_url.txt b/doc/examples/biomodels/BIOMD0000000574/BIOMD0000000574_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000574_url.txt rename to doc/examples/biomodels/BIOMD0000000574/BIOMD0000000574_url.txt index c735f72b5..10f4b21aa 100644 --- a/doc/examples/biomodels/BIOMD0000000574_url.txt +++ b/doc/examples/biomodels/BIOMD0000000574/BIOMD0000000574_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1405060000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000575_url.txt b/doc/examples/biomodels/BIOMD0000000575/BIOMD0000000575_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000575_url.txt rename to doc/examples/biomodels/BIOMD0000000575/BIOMD0000000575_url.txt index 6ee7e0668..3d6fbdddc 100644 --- a/doc/examples/biomodels/BIOMD0000000575_url.txt +++ b/doc/examples/biomodels/BIOMD0000000575/BIOMD0000000575_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1504130001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000576_url.txt b/doc/examples/biomodels/BIOMD0000000576/BIOMD0000000576_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000576_url.txt rename to doc/examples/biomodels/BIOMD0000000576/BIOMD0000000576_url.txt index b886e34d3..62563e79c 100644 --- a/doc/examples/biomodels/BIOMD0000000576_url.txt +++ b/doc/examples/biomodels/BIOMD0000000576/BIOMD0000000576_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1506290000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000577_url.txt b/doc/examples/biomodels/BIOMD0000000577/BIOMD0000000577_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000577_url.txt rename to doc/examples/biomodels/BIOMD0000000577/BIOMD0000000577_url.txt index e2b3ad4a3..ce4c68ed0 100644 --- a/doc/examples/biomodels/BIOMD0000000577_url.txt +++ b/doc/examples/biomodels/BIOMD0000000577/BIOMD0000000577_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1506010000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000578_url.txt b/doc/examples/biomodels/BIOMD0000000578/BIOMD0000000578_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000578_url.txt rename to doc/examples/biomodels/BIOMD0000000578/BIOMD0000000578_url.txt index dcd7d69a4..249f4b1f7 100644 --- a/doc/examples/biomodels/BIOMD0000000578_url.txt +++ b/doc/examples/biomodels/BIOMD0000000578/BIOMD0000000578_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1501210000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000579_url.txt b/doc/examples/biomodels/BIOMD0000000579/BIOMD0000000579_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000579_url.txt rename to doc/examples/biomodels/BIOMD0000000579/BIOMD0000000579_url.txt index e12d56d66..99477229e 100644 --- a/doc/examples/biomodels/BIOMD0000000579_url.txt +++ b/doc/examples/biomodels/BIOMD0000000579/BIOMD0000000579_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1507210000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000580_url.txt b/doc/examples/biomodels/BIOMD0000000580/BIOMD0000000580_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000580_url.txt rename to doc/examples/biomodels/BIOMD0000000580/BIOMD0000000580_url.txt index 728ab348b..b4562a162 100644 --- a/doc/examples/biomodels/BIOMD0000000580_url.txt +++ b/doc/examples/biomodels/BIOMD0000000580/BIOMD0000000580_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1506230002() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000581_url.txt b/doc/examples/biomodels/BIOMD0000000581/BIOMD0000000581_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000581_url.txt rename to doc/examples/biomodels/BIOMD0000000581/BIOMD0000000581_url.txt index 038aedc2f..797790187 100644 --- a/doc/examples/biomodels/BIOMD0000000581_url.txt +++ b/doc/examples/biomodels/BIOMD0000000581/BIOMD0000000581_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1506230001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000582_url.txt b/doc/examples/biomodels/BIOMD0000000582/BIOMD0000000582_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000582_url.txt rename to doc/examples/biomodels/BIOMD0000000582/BIOMD0000000582_url.txt index 97905a504..387f5fbc6 100644 --- a/doc/examples/biomodels/BIOMD0000000582_url.txt +++ b/doc/examples/biomodels/BIOMD0000000582/BIOMD0000000582_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1506230000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000583_url.txt b/doc/examples/biomodels/BIOMD0000000583/BIOMD0000000583_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000583_url.txt rename to doc/examples/biomodels/BIOMD0000000583/BIOMD0000000583_url.txt index 5d6431c59..0170bb5f0 100644 --- a/doc/examples/biomodels/BIOMD0000000583_url.txt +++ b/doc/examples/biomodels/BIOMD0000000583/BIOMD0000000583_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *C__difficile_Host_Interactions_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000584_url.txt b/doc/examples/biomodels/BIOMD0000000584/BIOMD0000000584_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000584_url.txt rename to doc/examples/biomodels/BIOMD0000000584/BIOMD0000000584_url.txt index 33a21ff48..d8e376eae 100644 --- a/doc/examples/biomodels/BIOMD0000000584_url.txt +++ b/doc/examples/biomodels/BIOMD0000000584/BIOMD0000000584_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1507170000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000585_url.txt b/doc/examples/biomodels/BIOMD0000000585/BIOMD0000000585_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000585_url.txt rename to doc/examples/biomodels/BIOMD0000000585/BIOMD0000000585_url.txt index a9f3e46f5..f1fc19fe7 100644 --- a/doc/examples/biomodels/BIOMD0000000585_url.txt +++ b/doc/examples/biomodels/BIOMD0000000585/BIOMD0000000585_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1509240000() // Compartments and Species: diff --git a/doc/examples/biomodels/PC_10.txt b/doc/examples/biomodels/BIOMD0000000585/PC_10.txt similarity index 99% rename from doc/examples/biomodels/PC_10.txt rename to doc/examples/biomodels/BIOMD0000000585/PC_10.txt index cd22fde0f..0fac8771a 100644 --- a/doc/examples/biomodels/PC_10.txt +++ b/doc/examples/biomodels/BIOMD0000000585/PC_10.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *PC_IFNg10() // Compartments and Species: diff --git a/doc/examples/biomodels/PC_100.txt b/doc/examples/biomodels/BIOMD0000000585/PC_100.txt similarity index 99% rename from doc/examples/biomodels/PC_100.txt rename to doc/examples/biomodels/BIOMD0000000585/PC_100.txt index 6fdda80f2..a70ab4cae 100644 --- a/doc/examples/biomodels/PC_100.txt +++ b/doc/examples/biomodels/BIOMD0000000585/PC_100.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *PC_IFNg100() // Compartments and Species: diff --git a/doc/examples/biomodels/PSC_1.txt b/doc/examples/biomodels/BIOMD0000000585/PSC_1.txt similarity index 99% rename from doc/examples/biomodels/PSC_1.txt rename to doc/examples/biomodels/BIOMD0000000585/PSC_1.txt index c12c8afaa..6e2348e40 100644 --- a/doc/examples/biomodels/PSC_1.txt +++ b/doc/examples/biomodels/BIOMD0000000585/PSC_1.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *PSC_1() // Compartments and Species: diff --git a/doc/examples/biomodels/PSC_100.txt b/doc/examples/biomodels/BIOMD0000000585/PSC_100.txt similarity index 99% rename from doc/examples/biomodels/PSC_100.txt rename to doc/examples/biomodels/BIOMD0000000585/PSC_100.txt index b778a026d..037917f41 100644 --- a/doc/examples/biomodels/PSC_100.txt +++ b/doc/examples/biomodels/BIOMD0000000585/PSC_100.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *js_psc100_rationeu_1e8() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000586_url.txt b/doc/examples/biomodels/BIOMD0000000586/BIOMD0000000586_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000586_url.txt rename to doc/examples/biomodels/BIOMD0000000586/BIOMD0000000586_url.txt index bffb4bbdf..459736f88 100644 --- a/doc/examples/biomodels/BIOMD0000000586_url.txt +++ b/doc/examples/biomodels/BIOMD0000000586/BIOMD0000000586_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1512100000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000587_url.txt b/doc/examples/biomodels/BIOMD0000000587/BIOMD0000000587_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000587_url.txt rename to doc/examples/biomodels/BIOMD0000000587/BIOMD0000000587_url.txt index 30e3a71cf..784503b5a 100644 --- a/doc/examples/biomodels/BIOMD0000000587_url.txt +++ b/doc/examples/biomodels/BIOMD0000000587/BIOMD0000000587_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1512100001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000588_url.txt b/doc/examples/biomodels/BIOMD0000000588/BIOMD0000000588_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000588_url.txt rename to doc/examples/biomodels/BIOMD0000000588/BIOMD0000000588_url.txt index a3ac89ed2..f177b7118 100644 --- a/doc/examples/biomodels/BIOMD0000000588_url.txt +++ b/doc/examples/biomodels/BIOMD0000000588/BIOMD0000000588_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1601290000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000589_url.txt b/doc/examples/biomodels/BIOMD0000000589/BIOMD0000000589_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000589_url.txt rename to doc/examples/biomodels/BIOMD0000000589/BIOMD0000000589_url.txt index ba84236cc..6c18b3ba4 100644 --- a/doc/examples/biomodels/BIOMD0000000589_url.txt +++ b/doc/examples/biomodels/BIOMD0000000589/BIOMD0000000589_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *ASC_GSH_pathway() // Compartments and Species: diff --git a/doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 10a.txt b/doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 10a.txt similarity index 99% rename from doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 10a.txt rename to doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 10a.txt index 196fd9fd4..35a5c9f1b 100644 --- a/doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 10a.txt +++ b/doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 10a.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *ASC_GSH_pathway() // Compartments and Species: diff --git a/doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 10b.txt b/doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 10b.txt similarity index 99% rename from doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 10b.txt rename to doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 10b.txt index 5ef75d2a1..848c53db1 100644 --- a/doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 10b.txt +++ b/doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 10b.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *ASC_GSH_pathway() // Compartments and Species: diff --git a/doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 4.txt b/doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 4.txt similarity index 99% rename from doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 4.txt rename to doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 4.txt index 7ef055182..30c34c782 100644 --- a/doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 4.txt +++ b/doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 4.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *ASC_GSH_pathway() // Compartments and Species: diff --git a/doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 5.txt b/doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 5.txt similarity index 99% rename from doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 5.txt rename to doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 5.txt index a0aac9e66..eb0d04c42 100644 --- a/doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 5.txt +++ b/doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 5.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *ASC_GSH_pathway() // Compartments and Species: diff --git a/doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 6.txt b/doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 6.txt similarity index 99% rename from doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 6.txt rename to doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 6.txt index 445d7fe83..d3a957223 100644 --- a/doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 6.txt +++ b/doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 6.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *ASC_GSH_pathway() // Compartments and Species: diff --git a/doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 7.txt b/doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 7.txt similarity index 99% rename from doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 7.txt rename to doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 7.txt index 2dd878e6a..42244accf 100644 --- a/doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 7.txt +++ b/doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 7.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *ASC_GSH_pathway() // Compartments and Species: diff --git a/doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 8.txt b/doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 8.txt similarity index 99% rename from doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 8.txt rename to doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 8.txt index 737bd58bd..3caccc5cb 100644 --- a/doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 8.txt +++ b/doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 8.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *ASC_GSH_pathway() // Compartments and Species: diff --git a/doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 9.txt b/doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 9.txt similarity index 99% rename from doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 9.txt rename to doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 9.txt index 567ba1576..3085e3d1b 100644 --- a/doc/examples/biomodels/Valero et al 2015 ASC-GSH-Fig 9.txt +++ b/doc/examples/biomodels/BIOMD0000000589/Valero et al 2015 ASC-GSH-Fig 9.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *ASC_GSH_pathway() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000590_url.txt b/doc/examples/biomodels/BIOMD0000000590/BIOMD0000000590_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000590_url.txt rename to doc/examples/biomodels/BIOMD0000000590/BIOMD0000000590_url.txt index d7858cb09..51b64a25a 100644 --- a/doc/examples/biomodels/BIOMD0000000590_url.txt +++ b/doc/examples/biomodels/BIOMD0000000590/BIOMD0000000590_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1512160000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000591_url.txt b/doc/examples/biomodels/BIOMD0000000591/BIOMD0000000591_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000591_url.txt rename to doc/examples/biomodels/BIOMD0000000591/BIOMD0000000591_url.txt index 8a1a13a0e..8fb355ffb 100644 --- a/doc/examples/biomodels/BIOMD0000000591_url.txt +++ b/doc/examples/biomodels/BIOMD0000000591/BIOMD0000000591_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1501220000() // Compartments and Species: diff --git a/doc/examples/biomodels/Model_Fig5D.txt b/doc/examples/biomodels/BIOMD0000000591/Model_Fig5D.txt similarity index 98% rename from doc/examples/biomodels/Model_Fig5D.txt rename to doc/examples/biomodels/BIOMD0000000591/Model_Fig5D.txt index 94d906e75..c0056db09 100644 --- a/doc/examples/biomodels/Model_Fig5D.txt +++ b/doc/examples/biomodels/BIOMD0000000591/Model_Fig5D.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Boehm2014___isoform_specific_dimerization_of_pSTAT5A_and_pSTAT5B() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000592_url.txt b/doc/examples/biomodels/BIOMD0000000592/BIOMD0000000592_url.txt similarity index 96% rename from doc/examples/biomodels/BIOMD0000000592_url.txt rename to doc/examples/biomodels/BIOMD0000000592/BIOMD0000000592_url.txt index e37640051..7b6098540 100644 --- a/doc/examples/biomodels/BIOMD0000000592_url.txt +++ b/doc/examples/biomodels/BIOMD0000000592/BIOMD0000000592_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1411170000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000593_url.txt b/doc/examples/biomodels/BIOMD0000000593/BIOMD0000000593_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000593_url.txt rename to doc/examples/biomodels/BIOMD0000000593/BIOMD0000000593_url.txt index 0ac91cc2b..682fe4048 100644 --- a/doc/examples/biomodels/BIOMD0000000593_url.txt +++ b/doc/examples/biomodels/BIOMD0000000593/BIOMD0000000593_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1411170001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000594_url.txt b/doc/examples/biomodels/BIOMD0000000594/BIOMD0000000594_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000594_url.txt rename to doc/examples/biomodels/BIOMD0000000594/BIOMD0000000594_url.txt index 44af394c1..0cf65a639 100644 --- a/doc/examples/biomodels/BIOMD0000000594_url.txt +++ b/doc/examples/biomodels/BIOMD0000000594/BIOMD0000000594_url.txt @@ -1,16 +1,16 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1505190001() // Compartments and Species: compartment cell; - species Cbl in cell, Grb2 in cell, CG in cell, $Tyr in cell, EGFR_10UU in cell; + species Cbl in cell, Grb2 in cell, CG in cell, Tyr in cell, EGFR_10UU in cell; species EGFR_10CU in cell, EGFR_10LU in cell, EGFR_01UU in cell, EGFR_01UG in cell; species EGFR_01UL in cell, EGFR_11UU in cell, EGFR_11CU in cell, EGFR_11LU in cell; species EGFR_11UG in cell, EGFR_11UL in cell, EGFR_11CG in cell, EGFR_11CC in cell; species EGFR_11LG in cell, EGFR_02UU in cell, EGFR_02UG in cell, EGFR_02UL in cell; species EGFR_12UU in cell, EGFR_12CU in cell, EGFR_12LU in cell, EGFR_12UG in cell; species EGFR_12UL in cell, EGFR_12CG in cell, EGFR_12CC in cell, EGFR_12LG in cell; - species $Ub in cell, $TyrNorm in cell, $UbNorm in cell, EGFR_00UU in cell; + species Ub in cell, TyrNorm in cell, UbNorm in cell, EGFR_00UU in cell; // Assignment Rules: Tyr := EGFR_10UU + EGFR_10CU + EGFR_10LU + 1*(EGFR_01UU + EGFR_01UG + EGFR_01UL) + 2*(EGFR_11UU + EGFR_11CU + EGFR_11LU + EGFR_11UG + EGFR_11UL + EGFR_11CG + EGFR_11CC + EGFR_11LG) + 2*(EGFR_02UU + EGFR_02UG + EGFR_02UL) + 3*(EGFR_12UU + EGFR_12CU + EGFR_12LU + EGFR_12UG + EGFR_12UL + EGFR_12CG + EGFR_12CC + EGFR_12LG); diff --git a/doc/examples/biomodels/BIOMD0000000595_url.txt b/doc/examples/biomodels/BIOMD0000000595/BIOMD0000000595_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000595_url.txt rename to doc/examples/biomodels/BIOMD0000000595/BIOMD0000000595_url.txt index 66d1279b2..5bf85830a 100644 --- a/doc/examples/biomodels/BIOMD0000000595_url.txt +++ b/doc/examples/biomodels/BIOMD0000000595/BIOMD0000000595_url.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1505190000() // Compartments and Species: compartment cell; - species L in cell, Cbl in cell, Grb2 in cell, CG in cell, $PY in cell, Rc10UU in cell; + species L in cell, Cbl in cell, Grb2 in cell, CG in cell, PY in cell, Rc10UU in cell; species Rc10CU in cell, Rc10LU in cell, RcL10UU in cell, RcL10CU in cell; species RcL10LU in cell, R10UU in cell, R10CU in cell, R10LU in cell, RL10UU in cell; species RL10CU in cell, RL10LU in cell, Di10UU in cell, Di10CU in cell; @@ -52,8 +52,8 @@ model *MODEL1505190000() species DiL12UL in cell, DiL12CG in cell, DiL12CC in cell, DiL12LG in cell; species DaL12UU in cell, DaL12CU in cell, DaL12LU in cell, DaL12UG in cell; species DaL12UL in cell, DaL12CG in cell, DaL12CC in cell, DaL12LG in cell; - species $Ub in cell, $PYNorm in cell, $UbNorm in cell, $SumM in cell, R00UU in cell; - species $SumML in cell, RL00UU in cell, Rc00UU in cell, RcL00UU in cell; + species Ub in cell, PYNorm in cell, UbNorm in cell, SumM in cell, R00UU in cell; + species SumML in cell, RL00UU in cell, Rc00UU in cell, RcL00UU in cell; species Di00UU in cell, Da00UU in cell, DiL00UU in cell, DaL00UU in cell; // Assignment Rules: diff --git a/doc/examples/biomodels/Philipson2015.txt b/doc/examples/biomodels/BIOMD0000000596/Philipson2015.txt similarity index 99% rename from doc/examples/biomodels/Philipson2015.txt rename to doc/examples/biomodels/BIOMD0000000596/Philipson2015.txt index 13e8f147c..6230a63e7 100644 --- a/doc/examples/biomodels/Philipson2015.txt +++ b/doc/examples/biomodels/BIOMD0000000596/Philipson2015.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 // Warnings from automatic translation: // Layout error: unable to add alias #1 for species 'HP' to model, because it is not connected to any reactions. Antimony requires that all species and species aliases connect to some reaction. @@ -141,7 +141,7 @@ model *Philipson2015___Innate_immune_response_modulated_by_NLRX1() time_unit is "time"; unit_0 is "1"; - # General layout options + // General layout options model.layout = on model.layout.size = {1000, 1000} model.layout.background = "#FFFFFFFF" diff --git a/doc/examples/biomodels/BIOMD0000000597_url.txt b/doc/examples/biomodels/BIOMD0000000597/BIOMD0000000597_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000597_url.txt rename to doc/examples/biomodels/BIOMD0000000597/BIOMD0000000597_url.txt index ba4972d46..83980d02b 100644 --- a/doc/examples/biomodels/BIOMD0000000597_url.txt +++ b/doc/examples/biomodels/BIOMD0000000597/BIOMD0000000597_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1510190000() // Compartments and Species: @@ -73,7 +73,7 @@ model *MODEL1510190000() cEC_degr: cEC => ; def*((m36*cCOP1n*cEC + m37*cCOP1d*cEC + m32*cEC*(1 + p24*L*(p28*cG/(p29 + m19 + p17*cE3n) + (p18*cEG + p17*cE3n*p28*cG/(p29 + m19 + p17*cE3n))/(m9*cCOP1n + m10*cCOP1d + p31))^d/((p28*cG/(p29 + m19 + p17*cE3n) + (p18*cEG + p17*cE3n*p28*cG/(p29 + m19 + p17*cE3n))/(m9*cCOP1n + m10*cCOP1d + p31))^d + g7^d)))/def); // Events: - event_1: at time > 314: amplitudeStep1 = 0, offsetStep1 = 1; + event_1: at time > 314: offsetStep1 = 1, amplitudeStep1 = 0; // Species initializations: cCOP1c = 0.3269; diff --git a/doc/examples/biomodels/BIOMD0000000598_url.txt b/doc/examples/biomodels/BIOMD0000000598/BIOMD0000000598_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000598_url.txt rename to doc/examples/biomodels/BIOMD0000000598/BIOMD0000000598_url.txt index 37771a64e..5b1bbe52e 100644 --- a/doc/examples/biomodels/BIOMD0000000598_url.txt +++ b/doc/examples/biomodels/BIOMD0000000598/BIOMD0000000598_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1510190001() // Compartments and Species: @@ -73,7 +73,7 @@ model *MODEL1510190001() cEC_degr: cEC => ; def*((m36*cCOP1n*cEC + m37*cCOP1d*cEC + m32*cEC*(1 + p24*L*(p28*cG/(p29 + m19 + p17*cE3n) + (p18*cEG + p17*cE3n*p28*cG/(p29 + m19 + p17*cE3n))/(m9*cCOP1n + m10*cCOP1d + p31))^d/((p28*cG/(p29 + m19 + p17*cE3n) + (p18*cEG + p17*cE3n*p28*cG/(p29 + m19 + p17*cE3n))/(m9*cCOP1n + m10*cCOP1d + p31))^d + g7^d)))/def); // Events: - event_1: at time > 314: amplitudeStep1 = 0, offsetStep1 = 1; + event_1: at time > 314: offsetStep1 = 1, amplitudeStep1 = 0; // Species initializations: cCOP1c = 0.3269; diff --git a/doc/examples/biomodels/BIOMD0000000599_url.txt b/doc/examples/biomodels/BIOMD0000000599/BIOMD0000000599_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000599_url.txt rename to doc/examples/biomodels/BIOMD0000000599/BIOMD0000000599_url.txt index 9fd17549b..4e425a760 100644 --- a/doc/examples/biomodels/BIOMD0000000599_url.txt +++ b/doc/examples/biomodels/BIOMD0000000599/BIOMD0000000599_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Coggins2014___CXCL12_dependent_recruitment_of_beta_arrestin() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000600_url.txt b/doc/examples/biomodels/BIOMD0000000600/BIOMD0000000600_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000600_url.txt rename to doc/examples/biomodels/BIOMD0000000600/BIOMD0000000600_url.txt index 65cb0b787..fd8ca2959 100644 --- a/doc/examples/biomodels/BIOMD0000000600_url.txt +++ b/doc/examples/biomodels/BIOMD0000000600/BIOMD0000000600_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Celli_re2011___Plasticity_of_TGF___Signalling() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000601_url.txt b/doc/examples/biomodels/BIOMD0000000601/BIOMD0000000601_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000601_url.txt rename to doc/examples/biomodels/BIOMD0000000601/BIOMD0000000601_url.txt index 90b25bee2..88f83c112 100644 --- a/doc/examples/biomodels/BIOMD0000000601_url.txt +++ b/doc/examples/biomodels/BIOMD0000000601/BIOMD0000000601_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1406180001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000602_url.txt b/doc/examples/biomodels/BIOMD0000000602/BIOMD0000000602_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000602_url.txt rename to doc/examples/biomodels/BIOMD0000000602/BIOMD0000000602_url.txt index 9ae2b0c72..03311e733 100644 --- a/doc/examples/biomodels/BIOMD0000000602_url.txt +++ b/doc/examples/biomodels/BIOMD0000000602/BIOMD0000000602_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Stavrum2013___Tryptophan_Metabolism_in_Liver() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000603_url.txt b/doc/examples/biomodels/BIOMD0000000603/BIOMD0000000603_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000603_url.txt rename to doc/examples/biomodels/BIOMD0000000603/BIOMD0000000603_url.txt index c14b3c0e4..f7d63067e 100644 --- a/doc/examples/biomodels/BIOMD0000000603_url.txt +++ b/doc/examples/biomodels/BIOMD0000000603/BIOMD0000000603_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *PetelenzKuehn_osmoadaptation_WT() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000604_url.txt b/doc/examples/biomodels/BIOMD0000000604/BIOMD0000000604_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000604_url.txt rename to doc/examples/biomodels/BIOMD0000000604/BIOMD0000000604_url.txt index c55ac6d59..a16938291 100644 --- a/doc/examples/biomodels/BIOMD0000000604_url.txt +++ b/doc/examples/biomodels/BIOMD0000000604/BIOMD0000000604_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *PetelenzKuehn_osmoadaptation_pfk2627D() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000605_url.txt b/doc/examples/biomodels/BIOMD0000000605/BIOMD0000000605_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000605_url.txt rename to doc/examples/biomodels/BIOMD0000000605/BIOMD0000000605_url.txt index 48fe60c7e..cff39bcf9 100644 --- a/doc/examples/biomodels/BIOMD0000000605_url.txt +++ b/doc/examples/biomodels/BIOMD0000000605/BIOMD0000000605_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *PetelenzKuehn_osmoadaptation_HOG1att() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000606_url.txt b/doc/examples/biomodels/BIOMD0000000606/BIOMD0000000606_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000606_url.txt rename to doc/examples/biomodels/BIOMD0000000606/BIOMD0000000606_url.txt index 2ed374279..e344da05b 100644 --- a/doc/examples/biomodels/BIOMD0000000606_url.txt +++ b/doc/examples/biomodels/BIOMD0000000606/BIOMD0000000606_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *PetelenzKuehn_osmoadaptation_hog1D() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000607_url.txt b/doc/examples/biomodels/BIOMD0000000607/BIOMD0000000607_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000607_url.txt rename to doc/examples/biomodels/BIOMD0000000607/BIOMD0000000607_url.txt index db0de882e..eca93c5a1 100644 --- a/doc/examples/biomodels/BIOMD0000000607_url.txt +++ b/doc/examples/biomodels/BIOMD0000000607/BIOMD0000000607_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *PetelenzKuehn_osmoadaptation_fps1D1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000608_url.txt b/doc/examples/biomodels/BIOMD0000000608/BIOMD0000000608_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000608_url.txt rename to doc/examples/biomodels/BIOMD0000000608/BIOMD0000000608_url.txt index 525b8b8f1..8bf4f45c2 100644 --- a/doc/examples/biomodels/BIOMD0000000608_url.txt +++ b/doc/examples/biomodels/BIOMD0000000608/BIOMD0000000608_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1603310000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000609_url.txt b/doc/examples/biomodels/BIOMD0000000609/BIOMD0000000609_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000609_url.txt rename to doc/examples/biomodels/BIOMD0000000609/BIOMD0000000609_url.txt index 50be46680..903051245 100644 --- a/doc/examples/biomodels/BIOMD0000000609_url.txt +++ b/doc/examples/biomodels/BIOMD0000000609/BIOMD0000000609_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Reddyhoff2015() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000610_url.txt b/doc/examples/biomodels/BIOMD0000000610/BIOMD0000000610_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000610_url.txt rename to doc/examples/biomodels/BIOMD0000000610/BIOMD0000000610_url.txt index 360599a34..3477bd84a 100644 --- a/doc/examples/biomodels/BIOMD0000000610_url.txt +++ b/doc/examples/biomodels/BIOMD0000000610/BIOMD0000000610_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *PetelenzKuehn_osmoadaptation_gpd1D() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000611_url.txt b/doc/examples/biomodels/BIOMD0000000611/BIOMD0000000611_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000611_url.txt rename to doc/examples/biomodels/BIOMD0000000611/BIOMD0000000611_url.txt index 5189bab57..81b8dd31a 100644 --- a/doc/examples/biomodels/BIOMD0000000611_url.txt +++ b/doc/examples/biomodels/BIOMD0000000611/BIOMD0000000611_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1511160000() // Compartments and Species: @@ -35,7 +35,7 @@ model *MODEL1511160000() species mwe70b2c96_44b9_48eb_967a_7eb850a916a6 in mwa76931f0_7e48_4dcd_835f_4a2db486ed1b; species mw64e9cef3_5dd3_43f3_ad04_58e8fc07a91b in mwa76931f0_7e48_4dcd_835f_4a2db486ed1b; species mw6d041b25_87db_4394_9b8b_7ac61e01f359 in mwa76931f0_7e48_4dcd_835f_4a2db486ed1b; - species $mw85e2714d_e6e5_47d5_9ffc_d90573faebe1 in mwa76931f0_7e48_4dcd_835f_4a2db486ed1b; + species mw85e2714d_e6e5_47d5_9ffc_d90573faebe1 in mwa76931f0_7e48_4dcd_835f_4a2db486ed1b; species mwd68cbf38_9266_4dfb_aa00_f817c3421aec in mwa76931f0_7e48_4dcd_835f_4a2db486ed1b; species mwa6be116e_72f1_439e_bca6_eb61f79cc68e in mwa76931f0_7e48_4dcd_835f_4a2db486ed1b; species mw6a8501d2_9479_41ae_8616_1e8d0e1bbfa9 in mwa76931f0_7e48_4dcd_835f_4a2db486ed1b; diff --git a/doc/examples/biomodels/BIOMD0000000612_url.txt b/doc/examples/biomodels/BIOMD0000000612/BIOMD0000000612_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000612_url.txt rename to doc/examples/biomodels/BIOMD0000000612/BIOMD0000000612_url.txt index 72b3a53be..c625b5da2 100644 --- a/doc/examples/biomodels/BIOMD0000000612_url.txt +++ b/doc/examples/biomodels/BIOMD0000000612/BIOMD0000000612_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1602290000() // Compartments and Species: @@ -97,7 +97,7 @@ model *MODEL1602290000() AddLOAD1: at X > 300: LOAD = 1; AddLOAD2: at X > 600: LOAD = 1; AddPTH1: at X > 625: PTH = 150; - AddPTH2: at X > 1000: X = 0, PTH = 170; + AddPTH2: at X > 1000: PTH = 170, X = 0; // Species initializations: Bone = 2000; diff --git a/doc/examples/biomodels/BIOMD0000000613_url.txt b/doc/examples/biomodels/BIOMD0000000613/BIOMD0000000613_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000613_url.txt rename to doc/examples/biomodels/BIOMD0000000613/BIOMD0000000613_url.txt index 19dd90ec1..3b5db9537 100644 --- a/doc/examples/biomodels/BIOMD0000000613_url.txt +++ b/doc/examples/biomodels/BIOMD0000000613/BIOMD0000000613_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1604270004() // Compartments and Species: @@ -216,7 +216,7 @@ model *MODEL1604270004() Bcl2_degradation: BCL2 => ; bcl2Kout*BCL2; // Events: - Event: at 0 after (time == teri_times_initial) || ((time == (event_counter + teri_times_initial)) && (time < (teri_times_interval*teri_number_of_doses + teri_times_initial))), fromTrigger=false: TERISC = teri_dose_mcg*1000000/4117.8, event_counter = event_counter + teri_times_interval; + Event: at 0 after (time == teri_times_initial) || ((time == (event_counter + teri_times_initial)) && (time < (teri_times_interval*teri_number_of_doses + teri_times_initial))), fromTrigger=false: event_counter = event_counter + teri_times_interval, TERISC = teri_dose_mcg*1000000/4117.8; // Species initializations: PTH = 53.9; diff --git a/doc/examples/biomodels/BIOMD0000000614_url.txt b/doc/examples/biomodels/BIOMD0000000614/BIOMD0000000614_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000614_url.txt rename to doc/examples/biomodels/BIOMD0000000614/BIOMD0000000614_url.txt index 910c18f73..b5c565191 100644 --- a/doc/examples/biomodels/BIOMD0000000614_url.txt +++ b/doc/examples/biomodels/BIOMD0000000614/BIOMD0000000614_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kamihira2000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000615_url.txt b/doc/examples/biomodels/BIOMD0000000615/BIOMD0000000615_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000615_url.txt rename to doc/examples/biomodels/BIOMD0000000615/BIOMD0000000615_url.txt index f0fe48962..2a7ac2608 100644 --- a/doc/examples/biomodels/BIOMD0000000615_url.txt +++ b/doc/examples/biomodels/BIOMD0000000615/BIOMD0000000615_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1608150000() // Compartments and Species: @@ -58,7 +58,7 @@ model *MODEL1608150000() unit length = metre; unit area = metre^2; unit volume = litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = mole; unit extent = substance; unit mole_per_volume = mole / litre; diff --git a/doc/examples/biomodels/BIOMD0000000616_url.txt b/doc/examples/biomodels/BIOMD0000000616/BIOMD0000000616_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000616_url.txt rename to doc/examples/biomodels/BIOMD0000000616/BIOMD0000000616_url.txt index 594379111..2fe9ef296 100644 --- a/doc/examples/biomodels/BIOMD0000000616_url.txt +++ b/doc/examples/biomodels/BIOMD0000000616/BIOMD0000000616_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1608160000() // Compartments and Species: @@ -47,7 +47,7 @@ model *MODEL1608160000() unit length = metre; unit area = metre^2; unit volume = litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = mole; unit extent = substance; unit mole_per_volume = mole / litre; diff --git a/doc/examples/biomodels/BIOMD0000000617_url.txt b/doc/examples/biomodels/BIOMD0000000617/BIOMD0000000617_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000617_url.txt rename to doc/examples/biomodels/BIOMD0000000617/BIOMD0000000617_url.txt index c35671dc2..790e99afd 100644 --- a/doc/examples/biomodels/BIOMD0000000617_url.txt +++ b/doc/examples/biomodels/BIOMD0000000617/BIOMD0000000617_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1609120000() // Compartments and Species: @@ -59,7 +59,7 @@ model *MODEL1609120000() unit substance = 1e-3 mole; unit length = metre; unit area = metre^2; - unit time_unit = time_unit; + unit time_unit = second; unit extent = substance; unit substance_per_volume = 1e-3 mole / 1e-3 litre; unit substance_per_volume_litre = 1e-3 mole * litre / 1e-3 litre; diff --git a/doc/examples/biomodels/BIOMD0000000618_url.txt b/doc/examples/biomodels/BIOMD0000000618/BIOMD0000000618_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000618_url.txt rename to doc/examples/biomodels/BIOMD0000000618/BIOMD0000000618_url.txt index 815d3aa11..befed7395 100644 --- a/doc/examples/biomodels/BIOMD0000000618_url.txt +++ b/doc/examples/biomodels/BIOMD0000000618/BIOMD0000000618_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1607270000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000619_url.txt b/doc/examples/biomodels/BIOMD0000000619/BIOMD0000000619_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000619_url.txt rename to doc/examples/biomodels/BIOMD0000000619/BIOMD0000000619_url.txt index 421d72aea..3a954f418 100644 --- a/doc/examples/biomodels/BIOMD0000000619_url.txt +++ b/doc/examples/biomodels/BIOMD0000000619/BIOMD0000000619_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1509230010() // Compartments and Species: @@ -25,25 +25,25 @@ model *MODEL1509230010() // Species initializations: CArt = 0; - CArt has substance_per_volume; + CArt has substance; CGut = 0; - CGut has substance_per_volume; + CGut has substance; AGutlumen = APAP_Dose; - AGutlumen has substance_per_volume; + AGutlumen has substance; CLung = 0; - CLung has substance_per_volume; + CLung has substance; CVen = 0; - CVen has substance_per_volume; + CVen has substance; CRest = 0; - CRest has substance_per_volume; + CRest has substance; CLiver = 0; - CLiver has substance_per_volume; + CLiver has substance; CMetabolized = 0; - CMetabolized has substance_per_volume; + CMetabolized has substance; CKidney = 0; - CKidney has substance_per_volume; + CKidney has substance; CTubules = 0; - CTubules has substance_per_volume; + CTubules has substance; // Compartment initializations: VArt = VTotal*VArt_fraction_VTotal; @@ -147,7 +147,7 @@ model *MODEL1509230010() unit substance = mole; unit grams2mol = gram / mole; unit BW_ref_unit = kilogram; - unit substance_per_volume = mole / litre; + unit substance_volume = mole * litre; // Display Names: time_unit is "hour"; diff --git a/doc/examples/biomodels/BIOMD0000000620_url.txt b/doc/examples/biomodels/BIOMD0000000620/BIOMD0000000620_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000620_url.txt rename to doc/examples/biomodels/BIOMD0000000620/BIOMD0000000620_url.txt index e8a3901c7..6a6473b60 100644 --- a/doc/examples/biomodels/BIOMD0000000620_url.txt +++ b/doc/examples/biomodels/BIOMD0000000620/BIOMD0000000620_url.txt @@ -1,11 +1,11 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1604270002() // Compartments and Species: species IL1b, IL1Ra, Anakinra, Proinsulin, Insulin, TigB, B, f, Anakinrasc; - species Glucose, $a1c1, $rbc1, $a1c2, $rbc2, $a1c3, $rbc3, $a1c4, $rbc4; - species $a1c5, $rbc5, $a1c6, $rbc6, $a1c7, $rbc7, $a1c8, $rbc8, $a1c9, $rbc9; - species $a1c10, $rbc10, $a1c11, $rbc11, $a1c12, $rbc12, $hba1c; + species Glucose, a1c1, rbc1, a1c2, rbc2, a1c3, rbc3, a1c4, rbc4, a1c5, rbc5; + species a1c6, rbc6, a1c7, rbc7, a1c8, rbc8, a1c9, rbc9, a1c10, rbc10, a1c11; + species rbc11, a1c12, rbc12, $hba1c; // Assignment Rules: hba1c := 100*(a1c1 + a1c2 + a1c3 + a1c4 + a1c5 + a1c6 + a1c7 + a1c8 + a1c9 + a1c10 + a1c11 + a1c12)/(a1c1 + a1c2 + a1c3 + a1c4 + a1c5 + a1c6 + a1c7 + a1c8 + a1c9 + a1c10 + a1c11 + a1c12 + rbc1 + rbc2 + rbc3 + rbc4 + rbc5 + rbc6 + rbc7 + rbc8 + rbc9 + rbc10 + rbc11 + rbc12); @@ -63,7 +63,7 @@ model *MODEL1604270002() Proinsulin_elimination: Proinsulin => ; 0.1*Kxi*Proinsulin; // Events: - Anakinra_Administration_event: at 0 after (time == Anakinra_dose_counter) && (Anakinra_dose_counter < 91): Anakinra_dose_counter = Anakinra_dose_counter + 1, Anakinrasc = Anakinrasc + 100000*Ana_on; + Anakinra_Administration_event: at 0 after (time == Anakinra_dose_counter) && (Anakinra_dose_counter < 91): Anakinrasc = Anakinrasc + 100000*Ana_on, Anakinra_dose_counter = Anakinra_dose_counter + 1; // Species initializations: IL1b = 5; diff --git a/doc/examples/biomodels/BIOMD0000000621_url.txt b/doc/examples/biomodels/BIOMD0000000621/BIOMD0000000621_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000621_url.txt rename to doc/examples/biomodels/BIOMD0000000621/BIOMD0000000621_url.txt index ca22d3685..f51369e4d 100644 --- a/doc/examples/biomodels/BIOMD0000000621_url.txt +++ b/doc/examples/biomodels/BIOMD0000000621/BIOMD0000000621_url.txt @@ -1,11 +1,11 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1611040000() // Compartments and Species: species IL1b, IL1Ra, Anakinra, Proinsulin, Insulin, TigB, B, f, Anakinrasc; - species Glucose, $a1c1, $rbc1, $a1c2, $rbc2, $a1c3, $rbc3, $a1c4, $rbc4; - species $a1c5, $rbc5, $a1c6, $rbc6, $a1c7, $rbc7, $a1c8, $rbc8, $a1c9, $rbc9; - species $a1c10, $rbc10, $a1c11, $rbc11, $a1c12, $rbc12, $hba1c; + species Glucose, a1c1, rbc1, a1c2, rbc2, a1c3, rbc3, a1c4, rbc4, a1c5, rbc5; + species a1c6, rbc6, a1c7, rbc7, a1c8, rbc8, a1c9, rbc9, a1c10, rbc10, a1c11; + species rbc11, a1c12, rbc12, $hba1c; // Assignment Rules: hba1c := 100*(a1c1 + a1c2 + a1c3 + a1c4 + a1c5 + a1c6 + a1c7 + a1c8 + a1c9 + a1c10 + a1c11 + a1c12)/(a1c1 + a1c2 + a1c3 + a1c4 + a1c5 + a1c6 + a1c7 + a1c8 + a1c9 + a1c10 + a1c11 + a1c12 + rbc1 + rbc2 + rbc3 + rbc4 + rbc5 + rbc6 + rbc7 + rbc8 + rbc9 + rbc10 + rbc11 + rbc12); @@ -63,7 +63,7 @@ model *MODEL1611040000() Proinsulin_elimination: Proinsulin => ; 0.1*Kxi*Proinsulin; // Events: - Anakinra_Administration_event: at 0 after (time == Anakinra_dose_counter) && (Anakinra_dose_counter < 91): Anakinra_dose_counter = Anakinra_dose_counter + 1, Anakinrasc = Anakinrasc + 100000*Ana_on; + Anakinra_Administration_event: at 0 after (time == Anakinra_dose_counter) && (Anakinra_dose_counter < 91): Anakinrasc = Anakinrasc + 100000*Ana_on, Anakinra_dose_counter = Anakinra_dose_counter + 1; // Species initializations: IL1b = 0.05; diff --git a/doc/examples/biomodels/BIOMD0000000622_url.txt b/doc/examples/biomodels/BIOMD0000000622/BIOMD0000000622_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000622_url.txt rename to doc/examples/biomodels/BIOMD0000000622/BIOMD0000000622_url.txt index 3874ca3cd..174925ccd 100644 --- a/doc/examples/biomodels/BIOMD0000000622_url.txt +++ b/doc/examples/biomodels/BIOMD0000000622/BIOMD0000000622_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1611160000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000623_url.txt b/doc/examples/biomodels/BIOMD0000000623/BIOMD0000000623_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000623_url.txt rename to doc/examples/biomodels/BIOMD0000000623/BIOMD0000000623_url.txt index c57b44b9a..94d143a1d 100644 --- a/doc/examples/biomodels/BIOMD0000000623_url.txt +++ b/doc/examples/biomodels/BIOMD0000000623/BIOMD0000000623_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1611280000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000624_url.txt b/doc/examples/biomodels/BIOMD0000000624/BIOMD0000000624_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000624_url.txt rename to doc/examples/biomodels/BIOMD0000000624/BIOMD0000000624_url.txt index 0c9cc158f..69b680873 100644 --- a/doc/examples/biomodels/BIOMD0000000624_url.txt +++ b/doc/examples/biomodels/BIOMD0000000624/BIOMD0000000624_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1509230011() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000625_url.txt b/doc/examples/biomodels/BIOMD0000000625/BIOMD0000000625_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000625_url.txt rename to doc/examples/biomodels/BIOMD0000000625/BIOMD0000000625_url.txt index ef25c639e..8dc3e402d 100644 --- a/doc/examples/biomodels/BIOMD0000000625_url.txt +++ b/doc/examples/biomodels/BIOMD0000000625/BIOMD0000000625_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Leber2016___Expanded_model_of_Tfh_Tfr_differentiation___Helicobacter_pylori_infection_1_1() // Compartments and Species: @@ -16,7 +16,7 @@ model *Leber2016___Expanded_model_of_Tfh_Tfr_differentiation___Helicobacter_pylo NaiveCD4_Death: NaiveCD4 => ; compartment_*NaiveCD4_Death_k1*NaiveCD4; nTreg_Source: => nTreg; compartment_*nTreg_Source_v; nTreg_Death: nTreg => ; compartment_*nTreg_Death_k1*nTreg; - Tfh_Differentiation: NaiveCD4 => Tfh; compartment_*(Tfh_Differentiation_gamma*NaiveCD4*Bcl6/(Tfh_Differentiation_alpha + IL10)); + Tfh_Differentiation: NaiveCD4 => Tfh; compartment_*(Tfh_Differentiation_gamma_*NaiveCD4*Bcl6/(Tfh_Differentiation_alpha + IL10)); Tfr_Differentiation: nTreg => Tfr; compartment_*(Tfr_Differentiation_gamma1*nTreg*Bcl6 + Tfr_Differentiation_gamma2*nTreg*CXCR5); Tfh_Death: Tfh => ; compartment_*Tfh_Death_k1*Tfh; Tfr_Death: Tfr => ; compartment_*Tfr_Death_k1*Tfr; @@ -81,7 +81,7 @@ model *Leber2016___Expanded_model_of_Tfh_Tfr_differentiation___Helicobacter_pylo nTreg_Source_v = 10; nTreg_Death_k1 = 0.03; Tfh_Differentiation_alpha = 0.1; - Tfh_Differentiation_gamma = 0.364318; + Tfh_Differentiation_gamma_ = 0.364318; Tfr_Differentiation_gamma1 = 0.0555708; Tfr_Differentiation_gamma2 = 0.111444; Tfh_Death_k1 = 0.03; diff --git a/doc/examples/biomodels/BIOMD0000000626_url.txt b/doc/examples/biomodels/BIOMD0000000626/BIOMD0000000626_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000626_url.txt rename to doc/examples/biomodels/BIOMD0000000626/BIOMD0000000626_url.txt index 2002d2fc6..b275e009d 100644 --- a/doc/examples/biomodels/BIOMD0000000626_url.txt +++ b/doc/examples/biomodels/BIOMD0000000626/BIOMD0000000626_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ray2013___Meiotic_initiation_in_S__cerevisiae() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000627_url.txt b/doc/examples/biomodels/BIOMD0000000627/BIOMD0000000627_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000627_url.txt rename to doc/examples/biomodels/BIOMD0000000627/BIOMD0000000627_url.txt index 725ae38ae..4da92c9e9 100644 --- a/doc/examples/biomodels/BIOMD0000000627_url.txt +++ b/doc/examples/biomodels/BIOMD0000000627/BIOMD0000000627_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Brain_Energy_Metabolism_with_PPP() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000628_url.txt b/doc/examples/biomodels/BIOMD0000000628/BIOMD0000000628_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000628_url.txt rename to doc/examples/biomodels/BIOMD0000000628/BIOMD0000000628_url.txt index 69490fc69..3df8791bd 100644 --- a/doc/examples/biomodels/BIOMD0000000628_url.txt +++ b/doc/examples/biomodels/BIOMD0000000628/BIOMD0000000628_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1703070000() // Compartments and Species: @@ -735,9 +735,9 @@ model *MODEL1703070000() reaction_197: => Ca; Spine*parameter_1; // Events: - event_1: at parameter_6 == 1: parameter_7 = time, parameter_1 = parameter_8; - event_2: at (parameter_6 == 1) && (time == (parameter_7 + parameter_9)): parameter_7 = 0, parameter_6 = 0, parameter_1 = 0; - event_3: at (time == ModelValue_128) || ((time == (ModelValue_128 + parameter_3/ModelValue_131)) && (time < (ModelValue_128 + ModelValue_130/ModelValue_131))): parameter_3 = parameter_3 + 1, parameter_6 = 1; + event_1: at parameter_6 == 1: parameter_1 = parameter_8, parameter_7 = time; + event_2: at (parameter_6 == 1) && (time == (parameter_7 + parameter_9)): parameter_1 = 0, parameter_6 = 0, parameter_7 = 0; + event_3: at (time == ModelValue_128) || ((time == (ModelValue_128 + parameter_3/ModelValue_131)) && (time < (ModelValue_128 + ModelValue_130/ModelValue_131))): parameter_6 = 1, parameter_3 = parameter_3 + 1; // Species initializations: CamR = 1.45e-09; diff --git a/doc/examples/biomodels/BIOMD0000000629_url.txt b/doc/examples/biomodels/BIOMD0000000629/BIOMD0000000629_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000629_url.txt rename to doc/examples/biomodels/BIOMD0000000629/BIOMD0000000629_url.txt index 676b6f626..08f0f1d0e 100644 --- a/doc/examples/biomodels/BIOMD0000000629_url.txt +++ b/doc/examples/biomodels/BIOMD0000000629/BIOMD0000000629_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Haffez2017_RAR_interaction_with_synthetic_analogues() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000630_url.txt b/doc/examples/biomodels/BIOMD0000000630/BIOMD0000000630_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000630_url.txt rename to doc/examples/biomodels/BIOMD0000000630/BIOMD0000000630_url.txt index a561a6a54..3192e5b11 100644 --- a/doc/examples/biomodels/BIOMD0000000630_url.txt +++ b/doc/examples/biomodels/BIOMD0000000630/BIOMD0000000630_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Venkatraman2011___PLS_UPA_behaviour_in_the_presence_of_substrate_competition_1_1_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000631_url.txt b/doc/examples/biomodels/BIOMD0000000631/BIOMD0000000631_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000631_url.txt rename to doc/examples/biomodels/BIOMD0000000631/BIOMD0000000631_url.txt index 77ccd6292..ea4dbba9f 100644 --- a/doc/examples/biomodels/BIOMD0000000631_url.txt +++ b/doc/examples/biomodels/BIOMD0000000631/BIOMD0000000631_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1601130000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000632_url.txt b/doc/examples/biomodels/BIOMD0000000632/BIOMD0000000632_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000632_url.txt rename to doc/examples/biomodels/BIOMD0000000632/BIOMD0000000632_url.txt index 3252fe08a..45e65a14e 100644 --- a/doc/examples/biomodels/BIOMD0000000632_url.txt +++ b/doc/examples/biomodels/BIOMD0000000632/BIOMD0000000632_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1505080000() // Compartments and Species: @@ -35,7 +35,7 @@ model *MODEL1505080000() va4: p53 => ; compartment_*k4a*p53; // Events: - DNADamage: at 0 after time > 0: DNADamageS = (1 - prop_C)*DNAdamagefoci_0, DNADamageC = prop_C*DNAdamagefoci_0, TAF = ModelValue_9_0 + k_TAF*Gy^(1/2); + DNADamage: at 0 after time > 0: TAF = ModelValue_9_0 + k_TAF*Gy^(1/2), DNADamageC = prop_C*DNAdamagefoci_0, DNADamageS = (1 - prop_C)*DNAdamagefoci_0; // Species initializations: CycE = CycE_0; diff --git a/doc/examples/biomodels/BIOMD0000000633_url.txt b/doc/examples/biomodels/BIOMD0000000633/BIOMD0000000633_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000633_url.txt rename to doc/examples/biomodels/BIOMD0000000633/BIOMD0000000633_url.txt index 8c5fc8c73..fa3dd9f17 100644 --- a/doc/examples/biomodels/BIOMD0000000633_url.txt +++ b/doc/examples/biomodels/BIOMD0000000633/BIOMD0000000633_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000633() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000634_url.txt b/doc/examples/biomodels/BIOMD0000000634/BIOMD0000000634_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000634_url.txt rename to doc/examples/biomodels/BIOMD0000000634/BIOMD0000000634_url.txt index 149664097..26f52e20f 100644 --- a/doc/examples/biomodels/BIOMD0000000634_url.txt +++ b/doc/examples/biomodels/BIOMD0000000634/BIOMD0000000634_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1704060000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000635_url.txt b/doc/examples/biomodels/BIOMD0000000635/BIOMD0000000635_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000635_url.txt rename to doc/examples/biomodels/BIOMD0000000635/BIOMD0000000635_url.txt index 3cfa3bd7a..4eb8ecb1c 100644 --- a/doc/examples/biomodels/BIOMD0000000635_url.txt +++ b/doc/examples/biomodels/BIOMD0000000635/BIOMD0000000635_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1502200000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000636_url.txt b/doc/examples/biomodels/BIOMD0000000636/BIOMD0000000636_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000636_url.txt rename to doc/examples/biomodels/BIOMD0000000636/BIOMD0000000636_url.txt index bcc474edc..d8b6d8bcf 100644 --- a/doc/examples/biomodels/BIOMD0000000636_url.txt +++ b/doc/examples/biomodels/BIOMD0000000636/BIOMD0000000636_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1502200001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000637_url.txt b/doc/examples/biomodels/BIOMD0000000637/BIOMD0000000637_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000637_url.txt rename to doc/examples/biomodels/BIOMD0000000637/BIOMD0000000637_url.txt index 1f3df2d09..72cd5692b 100644 --- a/doc/examples/biomodels/BIOMD0000000637_url.txt +++ b/doc/examples/biomodels/BIOMD0000000637/BIOMD0000000637_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1610220000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000638_url.txt b/doc/examples/biomodels/BIOMD0000000638/BIOMD0000000638_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000638_url.txt rename to doc/examples/biomodels/BIOMD0000000638/BIOMD0000000638_url.txt index 8c9cf35a1..0f150b823 100644 --- a/doc/examples/biomodels/BIOMD0000000638_url.txt +++ b/doc/examples/biomodels/BIOMD0000000638/BIOMD0000000638_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1610220001() // Compartments and Species: @@ -189,7 +189,7 @@ model *MODEL1610220001() unit length = metre; unit area = metre^2; unit volume = 1e-15 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = item; unit extent = substance; unit substance_per_volume = item / 1e-15 litre; diff --git a/doc/examples/biomodels/BIOMD0000000639_url.txt b/doc/examples/biomodels/BIOMD0000000639/BIOMD0000000639_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000639_url.txt rename to doc/examples/biomodels/BIOMD0000000639/BIOMD0000000639_url.txt index a640edc52..8bf4065ef 100644 --- a/doc/examples/biomodels/BIOMD0000000639_url.txt +++ b/doc/examples/biomodels/BIOMD0000000639/BIOMD0000000639_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1602280001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000640_url.txt b/doc/examples/biomodels/BIOMD0000000640/BIOMD0000000640_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000640_url.txt rename to doc/examples/biomodels/BIOMD0000000640/BIOMD0000000640_url.txt index 38b40e04e..914277576 100644 --- a/doc/examples/biomodels/BIOMD0000000640_url.txt +++ b/doc/examples/biomodels/BIOMD0000000640/BIOMD0000000640_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1702270000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000641_url.txt b/doc/examples/biomodels/BIOMD0000000641/BIOMD0000000641_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000641_url.txt rename to doc/examples/biomodels/BIOMD0000000641/BIOMD0000000641_url.txt index 1e3c224af..3f02d06ca 100644 --- a/doc/examples/biomodels/BIOMD0000000641_url.txt +++ b/doc/examples/biomodels/BIOMD0000000641/BIOMD0000000641_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *BIOMD0000000641() // Compartments and Species: @@ -65,7 +65,7 @@ model *BIOMD0000000641() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 3600 second; unit substance = 1e-3 mole; unit extent = substance; unit substance_per_volume = 1e-3 mole / 1e-3 litre; diff --git a/doc/examples/biomodels/BIOMD0000000642_url.txt b/doc/examples/biomodels/BIOMD0000000642/BIOMD0000000642_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000642_url.txt rename to doc/examples/biomodels/BIOMD0000000642/BIOMD0000000642_url.txt index 8a0571e5e..de0a567c2 100644 --- a/doc/examples/biomodels/BIOMD0000000642_url.txt +++ b/doc/examples/biomodels/BIOMD0000000642/BIOMD0000000642_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Mufudza2012___Estrogen_effect_on_the_dynamics_of_breast_cancer() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000643_url.txt b/doc/examples/biomodels/BIOMD0000000643/BIOMD0000000643_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000643_url.txt rename to doc/examples/biomodels/BIOMD0000000643/BIOMD0000000643_url.txt index 4c88fc0b8..456871419 100644 --- a/doc/examples/biomodels/BIOMD0000000643_url.txt +++ b/doc/examples/biomodels/BIOMD0000000643/BIOMD0000000643_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1707020000() // Compartments and Species: @@ -95,7 +95,7 @@ model *MODEL1707020000() unit length = metre; unit area = metre^2; unit volume = litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-6 mole; unit extent = substance; unit substance_per_volume = 1e-6 mole / litre; diff --git a/doc/examples/biomodels/BIOMD0000000644_url.txt b/doc/examples/biomodels/BIOMD0000000644/BIOMD0000000644_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000644_url.txt rename to doc/examples/biomodels/BIOMD0000000644/BIOMD0000000644_url.txt index 533688c52..3ebffabc0 100644 --- a/doc/examples/biomodels/BIOMD0000000644_url.txt +++ b/doc/examples/biomodels/BIOMD0000000644/BIOMD0000000644_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1707020001() // Compartments and Species: @@ -100,7 +100,7 @@ model *MODEL1707020001() unit length = metre; unit area = metre^2; unit volume = litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-6 mole; unit extent = substance; unit substance_per_volume = 1e-6 mole / litre; diff --git a/doc/examples/biomodels/BIOMD0000000645_url.txt b/doc/examples/biomodels/BIOMD0000000645/BIOMD0000000645_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000645_url.txt rename to doc/examples/biomodels/BIOMD0000000645/BIOMD0000000645_url.txt index 361efbbb0..cdf66ee68 100644 --- a/doc/examples/biomodels/BIOMD0000000645_url.txt +++ b/doc/examples/biomodels/BIOMD0000000645/BIOMD0000000645_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Switching_behaviour_of_PP2A_inhibition_by_ARPP_16___mutual_inhibitions_and_PKA_inhibits_MAST3_and_dominant_negative_effect() // Compartments and Species: @@ -101,7 +101,7 @@ model *Switching_behaviour_of_PP2A_inhibition_by_ARPP_16___mutual_inhibitions_an unit length = metre; unit area = metre^2; unit volume = litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-6 mole; unit extent = substance; unit substance_per_volume = 1e-6 mole / litre; diff --git a/doc/examples/biomodels/BIOMD0000000646_url.txt b/doc/examples/biomodels/BIOMD0000000646/BIOMD0000000646_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000646_url.txt rename to doc/examples/biomodels/BIOMD0000000646/BIOMD0000000646_url.txt index be693ac05..70d9d14a8 100644 --- a/doc/examples/biomodels/BIOMD0000000646_url.txt +++ b/doc/examples/biomodels/BIOMD0000000646/BIOMD0000000646_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1708240001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000647_url.txt b/doc/examples/biomodels/BIOMD0000000647/BIOMD0000000647_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000647_url.txt rename to doc/examples/biomodels/BIOMD0000000647/BIOMD0000000647_url.txt index e54946de2..58f59ce2f 100644 --- a/doc/examples/biomodels/BIOMD0000000647_url.txt +++ b/doc/examples/biomodels/BIOMD0000000647/BIOMD0000000647_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kwang2003___The_influence_of_RKIP_on_the_ERK_signaling_pathway() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000648_url.txt b/doc/examples/biomodels/BIOMD0000000648/BIOMD0000000648_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000648_url.txt rename to doc/examples/biomodels/BIOMD0000000648/BIOMD0000000648_url.txt index e41bd41a4..31a9dac94 100644 --- a/doc/examples/biomodels/BIOMD0000000648_url.txt +++ b/doc/examples/biomodels/BIOMD0000000648/BIOMD0000000648_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Padala2017__ERK__PI3K_Akt_and_Wnt_signalling_network__normal() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000650_url.txt b/doc/examples/biomodels/BIOMD0000000650/BIOMD0000000650_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000650_url.txt rename to doc/examples/biomodels/BIOMD0000000650/BIOMD0000000650_url.txt index 6470b85b8..14768395d 100644 --- a/doc/examples/biomodels/BIOMD0000000650_url.txt +++ b/doc/examples/biomodels/BIOMD0000000650/BIOMD0000000650_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1708250002() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000651_url.txt b/doc/examples/biomodels/BIOMD0000000651/BIOMD0000000651_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000651_url.txt rename to doc/examples/biomodels/BIOMD0000000651/BIOMD0000000651_url.txt index d126a573e..03ad42e3b 100644 --- a/doc/examples/biomodels/BIOMD0000000651_url.txt +++ b/doc/examples/biomodels/BIOMD0000000651/BIOMD0000000651_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Nguyen2016___Feedback_regulation_in_cell_signalling__Lessons_for_cancer_therapeutics() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000652_url.txt b/doc/examples/biomodels/BIOMD0000000652/BIOMD0000000652_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000652_url.txt rename to doc/examples/biomodels/BIOMD0000000652/BIOMD0000000652_url.txt index 1b02b7a04..7b1e7919e 100644 --- a/doc/examples/biomodels/BIOMD0000000652_url.txt +++ b/doc/examples/biomodels/BIOMD0000000652/BIOMD0000000652_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Padala2017__ERK__PI3K_Akt_and_Wnt_signalling_network__normal() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000653_url.txt b/doc/examples/biomodels/BIOMD0000000653/BIOMD0000000653_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000653_url.txt rename to doc/examples/biomodels/BIOMD0000000653/BIOMD0000000653_url.txt index 045922f22..d79132a0f 100644 --- a/doc/examples/biomodels/BIOMD0000000653_url.txt +++ b/doc/examples/biomodels/BIOMD0000000653/BIOMD0000000653_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Padala2017__ERK__PI3K_Akt_and_Wnt_signalling_network__normal() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000654_url.txt b/doc/examples/biomodels/BIOMD0000000654/BIOMD0000000654_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000654_url.txt rename to doc/examples/biomodels/BIOMD0000000654/BIOMD0000000654_url.txt index fbd9bda12..b832fb36f 100644 --- a/doc/examples/biomodels/BIOMD0000000654_url.txt +++ b/doc/examples/biomodels/BIOMD0000000654/BIOMD0000000654_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Padala2017__ERK__PI3K_Akt_and_Wnt_signalling_network__Ras_mutated() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000655_url.txt b/doc/examples/biomodels/BIOMD0000000655/BIOMD0000000655_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000655_url.txt rename to doc/examples/biomodels/BIOMD0000000655/BIOMD0000000655_url.txt index 738c83b2e..32a48cdba 100644 --- a/doc/examples/biomodels/BIOMD0000000655_url.txt +++ b/doc/examples/biomodels/BIOMD0000000655/BIOMD0000000655_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Padala2017__ERK__PI3K_Akt_and_Wnt_signalling_network__PTEN_mutation() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000656_url.txt b/doc/examples/biomodels/BIOMD0000000656/BIOMD0000000656_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000656_url.txt rename to doc/examples/biomodels/BIOMD0000000656/BIOMD0000000656_url.txt index 1d5354339..f7d3fe7fd 100644 --- a/doc/examples/biomodels/BIOMD0000000656_url.txt +++ b/doc/examples/biomodels/BIOMD0000000656/BIOMD0000000656_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Padala2017__ERK__PI3K_Akt_and_Wnt_signalling_network__EGFR_overexpression() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000657.txt b/doc/examples/biomodels/BIOMD0000000657/BIOMD0000000657.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000657.txt rename to doc/examples/biomodels/BIOMD0000000657/BIOMD0000000657.txt index 6213fd46a..0e1d687f2 100644 --- a/doc/examples/biomodels/BIOMD0000000657.txt +++ b/doc/examples/biomodels/BIOMD0000000657/BIOMD0000000657.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1710040001() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000658_url.txt b/doc/examples/biomodels/BIOMD0000000658/BIOMD0000000658_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000658_url.txt rename to doc/examples/biomodels/BIOMD0000000658/BIOMD0000000658_url.txt index 4fdbaf25a..cd809a8bc 100644 --- a/doc/examples/biomodels/BIOMD0000000658_url.txt +++ b/doc/examples/biomodels/BIOMD0000000658/BIOMD0000000658_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Lee2003___Roles_of_APC_and_Axin_in_Wnt_Pathway__without_regulatory_loop() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000659_url.txt b/doc/examples/biomodels/BIOMD0000000659/BIOMD0000000659_url.txt similarity index 97% rename from doc/examples/biomodels/BIOMD0000000659_url.txt rename to doc/examples/biomodels/BIOMD0000000659/BIOMD0000000659_url.txt index 8ec1ca79b..386cd59a2 100644 --- a/doc/examples/biomodels/BIOMD0000000659_url.txt +++ b/doc/examples/biomodels/BIOMD0000000659/BIOMD0000000659_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Cursons2015___Regulation_of_ERK_MAPK_signaling_in_human_epidermis() // Compartments and Species: @@ -24,9 +24,9 @@ model *Cursons2015___Regulation_of_ERK_MAPK_signaling_in_human_epidermis() pERK_nuc' = (1/numHillTau)*(((funcHillMEKToERKNuc - funcHillERKToERKNuc)*numHillMax - pERK_nuc - numERKCytoToNucParam*pERK_nuc) + numCytoToNucVolRatio*numERKNucToCytoParam*pERK_cyto); // Events: - Position_0: at 0 after numTissuePos >= 0: CaM_memb = numCaMInputBaseline + numCaMInputAmp*((numTissuePos + 1)/2), Ca = numCaInputBaseline + numCaInputAmp*(numTissuePos/5); + Position_0: at 0 after numTissuePos >= 0: Ca = numCaInputBaseline + numCaInputAmp*(numTissuePos/5), CaM_memb = numCaMInputBaseline + numCaMInputAmp*((numTissuePos + 1)/2); Position_1: at 0 after numTissuePos >= 1: CaM_memb = numCaMInputBaseline + numCaMInputAmp*exp(1 - numTissuePos); - Position_5: at 0 after numTissuePos >= 5: CaM_memb = 0, Ca = numCaInputBaseline + numCaInputAmp*((7 - numTissuePos)/2); + Position_5: at 0 after numTissuePos >= 5: Ca = numCaInputBaseline + numCaInputAmp*((7 - numTissuePos)/2), CaM_memb = 0; Total_Rafc_input_less_than_0: at 0 after (funcHillCaToRaf - funcHillCaMToRaf - funcHillERKToRaf) <= 0: numTotalRafInputs = 0; Total_Raf_input_greater_than_0: at 0 after (funcHillCaToRaf - funcHillCaMToRaf - funcHillERKToRaf) > 0: numTotalRafInputs = funcHillCaToRaf - funcHillCaMToRaf - funcHillERKToRaf; diff --git a/doc/examples/biomodels/BIOMD0000000660_url.txt b/doc/examples/biomodels/BIOMD0000000660/BIOMD0000000660_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000660_url.txt rename to doc/examples/biomodels/BIOMD0000000660/BIOMD0000000660_url.txt index 17d87a0e8..b57207b5a 100644 --- a/doc/examples/biomodels/BIOMD0000000660_url.txt +++ b/doc/examples/biomodels/BIOMD0000000660/BIOMD0000000660_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Barr2017___Dynamics_of_p21_in_hTert_RPE1_cells() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000661_url.txt b/doc/examples/biomodels/BIOMD0000000661/BIOMD0000000661_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000661_url.txt rename to doc/examples/biomodels/BIOMD0000000661/BIOMD0000000661_url.txt index a3c585fc9..c0c7de68b 100644 --- a/doc/examples/biomodels/BIOMD0000000661_url.txt +++ b/doc/examples/biomodels/BIOMD0000000661/BIOMD0000000661_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Webb2002_FasFasLsystem_Tumour() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000662_url.txt b/doc/examples/biomodels/BIOMD0000000662/BIOMD0000000662_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000662_url.txt rename to doc/examples/biomodels/BIOMD0000000662/BIOMD0000000662_url.txt index bb5e52fed..4d001b93c 100644 --- a/doc/examples/biomodels/BIOMD0000000662_url.txt +++ b/doc/examples/biomodels/BIOMD0000000662/BIOMD0000000662_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Moore2004_CML_TcellInteration() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000663_url.txt b/doc/examples/biomodels/BIOMD0000000663/BIOMD0000000663_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000663_url.txt rename to doc/examples/biomodels/BIOMD0000000663/BIOMD0000000663_url.txt index a5b4d8709..f312abe04 100644 --- a/doc/examples/biomodels/BIOMD0000000663_url.txt +++ b/doc/examples/biomodels/BIOMD0000000663/BIOMD0000000663_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000664_url.txt b/doc/examples/biomodels/BIOMD0000000664/BIOMD0000000664_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000664_url.txt rename to doc/examples/biomodels/BIOMD0000000664/BIOMD0000000664_url.txt index 879290faa..4c95d3da6 100644 --- a/doc/examples/biomodels/BIOMD0000000664_url.txt +++ b/doc/examples/biomodels/BIOMD0000000664/BIOMD0000000664_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Muller2008_MAPKactivation_Dynamics() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000665_url.txt b/doc/examples/biomodels/BIOMD0000000665/BIOMD0000000665_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000665_url.txt rename to doc/examples/biomodels/BIOMD0000000665/BIOMD0000000665_url.txt index 6c608801c..d891d7546 100644 --- a/doc/examples/biomodels/BIOMD0000000665_url.txt +++ b/doc/examples/biomodels/BIOMD0000000665/BIOMD0000000665_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Fallon2000_IL2dynamics() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000666_url.txt b/doc/examples/biomodels/BIOMD0000000666/BIOMD0000000666_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000666_url.txt rename to doc/examples/biomodels/BIOMD0000000666/BIOMD0000000666_url.txt index df9d521dc..5357a5897 100644 --- a/doc/examples/biomodels/BIOMD0000000666_url.txt +++ b/doc/examples/biomodels/BIOMD0000000666/BIOMD0000000666_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Pappalardo2016___PI3K_AKT_and_MAPK_Signaling_Pathways_in_Melanoma_Cancer() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000667_url.txt b/doc/examples/biomodels/BIOMD0000000667/BIOMD0000000667_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000667_url.txt rename to doc/examples/biomodels/BIOMD0000000667/BIOMD0000000667_url.txt index 275c0993a..22595b751 100644 --- a/doc/examples/biomodels/BIOMD0000000667_url.txt +++ b/doc/examples/biomodels/BIOMD0000000667/BIOMD0000000667_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hornberg2005_MAPKsignalling() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000668_url.txt b/doc/examples/biomodels/BIOMD0000000668/BIOMD0000000668_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000668_url.txt rename to doc/examples/biomodels/BIOMD0000000668/BIOMD0000000668_url.txt index c5b2a52eb..823e52fdf 100644 --- a/doc/examples/biomodels/BIOMD0000000668_url.txt +++ b/doc/examples/biomodels/BIOMD0000000668/BIOMD0000000668_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zhu2015___combined_gemcitabine_and_birinapant_in_pancreatic_cancer_cells___basic_PD_model() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000669_url.txt b/doc/examples/biomodels/BIOMD0000000669/BIOMD0000000669_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000669_url.txt rename to doc/examples/biomodels/BIOMD0000000669/BIOMD0000000669_url.txt index e54b180ec..87a7d20ed 100644 --- a/doc/examples/biomodels/BIOMD0000000669_url.txt +++ b/doc/examples/biomodels/BIOMD0000000669/BIOMD0000000669_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zhu2015___combined_gemcitabine_and_birinapant_in_pancreatic_cancer_cells___mechanistic_PD_model() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000670_url.txt b/doc/examples/biomodels/BIOMD0000000670/BIOMD0000000670_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000670_url.txt rename to doc/examples/biomodels/BIOMD0000000670/BIOMD0000000670_url.txt index ff8e9aa7c..07a083e41 100644 --- a/doc/examples/biomodels/BIOMD0000000670_url.txt +++ b/doc/examples/biomodels/BIOMD0000000670/BIOMD0000000670_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Owen1998___tumour_growth_model() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000671_url.txt b/doc/examples/biomodels/BIOMD0000000671/BIOMD0000000671_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000671_url.txt rename to doc/examples/biomodels/BIOMD0000000671/BIOMD0000000671_url.txt index f844f52a8..d91c780d5 100644 --- a/doc/examples/biomodels/BIOMD0000000671_url.txt +++ b/doc/examples/biomodels/BIOMD0000000671/BIOMD0000000671_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Murphy2016___Differences_in_predictions_of_ODE_models_of_tumor_growth() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000672_url.txt b/doc/examples/biomodels/BIOMD0000000672/BIOMD0000000672_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000672_url.txt rename to doc/examples/biomodels/BIOMD0000000672/BIOMD0000000672_url.txt index 2652959e8..565164107 100644 --- a/doc/examples/biomodels/BIOMD0000000672_url.txt +++ b/doc/examples/biomodels/BIOMD0000000672/BIOMD0000000672_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Brown1997___Plasma_Melatonin_Levels() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000673_url.txt b/doc/examples/biomodels/BIOMD0000000673/BIOMD0000000673_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000673_url.txt rename to doc/examples/biomodels/BIOMD0000000673/BIOMD0000000673_url.txt index e903fb08d..02f031396 100644 --- a/doc/examples/biomodels/BIOMD0000000673_url.txt +++ b/doc/examples/biomodels/BIOMD0000000673/BIOMD0000000673_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Lockwood2006___AlzheimersDisease_PBPK_model() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000674_url.txt b/doc/examples/biomodels/BIOMD0000000674/BIOMD0000000674_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000674_url.txt rename to doc/examples/biomodels/BIOMD0000000674/BIOMD0000000674_url.txt index 615d754e1..c7570d925 100644 --- a/doc/examples/biomodels/BIOMD0000000674_url.txt +++ b/doc/examples/biomodels/BIOMD0000000674/BIOMD0000000674_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Reyes_Palomares2012___a_combined_model_hepatic_polyamine_and_sulfur_aminoacid_metabolism___version1_1() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000675.txt b/doc/examples/biomodels/BIOMD0000000675/BIOMD0000000675.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000675.txt rename to doc/examples/biomodels/BIOMD0000000675/BIOMD0000000675.txt index 32f55d81d..f597c7960 100644 --- a/doc/examples/biomodels/BIOMD0000000675.txt +++ b/doc/examples/biomodels/BIOMD0000000675/BIOMD0000000675.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Chen2000_CellCycle() // Compartments and Species: @@ -46,8 +46,8 @@ model *Chen2000_CellCycle() // Events: Event_detection_for_END_M: at SPN >= 1: END_M = time; - Event_detection_for_Cell_Division_and_BUD_SPN_reset: at Clb2 < 0.3: SPN = 0, BUD = 0, mass = exp(-1*mu*D)*mass; - Event_detection_for_START_S: at ORI > 1: END_M = time + 1000, START_S = time; + Event_detection_for_Cell_Division_and_BUD_SPN_reset: at Clb2 < 0.3: mass = exp(-1*mu*D)*mass, BUD = 0, SPN = 0; + Event_detection_for_START_S: at ORI > 1: START_S = time, END_M = time + 1000; Event_detection_for_ORI_reset: at (Clb2 + Clb5) < 0.2: ORI = 0; // Species initializations: diff --git a/doc/examples/biomodels/BIOMD0000000676_url.txt b/doc/examples/biomodels/BIOMD0000000676/BIOMD0000000676_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000676_url.txt rename to doc/examples/biomodels/BIOMD0000000676/BIOMD0000000676_url.txt index 574d1e5d1..4a6100fa6 100644 --- a/doc/examples/biomodels/BIOMD0000000676_url.txt +++ b/doc/examples/biomodels/BIOMD0000000676/BIOMD0000000676_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Chen2006___Nitric_Oxide_Release_from_Endothelial_Cells() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000677_url.txt b/doc/examples/biomodels/BIOMD0000000677/BIOMD0000000677_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000677_url.txt rename to doc/examples/biomodels/BIOMD0000000677/BIOMD0000000677_url.txt index ee7951295..784265bc2 100644 --- a/doc/examples/biomodels/BIOMD0000000677_url.txt +++ b/doc/examples/biomodels/BIOMD0000000677/BIOMD0000000677_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Holmes2006___Muscle_Contraction() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000678_url.txt b/doc/examples/biomodels/BIOMD0000000678/BIOMD0000000678_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000678_url.txt rename to doc/examples/biomodels/BIOMD0000000678/BIOMD0000000678_url.txt index 526340f6b..56140c09d 100644 --- a/doc/examples/biomodels/BIOMD0000000678_url.txt +++ b/doc/examples/biomodels/BIOMD0000000678/BIOMD0000000678_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Tomida2003___NFAT_functions_Calcium_Oscillation() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000679_urn.txt b/doc/examples/biomodels/BIOMD0000000679/BIOMD0000000679_urn.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000679_urn.txt rename to doc/examples/biomodels/BIOMD0000000679/BIOMD0000000679_urn.txt index f3e3efca2..337708f84 100644 --- a/doc/examples/biomodels/BIOMD0000000679_urn.txt +++ b/doc/examples/biomodels/BIOMD0000000679/BIOMD0000000679_urn.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Waugh2006___Diabetic_Wound_Healing___Macrophage_Dynamics() // Compartments and Species: diff --git a/doc/examples/biomodels/Waugh2006_1.txt b/doc/examples/biomodels/BIOMD0000000679/Waugh2006_1.txt similarity index 99% rename from doc/examples/biomodels/Waugh2006_1.txt rename to doc/examples/biomodels/BIOMD0000000679/Waugh2006_1.txt index ae8ee39e7..afc4aac14 100644 --- a/doc/examples/biomodels/Waugh2006_1.txt +++ b/doc/examples/biomodels/BIOMD0000000679/Waugh2006_1.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Waugh2006___Diabetic_Wound_Healing___Macrophage_Dynamics() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000680_url.txt b/doc/examples/biomodels/BIOMD0000000680/BIOMD0000000680_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000680_url.txt rename to doc/examples/biomodels/BIOMD0000000680/BIOMD0000000680_url.txt index 5dec3a783..ed02739e1 100644 --- a/doc/examples/biomodels/BIOMD0000000680_url.txt +++ b/doc/examples/biomodels/BIOMD0000000680/BIOMD0000000680_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Waugh2006___Diabetic_Wound_Healing___TGF_B_Dynamics() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000681_url.txt b/doc/examples/biomodels/BIOMD0000000681/BIOMD0000000681_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000681_url.txt rename to doc/examples/biomodels/BIOMD0000000681/BIOMD0000000681_url.txt index 2b3b6527c..8e87c7544 100644 --- a/doc/examples/biomodels/BIOMD0000000681_url.txt +++ b/doc/examples/biomodels/BIOMD0000000681/BIOMD0000000681_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Waugh2006___Diabetic_Wound_Healing___Treated_and_Untreated_Macrophage_Dynamics() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000682_url.txt b/doc/examples/biomodels/BIOMD0000000682/BIOMD0000000682_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000682_url.txt rename to doc/examples/biomodels/BIOMD0000000682/BIOMD0000000682_url.txt index 287e16b7d..69defffff 100644 --- a/doc/examples/biomodels/BIOMD0000000682_url.txt +++ b/doc/examples/biomodels/BIOMD0000000682/BIOMD0000000682_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wierschem2004_PancreaticIslets_ActionPotentials() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000683.txt b/doc/examples/biomodels/BIOMD0000000683/BIOMD0000000683.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000683.txt rename to doc/examples/biomodels/BIOMD0000000683/BIOMD0000000683.txt index dd5f31b0e..a93095061 100644 --- a/doc/examples/biomodels/BIOMD0000000683.txt +++ b/doc/examples/biomodels/BIOMD0000000683/BIOMD0000000683.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wodarz1999_CTL_memory_response_HIV() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000683_urn.txt b/doc/examples/biomodels/BIOMD0000000683/BIOMD0000000683_urn.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000683_urn.txt rename to doc/examples/biomodels/BIOMD0000000683/BIOMD0000000683_urn.txt index 33b953207..89e75e379 100644 --- a/doc/examples/biomodels/BIOMD0000000683_urn.txt +++ b/doc/examples/biomodels/BIOMD0000000683/BIOMD0000000683_urn.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wodarz1999_CTL_memory_response_HIV() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000684_url.txt b/doc/examples/biomodels/BIOMD0000000684/BIOMD0000000684_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000684_url.txt rename to doc/examples/biomodels/BIOMD0000000684/BIOMD0000000684_url.txt index 760a8e694..131eb8ef1 100644 --- a/doc/examples/biomodels/BIOMD0000000684_url.txt +++ b/doc/examples/biomodels/BIOMD0000000684/BIOMD0000000684_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wodarz2003_ImmunologicalMemory() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000685_url.txt b/doc/examples/biomodels/BIOMD0000000685/BIOMD0000000685_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000685_url.txt rename to doc/examples/biomodels/BIOMD0000000685/BIOMD0000000685_url.txt index c0a1ce5f4..6a8a1de16 100644 --- a/doc/examples/biomodels/BIOMD0000000685_url.txt +++ b/doc/examples/biomodels/BIOMD0000000685/BIOMD0000000685_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wodarz2003_CTL_cross_priming() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000686_url.txt b/doc/examples/biomodels/BIOMD0000000686/BIOMD0000000686_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000686_url.txt rename to doc/examples/biomodels/BIOMD0000000686/BIOMD0000000686_url.txt index fb8ccb8b5..1a4cc799d 100644 --- a/doc/examples/biomodels/BIOMD0000000686_url.txt +++ b/doc/examples/biomodels/BIOMD0000000686/BIOMD0000000686_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wodarz2007_CTL_inflation_Model_A() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000687_url.txt b/doc/examples/biomodels/BIOMD0000000687/BIOMD0000000687_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000687_url.txt rename to doc/examples/biomodels/BIOMD0000000687/BIOMD0000000687_url.txt index cb6b6679d..1dac7101d 100644 --- a/doc/examples/biomodels/BIOMD0000000687_url.txt +++ b/doc/examples/biomodels/BIOMD0000000687/BIOMD0000000687_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wodarz2007_CTLinflation_ModelB() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000688_url.txt b/doc/examples/biomodels/BIOMD0000000688/BIOMD0000000688_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000688_url.txt rename to doc/examples/biomodels/BIOMD0000000688/BIOMD0000000688_url.txt index 4704f0803..21173cb68 100644 --- a/doc/examples/biomodels/BIOMD0000000688_url.txt +++ b/doc/examples/biomodels/BIOMD0000000688/BIOMD0000000688_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wodarz2007_CTL_inflation_Model_C() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000689_url.txt b/doc/examples/biomodels/BIOMD0000000689/BIOMD0000000689_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000689_url.txt rename to doc/examples/biomodels/BIOMD0000000689/BIOMD0000000689_url.txt index 8b6556ed1..0b644c294 100644 --- a/doc/examples/biomodels/BIOMD0000000689_url.txt +++ b/doc/examples/biomodels/BIOMD0000000689/BIOMD0000000689_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Thiaville2016___Folate_pathway_model_with_induced_PanB_reaction() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000690_url.txt b/doc/examples/biomodels/BIOMD0000000690/BIOMD0000000690_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000690_url.txt rename to doc/examples/biomodels/BIOMD0000000690/BIOMD0000000690_url.txt index 077542f03..e52d19ead 100644 --- a/doc/examples/biomodels/BIOMD0000000690_url.txt +++ b/doc/examples/biomodels/BIOMD0000000690/BIOMD0000000690_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Thiaville2016___Folate_pathway_model_with_induced_PanB_reaction_and_folate_pathway() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000691_url.txt b/doc/examples/biomodels/BIOMD0000000691/BIOMD0000000691_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000691_url.txt rename to doc/examples/biomodels/BIOMD0000000691/BIOMD0000000691_url.txt index fcb70a63f..0038edbd8 100644 --- a/doc/examples/biomodels/BIOMD0000000691_url.txt +++ b/doc/examples/biomodels/BIOMD0000000691/BIOMD0000000691_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wolf2000___Cellular_interaction_on_glycolytic_oscillations_in_yeast() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000692_url.txt b/doc/examples/biomodels/BIOMD0000000692/BIOMD0000000692_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000692_url.txt rename to doc/examples/biomodels/BIOMD0000000692/BIOMD0000000692_url.txt index 4a67dff48..c38c527d3 100644 --- a/doc/examples/biomodels/BIOMD0000000692_url.txt +++ b/doc/examples/biomodels/BIOMD0000000692/BIOMD0000000692_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Phillips2003___The_Mechanism_of_Ras_GTPase_Activation_by_Neurofibromin() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000693_url.txt b/doc/examples/biomodels/BIOMD0000000693/BIOMD0000000693_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000693_url.txt rename to doc/examples/biomodels/BIOMD0000000693/BIOMD0000000693_url.txt index 90a1d6d04..5fef9df50 100644 --- a/doc/examples/biomodels/BIOMD0000000693_url.txt +++ b/doc/examples/biomodels/BIOMD0000000693/BIOMD0000000693_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wang2008___Mimicking_the_inhibitory_effect_of_riluzole_on_membrane_conductance_in_skeletal_fibres() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000695_url.txt b/doc/examples/biomodels/BIOMD0000000695/BIOMD0000000695_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000695_url.txt rename to doc/examples/biomodels/BIOMD0000000695/BIOMD0000000695_url.txt index 11914c887..9f2eaa44f 100644 --- a/doc/examples/biomodels/BIOMD0000000695_url.txt +++ b/doc/examples/biomodels/BIOMD0000000695/BIOMD0000000695_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *FelixGarza2017___Blue_Light_Treatment_of_Psoriasis__simplified() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000696_url.txt b/doc/examples/biomodels/BIOMD0000000696/BIOMD0000000696_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000696_url.txt rename to doc/examples/biomodels/BIOMD0000000696/BIOMD0000000696_url.txt index 4a50a4809..bc673170f 100644 --- a/doc/examples/biomodels/BIOMD0000000696_url.txt +++ b/doc/examples/biomodels/BIOMD0000000696/BIOMD0000000696_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Boada2016___Incoherent_type_1_feed_forward_loop__I1_FFL() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000697_url.txt b/doc/examples/biomodels/BIOMD0000000697/BIOMD0000000697_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000697_url.txt rename to doc/examples/biomodels/BIOMD0000000697/BIOMD0000000697_url.txt index f73c069a8..1ced1bed2 100644 --- a/doc/examples/biomodels/BIOMD0000000697_url.txt +++ b/doc/examples/biomodels/BIOMD0000000697/BIOMD0000000697_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Cell_Cyle_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000698_url.txt b/doc/examples/biomodels/BIOMD0000000698/BIOMD0000000698_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000698_url.txt rename to doc/examples/biomodels/BIOMD0000000698/BIOMD0000000698_url.txt index f5efd8bc0..7d059f18f 100644 --- a/doc/examples/biomodels/BIOMD0000000698_url.txt +++ b/doc/examples/biomodels/BIOMD0000000698/BIOMD0000000698_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Reed2004___Methionine_Cycle() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000699_url.txt b/doc/examples/biomodels/BIOMD0000000699/BIOMD0000000699_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000699_url.txt rename to doc/examples/biomodels/BIOMD0000000699/BIOMD0000000699_url.txt index cd78bfb94..06c7e08f0 100644 --- a/doc/examples/biomodels/BIOMD0000000699_url.txt +++ b/doc/examples/biomodels/BIOMD0000000699/BIOMD0000000699_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Caydasi2012___Inhibition_of_Tem1_by_the_GAP_complex_in_Spindle_Position_Checkpoint() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000700_url.txt b/doc/examples/biomodels/BIOMD0000000700/BIOMD0000000700_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000700_url.txt rename to doc/examples/biomodels/BIOMD0000000700/BIOMD0000000700_url.txt index 58f929481..08da73d79 100644 --- a/doc/examples/biomodels/BIOMD0000000700_url.txt +++ b/doc/examples/biomodels/BIOMD0000000700/BIOMD0000000700_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Heldt2018___Proliferation_quiescence_decision_pormoted_by_p21_in_response_to_DNA_damage() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1202090001_FINAL.txt b/doc/examples/biomodels/BIOMD0000000701/MODEL1202090001_FINAL.txt similarity index 99% rename from doc/examples/biomodels/MODEL1202090001_FINAL.txt rename to doc/examples/biomodels/BIOMD0000000701/MODEL1202090001_FINAL.txt index 4f29310f6..643d5872b 100644 --- a/doc/examples/biomodels/MODEL1202090001_FINAL.txt +++ b/doc/examples/biomodels/BIOMD0000000701/MODEL1202090001_FINAL.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Caydasi2012___Inhibition_of_Tem1_by_the_GAP_complex_in_Spindle_Position_Checkpoint() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1202090001_url.txt b/doc/examples/biomodels/BIOMD0000000701/MODEL1202090001_url.txt similarity index 99% rename from doc/examples/biomodels/MODEL1202090001_url.txt rename to doc/examples/biomodels/BIOMD0000000701/MODEL1202090001_url.txt index 3c3d54347..fae5990da 100644 --- a/doc/examples/biomodels/MODEL1202090001_url.txt +++ b/doc/examples/biomodels/BIOMD0000000701/MODEL1202090001_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *hotspotassociation() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000702_url.txt b/doc/examples/biomodels/BIOMD0000000702/BIOMD0000000702_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000702_url.txt rename to doc/examples/biomodels/BIOMD0000000702/BIOMD0000000702_url.txt index b5a9c0cff..1793a2265 100644 --- a/doc/examples/biomodels/BIOMD0000000702_url.txt +++ b/doc/examples/biomodels/BIOMD0000000702/BIOMD0000000702_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Caydasi2012___Inhibition_of_Tem1_by_the_GAP_complex_in_Spindle_Position_Checkpoint() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000703_url.txt b/doc/examples/biomodels/BIOMD0000000703/BIOMD0000000703_url.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000703_url.txt rename to doc/examples/biomodels/BIOMD0000000703/BIOMD0000000703_url.txt index 408cd4a8f..e5388766b 100644 --- a/doc/examples/biomodels/BIOMD0000000703_url.txt +++ b/doc/examples/biomodels/BIOMD0000000703/BIOMD0000000703_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Diedrichs2018___A_data_entrained_computational_model_for_testing_the_regulatory_logic_of_the_vertebrate_unfolded_protein_response() // Compartments and Species: @@ -21,7 +21,7 @@ model *Diedrichs2018___A_data_entrained_computational_model_for_testing_the_regu A6_degr: A6 => ; ER*kdA6*A6; A6_syn: => A6; ER*(kdA6*A6_star + A6_syn_kcl*(U - U_star)*((A6tot_norm - A6)/(1 + B/KBA6))); U_degr: U => ; ER*(U_degr_delta*(U/(1 + U_degr_KII*(Ip - Ip_star)))*B); - A4_syn: => A4; ER*(kdA4*A4_star + A4_syn_gamma*(U - U_star)*Ep); + A4_syn: => A4; ER*(kdA4*A4_star + A4_syn_gamma_*(U - U_star)*Ep); A4_degr: A4 => ; ER*kdA4*A4; c_syn: => c; ER*(kdc*c_star + c_syn_muA4*(1 + c_syn_Kc4*A6)*((A4 - A4_star)^c_syn_n/((A4 - A4_star)^c_syn_n + c_syn_KA4c^c_syn_n*(1 + c_syn_Kth4c*A6)^c_syn_n))); c_degr: c => ; ER*kdc*c; @@ -147,7 +147,7 @@ model *Diedrichs2018___A_data_entrained_computational_model_for_testing_the_regu A6_syn_kcl = 4; U_degr_KII = 0.01; U_degr_delta = 1.5; - A4_syn_gamma = 0.001; + A4_syn_gamma_ = 0.001; c_syn_KA4c = 2; c_syn_Kc4 = 0.56; c_syn_Kth4c = 0.25; diff --git a/doc/examples/biomodels/BIOMD0000000704_url.txt b/doc/examples/biomodels/BIOMD0000000704/BIOMD0000000704_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000704_url.txt rename to doc/examples/biomodels/BIOMD0000000704/BIOMD0000000704_url.txt index 40de58645..813fe2dbd 100644 --- a/doc/examples/biomodels/BIOMD0000000704_url.txt +++ b/doc/examples/biomodels/BIOMD0000000704/BIOMD0000000704_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Aguda1999___G2_DNA_damage_checkpoint() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000705_url.txt b/doc/examples/biomodels/BIOMD0000000705/BIOMD0000000705_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000705_url.txt rename to doc/examples/biomodels/BIOMD0000000705/BIOMD0000000705_url.txt index 8e88a1bee..f01c84407 100644 --- a/doc/examples/biomodels/BIOMD0000000705_url.txt +++ b/doc/examples/biomodels/BIOMD0000000705/BIOMD0000000705_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Smith2010___Response_of_FOXO_Transcription_Factors_to_Post_Translational_Modifications_Made_by_Ageing_Related_Signalling_Pathways() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000706_url.txt b/doc/examples/biomodels/BIOMD0000000706/BIOMD0000000706_url.txt similarity index 99% rename from doc/examples/biomodels/BIOMD0000000706_url.txt rename to doc/examples/biomodels/BIOMD0000000706/BIOMD0000000706_url.txt index 077627d8b..f004863e9 100644 --- a/doc/examples/biomodels/BIOMD0000000706_url.txt +++ b/doc/examples/biomodels/BIOMD0000000706/BIOMD0000000706_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Smith2010___Response_of_FOXO_Transcription_Factors_to_Post_Translational_Modifications_Made_by_Ageing_Related_Signalling_Pathways() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1006230047.txt b/doc/examples/biomodels/BIOMD0000000707/MODEL1006230047.txt similarity index 99% rename from doc/examples/biomodels/MODEL1006230047.txt rename to doc/examples/biomodels/BIOMD0000000707/MODEL1006230047.txt index e8aebed16..5ea1cf4a9 100644 --- a/doc/examples/biomodels/MODEL1006230047.txt +++ b/doc/examples/biomodels/BIOMD0000000707/MODEL1006230047.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Liu2017 - Dynamics of Avian Influenza with Logistic Growth.txt b/doc/examples/biomodels/BIOMD0000000708/Liu2017 - Dynamics of Avian Influenza with Logistic Growth.txt similarity index 99% rename from doc/examples/biomodels/Liu2017 - Dynamics of Avian Influenza with Logistic Growth.txt rename to doc/examples/biomodels/BIOMD0000000708/Liu2017 - Dynamics of Avian Influenza with Logistic Growth.txt index 08935bd2d..7baa2cc05 100644 --- a/doc/examples/biomodels/Liu2017 - Dynamics of Avian Influenza with Logistic Growth.txt +++ b/doc/examples/biomodels/BIOMD0000000708/Liu2017 - Dynamics of Avian Influenza with Logistic Growth.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Liu2017___Dynamics_of_Avian_Influenza_with_Logistic_Growth() // Compartments and Species: diff --git a/doc/examples/biomodels/Liu2017 - Dynamics of Avian Influenza with Allee Growth Effect.txt b/doc/examples/biomodels/BIOMD0000000709/Liu2017 - Dynamics of Avian Influenza with Allee Growth Effect.txt similarity index 99% rename from doc/examples/biomodels/Liu2017 - Dynamics of Avian Influenza with Allee Growth Effect.txt rename to doc/examples/biomodels/BIOMD0000000709/Liu2017 - Dynamics of Avian Influenza with Allee Growth Effect.txt index b8cd6b62c..1db431859 100644 --- a/doc/examples/biomodels/Liu2017 - Dynamics of Avian Influenza with Allee Growth Effect.txt +++ b/doc/examples/biomodels/BIOMD0000000709/Liu2017 - Dynamics of Avian Influenza with Allee Growth Effect.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Liu2017___Dynamics_of_Avian_Influenza_with_Allee_Growth_Effect() // Compartments and Species: diff --git a/doc/examples/biomodels/Hernandez-Vargas2012 - Innate immune system dynamics to Influenza virus.txt b/doc/examples/biomodels/BIOMD0000000710/Hernandez-Vargas2012 - Innate immune system dynamics to Influenza virus.txt similarity index 99% rename from doc/examples/biomodels/Hernandez-Vargas2012 - Innate immune system dynamics to Influenza virus.txt rename to doc/examples/biomodels/BIOMD0000000710/Hernandez-Vargas2012 - Innate immune system dynamics to Influenza virus.txt index 558ca019a..7ebbc7699 100644 --- a/doc/examples/biomodels/Hernandez-Vargas2012 - Innate immune system dynamics to Influenza virus.txt +++ b/doc/examples/biomodels/BIOMD0000000710/Hernandez-Vargas2012 - Innate immune system dynamics to Influenza virus.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hernandez_Vargas2012___Innate_Immune_System_ynamics_to_Influenza_virus() // Compartments and Species: diff --git a/doc/examples/biomodels/Hancioglu2007 - Human Immune Response to Influenza A virus.txt b/doc/examples/biomodels/BIOMD0000000711/Hancioglu2007 - Human Immune Response to Influenza A virus.txt similarity index 99% rename from doc/examples/biomodels/Hancioglu2007 - Human Immune Response to Influenza A virus.txt rename to doc/examples/biomodels/BIOMD0000000711/Hancioglu2007 - Human Immune Response to Influenza A virus.txt index 5e648acb8..6dca44a3c 100644 --- a/doc/examples/biomodels/Hancioglu2007 - Human Immune Response to Influenza A virus.txt +++ b/doc/examples/biomodels/BIOMD0000000711/Hancioglu2007 - Human Immune Response to Influenza A virus.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hancioglu2007___Human_Immune_Response_to_Influenza_A_virus_Infection() // Compartments and Species: diff --git a/doc/examples/biomodels/Jena5258.txt b/doc/examples/biomodels/BIOMD0000000712/Jena5258.txt similarity index 98% rename from doc/examples/biomodels/Jena5258.txt rename to doc/examples/biomodels/BIOMD0000000712/Jena5258.txt index 7f438bbf5..c4c3c7219 100644 --- a/doc/examples/biomodels/Jena5258.txt +++ b/doc/examples/biomodels/BIOMD0000000712/Jena5258.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/PVR.txt b/doc/examples/biomodels/BIOMD0000000713/PVR.txt similarity index 98% rename from doc/examples/biomodels/PVR.txt rename to doc/examples/biomodels/BIOMD0000000713/PVR.txt index a9f7a2a5d..885c83559 100644 --- a/doc/examples/biomodels/PVR.txt +++ b/doc/examples/biomodels/BIOMD0000000713/PVR.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/HealthyOutcome.txt b/doc/examples/biomodels/BIOMD0000000714/HealthyOutcome.txt similarity index 99% rename from doc/examples/biomodels/HealthyOutcome.txt rename to doc/examples/biomodels/BIOMD0000000714/HealthyOutcome.txt index 24d4b3a7b..66b85e29c 100644 --- a/doc/examples/biomodels/HealthyOutcome.txt +++ b/doc/examples/biomodels/BIOMD0000000714/HealthyOutcome.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Reynolds2006___Reduced_model_of_the_acute_inflammatory_response() // Compartments and Species: diff --git a/doc/examples/biomodels/Epidemic Model with the impact of Media Reactions.txt b/doc/examples/biomodels/BIOMD0000000715/Epidemic Model with the impact of Media Reactions.txt similarity index 99% rename from doc/examples/biomodels/Epidemic Model with the impact of Media Reactions.txt rename to doc/examples/biomodels/BIOMD0000000715/Epidemic Model with the impact of Media Reactions.txt index 9dd9fe218..678ee7924 100644 --- a/doc/examples/biomodels/Epidemic Model with the impact of Media Reactions.txt +++ b/doc/examples/biomodels/BIOMD0000000715/Epidemic Model with the impact of Media Reactions.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/BI reactions.txt b/doc/examples/biomodels/BIOMD0000000716/BI reactions.txt similarity index 99% rename from doc/examples/biomodels/BI reactions.txt rename to doc/examples/biomodels/BIOMD0000000716/BI reactions.txt index a20dc9fcb..0cf34b386 100644 --- a/doc/examples/biomodels/BI reactions.txt +++ b/doc/examples/biomodels/BIOMD0000000716/BI reactions.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/HSI reactions.txt b/doc/examples/biomodels/BIOMD0000000717/HSI reactions.txt similarity index 99% rename from doc/examples/biomodels/HSI reactions.txt rename to doc/examples/biomodels/BIOMD0000000717/HSI reactions.txt index fc2d565a7..71d3a07ff 100644 --- a/doc/examples/biomodels/HSI reactions.txt +++ b/doc/examples/biomodels/BIOMD0000000717/HSI reactions.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Li2008.txt b/doc/examples/biomodels/BIOMD0000000718/Li2008.txt similarity index 99% rename from doc/examples/biomodels/Li2008.txt rename to doc/examples/biomodels/BIOMD0000000718/Li2008.txt index 904384cac..46ef7ec9c 100644 --- a/doc/examples/biomodels/Li2008.txt +++ b/doc/examples/biomodels/BIOMD0000000718/Li2008.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Li2008___Caulobacter_Cell_Cycle() // Compartments and Species: diff --git a/doc/examples/biomodels/Tsai2014.txt b/doc/examples/biomodels/BIOMD0000000719/Tsai2014.txt similarity index 99% rename from doc/examples/biomodels/Tsai2014.txt rename to doc/examples/biomodels/BIOMD0000000719/Tsai2014.txt index 26bfa9ed4..8aadae67b 100644 --- a/doc/examples/biomodels/Tsai2014.txt +++ b/doc/examples/biomodels/BIOMD0000000719/Tsai2014.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Tsai2014___Cell_cycle_duration_control_by_oscillatory_Dynamics__in_Early_Xenopus_laevis_Embryos() // Compartments and Species: diff --git a/doc/examples/biomodels/Yan2012.txt b/doc/examples/biomodels/BIOMD0000000720/Yan2012.txt similarity index 99% rename from doc/examples/biomodels/Yan2012.txt rename to doc/examples/biomodels/BIOMD0000000720/Yan2012.txt index f1f762173..e8342672d 100644 --- a/doc/examples/biomodels/Yan2012.txt +++ b/doc/examples/biomodels/BIOMD0000000720/Yan2012.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Yan2014___Rb_E2F_pathway_dynamics_with_miR449() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000721/Model.txt b/doc/examples/biomodels/BIOMD0000000721/Model.txt new file mode 100644 index 000000000..540d4a38e --- /dev/null +++ b/doc/examples/biomodels/BIOMD0000000721/Model.txt @@ -0,0 +1,117 @@ +// Created by libAntimony v3.2.0 +model *New_Model() + + // Compartments and Species: + compartment Bone; + species Osteocytes__S in Bone, Pre_Osteoblasts__P in Bone, Osteoblasts__B in Bone; + species Osteoclasts__C in Bone, Bone_volume__z in Bone; + + // Reactions: + Differentiation_of_Osteoblast_to_Osteocytes: Osteoblasts__B => Osteocytes__S; Bone*(alpha_1*Osteoblasts__B^g_31*(1 - Osteocytes__S/K_S)); + Differentiation_of_MSC_cells_to_Pre_Osteoblast_cells: => Pre_Osteoblasts__P; Bone*(alpha_2*Osteocytes__S^g_21*(1 - Osteocytes__S/K_S)*g_22); + Proliferation_of_pre_osteoblasts: => Pre_Osteoblasts__P; Bone*(alpha_3*Pre_Osteoblasts__P^g_32*(1 - Osteocytes__S/K_S)); + Differentiation_of_Pre_Osteoblast_to_mature_osteoblast: Pre_Osteoblasts__P => Osteoblasts__B; Bone*(beta_1*Pre_Osteoblasts__P^f_12*Osteoclasts__C^f_14); + Apoptosis_of_pre_osteoblast: Pre_Osteoblasts__P => ; Bone*delta*Pre_Osteoblasts__P; + Apoptosis_of_osteoblasts: Osteoblasts__B => ; Bone*(beta_2*Osteoblasts__B^f_23); + Differentiation_of_pre_osteoclast_to_osteoclasts: => Osteoclasts__C; Bone*(alpha_4*Osteocytes__S^g_41*Pre_Osteoblasts__P^g_42*(epsilon + Osteoblasts__B)^g_43*(1 - Osteocytes__S/K_S)^g_44); + Apoptosis_of_osteoclasts: Osteoclasts__C => ; Bone*(beta_3*Osteoclasts__C^f_34); + Resorption_of_bone: Bone_volume__z => ; Bone*(k1*Osteoclasts__C); + Formation_of_bone: => Bone_volume__z; Bone*(k2*Osteoblasts__B); + + // Species initializations: + Osteocytes__S = K_S - rho; + Pre_Osteoblasts__P = 0; + Osteoblasts__B = 0; + Osteoclasts__C = 0; + Bone_volume__z = 100; + + // Compartment initializations: + Bone = 1; + + // Variable initializations: + K_S = 200; + rho = 20; + alpha_1 = 0.5; + alpha_2 = 0.1; + alpha_3 = 0.1; + beta_1 = 0.1; + delta = 0.1; + beta_2 = 0.1; + alpha_4 = 0.1; + k1 = 0.7; + k2 = 0.015445; + g_31 = 1; + g_21 = 2; + g_22 = 1; + g_32 = 1; + g_41 = 1; + g_42 = 1; + g_43 = -1; + g_44 = 1; + f_12 = 1; + f_14 = 1; + f_23 = 1; + f_34 = 1; + epsilon = 1; + beta_3 = 0.1; + + // Other declarations: + const Bone, K_S, rho, alpha_1, alpha_2, alpha_3, beta_1, delta, beta_2; + const alpha_4, k1, k2, g_31, g_21, g_22, g_32, g_41, g_42, g_43, g_44, f_12; + const f_14, f_23, f_34, epsilon, beta_3; + + // Unit definitions: + unit volume = 1e-3 litre; + unit time_unit = 86400 second; + unit substance = 1e-3 mole; + + // Display Names: + time_unit is "time"; + Osteocytes__S is "Osteocytes (S)"; + Pre_Osteoblasts__P is "Pre-Osteoblasts (P)"; + Osteoblasts__B is "Osteoblasts (B)"; + Osteoclasts__C is "Osteoclasts (C)"; + Bone_volume__z is "Bone volume (z)"; + Differentiation_of_Osteoblast_to_Osteocytes is "Differentiation of Osteoblast to Osteocytes"; + Differentiation_of_MSC_cells_to_Pre_Osteoblast_cells is "Differentiation of MSC cells to Pre-Osteoblast cells"; + Proliferation_of_pre_osteoblasts is "Proliferation of pre-osteoblasts"; + Differentiation_of_Pre_Osteoblast_to_mature_osteoblast is "Differentiation of Pre-Osteoblast to mature osteoblast"; + Apoptosis_of_pre_osteoblast is "Apoptosis of pre-osteoblast"; + Apoptosis_of_osteoblasts is "Apoptosis of osteoblasts"; + Differentiation_of_pre_osteoclast_to_osteoclasts is "Differentiation of pre-osteoclast to osteoclasts"; + Apoptosis_of_osteoclasts is "Apoptosis of osteoclasts"; + Resorption_of_bone is "Resorption of bone"; + Formation_of_bone is "Formation of bone"; + + // CV terms: + Bone hasProperty "http://identifiers.org/bto/BTO:0000140" + Osteocytes__S identity "http://identifiers.org/bto/BTO:0002038" + Pre_Osteoblasts__P isVersionOf "http://identifiers.org/bto/BTO:0001593" + Osteoblasts__B identity "http://identifiers.org/bto/BTO:0001593" + Osteoclasts__C identity "http://identifiers.org/bto/BTO:0000968" + Differentiation_of_Osteoblast_to_Osteocytes isVersionOf "http://identifiers.org/omit/0003784" + Differentiation_of_MSC_cells_to_Pre_Osteoblast_cells isVersionOf "http://identifiers.org/omit/0003784" + Proliferation_of_pre_osteoblasts isVersionOf "http://identifiers.org/go/GO:0033687" + Differentiation_of_Pre_Osteoblast_to_mature_osteoblast isVersionOf "http://identifiers.org/omit/0003784" + Apoptosis_of_pre_osteoblast isVersionOf "http://identifiers.org/ncit/C17557" + Apoptosis_of_osteoblasts isVersionOf "http://identifiers.org/ncit/C17557" + Differentiation_of_pre_osteoclast_to_osteoclasts isVersionOf "http://identifiers.org/omit/0003784" + Apoptosis_of_osteoclasts isVersionOf "http://identifiers.org/ncit/C17557" + Resorption_of_bone isVersionOf "http://identifiers.org/omit/0003220" + Formation_of_bone isVersionOf "http://identifiers.org/ncit/C53954" + + model model_source "http://identifiers.org/biomodels.db/MODEL1811150001", + "http://identifiers.org/biomodels.db/BIOMD0000000721" + model hasProperty "http://identifiers.org/mamo/MAMO_0000046" + model hasProperty "http://identifiers.org/go/GO:0046849" + model hasTaxon "http://identifiers.org/taxonomy/9606" + model isDescribedBy "http://identifiers.org/pubmed/23717504" + model created "2018-11-14T09:09:52Z" + model modified "2018-11-14T09:09:52Z" + model creator1.givenName "Sarubini" + model creator1.familyName "Kananathan" + model creator1.organization "EMBL-EBI" + model creator1.email "sarubini.kananathan@hotmail.co.uk" +end + +New_Model is "Graham2013 - Role of osteocytes in targeted bone remodeling" diff --git a/doc/examples/biomodels/Wound Healing with Normal health condition.txt b/doc/examples/biomodels/BIOMD0000000722/Wound Healing with Normal health condition.txt similarity index 99% rename from doc/examples/biomodels/Wound Healing with Normal health condition.txt rename to doc/examples/biomodels/BIOMD0000000722/Wound Healing with Normal health condition.txt index ed57d057f..6a8ad02ef 100644 --- a/doc/examples/biomodels/Wound Healing with Normal health condition.txt +++ b/doc/examples/biomodels/BIOMD0000000722/Wound Healing with Normal health condition.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Weis2014.txt b/doc/examples/biomodels/BIOMD0000000723/Weis2014.txt similarity index 99% rename from doc/examples/biomodels/Weis2014.txt rename to doc/examples/biomodels/BIOMD0000000723/Weis2014.txt index 7330ef4e1..9cba78965 100644 --- a/doc/examples/biomodels/Weis2014.txt +++ b/doc/examples/biomodels/BIOMD0000000723/Weis2014.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Weis2014___Data_driven_Mammalian_Cell_Cycle_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Theinmozhi_2018.txt b/doc/examples/biomodels/BIOMD0000000724/Theinmozhi_2018.txt similarity index 99% rename from doc/examples/biomodels/Theinmozhi_2018.txt rename to doc/examples/biomodels/BIOMD0000000724/Theinmozhi_2018.txt index 7195f33a5..380b4a5d1 100644 --- a/doc/examples/biomodels/Theinmozhi_2018.txt +++ b/doc/examples/biomodels/BIOMD0000000724/Theinmozhi_2018.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *_30356330_Theinmozhi_PDL1_TCR_regulation() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1511020000_urn.txt b/doc/examples/biomodels/BIOMD0000000725/MODEL1511020000_urn.txt similarity index 99% rename from doc/examples/biomodels/MODEL1511020000_urn.txt rename to doc/examples/biomodels/BIOMD0000000725/MODEL1511020000_urn.txt index f06b52c52..fe406b13d 100644 --- a/doc/examples/biomodels/MODEL1511020000_urn.txt +++ b/doc/examples/biomodels/BIOMD0000000725/MODEL1511020000_urn.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1511020000() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000725/Model.txt b/doc/examples/biomodels/BIOMD0000000725/Model.txt new file mode 100644 index 000000000..6f0109b15 --- /dev/null +++ b/doc/examples/biomodels/BIOMD0000000725/Model.txt @@ -0,0 +1,404 @@ +// Created by libAntimony v3.2.0 +model *Salcedo_Sora2016___Microbial_folate_biosynthesis_and_utilisation() + + // Compartments and Species: + compartment compartment_; + species DAHP in compartment_, $PEP in compartment_, Pi in compartment_; + species DHQ in compartment_, $EP in compartment_, DHSK in compartment_; + species SK in compartment_, SKP in compartment_, CVPSK in compartment_; + species CM in compartment_, $Gln in compartment_, Glu in compartment_, ADC in compartment_; + species Pyr in compartment_, pABA in compartment_, DHNTP in compartment_; + species $GTP in compartment_, AHMDHP in compartment_, HAD in compartment_; + species PTHP in compartment_, AHMDPP in compartment_, DHP in compartment_; + species DHF in compartment_, THF in compartment_, THFGlu in compartment_; + species $Gly in compartment_, $Ser in compartment_, myTHFGlu in compartment_; + species MTHFGlu in compartment_, $Hcy in compartment_, Met in compartment_; + species dTMP in compartment_, $dUMP in compartment_, meTHFGlu in compartment_; + species fTHFGlu in compartment_, fmtRNA in compartment_, $mtRNA in compartment_; + species COTwo in compartment_, ADP in compartment_, $ATP in compartment_; + species NADP in compartment_, $NADPH in compartment_, AMP in compartment_; + species DLp in compartment_, SAmDLp in compartment_, $Lp in compartment_; + species NAD in compartment_, $NADH in compartment_, Ammonia in compartment_; + species Formyl in compartment_, ffTHFGlu in compartment_; + + // Reactions: + R1: $PEP + $EP => DAHP + Pi; compartment_*(R1_vmax*EP*PEP/(R1_kpep*R1_kep + R1_kpep*EP + R1_kep*PEP + EP*PEP)); + R2: DAHP => DHQ + Pi; compartment_*(R2_V*DAHP/(R2_Km + DAHP)); + R3: DHQ => DHSK; compartment_*(R3_V*DHQ/(R3_Km + DHQ)); + R4: DHSK + $NADPH => SK + NADP; compartment_*(R4_vmax*DHSK*NADPH/(R4_kdhsk*R4_knadph + R4_kdhsk*NADPH + R4_knadph*DHSK + DHSK*NADPH)); + R5: SK + $ATP => SKP + ADP + Pi; compartment_*(R5_vmax*SK*ATP/(R5_ksk*R5_katp + R5_ksk*ATP + R5_katp*SK + SK*ATP)); + R6: SKP + $PEP => CVPSK + Pi; compartment_*(R6_vmax*SKP*PEP/(R6_kpep*R6_kskp + R6_kpep*PEP + R6_kskp*SKP + PEP*SKP)); + R7: CVPSK => CM + Pi; compartment_*(R7_V*CVPSK/(R7_Km + CVPSK)); + R8: CM + $Gln => ADC + Glu; compartment_*(R8_vmax*CM*Gln/(R8_kcm*R8_kgln + R8_kcm*Gln + R8_kgln*CM + CM*Gln)); + R9: ADC => pABA + Pyr; compartment_*(R9_V*ADC/(R9_Km + ADC)); + R10: $GTP => DHNTP + Formyl; compartment_*(R10_vmax*GTP/(R10_kgtp*(1 + THF/R10_kiTHF) + GTP)); + R11: DHNTP => AHMDHP + HAD + Pi; compartment_*(R11_V*DHNTP/(R11_Km + DHNTP)); + R27: DHNTP => PTHP + Pi; compartment_*(R27_V*DHNTP/(R27_Km + DHNTP)); + R12: AHMDHP + $ATP => AHMDPP + AMP; compartment_*(R12_vmax*ATP*AHMDHP/(R12_kahmdhp*R12_katp + R12_katp*ATP + R12_kahmdhp*AHMDHP + ATP*AHMDHP)); + R14: DHP + Glu + $ATP => DHF + ADP + Pi; compartment_*(R14_vmax*DHP*Glu*ATP/(R14_kdhp*R14_kglu*R14_katp + R14_kdhp*(Glu + ATP) + R14_kglu*(DHP + ATP) + R14_katp*(Glu + ATP) + DHP*Glu*ATP)); + R15: DHF + $NADPH => THF + NADP; compartment_*(R15_vmax*DHF*NADPH/(R15_kdhf*R15_knadph + R15_kdhf*NADPH + R15_knadph*DHF + DHF*NADPH)); + R16: THF + Glu + $ATP => THFGlu + ADP + Pi; compartment_*(R16_vmax*THF*Glu*ATP/(R16_kthf*(1 + DHF/R16_kidhf)*R16_kglu*R16_katp + R16_kthf*(Glu + ATP) + R16_kglu*(THF + ATP) + R16_katp*(THF + Glu) + THF*Glu*ATP)); + R17: THFGlu + $Ser -> myTHFGlu + $Gly; compartment_*(R17_vmax*THFGlu*Ser/(R17_kthfglu*(1 + THF/R17_kithf)*R17_kser + R17_kthfglu*Ser + R17_kser*THFGlu + THFGlu*Ser)); + R18b: DLp + $Gly -> SAmDLp + COTwo; compartment_*(R18b_vmax*DLp*Gly/(R18b_kgly*R18b_kdlp + R18b_kgly*Gly + R18b_kdlp*DLp + DLp*Gly)); + R19: myTHFGlu + $NADPH => MTHFGlu + NADP; compartment_*(R19_vmax*myTHFGlu*NADPH/(R19_kmythfglu*(1 + DHF/R19_kidhf)*R19_knadph + R19_kmythfglu*NADPH + R19_knadph*myTHFGlu + myTHFGlu*NADPH)); + R20: MTHFGlu + $Hcy => THFGlu + Met; compartment_*(R20_vmax*MTHFGlu*Hcy/(R20_kmthfglu*R20_khcy + R20_kmthfglu*Hcy + R20_khcy*MTHFGlu + MTHFGlu*Hcy)); + R21: myTHFGlu + $dUMP => dTMP + DHF; compartment_*(R21_vmax*myTHFGlu*dUMP/(R21_kmythfglu*(1 + DHF/R21_kidhf)*R21_kdump + R21_kmythfglu*dUMP + R21_kdump*myTHFGlu + myTHFGlu*dUMP)); + R22: myTHFGlu + NADP -> meTHFGlu + $NADPH; compartment_*(R22_vmax*myTHFGlu*NADP/(R22_kmythfglu*(1 + DHF/R22_kidhf)*R22_knadp + R22_kmythfglu*NADP + R22_knadp*myTHFGlu + myTHFGlu*NADP)); + R25: fTHFGlu + $mtRNA -> fmtRNA + THFGlu; compartment_*(R25_vmax*fTHFGlu*mtRNA/(R25_kfthfglu*R25_kmtrna + R25_kfthfglu*mtRNA + R25_kmtrna*fTHFGlu + fTHFGlu*mtRNA)); + R26: fTHFGlu + NADP -> THFGlu + COTwo + $NADPH; compartment_*(R26_vmax*fTHFGlu*NADP/(R26_kfthfglu*R26_knadp + R26_kfthfglu*NADP + R26_knadp*fTHFGlu + fTHFGlu*NADP)); + R18c: THFGlu + SAmDLp -> myTHFGlu + $Lp + Ammonia; compartment_*(R18c_vmax*THFGlu*SAmDLp/(R18c_kthfglu*R18c_ksamdlp + R18c_kthfglu*SAmDLp + R18c_ksamdlp*THFGlu + THFGlu*SAmDLp)); + R18a: $Lp + $NADH -> DLp + NAD; compartment_*(R18a_vmax*NADH*Lp/(R18a_knadh*R18a_klp + R18a_knadh*Lp + R18a_klp*NADH + NADH*Lp)); + R13: AHMDPP + pABA => DHP + Pi; compartment_*(R13_vmax*AHMDPP*pABA/(R13_kahmdpp*R13_kpaba + R13_kpaba*AHMDPP + R13_kahmdpp*pABA + AHMDPP*pABA)); + R24: fTHFGlu + ADP + Pi -> THFGlu + $ATP + Formyl; compartment_*(R24_vmax*fTHFGlu*ADP*Pi/(R24_kthfglu*R24_kformyl*R24_katp + R24_kthfglu*(ADP + Pi) + R24_kformyl*(fTHFGlu + Pi) + R24_katp*(ADP + fTHFGlu) + fTHFGlu*ADP*Pi)); + R23: meTHFGlu -> fTHFGlu; compartment_*(R23_k1*meTHFGlu - R23_k2*fTHFGlu); + R28: meTHFGlu => ffTHFGlu; compartment_*(R28_V*meTHFGlu/(R28_Km + meTHFGlu)); + R29: $ATP + ffTHFGlu => ADP + Pi + meTHFGlu; compartment_*(R29_vmax*ATP*ffTHFGlu/(R29_katp*R29_kffthfglu + R29_katp*ffTHFGlu + R29_kffthfglu*ATP + ATP*ffTHFGlu)); + + // Species initializations: + DAHP = 0.9796078511; + PEP = 16.01031821; + Pi = 2.725541316; + DHQ = 0.9994087764; + EP = 107.502052; + DHSK = 1.92788104; + SK = 5.06777189; + SKP = 2; + CVPSK = 0.9174312684; + CM = 1.009195849; + Gln = 381.0009289; + Glu = 959.9999225; + ADC = 0.9907047071; + Pyr = 1.000006539; + pABA = 1.00378139; + DHNTP = 4; + GTP = 487.4867469; + AHMDHP = 2.01877235; + HAD = 2.002305849; + PTHP = 1.002298517; + AHMDPP = 0.9873083466; + DHP = 0.9963801483; + DHF = 1.142744159; + THF = 8; + THFGlu = 1; + Gly = 499.9974679; + Ser = 6.803576818; + myTHFGlu = 1.04350884; + MTHFGlu = 1.000096392; + Hcy = 1.000182797; + Met = 0.9998172031; + dTMP = 0.9974700923; + dUMP = 20.00252991; + meTHFGlu = 0.9082384182; + fTHFGlu = 1.83347183; + fmtRNA = 0.9968760756; + mtRNA = 1.003123924; + COTwo = 0.988683328; + ADP = 2.828115142; + ATP = 963.0188351; + NADP = 2; + NADPH = 12.19849409; + AMP = 0.983533495; + DLp = 0.7017503089; + SAmDLp = 1.000015336; + Lp = 1.298234355; + NAD = 0.7017656449; + NADH = 8.349823436; + Ammonia = 0.9895374253; + Formyl = 8; + ffTHFGlu = 1; + + // Compartment initializations: + compartment_ = 1; + + // Variable initializations: + R1_kep = 285; + R1_kpep = 36; + R1_vmax = 578.76; + R2_Km = 4.7; + R2_V = 7.462; + R3_Km = 58; + R3_V = 116.48; + R4_kdhsk = 30; + R4_knadph = 11; + R4_vmax = 17290; + R5_katp = 151.5; + R5_ksk = 200; + R5_vmax = 18200; + R6_kpep = 93; + R6_kskp = 80; + R6_vmax = 1547; + R7_Km = 12.7; + R7_V = 728; + R8_kcm = 13; + R8_kgln = 1100; + R8_vmax = 26; + R9_Km = 1.1; + R9_V = 2.2; + R10_kgtp = 17.6; + R10_kiTHF = 0.157; + R10_vmax = 1515.15; + R11_Km = 7.4; + R11_V = 792.064; + R27_Km = 10; + R27_V = 22.659; + R12_kahmdhp = 3.6; + R12_katp = 15; + R12_vmax = 382.2; + R14_katp = 100; + R14_kdhp = 1; + R14_kglu = 1380; + R14_vmax = 2.821; + R15_kdhf = 3; + R15_knadph = 6.12; + R15_vmax = 3000; + R16_katp = 128; + R16_kglu = 740; + R16_kidhf = 3.1; + R16_kthf = 26; + R16_vmax = 84.63; + R17_kithf = 0.157; + R17_kser = 700; + R17_kthfglu = 40; + R17_vmax = 682.5; + R18b_kdlp = 290; + R18b_kgly = 4505; + R18b_vmax = 751.66; + R19_kidhf = 0.428; + R19_kmythfglu = 33; + R19_knadph = 19; + R19_vmax = 738.92; + R20_khcy = 17; + R20_kmthfglu = 30; + R20_vmax = 379.925; + R21_kdump = 5.4; + R21_kidhf = 0.428; + R21_kmythfglu = 17; + R21_vmax = 49.14; + R22_kidhf = 0.428; + R22_kmythfglu = 25; + R22_knadp = 22; + R22_vmax = 1892.8; + R25_kfthfglu = 12.15; + R25_kmtrna = 1.07; + R25_vmax = 116.48; + R26_kfthfglu = 7.85; + R26_knadp = 0.9; + R26_vmax = 59.332; + R18c_ksamdlp = 290; + R18c_kthfglu = 67.7; + R18c_vmax = 196.56; + R18a_klp = 1280; + R18a_knadh = 58; + R18a_vmax = 5432.7; + R13_kahmdpp = 3.15; + R13_kpaba = 2.6; + R13_vmax = 105.014; + R24_katp = 74.5; + R24_kformyl = 3190; + R24_kthfglu = 134; + R24_vmax = 15315.3; + R23_k1 = 0.08; + R23_k2 = 0.031; + R28_Km = 67; + R28_V = 200; + R29_katp = 50; + R29_kffthfglu = 5; + R29_vmax = 500; + + // Other declarations: + const compartment_; + + // Unit definitions: + unit time_unit = 60 second; + unit substance = 1e-6 mole; + + // Display Names: + time_unit is "time"; + compartment_ is "Single celled micro-organism"; + R1 is "R1 - Synthesis of 3-Deoxy-7-phosphoheptulonate"; + R2 is "R2 - 2-Dehydro-3-deoxy-D-arabino-heptonate 7-phosphate phosphate-lyase (3-Dehydroquinate synthase)"; + R3 is "R3 - 3-Dehydroquinate hydro-lyase (3-Dehydroquinate dehydratase)"; + R4 is "R4 - Shikimate:NADP + 3-oxidoreductase (Shikimate 5-dehydrogenase)"; + R5 is "R5 - ATP:Shikimate 3-phosphotransferase (Shikimate kinase)"; + R6 is "R6 - Phosphoenolpyruvate:3-phosphoshikimate 5-O-(1-carboxyvinyl)-transferase"; + R7 is "R7 - 5-O-(1-Carboxyvinyl)-3-phosphoshikimate phosphate-lyase (chorismate synthase)"; + R8 is "R8 - Aminodeoxychorismate synthase"; + R9 is "R9 - Aminodeoxychorismate lyase"; + R10 is "R10 - GTP 7,8,9-dihydrolase (GTP cyclohydrolase I)"; + R11 is "R11 - Dihydroneopterin aldolase"; + R27 is "R27 - 6-Pyruvoyltetrahydropterin synthase"; + R12 is "R12 - 2-Amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase"; + R14 is "R14 - 7,8-Dihydrofolate synthase"; + R15 is "R15 - Dihydrofolate reductase"; + R16 is "R16 - Folylpoly-gamma-glutamate synthase"; + R17 is "R17 - Serine hydroxymethyltransferase"; + R18b is "R18b - Glycine decarboxylase (P protein)"; + R19 is "R19 - 5,10-Methylenetetrahydrofolate reductase"; + R20 is "R20 - Methionine synthase"; + R21 is "R21 - Thymidylate synthase"; + R22 is "R22 - 5,10-Methylenetetrahydrofolate dehydrogenase"; + R25 is "R25 - Methionyl-tRNA formyltransferase"; + R26 is "R26 - 10-Formyltetrahydrofolate dehydrogenase"; + R18c is "R18c - S-Aminomethyldihydrolipoylprotein:tetrahydrofolate aminomethyltransferase (T protein)"; + R18a is "R18a - Dihydrolipoamide dehydrogenase"; + R13 is "R13 - Dihydropteroate synthase"; + R24 is "R24 - 10-Formyltetrahydrofolate synthetase"; + R23 is "R23 - 5,10-Methenyltetrahydrofolate cyclohydrolase"; + R28 is "R28 - S-Aminomethyldihydrolipoylprotein:tetrahydrofolate aminomethyltransferase (T protein)"; + R29 is "R29 - 5-formyltetrahydrofolate cyclo-ligase"; + + // CV terms: + DAHP identity "http://identifiers.org/kegg.compound/C04691" + PEP identity "http://identifiers.org/kegg.compound/C00074" + Pi identity "http://identifiers.org/kegg.compound/C00009" + DHQ identity "http://identifiers.org/kegg.compound/C00944" + EP identity "http://identifiers.org/kegg.compound/C00279" + DHSK identity "http://identifiers.org/kegg.compound/C02637" + SK identity "http://identifiers.org/kegg.compound/C00493" + SKP identity "http://identifiers.org/kegg.compound/C03175" + CVPSK identity "http://identifiers.org/kegg.compound/C01269" + CM identity "http://identifiers.org/kegg.compound/C00251" + Gln identity "http://identifiers.org/kegg.compound/C00064" + Glu identity "http://identifiers.org/kegg.compound/C00025" + ADC identity "http://identifiers.org/kegg.compound/C11355" + Pyr identity "http://identifiers.org/kegg.compound/C00022" + pABA identity "http://identifiers.org/kegg.compound/C00568" + DHNTP identity "http://identifiers.org/kegg.compound/C04895" + GTP identity "http://identifiers.org/kegg.compound/C00044" + AHMDHP identity "http://identifiers.org/kegg.compound/C01300" + HAD identity "http://identifiers.org/kegg.compound/C00266" + PTHP identity "http://identifiers.org/kegg.compound/C03684" + AHMDPP identity "http://identifiers.org/kegg.compound/C04807" + DHP identity "http://identifiers.org/kegg.compound/C00921" + DHF identity "http://identifiers.org/kegg.compound/C00415" + THF identity "http://identifiers.org/kegg.compound/C00101" + THFGlu identity "http://identifiers.org/kegg.compound/C03541" + Gly identity "http://identifiers.org/kegg.compound/C00037" + Ser identity "http://identifiers.org/kegg.compound/C00065" + myTHFGlu identity "http://identifiers.org/kegg.compound/C00143" + MTHFGlu identity "http://identifiers.org/kegg.compound/C00440" + Hcy identity "http://identifiers.org/kegg.compound/C00155" + Met identity "http://identifiers.org/kegg.compound/C00073" + dTMP identity "http://identifiers.org/kegg.compound/C00364" + dUMP identity "http://identifiers.org/kegg.compound/C00365" + meTHFGlu identity "http://identifiers.org/kegg.compound/C00445" + fTHFGlu identity "http://identifiers.org/kegg.compound/C00234" + fmtRNA identity "http://identifiers.org/kegg.compound/C03294" + mtRNA identity "http://identifiers.org/kegg.compound/C02430" + ADP identity "http://identifiers.org/kegg.compound/C00008" + ATP identity "http://identifiers.org/kegg.compound/C00002" + NADP identity "http://identifiers.org/kegg.compound/C00006" + NADPH identity "http://identifiers.org/kegg.compound/C00005" + AMP identity "http://identifiers.org/kegg.compound/C00020" + DLp identity "http://identifiers.org/kegg.compound/C02972" + SAmDLp identity "http://identifiers.org/kegg.compound/C01242" + Lp identity "http://identifiers.org/kegg.compound/C02051" + NAD identity "http://identifiers.org/kegg.compound/C00003" + NADH identity "http://identifiers.org/kegg.compound/C00004" + Ammonia identity "http://identifiers.org/kegg.compound/C00014" + Formyl identity "http://identifiers.org/kegg.compound/C00058" + ffTHFGlu identity "http://identifiers.org/kegg.compound/C03479" + R1 isVersionOf "http://identifiers.org/kegg.reaction/R01826" + R2 isVersionOf "http://identifiers.org/kegg.reaction/R03083" + R3 isVersionOf "http://identifiers.org/kegg.reaction/R03084" + R4 isVersionOf "http://identifiers.org/kegg.reaction/R02413" + R5 isVersionOf "http://identifiers.org/kegg.reaction/R02412" + R6 isVersionOf "http://identifiers.org/kegg.reaction/R03460" + R7 isVersionOf "http://identifiers.org/kegg.reaction/R01714" + R8 isVersionOf "http://identifiers.org/kegg.reaction/R01716" + R9 isVersionOf "http://identifiers.org/kegg.reaction/R05553" + R10 isVersionOf "http://identifiers.org/kegg.reaction/R00424" + R11 isVersionOf "http://identifiers.org/kegg.reaction/R03504" + R27 isVersionOf "http://identifiers.org/kegg.reaction/R04286" + R12 isVersionOf "http://identifiers.org/kegg.reaction/R03503" + R14 isVersionOf "http://identifiers.org/kegg.reaction/R02237" + R15 isVersionOf "http://identifiers.org/kegg.reaction/R00939" + R16 isVersionOf "http://identifiers.org/kegg.reaction/R04241" + R17 isVersionOf "http://identifiers.org/kegg.reaction/R00945" + R18b isVersionOf "http://identifiers.org/kegg.reaction/R03425" + R19 isVersionOf "http://identifiers.org/kegg.reaction/R01224" + R20 isVersionOf "http://identifiers.org/kegg.reaction/R00946" + R21 isVersionOf "http://identifiers.org/kegg.reaction/R02101" + R22 isVersionOf "http://identifiers.org/kegg.reaction/R01220" + R25 isVersionOf "http://identifiers.org/kegg.reaction/R03940" + R26 isVersionOf "http://identifiers.org/kegg.reaction/R00941" + R18c isVersionOf "http://identifiers.org/kegg.reaction/R04125" + R18a isVersionOf "http://identifiers.org/kegg.reaction/R03815" + R13 isVersionOf "http://identifiers.org/kegg.reaction/R03067" + R24 isVersionOf "http://identifiers.org/kegg.reaction/R00943" + R23 isVersionOf "http://identifiers.org/kegg.reaction/R01655" + R28 isVersionOf "http://identifiers.org/kegg.reaction/R02300" + R29 isVersionOf "http://identifiers.org/kegg.reaction/R02301" + + model model_source "http://identifiers.org/biomodels.db/MODEL1511020000", + "http://identifiers.org/biomodels.db/BIOMD0000000725" + model identity "http://identifiers.org/biomodels.db/MODEL1511020000" + model hasProperty "http://identifiers.org/ncit/C38809" + model hasProperty "http://identifiers.org/ncit/C14329" + model hasProperty "http://identifiers.org/pw/PW:0001369" + model hasProperty "http://identifiers.org/efo/0005741" + model hasProperty "http://identifiers.org/mamo/MAMO_0000046" + model isDescribedBy "http://identifiers.org/doi/10.1039/C5MB00801H" + model created "2015-06-28T14:24:15Z" + model modified "2015-06-28T14:24:15Z" + model creator1.givenName "Mark T." + model creator1.familyName "McAuley" + model creator1.organization "University of Chester, UK" + model creator1.email "m.mcauley@chester.ac.uk" + model creator2.givenName "J. Enrique" + model creator2.familyName "Salcedo-Sora" + model creator2.organization "Liverpool Hope University, UK" + model creator2.email "salcede@hope.ac.uk" + model creator3.givenName "Sarubini" + model creator3.familyName "Kananathan" + model creator3.organization "EMBL-EBI" + model creator3.email "sarubini.kananathan@hotmail.co.uk" + + // Notes: + model notes ``` +Salcedo-Sora2016 - Microbial folate biosynthesis and utilisation + + +This model is described in the article: + + +[ A mathematical model of microbial folate biosynthesis and utilisation: implications for antifolate development.](http://identifiers.org/pubmed/26794619 "Access to this publication") + + +Enrique Salcedo-Sora J, Mc Auley MT. + +Mol Biosyst. 2016 Jan 21. +Abstract: + + +The metabolic biochemistry of folate biosynthesis and utilisation has evolved +into a complex network of reactions. Although this complexity represents challenges +to the field of folate research it has also provided a renewed source for antimetabolite +targets. A range of improved folate chemotherapy continues to be developed and applied +particularly to cancer and chronic inflammatory diseases. However, new or better +antifolates against infectious diseases remain much more elusive. In this paper we +describe the assembly of a generic deterministic mathematical model of microbial +folate metabolism. Our aim is to explore how a mathematical model could be used to +explore the dynamics of this inherently complex set of biochemical reactions. Using +the model it was found that: (1) a particular small set of folate intermediates are +overrepresented, (2) inhibitory profiles can be quantified by the level of key folate +products, (3) using the model to scan for the most effective combinatorial inhibitions +of folate enzymes we identified specific targets which could complement current antifolates, +and (4) the model substantiates the case for a substrate cycle in the folinic acid +biosynthesis reaction. Our model is coded in the systems biology markup language +and has been deposited in the BioModels Database (MODEL1511020000), this makes it +accessible to the community as a whole. + + +This model is hosted on [BioModels Database](http://www.ebi.ac.uk/biomodels/) and identified by: [MODEL1511020000](http://identifiers.org/biomodels.db/MODEL1511020000). + +To cite BioModels Database, please use: [BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models](http://identifiers.org/pubmed/20587024 "Latest BioModels Database publication"). + + +To the extent possible under law, all copyright and related or neighbouring rights +to this encoded model have been dedicated to the public domain worldwide. Please +refer to [CC0 Public Domain Dedication](http://creativecommons.org/publicdomain/zero/1.0/ "Access to: CC0 1.0 Universal (CC0 1.0), Public Domain Dedication") for more information. +``` +end + +Salcedo_Sora2016___Microbial_folate_biosynthesis_and_utilisation is "Salcedo-Sora2016 - Microbial folate biosynthesis and utilisation" diff --git a/doc/examples/biomodels/BIOMD0000000726/Model.txt b/doc/examples/biomodels/BIOMD0000000726/Model.txt new file mode 100644 index 000000000..9c4c62357 --- /dev/null +++ b/doc/examples/biomodels/BIOMD0000000726/Model.txt @@ -0,0 +1,160 @@ +// Created by libAntimony v3.2.0 +model *Ruan2017___Transmission_dynamics_and_control_of_rabies_in_China() + + // Compartments and Species: + compartment compartment_, Human_Population; + species S_d in compartment_, E_d in compartment_, I_d in compartment_, R_d in compartment_; + species S_h in Human_Population, E_h in Human_Population, I_h in Human_Population; + species R_h in Human_Population; + + // Reactions: + reaction_1: => S_d; compartment_*A; + reaction_2: R_d => S_d; compartment_*lambda*R_d; + reaction_3: E_d => S_d; compartment_*(sigma*(1 - gamma_)*E_d); + reaction_4: S_d => E_d; compartment_*(beta*S_d*I_d); + reaction_5: S_d => ; compartment_*m*S_d; + reaction_6: E_d => I_d; compartment_*(sigma*gamma_*E_d); + reaction_7: E_d => ; compartment_*m*E_d; + reaction_8: I_d => ; compartment_*m*I_d; + reaction_9: S_d => R_d; compartment_*k*S_d; + reaction_10: E_d => R_d; compartment_*k*E_d; + reaction_11: I_d => ; compartment_*mu*I_d; + reaction_12: R_d => ; compartment_*m*R_d; + reaction_13: => S_h; Human_Population*B; + reaction_14: R_h => S_h; Human_Population*lambda_h*R_h; + reaction_15: E_h => S_h; Human_Population*(sigma_h*(1 - gamma_h)*E_h); + reaction_16: S_h => ; Human_Population*m_h*S_h; + reaction_17: S_h => E_h; beta_dh*S_h*I_d; + reaction_18: E_h => I_h; Human_Population*(sigma_h*gamma_h*E_h); + reaction_19: E_h => ; Human_Population*m_h*E_h; + reaction_20: E_h => R_h; Human_Population*k_h*E_h; + reaction_21: I_h => ; Human_Population*m_h*I_h; + reaction_22: I_h => ; Human_Population*mu_h*I_h; + reaction_23: R_h => ; Human_Population*m_h*R_h; + + // Species initializations: + S_d = 35000000; + E_d = 200000; + I_d = 100000; + R_d = 200000; + S_h = 1290000000; + E_h = 250; + I_h = 89; + R_h = 200000; + + // Compartment initializations: + compartment_ = 1; + Human_Population = 1; + + // Variable initializations: + A = 3000000; + lambda = 1; + gamma_ = 0.4; + sigma = 6; + m = 0.08; + beta = 1.58e-07; + k = 0.09; + mu = 1; + B = 15400000; + lambda_h = 1; + gamma_h = 0.4; + sigma_h = 6; + m_h = 0.003; + beta_dh = 2.29e-12; + k_h = 0.54; + mu_h = 1.34; + + // Other declarations: + const compartment_, Human_Population, A, lambda, gamma_, sigma, m, beta; + const k, mu, B, lambda_h, gamma_h, sigma_h, m_h, beta_dh, k_h, mu_h; + + // Unit definitions: + unit time_unit = 86400 second; + + // Display Names: + time_unit is "time"; + compartment_ is "Dog Population"; + Human_Population is "Human Population"; + S_d is "Susceptible dogs (S_d)"; + E_d is "Exposed dogs (E_d)"; + I_d is "Infectious dogs (I_d)"; + R_d is "Recovered dogs (R_d)"; + S_h is "Susceptible humans (S_h)"; + E_h is "Exposed humans (E_h)"; + I_h is "Infectious humans (I_h)"; + R_h is "Recovered humans (R_h)"; + gamma_ is "gamma"; + reaction_1 is "Birth of susceptible dogs"; + reaction_2 is "Loss of immunity in recovered dogs"; + reaction_3 is "Exposed dogs that do not get infected"; + reaction_4 is "Exposure of virus to susceptible dogs"; + reaction_5 is "Natural death of susceptible dogs"; + reaction_6 is "Infection of exposed dogs"; + reaction_7 is "Natural death of exposed dogs"; + reaction_8 is "Natural death of infected dogs"; + reaction_9 is "Vaccination of susceptible dogs"; + reaction_10 is "Vaccination of exposed dogs"; + reaction_11 is "Disease related death of infected dogs"; + reaction_12 is "Natural death of recovered dogs"; + reaction_13 is "Birth of susceptible humans"; + reaction_14 is "Loss of immunity in recovered humans"; + reaction_15 is "Exposure humans that were not infected"; + reaction_16 is "Natural death of susceptible humans"; + reaction_17 is "Exposure of virus to susceptible humans"; + reaction_18 is "Infection of exposed humans"; + reaction_19 is "Natural death of exposed humans"; + reaction_20 is "Vaccination of exposed humans"; + reaction_21 is "Natural death of infected humans"; + reaction_22 is "Disease related death of infected humans"; + reaction_23 is "Natural death of recovered humans"; + + // CV terms: + compartment_ identity "http://identifiers.org/obi/OBI:0000181" + compartment_ hasTaxon "http://identifiers.org/taxonomy/9615" + Human_Population identity "http://identifiers.org/obi/OBI:0000181" + Human_Population hasTaxon "http://identifiers.org/taxonomy/9606" + S_d isVersionOf "http://identifiers.org/ido/0000514" + S_d hasTaxon "http://identifiers.org/taxonomy/9615" + E_d hasProperty "http://identifiers.org/efo/0000487" + E_d hasTaxon "http://identifiers.org/taxonomy/9615" + I_d isVersionOf "http://identifiers.org/ido/0000511" + I_d hasTaxon "http://identifiers.org/taxonomy/9615" + R_d hasProperty "http://identifiers.org/ncit/C49498" + R_d hasTaxon "http://identifiers.org/taxonomy/9615" + S_h isVersionOf "http://identifiers.org/ido/0000514" + S_h hasTaxon "http://identifiers.org/taxonomy/9606" + E_h hasProperty "http://identifiers.org/efo/0000487" + E_h hasTaxon "http://identifiers.org/taxonomy/9606" + I_h isVersionOf "http://identifiers.org/ido/0000511" + I_h hasTaxon "http://identifiers.org/taxonomy/9606" + R_h hasProperty "http://identifiers.org/ncit/C49498" + R_h hasTaxon "http://identifiers.org/taxonomy/9606" + reaction_5 isVersionOf "http://identifiers.org/sbo/SBO:0000179" + reaction_7 isVersionOf "http://identifiers.org/sbo/SBO:0000179" + reaction_8 isVersionOf "http://identifiers.org/sbo/SBO:0000179" + reaction_9 isPartOf "http://identifiers.org/efo/0004292" + reaction_10 isPartOf "http://identifiers.org/efo/0004292" + reaction_12 isVersionOf "http://identifiers.org/sbo/SBO:0000179" + reaction_16 isVersionOf "http://identifiers.org/sbo/SBO:0000179" + reaction_19 isVersionOf "http://identifiers.org/sbo/SBO:0000179" + reaction_20 isPartOf "http://identifiers.org/efo/0004292" + reaction_21 isVersionOf "http://identifiers.org/sbo/SBO:0000179" + reaction_23 isVersionOf "http://identifiers.org/sbo/SBO:0000179" + + model model_source "http://identifiers.org/biomodels.db/MODEL1808280012", + "http://identifiers.org/biomodels.db/BIOMD0000000726" + model hasProperty "http://identifiers.org/mamo/MAMO_0000046" + model hasProperty "http://identifiers.org/ncit/C28182" + model hasTaxon "http://identifiers.org/taxonomy/11292" + model hasTaxon "http://identifiers.org/taxonomy/9606" + model hasTaxon "http://identifiers.org/taxonomy/9615" + model isDescribedBy "http://identifiers.org/pubmed/28188732" + model created "2018-07-10T14:56:12Z" + model modified "2018-07-10T14:56:12Z" + model creator1.givenName "Sarubini" + model creator1.familyName "Kananathan" + model creator1.organization "EMBL-EBI" + model creator1.email "sarubini.kananathan@hotmail.co.uk" +end + +Ruan2017___Transmission_dynamics_and_control_of_rabies_in_China is "Ruan2017 - Transmission dynamics and control of rabies in China" diff --git a/doc/examples/biomodels/Li2009.txt b/doc/examples/biomodels/BIOMD0000000727/Li2009.txt similarity index 99% rename from doc/examples/biomodels/Li2009.txt rename to doc/examples/biomodels/BIOMD0000000727/Li2009.txt index ecd6d587e..1d055e4fd 100644 --- a/doc/examples/biomodels/Li2009.txt +++ b/doc/examples/biomodels/BIOMD0000000727/Li2009.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Li2009__Assymetric_Caulobacter_cell_cycle() // Compartments and Species: @@ -73,8 +73,8 @@ model *Li2009__Assymetric_Caulobacter_cell_cycle() DivK_P_decay: DivK_P => ; Caulobacter*kd_DivK*DivK_P; // Events: - Ini_equal_0_05Count: at Ini >= (0.05*Count): hcori = 1, Ini = 0, DNA_ = DNA_ + Ini, Elong = Elong + Ini, Count = Count*2; - Z_equals_0: at Z <= 0.1: DNA_ = DNA_/2, Elong = Elong/2, Zring = 0, Count = Count/2; + Ini_equal_0_05Count: at Ini >= (0.05*Count): Count = Count*2, Elong = Elong + Ini, DNA_ = DNA_ + Ini, Ini = 0, hcori = 1; + Z_equals_0: at Z <= 0.1: Count = Count/2, Zring = 0, Elong = Elong/2, DNA_ = DNA_/2; Elong_reset_by_count: at Elong >= (Count/2): Elong = 0; hcori_reset_by_Elong: at (Elong*2) >= (Pelong*Count): hcori = 1; hctrA_reset_by_Elong: at (Elong*2) >= (PctrA*Count): hctrA = 1; diff --git a/doc/examples/biomodels/Norell1990.txt b/doc/examples/biomodels/BIOMD0000000728/Norell1990.txt similarity index 98% rename from doc/examples/biomodels/Norell1990.txt rename to doc/examples/biomodels/BIOMD0000000728/Norell1990.txt index 37678615d..9b42624c7 100644 --- a/doc/examples/biomodels/Norell1990.txt +++ b/doc/examples/biomodels/BIOMD0000000728/Norell1990.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Norel1990___MPF_and_Cyclin_Oscillations() // Compartments and Species: diff --git a/doc/examples/biomodels/Goldbeter1996.txt b/doc/examples/biomodels/BIOMD0000000729/Goldbeter1996.txt similarity index 99% rename from doc/examples/biomodels/Goldbeter1996.txt rename to doc/examples/biomodels/BIOMD0000000729/Goldbeter1996.txt index 81f919c13..7f6517072 100644 --- a/doc/examples/biomodels/Goldbeter1996.txt +++ b/doc/examples/biomodels/BIOMD0000000729/Goldbeter1996.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Goldbeter1996___Cyclin_Cdc2_kinase_Oscillations() // Compartments and Species: diff --git a/doc/examples/biomodels/Gerard2009.txt b/doc/examples/biomodels/BIOMD0000000730/Gerard2009.txt similarity index 99% rename from doc/examples/biomodels/Gerard2009.txt rename to doc/examples/biomodels/BIOMD0000000730/Gerard2009.txt index dd584a73c..11324deec 100644 --- a/doc/examples/biomodels/Gerard2009.txt +++ b/doc/examples/biomodels/BIOMD0000000730/Gerard2009.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Gerard2009() // Compartments and Species: diff --git a/doc/examples/biomodels/22051568_Tessi.txt b/doc/examples/biomodels/BIOMD0000000731/22051568_Tessi.txt similarity index 99% rename from doc/examples/biomodels/22051568_Tessi.txt rename to doc/examples/biomodels/BIOMD0000000731/22051568_Tessi.txt index fe688e44f..38b67f7b4 100644 --- a/doc/examples/biomodels/22051568_Tessi.txt +++ b/doc/examples/biomodels/BIOMD0000000731/22051568_Tessi.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Robertson_Tessi_M__2012() // Compartments and Species: @@ -173,7 +173,7 @@ model *Robertson_Tessi_M__2012() const S4, tc, ts, t1, I2; // Unit definitions: - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / 1e-3 second; unit unit_1 = 1 / dimensionless^-0; diff --git a/doc/examples/biomodels/Kirschner_1998.txt b/doc/examples/biomodels/BIOMD0000000732/Kirschner_1998.txt similarity index 99% rename from doc/examples/biomodels/Kirschner_1998.txt rename to doc/examples/biomodels/BIOMD0000000732/Kirschner_1998.txt index 7e1eb01f7..3ec700a97 100644 --- a/doc/examples/biomodels/Kirschner_1998.txt +++ b/doc/examples/biomodels/BIOMD0000000732/Kirschner_1998.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kirschner1998_Immunotherapy_Tumour() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1006230038_urn.txt b/doc/examples/biomodels/BIOMD0000000732/MODEL1006230038_urn.txt similarity index 99% rename from doc/examples/biomodels/MODEL1006230038_urn.txt rename to doc/examples/biomodels/BIOMD0000000732/MODEL1006230038_urn.txt index 38c6d81a2..f52435574 100644 --- a/doc/examples/biomodels/MODEL1006230038_urn.txt +++ b/doc/examples/biomodels/BIOMD0000000732/MODEL1006230038_urn.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kirschner1998_Immunotherapy_Tumour() // Compartments and Species: diff --git a/doc/examples/biomodels/Moore_2004_fig6.txt b/doc/examples/biomodels/BIOMD0000000733/Moore_2004_fig6.txt similarity index 99% rename from doc/examples/biomodels/Moore_2004_fig6.txt rename to doc/examples/biomodels/BIOMD0000000733/Moore_2004_fig6.txt index b5601f0b3..8c3babbc5 100644 --- a/doc/examples/biomodels/Moore_2004_fig6.txt +++ b/doc/examples/biomodels/BIOMD0000000733/Moore_2004_fig6.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Moore_2004() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000734.txt b/doc/examples/biomodels/BIOMD0000000734/BIOMD0000000734.txt similarity index 98% rename from doc/examples/biomodels/BIOMD0000000734.txt rename to doc/examples/biomodels/BIOMD0000000734/BIOMD0000000734.txt index 6f9bf60f1..fd63b1fc0 100644 --- a/doc/examples/biomodels/BIOMD0000000734.txt +++ b/doc/examples/biomodels/BIOMD0000000734/BIOMD0000000734.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Mouse_Iron_Distribution___Rich_and_Deficient_iron_diets__tracer() // Compartments and Species: @@ -358,11 +358,10 @@ This model includes the radioiron tracer species. Differences in parameter values between deficient, rich, and adequate diets: -| | -||---------------|------------|---------------|| -| | **Adequate** | 0.00377422 | 1.7393e-08 | | -| | **Deficient** | 0 | 8.54927e-09 | | -| | **Rich** | 0.00415624 | 2.30942e-08 | | +| **Diet** | **vDiet** | **vhepcidin** | +| **Adequate** | 0.00377422 | 1.7393e-08 | +| **Deficient** | 0 | 8.54927e-09 | +| **Rich** | 0.00415624 | 2.30942e-08 | ``` end diff --git a/doc/examples/biomodels/MODEL1605030002_urn.txt b/doc/examples/biomodels/BIOMD0000000735/MODEL1605030002_urn.txt similarity index 99% rename from doc/examples/biomodels/MODEL1605030002_urn.txt rename to doc/examples/biomodels/BIOMD0000000735/MODEL1605030002_urn.txt index 8523be033..0d11e9eb5 100644 --- a/doc/examples/biomodels/MODEL1605030002_urn.txt +++ b/doc/examples/biomodels/BIOMD0000000735/MODEL1605030002_urn.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1605030002() // Compartments and Species: diff --git a/doc/examples/biomodels/Parmar2017_Adequate_tracer.txt b/doc/examples/biomodels/BIOMD0000000735/Parmar2017_Adequate_tracer.txt similarity index 99% rename from doc/examples/biomodels/Parmar2017_Adequate_tracer.txt rename to doc/examples/biomodels/BIOMD0000000735/Parmar2017_Adequate_tracer.txt index 4485b5ea4..034ff859b 100644 --- a/doc/examples/biomodels/Parmar2017_Adequate_tracer.txt +++ b/doc/examples/biomodels/BIOMD0000000735/Parmar2017_Adequate_tracer.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Mouse_Iron_Distribution___Adequate_iron_diet__tracer() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1605030003_urn.txt b/doc/examples/biomodels/BIOMD0000000736/MODEL1605030003_urn.txt similarity index 99% rename from doc/examples/biomodels/MODEL1605030003_urn.txt rename to doc/examples/biomodels/BIOMD0000000736/MODEL1605030003_urn.txt index 6181a8ff5..26a0c259c 100644 --- a/doc/examples/biomodels/MODEL1605030003_urn.txt +++ b/doc/examples/biomodels/BIOMD0000000736/MODEL1605030003_urn.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1605030003() // Compartments and Species: diff --git a/doc/examples/biomodels/Parmar2017_Adequate_diet_Anemia_NoTracer.txt b/doc/examples/biomodels/BIOMD0000000736/Parmar2017_Adequate_diet_Anemia_NoTracer.txt similarity index 99% rename from doc/examples/biomodels/Parmar2017_Adequate_diet_Anemia_NoTracer.txt rename to doc/examples/biomodels/BIOMD0000000736/Parmar2017_Adequate_diet_Anemia_NoTracer.txt index 6591d6830..cd33f628d 100644 --- a/doc/examples/biomodels/Parmar2017_Adequate_diet_Anemia_NoTracer.txt +++ b/doc/examples/biomodels/BIOMD0000000736/Parmar2017_Adequate_diet_Anemia_NoTracer.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Mouse_Iron_Distribution___Adequate_iron_diet() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1605030004_urn.txt b/doc/examples/biomodels/BIOMD0000000737/MODEL1605030004_urn.txt similarity index 99% rename from doc/examples/biomodels/MODEL1605030004_urn.txt rename to doc/examples/biomodels/BIOMD0000000737/MODEL1605030004_urn.txt index b4c3fe34a..eca45b38e 100644 --- a/doc/examples/biomodels/MODEL1605030004_urn.txt +++ b/doc/examples/biomodels/BIOMD0000000737/MODEL1605030004_urn.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1605030004() // Compartments and Species: diff --git a/doc/examples/biomodels/Parmar2017_Deficient_NoTracer.txt b/doc/examples/biomodels/BIOMD0000000737/Parmar2017_Deficient_NoTracer.txt similarity index 99% rename from doc/examples/biomodels/Parmar2017_Deficient_NoTracer.txt rename to doc/examples/biomodels/BIOMD0000000737/Parmar2017_Deficient_NoTracer.txt index c001f8a51..50136a23d 100644 --- a/doc/examples/biomodels/Parmar2017_Deficient_NoTracer.txt +++ b/doc/examples/biomodels/BIOMD0000000737/Parmar2017_Deficient_NoTracer.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Mouse_Iron_Distribution___Deficient_iron_diet() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1605030005_urn.txt b/doc/examples/biomodels/BIOMD0000000738/MODEL1605030005_urn.txt similarity index 99% rename from doc/examples/biomodels/MODEL1605030005_urn.txt rename to doc/examples/biomodels/BIOMD0000000738/MODEL1605030005_urn.txt index 1a26b0cb0..72949b794 100644 --- a/doc/examples/biomodels/MODEL1605030005_urn.txt +++ b/doc/examples/biomodels/BIOMD0000000738/MODEL1605030005_urn.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1605030005() // Compartments and Species: diff --git a/doc/examples/biomodels/Parmar2017_Rich_NoTracer.txt b/doc/examples/biomodels/BIOMD0000000738/Parmar2017_Rich_NoTracer.txt similarity index 99% rename from doc/examples/biomodels/Parmar2017_Rich_NoTracer.txt rename to doc/examples/biomodels/BIOMD0000000738/Parmar2017_Rich_NoTracer.txt index 83f0c89bd..8b306e92b 100644 --- a/doc/examples/biomodels/Parmar2017_Rich_NoTracer.txt +++ b/doc/examples/biomodels/BIOMD0000000738/Parmar2017_Rich_NoTracer.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Mouse_Iron_Distribution___Rich_iron_diet() // Compartments and Species: diff --git a/doc/examples/biomodels/Bravo2012.txt b/doc/examples/biomodels/BIOMD0000000739/Bravo2012.txt similarity index 99% rename from doc/examples/biomodels/Bravo2012.txt rename to doc/examples/biomodels/BIOMD0000000739/Bravo2012.txt index b972be585..2641b5d77 100644 --- a/doc/examples/biomodels/Bravo2012.txt +++ b/doc/examples/biomodels/BIOMD0000000739/Bravo2012.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bravo2012___Modelling_blood_coagulation_factor_Va_inactivation_by_APC() // Compartments and Species: diff --git a/doc/examples/biomodels/Panteleev2010_full_model.txt b/doc/examples/biomodels/BIOMD0000000740/Panteleev2010_full_model.txt similarity index 99% rename from doc/examples/biomodels/Panteleev2010_full_model.txt rename to doc/examples/biomodels/BIOMD0000000740/Panteleev2010_full_model.txt index be190df90..80cae61b8 100644 --- a/doc/examples/biomodels/Panteleev2010_full_model.txt +++ b/doc/examples/biomodels/BIOMD0000000740/Panteleev2010_full_model.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Panteleev2010___Blood_Coagulation__Full_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Eftimie2018.txt b/doc/examples/biomodels/BIOMD0000000741/Eftimie2018.txt similarity index 99% rename from doc/examples/biomodels/Eftimie2018.txt rename to doc/examples/biomodels/BIOMD0000000741/Eftimie2018.txt index 8ea7be8e8..c1cc25bd6 100644 --- a/doc/examples/biomodels/Eftimie2018.txt +++ b/doc/examples/biomodels/BIOMD0000000741/Eftimie2018.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Eftimie2018___Cancer_and_Immune_biomarkers() // Compartments and Species: @@ -96,7 +96,7 @@ model *Eftimie2018___Cancer_and_Immune_biomarkers() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / 1e3 second; unit unit_1 = 1 / dimensionless^-0; diff --git a/doc/examples/biomodels/Garcia2018basic.txt b/doc/examples/biomodels/BIOMD0000000742/Garcia2018basic.txt similarity index 99% rename from doc/examples/biomodels/Garcia2018basic.txt rename to doc/examples/biomodels/BIOMD0000000742/Garcia2018basic.txt index 035e19b6f..f881a9caa 100644 --- a/doc/examples/biomodels/Garcia2018basic.txt +++ b/doc/examples/biomodels/BIOMD0000000742/Garcia2018basic.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Garcia2018basic___cancer_and_immune_cell_count_basic_model() // Compartments and Species: @@ -44,7 +44,7 @@ model *Garcia2018basic___cancer_and_immune_cell_count_basic_model() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / 1e3 second; unit unit_1 = 1 / dimensionless^-0; diff --git a/doc/examples/biomodels/Gallaher2018.txt b/doc/examples/biomodels/BIOMD0000000743/Gallaher2018.txt similarity index 99% rename from doc/examples/biomodels/Gallaher2018.txt rename to doc/examples/biomodels/BIOMD0000000743/Gallaher2018.txt index 6ce039690..5f9b95752 100644 --- a/doc/examples/biomodels/Gallaher2018.txt +++ b/doc/examples/biomodels/BIOMD0000000743/Gallaher2018.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Gallaher2018___Tumor_Immune_dynamics_in_multiple_myeloma() // Compartments and Species: @@ -108,7 +108,7 @@ model *Gallaher2018___Tumor_Immune_dynamics_in_multiple_myeloma() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / 86400e-1 second; unit unit_1 = 1 / dimensionless^-0; diff --git a/doc/examples/biomodels/BIOMD0000000744/Hu2019.txt b/doc/examples/biomodels/BIOMD0000000744/Hu2019.txt new file mode 100644 index 000000000..cda8bbd14 --- /dev/null +++ b/doc/examples/biomodels/BIOMD0000000744/Hu2019.txt @@ -0,0 +1,266 @@ +// Created by libAntimony v3.2.0 +model *Hu2019___Pancreatic_cancer_dynamics() + + // Compartments and Species: + compartment Pancreatic_tumor; + species x in Pancreatic_tumor, y in Pancreatic_tumor, z in Pancreatic_tumor; + species w in Pancreatic_tumor, v in Pancreatic_tumor; + + // Reactions: + PCC_growth: => x; Pancreatic_tumor*(r1*x*(1 - x*b1)); + PCC_activation_by_PSC: => x; Pancreatic_tumor*(beta1*y*x*(1 - x*b1)); + PCC_death: x => ; Pancreatic_tumor*(delta1*x*z/(m1 + w)); + PSC_growth: => y; Pancreatic_tumor*(r2*y*(1 - b2*y)); + PSC_activation_by_tp_cytokine: => y; Pancreatic_tumor*((beta2*w/(k2 + w))*y*(1 - b2*y)); + PSC_death: y => ; Pancreatic_tumor*(u2*y); + effector_production: => z; Pancreatic_tumor*(beta3*z*v/((k3 + v)*(m3 + w))); + effector_prolif: => z; Pancreatic_tumor*r3; + effector_death: z => ; Pancreatic_tumor*(u3*z); + tp_cytokine_production: => w; Pancreatic_tumor*(beta4*x*z/(k4 + x)); + tp_decay: w => ; Pancreatic_tumor*(u4*w); + tp_stimulation_by_PSC: => w; Pancreatic_tumor*(r4*x*y/(m4 + v)); + ts_production: => v; Pancreatic_tumor*(beta5*x*z/(k5 + x)); + ts_decay: v => ; Pancreatic_tumor*(u5*v); + + // Species initializations: + x = 1000000000; + x has substance_per_volume; + y = 5600000; + y has substance_per_volume; + z = 190000000; + z has substance_per_volume; + w = 50000; + w has substance_per_volume; + v = 9.4; + v has substance_per_volume; + + // Compartment initializations: + Pancreatic_tumor = 1; + Pancreatic_tumor has volume; + + // Variable initializations: + r1 = 0.0195; + r1 has unit_0; + b1 = 1.02e-11; + b1 has unit_1; + beta1 = 3.482115e-12; + beta1 has unit_0; + m1 = 100000000; + m1 has unit_1; + delta1 = 0.96; + delta1 has unit_0; + r2 = 0.00195; + r2 has unit_0; + beta2 = 0.125; + beta2 has unit_0; + k2 = 56000000000; + k2 has unit_1; + b2 = 1.7857e-09; + b2 has unit_1; + u2 = 0.015; + u2 has unit_0; + beta3 = 124.5; + beta3 has unit_0; + k3 = 20000000000; + k3 has unit_1; + m3 = 1000000; + m3 has unit_1; + r3 = 3500; + r3 has unit_0; + u3 = 0.02; + u3 has unit_0; + beta4 = 5.85; + beta4 has unit_0; + k4 = 1000000; + k4 has unit_1; + u4 = 0.034; + u4 has unit_0; + r4 = 12500; + r4 has unit_0; + m4 = 89000000000; + m4 has unit_1; + beta5 = 7.3; + beta5 has unit_0; + k5 = 1000000; + k5 has unit_1; + u5 = 0.034; + u5 has unit_0; + + // Other declarations: + const Pancreatic_tumor, r1, b1, beta1, m1, delta1, r2, beta2, k2, b2, u2; + const beta3, k3, m3, r3, u3, beta4, k4, u4, r4, m4, beta5, k5, u5; + + // Unit definitions: + unit length = metre; + unit area = metre^2; + unit volume = 1e-3 litre; + unit time_unit = 86400 second; + unit substance = 1e-3 mole; + unit unit_0 = 1 / 86400e-1 second; + unit unit_1 = 1 / dimensionless^-0; + unit extent = substance; + unit substance_per_volume = 1e-3 mole / 1e-3 litre; + + // Display Names: + time_unit is "time"; + unit_0 is "1/d"; + unit_1 is "1"; + Pancreatic_tumor is "Pancreatic tumor"; + PCC_growth is "PCC growth"; + PCC_activation_by_PSC is "PCC activation by PSC"; + PCC_death is "PCC death"; + PSC_growth is "PSC growth"; + PSC_activation_by_tp_cytokine is "PSC activation by tp cytokine"; + PSC_death is "PSC death"; + effector_production is "effector production"; + effector_prolif is "effector prolif."; + effector_death is "effector death"; + tp_cytokine_production is "tp cytokine production"; + tp_decay is "tp decay"; + tp_stimulation_by_PSC is "tp stimulation by PSC"; + ts_production is "ts production"; + ts_decay is "ts decay"; + + // CV terms: + Pancreatic_tumor isVersionOf "http://identifiers.org/bto/BTO:0000988" + Pancreatic_tumor isVersionOf "http://identifiers.org/ncit/C94498" + x isVersionOf "http://identifiers.org/ncit/C12917" + x isVersionOf "http://identifiers.org/cl/CL:0001064" + y identity "http://identifiers.org/ncit/C107531" + y identity "http://identifiers.org/cl/CL:0002410" + z hasVersion "http://identifiers.org/ncit/C12536" + z hasVersion "http://identifiers.org/ncit/C12542" + w isVersionOf "http://identifiers.org/ncit/C20464" + v isVersionOf "http://identifiers.org/ncit/C20464" + r1 isVersionOf "http://identifiers.org/sbo/SBO:0000610" + b1 origin "http://identifiers.org/sbo/SBO:0000661" + beta1 isVersionOf "http://identifiers.org/ncit/C94967" + m1 isVersionOf "http://identifiers.org/sbo/SBO:0000193" + delta1 isVersionOf "http://identifiers.org/ncit/C94967" + delta1 isPropertyOf "http://identifiers.org/go/GO:0001909" + r2 isVersionOf "http://identifiers.org/sbo/SBO:0000610" + beta2 isVersionOf "http://identifiers.org/ncit/C94967" + k2 isVersionOf "http://identifiers.org/sbo/SBO:0000193" + b2 origin "http://identifiers.org/sbo/SBO:0000661" + u2 isVersionOf "http://identifiers.org/ncit/C94967" + u2 isPropertyOf "http://identifiers.org/go/GO:0008219" + beta3 isVersionOf "http://identifiers.org/ncit/C94967" + k3 isVersionOf "http://identifiers.org/sbo/SBO:0000193" + m3 isVersionOf "http://identifiers.org/sbo/SBO:0000193" + r3 isVersionOf "http://identifiers.org/sbo/SBO:0000610" + u3 isVersionOf "http://identifiers.org/go/GO:0008219" + u3 isVersionOf "http://identifiers.org/ncit/C94967" + beta4 isVersionOf "http://identifiers.org/ncit/C94967" + beta4 isPropertyOf "http://identifiers.org/go/GO:0001816" + k4 isVersionOf "http://identifiers.org/sbo/SBO:0000193" + u4 isVersionOf "http://identifiers.org/ncit/C94967" + u4 isPropertyOf "http://identifiers.org/ncit/C40678" + r4 isVersionOf "http://identifiers.org/go/GO:0001816" + m4 isVersionOf "http://identifiers.org/sbo/SBO:0000193" + beta5 isVersionOf "http://identifiers.org/ncit/C94967" + beta5 isPropertyOf "http://identifiers.org/go/GO:0001816" + k5 isVersionOf "http://identifiers.org/sbo/SBO:0000193" + u5 isVersionOf "http://identifiers.org/ncit/C94967" + u5 isPropertyOf "http://identifiers.org/ncit/C40678" + PCC_growth isVersionOf "http://identifiers.org/sbo/SBO:0000393" + PCC_growth isVersionOf "http://identifiers.org/go/GO:0008283" + PCC_activation_by_PSC isVersionOf "http://identifiers.org/sbo/SBO:0000393" + PCC_activation_by_PSC isVersionOf "http://identifiers.org/go/GO:0008283" + PCC_death isVersionOf "http://identifiers.org/go/GO:0008219" + PCC_death isVersionOf "http://identifiers.org/sbo/SBO:0000179" + PSC_growth isVersionOf "http://identifiers.org/go/GO:0008283" + PSC_growth isVersionOf "http://identifiers.org/sbo/SBO:0000393" + PSC_activation_by_tp_cytokine isVersionOf "http://identifiers.org/sbo/SBO:0000393" + PSC_activation_by_tp_cytokine isVersionOf "http://identifiers.org/go/GO:0008283" + PSC_death isVersionOf "http://identifiers.org/go/GO:0008219" + PSC_death isVersionOf "http://identifiers.org/sbo/SBO:0000179" + effector_production isVersionOf "http://identifiers.org/go/GO:0046651" + effector_production isVersionOf "http://identifiers.org/sbo/SBO:0000393" + effector_prolif isVersionOf "http://identifiers.org/sbo/SBO:0000393" + effector_prolif isVersionOf "http://identifiers.org/go/GO:0046651" + effector_death isVersionOf "http://identifiers.org/go/GO:0008219" + effector_death isVersionOf "http://identifiers.org/sbo/SBO:0000179" + tp_cytokine_production isVersionOf "http://identifiers.org/sbo/SBO:0000393" + tp_cytokine_production isVersionOf "http://identifiers.org/go/GO:0001816" + tp_decay isVersionOf "http://identifiers.org/ncit/C40678" + tp_decay isVersionOf "http://identifiers.org/sbo/SBO:0000179" + tp_stimulation_by_PSC isVersionOf "http://identifiers.org/sbo/SBO:0000393" + tp_stimulation_by_PSC isVersionOf "http://identifiers.org/go/GO:0001816" + ts_production isVersionOf "http://identifiers.org/sbo/SBO:0000393" + ts_production isVersionOf "http://identifiers.org/go/GO:0001816" + ts_decay isVersionOf "http://identifiers.org/sbo/SBO:0000179" + ts_decay isVersionOf "http://identifiers.org/ncit/C40678" + + model model_source "http://identifiers.org/biomodels.db/MODEL1907050003", + "http://identifiers.org/biomodels.db/BIOMD0000000744" + model publication "http://identifiers.org/pubmed/30843136" + model isVersionOf "http://identifiers.org/go/GO:0002418" + model occursIn "http://identifiers.org/bto/BTO:0000988" + model hasProperty "http://identifiers.org/efo/0002618" + model hasProperty "http://identifiers.org/mamo/MAMO_0000046" + model hasTaxon "http://identifiers.org/taxonomy/9606" + model created "2019-07-04T08:26:17Z" + model modified "2019-07-04T08:26:17Z" + model creator1.givenName "Jinghao" + model creator1.familyName "Men" + model creator1.organization "University of Cambridge" + model creator1.email "jm2187@cam.ac.uk" + + // Notes: + model notes ``` +The paper describes a model on the size of pancreatic tumour. Created by COPASI +4.25 (Build 207) This model is described in the article: Modeling Pancreatic Cancer +Dynamics with Immunotherapy Xiaochuan Hu, Guoyi Ke and Sophia R.-J. Jang Bulletin +of Mathematical Biology (2019) 81:1885–1915 Abstract: We develop a mathematical +model of pancreatic cancer that includes pancreatic cancer cells, pancreatic stellate +cells, effector cells and tumor-promoting and tumor- suppressing cytokines to investigate +the effects of immunotherapies on patient survival. The model is first validated +using the survival data of two clinical trials. Local sen- sitivity analysis of the +parameters indicates there exists a critical activation rate of pro-tumor cytokines +beyond which the cancer can be eradicated if four adoptive trans- fers of immune +cells are applied. Optimal control theory is explored as a potential tool for searching +the best adoptive cellular immunotherapies. Combined immunother- apies between adoptive +ex vivo expanded immune cells and TGF-β inhibition by siRNA treatments are investigated. +This study concludes that mono-immunotherapy is unlikely to control the pancreatic +cancer and combined immunotherapies between anti-TGF-β and adoptive transfers of +immune cells can prolong patient survival. We show through numerical explorations +that how these two types of immunotherapies are scheduled is important to survival. +Applying TGF-β inhibition first followed by adoptive immune cell transfers can yield +better survival outcomes. This model is hosted on BioModels Database and identified +by: MODEL1907050003. To cite BioModels Database, please use: BioModels Database: +An enhanced, curated and annotated resource for published quantitative kinetic models . +To the extent possible under law, all copyright and related or neighbouring rights +to this encoded model have been dedicated to the public domain worldwide. Please +refer to CC0 Public Domain Dedication for more information. +``` + x notes "PCC population" + y notes "PSC population" + z notes "effector cells: CTL and NKinit. low: 1.3e8median: 1.9e8high: 2.56e8" + w notes "conc. of tumor-promoting cytokinepg/ml" + v notes "conc. of tumor-suppressing cytokinepg/ml" + r1 notes "intrinsic growth rate of PCC" + b1 notes "reciprocal of carrying capacity of PCC" + beta1 notes "maximum activation rate of PCC due to PSC" + m1 notes "conc. of tp cytokines at half-maximum of inhibition" + delta1 notes "maximum killing rate of pcc by effector cells" + r2 notes "intrinsic growth rate of PSC" + beta2 notes "maximum activation rate of PSC due to tp cytokine" + k2 notes "half saturation const. of PSC activation rate" + b2 notes "reciprocal of carrying capacity of PSC" + u2 notes "natural death rate of psc" + beta3 notes "maximum production rate of effector cells" + k3 notes "half saturation const. of effector cell production rate" + m3 notes "conc. of tp cytokines at half maximum of inhibition" + r3 notes "natural prolif. rate of effector cell" + u3 notes "apoptosis rate of effector cells" + beta4 notes "maximum production rate of tp cytokine" + k4 notes "half saturation const. of tp cytokine production" + u4 notes "decay rate of tp cytokines" + r4 notes "maximum production rate of tumor-promoting cytoking" + m4 notes "conc. of ts cytokines at half-maximum of inhibition" + beta5 notes "maximum production rate of ts cytokine" + k5 notes "half saturation const. of ts cytokine production" + u5 notes "decay rate of ts cytokines" +end + +Hu2019___Pancreatic_cancer_dynamics is "Hu2019 - Pancreatic cancer dynamics" diff --git a/doc/examples/biomodels/Jarrett2018.txt b/doc/examples/biomodels/BIOMD0000000745/Jarrett2018.txt similarity index 99% rename from doc/examples/biomodels/Jarrett2018.txt rename to doc/examples/biomodels/BIOMD0000000745/Jarrett2018.txt index 2c1e29fe6..fcb108d63 100644 --- a/doc/examples/biomodels/Jarrett2018.txt +++ b/doc/examples/biomodels/BIOMD0000000745/Jarrett2018.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Jarrett2018___trastuzumab_induced_immune_response_in_murine_HER2__breast_cancer_model_1() // Compartments and Species: @@ -68,7 +68,7 @@ model *Jarrett2018___trastuzumab_induced_immune_response_in_murine_HER2__breast_ unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / 1e-3 second; unit unit_1 = 1 / dimensionless^-0; diff --git a/doc/examples/biomodels/Saad2017-no checkpoint.txt b/doc/examples/biomodels/BIOMD0000000746/Saad2017-no checkpoint.txt similarity index 99% rename from doc/examples/biomodels/Saad2017-no checkpoint.txt rename to doc/examples/biomodels/BIOMD0000000746/Saad2017-no checkpoint.txt index ea6653f3d..fda59c4a6 100644 --- a/doc/examples/biomodels/Saad2017-no checkpoint.txt +++ b/doc/examples/biomodels/BIOMD0000000746/Saad2017-no checkpoint.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Saad2017___immune_checkpoint_and_BCG_in_superficial_bladder_cancer() // Compartments and Species: @@ -55,7 +55,7 @@ model *Saad2017___immune_checkpoint_and_BCG_in_superficial_bladder_cancer() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / 86400e-1 second; unit extent = substance; diff --git a/doc/examples/biomodels/Saad2017-no treatment.txt b/doc/examples/biomodels/BIOMD0000000746/Saad2017-no treatment.txt similarity index 99% rename from doc/examples/biomodels/Saad2017-no treatment.txt rename to doc/examples/biomodels/BIOMD0000000746/Saad2017-no treatment.txt index c7cf28d27..5fcbebcba 100644 --- a/doc/examples/biomodels/Saad2017-no treatment.txt +++ b/doc/examples/biomodels/BIOMD0000000746/Saad2017-no treatment.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Saad2017___immune_checkpoint_and_BCG_in_superficial_bladder_cancer() // Compartments and Species: @@ -64,7 +64,7 @@ model *Saad2017___immune_checkpoint_and_BCG_in_superficial_bladder_cancer() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / 86400e-1 second; unit unit_1 = 1 / dimensionless^-0; diff --git a/doc/examples/biomodels/Saad2017.txt b/doc/examples/biomodels/BIOMD0000000746/Saad2017.txt similarity index 99% rename from doc/examples/biomodels/Saad2017.txt rename to doc/examples/biomodels/BIOMD0000000746/Saad2017.txt index 0d8670f87..dbdd828b4 100644 --- a/doc/examples/biomodels/Saad2017.txt +++ b/doc/examples/biomodels/BIOMD0000000746/Saad2017.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Saad2017___immune_checkpoint_and_BCG_in_superficial_bladder_cancer() // Compartments and Species: @@ -67,7 +67,7 @@ model *Saad2017___immune_checkpoint_and_BCG_in_superficial_bladder_cancer() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / 86400e-1 second; unit unit_1 = 1 / dimensionless^-0; diff --git a/doc/examples/biomodels/Nagashima2002.txt b/doc/examples/biomodels/BIOMD0000000747/Nagashima2002.txt similarity index 99% rename from doc/examples/biomodels/Nagashima2002.txt rename to doc/examples/biomodels/BIOMD0000000747/Nagashima2002.txt index 8f1718a00..251ba6444 100644 --- a/doc/examples/biomodels/Nagashima2002.txt +++ b/doc/examples/biomodels/BIOMD0000000747/Nagashima2002.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Nagashima2002___Simulating_blood_coagulation_inhibitory_effects() // Compartments and Species: diff --git a/doc/examples/biomodels/Phan2017.txt b/doc/examples/biomodels/BIOMD0000000748/Phan2017.txt similarity index 99% rename from doc/examples/biomodels/Phan2017.txt rename to doc/examples/biomodels/BIOMD0000000748/Phan2017.txt index 7bc20f574..f10902e00 100644 --- a/doc/examples/biomodels/Phan2017.txt +++ b/doc/examples/biomodels/BIOMD0000000748/Phan2017.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Phan2017___innate_immune_in_oncolytic_virotherapy() // Compartments and Species: @@ -58,7 +58,7 @@ model *Phan2017___innate_immune_in_oncolytic_virotherapy() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-3 mole; unit unit_0 = 1 / dimensionless^-0; unit extent = substance; diff --git a/doc/examples/biomodels/Reppas2015.txt b/doc/examples/biomodels/BIOMD0000000749/Reppas2015.txt similarity index 99% rename from doc/examples/biomodels/Reppas2015.txt rename to doc/examples/biomodels/BIOMD0000000749/Reppas2015.txt index 6b974bbd7..803e97787 100644 --- a/doc/examples/biomodels/Reppas2015.txt +++ b/doc/examples/biomodels/BIOMD0000000749/Reppas2015.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Reppas2015___tumor_control_via_alternating_immunostimulating_and_immunosuppressive_phases() // Compartments and Species: @@ -62,7 +62,7 @@ model *Reppas2015___tumor_control_via_alternating_immunostimulating_and_immunosu unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / dimensionless^-0; unit unit_1 = 1 / 86400e-1 second; diff --git a/doc/examples/biomodels/Lolas2016.txt b/doc/examples/biomodels/BIOMD0000000750/Lolas2016.txt similarity index 99% rename from doc/examples/biomodels/Lolas2016.txt rename to doc/examples/biomodels/BIOMD0000000750/Lolas2016.txt index 71744fa0e..4a0f707db 100644 --- a/doc/examples/biomodels/Lolas2016.txt +++ b/doc/examples/biomodels/BIOMD0000000750/Lolas2016.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Lolas2016___tumour_induced_neoneurogenesis_and_perineural_tumour_growth() // Compartments and Species: @@ -153,7 +153,7 @@ model *Lolas2016___tumour_induced_neoneurogenesis_and_perineural_tumour_growth() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / 86400e-1 second; unit unit_1 = 86400e-1 second / (1e-3 metre)^3; diff --git a/doc/examples/biomodels/Wilkie2013b.txt b/doc/examples/biomodels/BIOMD0000000751/Wilkie2013b.txt similarity index 98% rename from doc/examples/biomodels/Wilkie2013b.txt rename to doc/examples/biomodels/BIOMD0000000751/Wilkie2013b.txt index 88d152b8a..359346ecb 100644 --- a/doc/examples/biomodels/Wilkie2013b.txt +++ b/doc/examples/biomodels/BIOMD0000000751/Wilkie2013b.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wilkie2013b___immune_induced_cancer_dormancy_and_immune_evasion_basic() // Compartments and Species: @@ -44,7 +44,7 @@ model *Wilkie2013b___immune_induced_cancer_dormancy_and_immune_evasion_basic() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-3 mole; unit unit_0 = 1 / dimensionless^-0; unit extent = substance; diff --git a/doc/examples/biomodels/Wilkie2013r.txt b/doc/examples/biomodels/BIOMD0000000752/Wilkie2013r.txt similarity index 99% rename from doc/examples/biomodels/Wilkie2013r.txt rename to doc/examples/biomodels/BIOMD0000000752/Wilkie2013r.txt index d8a0fb96e..fbd3465f1 100644 --- a/doc/examples/biomodels/Wilkie2013r.txt +++ b/doc/examples/biomodels/BIOMD0000000752/Wilkie2013r.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wilkie2013r___immune_induced_cancer_dormancy_and_immune_evasion_resistance() // Compartments and Species: @@ -54,7 +54,7 @@ model *Wilkie2013r___immune_induced_cancer_dormancy_and_immune_evasion_resistanc unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-3 mole; unit unit_0 = 1 / dimensionless^-0; unit extent = substance; diff --git a/doc/examples/biomodels/Figueredo2013_1.txt b/doc/examples/biomodels/BIOMD0000000753/Figueredo2013_1.txt similarity index 99% rename from doc/examples/biomodels/Figueredo2013_1.txt rename to doc/examples/biomodels/BIOMD0000000753/Figueredo2013_1.txt index 2eff790ee..8c0fe8130 100644 --- a/doc/examples/biomodels/Figueredo2013_1.txt +++ b/doc/examples/biomodels/BIOMD0000000753/Figueredo2013_1.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Figueredo2013_1___immunointeraction_base_model() // Compartments and Species: @@ -49,7 +49,7 @@ model *Figueredo2013_1___immunointeraction_base_model() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-3 mole; unit unit_0 = 1 / dimensionless^-0; unit extent = substance; diff --git a/doc/examples/biomodels/Figueredo2013_2.txt b/doc/examples/biomodels/BIOMD0000000754/Figueredo2013_2.txt similarity index 99% rename from doc/examples/biomodels/Figueredo2013_2.txt rename to doc/examples/biomodels/BIOMD0000000754/Figueredo2013_2.txt index 0cf16c641..1bb866444 100644 --- a/doc/examples/biomodels/Figueredo2013_2.txt +++ b/doc/examples/biomodels/BIOMD0000000754/Figueredo2013_2.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Figueredo2013_2___immunointeraction_model_with_IL2() // Compartments and Species: @@ -65,7 +65,7 @@ model *Figueredo2013_2___immunointeraction_model_with_IL2() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-3 mole; unit unit_0 = 1 / dimensionless^-0; unit extent = substance; diff --git a/doc/examples/biomodels/Hansen2019.txt b/doc/examples/biomodels/BIOMD0000000755/Hansen2019.txt similarity index 99% rename from doc/examples/biomodels/Hansen2019.txt rename to doc/examples/biomodels/BIOMD0000000755/Hansen2019.txt index 2a16eb9b6..f0aa16187 100644 --- a/doc/examples/biomodels/Hansen2019.txt +++ b/doc/examples/biomodels/BIOMD0000000755/Hansen2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hansen2019___Nine_species_reduced_model_of_blood_coagulation() // Compartments and Species: diff --git a/doc/examples/biomodels/Figueredo2013_3.txt b/doc/examples/biomodels/BIOMD0000000756/Figueredo2013_3.txt similarity index 99% rename from doc/examples/biomodels/Figueredo2013_3.txt rename to doc/examples/biomodels/BIOMD0000000756/Figueredo2013_3.txt index 1e5d90ac4..8c2f789b7 100644 --- a/doc/examples/biomodels/Figueredo2013_3.txt +++ b/doc/examples/biomodels/BIOMD0000000756/Figueredo2013_3.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Figueredo2013_3___immunointeraction_full_model() // Compartments and Species: @@ -83,7 +83,7 @@ model *Figueredo2013_3___immunointeraction_full_model() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-3 mole; unit unit_0 = 1 / dimensionless^-0; unit extent = substance; diff --git a/doc/examples/biomodels/Abernathy2016.txt b/doc/examples/biomodels/BIOMD0000000757/Abernathy2016.txt similarity index 99% rename from doc/examples/biomodels/Abernathy2016.txt rename to doc/examples/biomodels/BIOMD0000000757/Abernathy2016.txt index a11ef9fc8..53199b4da 100644 --- a/doc/examples/biomodels/Abernathy2016.txt +++ b/doc/examples/biomodels/BIOMD0000000757/Abernathy2016.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Abernathy2016___glioblastoma_treatment() // Compartments and Species: @@ -133,7 +133,7 @@ model *Abernathy2016___glioblastoma_treatment() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 3600 second; unit substance = 1e-3 mole; unit unit_0 = 1 / 3600e2 second; unit unit_1 = 1 / dimensionless^-0; diff --git a/doc/examples/biomodels/Babbs2012.txt b/doc/examples/biomodels/BIOMD0000000758/Babbs2012.txt similarity index 98% rename from doc/examples/biomodels/Babbs2012.txt rename to doc/examples/biomodels/BIOMD0000000758/Babbs2012.txt index 59ccfdb8c..00ee3e4d7 100644 --- a/doc/examples/biomodels/Babbs2012.txt +++ b/doc/examples/biomodels/BIOMD0000000758/Babbs2012.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Babbs2012___immunotherapy() // Compartments and Species: @@ -38,7 +38,7 @@ model *Babbs2012___immunotherapy() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / 86400e-1 second; unit extent = substance; diff --git a/doc/examples/biomodels/denBreems2015.txt b/doc/examples/biomodels/BIOMD0000000759/denBreems2015.txt similarity index 99% rename from doc/examples/biomodels/denBreems2015.txt rename to doc/examples/biomodels/BIOMD0000000759/denBreems2015.txt index 8ae3af854..55a4987ad 100644 --- a/doc/examples/biomodels/denBreems2015.txt +++ b/doc/examples/biomodels/BIOMD0000000759/denBreems2015.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *den_Breems2015___macrophage_in_cancer() // Compartments and Species: diff --git a/doc/examples/biomodels/Feizabadi2011_1.txt b/doc/examples/biomodels/BIOMD0000000760/Feizabadi2011_1.txt similarity index 99% rename from doc/examples/biomodels/Feizabadi2011_1.txt rename to doc/examples/biomodels/BIOMD0000000760/Feizabadi2011_1.txt index 933b9dbdd..595878128 100644 --- a/doc/examples/biomodels/Feizabadi2011_1.txt +++ b/doc/examples/biomodels/BIOMD0000000760/Feizabadi2011_1.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Feizabadi2011_1___immunodeficiency_in_cancer_core_model() // Compartments and Species: diff --git a/doc/examples/biomodels/Cappuccio2006 v2.0.txt b/doc/examples/biomodels/BIOMD0000000761/Cappuccio2006 v2.0.txt similarity index 99% rename from doc/examples/biomodels/Cappuccio2006 v2.0.txt rename to doc/examples/biomodels/BIOMD0000000761/Cappuccio2006 v2.0.txt index 3c85bf351..fdb4ebe8d 100644 --- a/doc/examples/biomodels/Cappuccio2006 v2.0.txt +++ b/doc/examples/biomodels/BIOMD0000000761/Cappuccio2006 v2.0.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/Kuznetsov1994.txt b/doc/examples/biomodels/BIOMD0000000762/Kuznetsov1994.txt similarity index 98% rename from doc/examples/biomodels/Kuznetsov1994.txt rename to doc/examples/biomodels/BIOMD0000000762/Kuznetsov1994.txt index 99b968465..3fef8cfbe 100644 --- a/doc/examples/biomodels/Kuznetsov1994.txt +++ b/doc/examples/biomodels/BIOMD0000000762/Kuznetsov1994.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kuznetsov1994___Nonlinear_dynamics_of_immunogenic_tumors() // Compartments and Species: diff --git a/doc/examples/biomodels/Dritschel2018.txt b/doc/examples/biomodels/BIOMD0000000763/Dritschel2018.txt similarity index 99% rename from doc/examples/biomodels/Dritschel2018.txt rename to doc/examples/biomodels/BIOMD0000000763/Dritschel2018.txt index cf4338931..37716d583 100644 --- a/doc/examples/biomodels/Dritschel2018.txt +++ b/doc/examples/biomodels/BIOMD0000000763/Dritschel2018.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *L2V4_Model_of_Dritschel2018___A_mathematical_model_of_cytotoxic_and_helper_T_cell_interactions_in_a_tumour_microenvironment() // Compartments and Species: diff --git a/doc/examples/biomodels/Malinzi2019.txt b/doc/examples/biomodels/BIOMD0000000764/Malinzi2019.txt similarity index 99% rename from doc/examples/biomodels/Malinzi2019.txt rename to doc/examples/biomodels/BIOMD0000000764/Malinzi2019.txt index cc4bae341..fb7311a57 100644 --- a/doc/examples/biomodels/Malinzi2019.txt +++ b/doc/examples/biomodels/BIOMD0000000764/Malinzi2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Malinzi2019___chemovirotherapy() // Compartments and Species: @@ -91,7 +91,7 @@ model *Malinzi2019___chemovirotherapy() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-3 mole; unit unit_0 = 1 / dimensionless^-0; unit extent = substance; diff --git a/doc/examples/biomodels/Mager2005.txt b/doc/examples/biomodels/BIOMD0000000765/Mager2005.txt similarity index 99% rename from doc/examples/biomodels/Mager2005.txt rename to doc/examples/biomodels/BIOMD0000000765/Mager2005.txt index 0a24eba8f..4810f15d3 100644 --- a/doc/examples/biomodels/Mager2005.txt +++ b/doc/examples/biomodels/BIOMD0000000765/Mager2005.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Mager2005___Quasi_equilibrium_pharmacokinetic_model_for_drugs_exhibiting_target_mediated_drug_disposition() // Compartments and Species: diff --git a/doc/examples/biomodels/Macnamara2015_1.txt b/doc/examples/biomodels/BIOMD0000000766/Macnamara2015_1.txt similarity index 99% rename from doc/examples/biomodels/Macnamara2015_1.txt rename to doc/examples/biomodels/BIOMD0000000766/Macnamara2015_1.txt index 64cf5f0b3..488654370 100644 --- a/doc/examples/biomodels/Macnamara2015_1.txt +++ b/doc/examples/biomodels/BIOMD0000000766/Macnamara2015_1.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Macnamara2015_1___virotherapy_full_model() // Compartments and Species: @@ -73,7 +73,7 @@ model *Macnamara2015_1___virotherapy_full_model() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / 86400e-1 second; unit unit_1 = 1 / dimensionless^-0; diff --git a/doc/examples/biomodels/Macnamara2015_2.txt b/doc/examples/biomodels/BIOMD0000000767/Macnamara2015_2.txt similarity index 98% rename from doc/examples/biomodels/Macnamara2015_2.txt rename to doc/examples/biomodels/BIOMD0000000767/Macnamara2015_2.txt index c137bb140..31b231a25 100644 --- a/doc/examples/biomodels/Macnamara2015_2.txt +++ b/doc/examples/biomodels/BIOMD0000000767/Macnamara2015_2.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Macnamara2015_2___virotherapy_virus_free_submodel() // Compartments and Species: @@ -49,7 +49,7 @@ model *Macnamara2015_2___virotherapy_virus_free_submodel() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / 86400e-1 second; unit unit_1 = 1 / dimensionless^-0; diff --git a/doc/examples/biomodels/Eftimie2010.txt b/doc/examples/biomodels/BIOMD0000000768/Eftimie2010.txt similarity index 99% rename from doc/examples/biomodels/Eftimie2010.txt rename to doc/examples/biomodels/BIOMD0000000768/Eftimie2010.txt index 03a5488ba..ac250cabe 100644 --- a/doc/examples/biomodels/Eftimie2010.txt +++ b/doc/examples/biomodels/BIOMD0000000768/Eftimie2010.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Eftimie2010___immunity_to_melanoma() // Compartments and Species: @@ -95,7 +95,7 @@ model *Eftimie2010___immunity_to_melanoma() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / 86400e-1 second; unit unit_1 = 1 / dimensionless^-0; diff --git a/doc/examples/biomodels/Eftimie2017_2.txt b/doc/examples/biomodels/BIOMD0000000769/Eftimie2017_2.txt similarity index 99% rename from doc/examples/biomodels/Eftimie2017_2.txt rename to doc/examples/biomodels/BIOMD0000000769/Eftimie2017_2.txt index df3e78060..df9afc051 100644 --- a/doc/examples/biomodels/Eftimie2017_2.txt +++ b/doc/examples/biomodels/BIOMD0000000769/Eftimie2017_2.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Eftimie2017_2___interaction_of_Th_and_macrophage_in_melanoma() // Compartments and Species: @@ -111,7 +111,7 @@ model *Eftimie2017_2___interaction_of_Th_and_macrophage_in_melanoma() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / 86400e-1 second; unit unit_1 = 1 / dimensionless^-0; diff --git a/doc/examples/biomodels/Eftimie2017_1.txt b/doc/examples/biomodels/BIOMD0000000770/Eftimie2017_1.txt similarity index 99% rename from doc/examples/biomodels/Eftimie2017_1.txt rename to doc/examples/biomodels/BIOMD0000000770/Eftimie2017_1.txt index b40a45e61..2982e561c 100644 --- a/doc/examples/biomodels/Eftimie2017_1.txt +++ b/doc/examples/biomodels/BIOMD0000000770/Eftimie2017_1.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Eftimie2017_1___interaction_of_Th_and_macrophage() // Compartments and Species: @@ -77,7 +77,7 @@ model *Eftimie2017_1___interaction_of_Th_and_macrophage() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / 86400e-1 second; unit unit_1 = 1 / dimensionless^-0; diff --git a/doc/examples/biomodels/Bazjer2008.txt b/doc/examples/biomodels/BIOMD0000000771/Bazjer2008.txt similarity index 98% rename from doc/examples/biomodels/Bazjer2008.txt rename to doc/examples/biomodels/BIOMD0000000771/Bazjer2008.txt index 6feb203ab..d8314c5fc 100644 --- a/doc/examples/biomodels/Bazjer2008.txt +++ b/doc/examples/biomodels/BIOMD0000000771/Bazjer2008.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bajzer2008___Modeling_of_cancer_virotherapy_with_recombinant_measles_viruses() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000772/Wang2019.txt b/doc/examples/biomodels/BIOMD0000000772/Wang2019.txt new file mode 100644 index 000000000..77874e5dc --- /dev/null +++ b/doc/examples/biomodels/BIOMD0000000772/Wang2019.txt @@ -0,0 +1,84 @@ +// Created by libAntimony v3.2.0 +model *Wang2019___A_mathematical_model_of_oncolytic_virotherapy_with_time_delay() + + // Compartments and Species: + compartment compartment_; + species x in compartment_, I in compartment_, y in compartment_, z in compartment_; + + // Reactions: + Uninfected_Cells_Proliferation: => x; compartment_*(r*x*(1 - (x + y)/k)); + Uninfected_Cells_Infection: x + y => I; compartment_*b*x*y; + Length_of_Eclipse_Phase: I => y; compartment_*(b*exp(-n*tau)*x*y); + Cytotoxicity: y => ; compartment_*a*y; + Immune_Kill: y => ; compartment_*(p*y*z); + Stimulation: => z; compartment_*(c*y*z); + Clearance: z => ; compartment_*d*z; + + // Species initializations: + x = 200; + I = 0; + y = 800; + z = 100; + + // Compartment initializations: + compartment_ = 1; + + // Variable initializations: + r = 0.206; + k = 2139; + b = 0.000448; + tau = 0; + a = 1; + p = 0.01; + c = 0.02; + d = 0.5; + n = 0.01; + + // Other declarations: + const compartment_, r, k, b, tau, a, p, c, d, n; + + // Unit definitions: + unit volume = 1e-3 litre; + unit time_unit = 86400 second; + unit substance = 1e-3 mole; + + // Display Names: + time_unit is "time"; + compartment_ is "compartment"; + + // CV terms: + compartment_ isVersionOf "http://identifiers.org/ncit/C94498" + x isVersionOf "http://identifiers.org/cl/CL:0000000" + I isVersionOf "http://identifiers.org/go/GO:0098689" + y isVersionOf "http://identifiers.org/bto/BTO:0000152" + z isVersionOf "http://identifiers.org/cl/CL:0000910" + Uninfected_Cells_Proliferation isVersionOf "http://identifiers.org/ncit/C18081" + Uninfected_Cells_Infection isVersionOf "http://identifiers.org/ncit/C3439" + Length_of_Eclipse_Phase isVersionOf "http://identifiers.org/go/GO:0098689" + Cytotoxicity isVersionOf "http://identifiers.org/ncit/C27988" + Immune_Kill isVersionOf "http://identifiers.org/go/GO:0001906" + Stimulation isVersionOf "http://identifiers.org/ncit/C39042" + Clearance isVersionOf "http://identifiers.org/go/GO:0008219" + + model publication "http://identifiers.org/pubmed/31137188" + model origin "http://identifiers.org/pubmed/11309314" + model model_source "http://identifiers.org/biomodels.db/MODEL1908010001", + "http://identifiers.org/biomodels.db/BIOMD0000000772" + model hasProperty "http://identifiers.org/ncit/C62713" + model hasProperty "http://identifiers.org/mamo/MAMO_0000089" + model created "2019-08-01T09:37:14Z" + model modified "2019-08-01T09:37:14Z" + model creator1.givenName "Johannes" + model creator1.familyName "Meyer" + model creator1.organization "EMBL-EBI" + model creator1.email "johannes.p.meyer@gmail.com" + + // Notes: + model notes ``` +A mathematical model describing oncolytic virotherapy with incorporation the viral +lytic cycle and the virus-specific CTL response. The thresholds for viral treatment +and virus-specific CTl response are also obtained. +``` +end + +Wang2019___A_mathematical_model_of_oncolytic_virotherapy_with_time_delay is "Wang2019 - A mathematical model of oncolytic virotherapy with time delay" diff --git a/doc/examples/biomodels/Wodarz2018_2.txt b/doc/examples/biomodels/BIOMD0000000773/Wodarz2018_2.txt similarity index 99% rename from doc/examples/biomodels/Wodarz2018_2.txt rename to doc/examples/biomodels/BIOMD0000000773/Wodarz2018_2.txt index 92480da8e..dce54ec0d 100644 --- a/doc/examples/biomodels/Wodarz2018_2.txt +++ b/doc/examples/biomodels/BIOMD0000000773/Wodarz2018_2.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wodarz2018_2___model_with_transit_amplifying_cells() // Compartments and Species: @@ -79,7 +79,7 @@ model *Wodarz2018_2___model_with_transit_amplifying_cells() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-3 mole; unit unit_0 = 1 / dimensionless^-0; unit extent = substance; diff --git a/doc/examples/biomodels/Wodarz2018_1.txt b/doc/examples/biomodels/BIOMD0000000774/Wodarz2018_1.txt similarity index 99% rename from doc/examples/biomodels/Wodarz2018_1.txt rename to doc/examples/biomodels/BIOMD0000000774/Wodarz2018_1.txt index d60ffa8cd..eed1d32f6 100644 --- a/doc/examples/biomodels/Wodarz2018_1.txt +++ b/doc/examples/biomodels/BIOMD0000000774/Wodarz2018_1.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wodarz2018_1___simple_model() // Compartments and Species: @@ -59,7 +59,7 @@ model *Wodarz2018_1___simple_model() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-3 mole; unit unit_0 = 1 / dimensionless^-0; unit extent = substance; diff --git a/doc/examples/biomodels/Iarosz2015.txt b/doc/examples/biomodels/BIOMD0000000775/Iarosz2015.txt similarity index 99% rename from doc/examples/biomodels/Iarosz2015.txt rename to doc/examples/biomodels/BIOMD0000000775/Iarosz2015.txt index bddf72956..dc988c9d1 100644 --- a/doc/examples/biomodels/Iarosz2015.txt +++ b/doc/examples/biomodels/BIOMD0000000775/Iarosz2015.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Iarosz2015___brain_tumor() // Compartments and Species: @@ -73,7 +73,7 @@ model *Iarosz2015___brain_tumor() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / 86400e-1 second; unit unit_1 = 1 / dimensionless^-0; diff --git a/doc/examples/biomodels/Monro2008.txt b/doc/examples/biomodels/BIOMD0000000776/Monro2008.txt similarity index 98% rename from doc/examples/biomodels/Monro2008.txt rename to doc/examples/biomodels/BIOMD0000000776/Monro2008.txt index 754a09a46..62e09937e 100644 --- a/doc/examples/biomodels/Monro2008.txt +++ b/doc/examples/biomodels/BIOMD0000000776/Monro2008.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Monro2008___chemotherapy_resistance() // Compartments and Species: @@ -47,7 +47,7 @@ model *Monro2008___chemotherapy_resistance() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / 86400e-1 second; unit unit_1 = 1 / dimensionless^-0; diff --git a/doc/examples/biomodels/Chakrabarty2010.txt b/doc/examples/biomodels/BIOMD0000000777/Chakrabarty2010.txt similarity index 99% rename from doc/examples/biomodels/Chakrabarty2010.txt rename to doc/examples/biomodels/BIOMD0000000777/Chakrabarty2010.txt index 8c62bff39..3f7918b6f 100644 --- a/doc/examples/biomodels/Chakrabarty2010.txt +++ b/doc/examples/biomodels/BIOMD0000000777/Chakrabarty2010.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Chakrabarty2010___A_control_theory_approach_to_cancer_remission_aided_by_an_optimal_therapy() // Compartments and Species: diff --git a/doc/examples/biomodels/Wei2017.txt b/doc/examples/biomodels/BIOMD0000000778/Wei2017.txt similarity index 99% rename from doc/examples/biomodels/Wei2017.txt rename to doc/examples/biomodels/BIOMD0000000778/Wei2017.txt index dff400ee0..f6b3ceaa5 100644 --- a/doc/examples/biomodels/Wei2017.txt +++ b/doc/examples/biomodels/BIOMD0000000778/Wei2017.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wei2017___tumor__T_cell_and_cytokine_interaction() // Compartments and Species: @@ -67,7 +67,7 @@ model *Wei2017___tumor__T_cell_and_cytokine_interaction() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / 86400e-1 second; unit unit_1 = 1 / dimensionless^-0; diff --git a/doc/examples/biomodels/dePillis2009.txt b/doc/examples/biomodels/BIOMD0000000779/dePillis2009.txt similarity index 99% rename from doc/examples/biomodels/dePillis2009.txt rename to doc/examples/biomodels/BIOMD0000000779/dePillis2009.txt index 747a778ef..801578f61 100644 --- a/doc/examples/biomodels/dePillis2009.txt +++ b/doc/examples/biomodels/BIOMD0000000779/dePillis2009.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *dePillis2009___Mathematical_model_creation_for_cancer_chemo_immunotherapy() // Compartments and Species: diff --git a/doc/examples/biomodels/Wang2016_1.txt b/doc/examples/biomodels/BIOMD0000000780/Wang2016_1.txt similarity index 99% rename from doc/examples/biomodels/Wang2016_1.txt rename to doc/examples/biomodels/BIOMD0000000780/Wang2016_1.txt index f78796649..ae19d28f2 100644 --- a/doc/examples/biomodels/Wang2016_1.txt +++ b/doc/examples/biomodels/BIOMD0000000780/Wang2016_1.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wang2016_1___oncolytic_efficacy_of_M1_virus_SNTM_model() // Compartments and Species: @@ -75,7 +75,7 @@ model *Wang2016_1___oncolytic_efficacy_of_M1_virus_SNTM_model() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-3 mole; unit unit_0 = 1 / dimensionless^-0; unit extent = substance; diff --git a/doc/examples/biomodels/Wang2016_2.txt b/doc/examples/biomodels/BIOMD0000000781/Wang2016_2.txt similarity index 99% rename from doc/examples/biomodels/Wang2016_2.txt rename to doc/examples/biomodels/BIOMD0000000781/Wang2016_2.txt index 676e7d838..6efdc9e71 100644 --- a/doc/examples/biomodels/Wang2016_2.txt +++ b/doc/examples/biomodels/BIOMD0000000781/Wang2016_2.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wang2016_2___oncolytic_efficacy_of_M1_virus_SNT_model() // Compartments and Species: @@ -59,7 +59,7 @@ model *Wang2016_2___oncolytic_efficacy_of_M1_virus_SNT_model() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-3 mole; unit unit_0 = 1 / dimensionless^-0; unit extent = substance; diff --git a/doc/examples/biomodels/Wang2016_3.txt b/doc/examples/biomodels/BIOMD0000000782/Wang2016_3.txt similarity index 98% rename from doc/examples/biomodels/Wang2016_3.txt rename to doc/examples/biomodels/BIOMD0000000782/Wang2016_3.txt index b34ebb869..3205f5d23 100644 --- a/doc/examples/biomodels/Wang2016_3.txt +++ b/doc/examples/biomodels/BIOMD0000000782/Wang2016_3.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wang2016_3___oncolytic_efficacy_of_M1_virus_SN_model() // Compartments and Species: @@ -46,7 +46,7 @@ model *Wang2016_3___oncolytic_efficacy_of_M1_virus_SN_model() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-3 mole; unit unit_0 = 1 / dimensionless^-0; unit extent = substance; diff --git a/doc/examples/biomodels/Dong2014.txt b/doc/examples/biomodels/BIOMD0000000783/Dong2014.txt similarity index 99% rename from doc/examples/biomodels/Dong2014.txt rename to doc/examples/biomodels/BIOMD0000000783/Dong2014.txt index db1560dfd..00592fb93 100644 --- a/doc/examples/biomodels/Dong2014.txt +++ b/doc/examples/biomodels/BIOMD0000000783/Dong2014.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Dong2014___Mathematical_modeling_on_helper_t_cells_in_a_tumor_immune_system() // Compartments and Species: diff --git a/doc/examples/biomodels/Lopez2014.txt b/doc/examples/biomodels/BIOMD0000000784/Lopez2014.txt similarity index 99% rename from doc/examples/biomodels/Lopez2014.txt rename to doc/examples/biomodels/BIOMD0000000784/Lopez2014.txt index c5b0b1500..a804fca56 100644 --- a/doc/examples/biomodels/Lopez2014.txt +++ b/doc/examples/biomodels/BIOMD0000000784/Lopez2014.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *L_pez2014___A_Validated_Mathematical_Model_of_Tumor_Growth_Including_Tumor_Host_Interaction_and_Cell_Mediated_Immune_Response() // Compartments and Species: diff --git a/doc/examples/biomodels/Sotolongo-Costa2003.txt b/doc/examples/biomodels/BIOMD0000000785/Sotolongo-Costa2003.txt similarity index 98% rename from doc/examples/biomodels/Sotolongo-Costa2003.txt rename to doc/examples/biomodels/BIOMD0000000785/Sotolongo-Costa2003.txt index cfb6d25c5..f19235615 100644 --- a/doc/examples/biomodels/Sotolongo-Costa2003.txt +++ b/doc/examples/biomodels/BIOMD0000000785/Sotolongo-Costa2003.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Sotolongo_Costa2003___Behavior_of_tumors_under_nonstationary_therapy() // Compartments and Species: diff --git a/doc/examples/biomodels/Lipniacki2004.txt b/doc/examples/biomodels/BIOMD0000000786/Lipniacki2004.txt similarity index 99% rename from doc/examples/biomodels/Lipniacki2004.txt rename to doc/examples/biomodels/BIOMD0000000786/Lipniacki2004.txt index 52233e7cb..c381f080a 100644 --- a/doc/examples/biomodels/Lipniacki2004.txt +++ b/doc/examples/biomodels/BIOMD0000000786/Lipniacki2004.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 // Warnings from automatic translation: // Layout error in model: unable to draw an arc between the species 'NFKB_nuc' and the reaction 'NFKB_export': 'NFKB_nuc' is not a participant in that reaction. @@ -126,7 +126,7 @@ model *Lipniacki2004___Mathematical_model_of_NFKB_regulatory_module() // Display Names: ModelValue_1 is "Initial for Kv"; - # General layout options + // General layout options model.layout = on model.layout.size = {10, 10} model.layout.background = "#FFFFFFFF" @@ -229,7 +229,7 @@ model *Lipniacki2004___Mathematical_model_of_NFKB_regulatory_module() IKKn_production.--.rxn_end = {728.96, 497.2} IKKn_production.--.species_end = {780.17, 536.37} IKKn_production.--.b1 = {742.54, 507.09} - IKKn_production.--.b2 = {764.74, 524.2} + IKKn_production.--.b2 = {764.74, 524.2} IKKn_production.IKK_neutral.rxn_end = {715.39, 487.31} IKKn_production.IKK_neutral.species_end = {677.6, 460.79} IKKn_production.IKK_neutral.b1 = {701.82, 477.43} @@ -464,7 +464,7 @@ model *Lipniacki2004___Mathematical_model_of_NFKB_regulatory_module() A20mRNA_degradation.--.species_end = {6, 404.85} A20mRNA_degradation.--.b1 = {48.69, 426.51} A20mRNA_degradation.--.b2 = {23.6, 414.24} - A20mRNA_degradation.--.position = {0, 401.56} + A20mRNA_degradation.--.position = {0, 401.56} A20mRNA_degradation.--.size = {1, 1} A20_translation.position = {182.29, 573.11} A20_translation.--.rxn_end = {174.52, 573.74} diff --git a/doc/examples/biomodels/Frascoli2014.txt b/doc/examples/biomodels/BIOMD0000000787/Frascoli2014.txt similarity index 98% rename from doc/examples/biomodels/Frascoli2014.txt rename to doc/examples/biomodels/BIOMD0000000787/Frascoli2014.txt index b798020b0..d91cd2550 100644 --- a/doc/examples/biomodels/Frascoli2014.txt +++ b/doc/examples/biomodels/BIOMD0000000787/Frascoli2014.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Frascoli2014___A_dynamical_model_of_tumour_immunotherapy() // Compartments and Species: diff --git a/doc/examples/biomodels/Schropp2019.txt b/doc/examples/biomodels/BIOMD0000000788/Schropp2019.txt similarity index 99% rename from doc/examples/biomodels/Schropp2019.txt rename to doc/examples/biomodels/BIOMD0000000788/Schropp2019.txt index d3a00a4c7..5b57c3147 100644 --- a/doc/examples/biomodels/Schropp2019.txt +++ b/doc/examples/biomodels/BIOMD0000000788/Schropp2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Schropp2019___Target_Mediated_Drug_Disposition_Model_for_Bispecific_Antibodies() // Compartments and Species: diff --git a/doc/examples/biomodels/Jenner2018.txt b/doc/examples/biomodels/BIOMD0000000789/Jenner2018.txt similarity index 98% rename from doc/examples/biomodels/Jenner2018.txt rename to doc/examples/biomodels/BIOMD0000000789/Jenner2018.txt index 5e55e5b44..62fe6ae3f 100644 --- a/doc/examples/biomodels/Jenner2018.txt +++ b/doc/examples/biomodels/BIOMD0000000789/Jenner2018.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Jenner2018___treatment_of_oncolytic_virus() // Compartments and Species: @@ -57,7 +57,7 @@ model *Jenner2018___treatment_of_oncolytic_virus() unit length = metre; unit area = metre^2; unit volume = 1 / dimensionless^-0; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / dimensionless^-0; unit unit_1 = 1 / 86400 second; diff --git a/doc/examples/biomodels/Alvarez2019.txt b/doc/examples/biomodels/BIOMD0000000790/Alvarez2019.txt similarity index 99% rename from doc/examples/biomodels/Alvarez2019.txt rename to doc/examples/biomodels/BIOMD0000000790/Alvarez2019.txt index a1f9ccb94..82740cf8d 100644 --- a/doc/examples/biomodels/Alvarez2019.txt +++ b/doc/examples/biomodels/BIOMD0000000790/Alvarez2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Alvarez2019___A_nonlinear_mathematical_model_of_cell_mediated_immune_response_for_tumor_phenotypic_heterogeneity() // Compartments and Species: diff --git a/doc/examples/biomodels/Wilson2012.txt b/doc/examples/biomodels/BIOMD0000000791/Wilson2012.txt similarity index 99% rename from doc/examples/biomodels/Wilson2012.txt rename to doc/examples/biomodels/BIOMD0000000791/Wilson2012.txt index eab93da7b..816d58ac8 100644 --- a/doc/examples/biomodels/Wilson2012.txt +++ b/doc/examples/biomodels/BIOMD0000000791/Wilson2012.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wilson2012___tumor_vaccine_efficacy() // Compartments and Species: @@ -75,7 +75,7 @@ model *Wilson2012___tumor_vaccine_efficacy() unit length = metre; unit area = metre^2; unit volume = 1 / dimensionless^-0; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / dimensionless^-0; unit unit_1 = 1 / 86400 second; diff --git a/doc/examples/biomodels/Hu2019.txt b/doc/examples/biomodels/BIOMD0000000792/Hu2019.txt similarity index 99% rename from doc/examples/biomodels/Hu2019.txt rename to doc/examples/biomodels/BIOMD0000000792/Hu2019.txt index aee63e72f..b2a88b1f6 100644 --- a/doc/examples/biomodels/Hu2019.txt +++ b/doc/examples/biomodels/BIOMD0000000792/Hu2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hu2019___Modeling_Pancreatic_Cancer_Dynamics_with_Immunotherapy() // Compartments and Species: diff --git a/doc/examples/biomodels/Chen2011_1.txt b/doc/examples/biomodels/BIOMD0000000793/Chen2011_1.txt similarity index 98% rename from doc/examples/biomodels/Chen2011_1.txt rename to doc/examples/biomodels/BIOMD0000000793/Chen2011_1.txt index 3061ea26a..20d4db300 100644 --- a/doc/examples/biomodels/Chen2011_1.txt +++ b/doc/examples/biomodels/BIOMD0000000793/Chen2011_1.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Chen2011_1___bone_marrow_invasion_absolute_model() // Compartments and Species: @@ -39,7 +39,7 @@ model *Chen2011_1___bone_marrow_invasion_absolute_model() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-3 mole; unit unit_0 = 1 / dimensionless^-0; unit extent = substance; diff --git a/doc/examples/biomodels/Chen2011_1swapped.txt b/doc/examples/biomodels/BIOMD0000000793/Chen2011_1swapped.txt similarity index 98% rename from doc/examples/biomodels/Chen2011_1swapped.txt rename to doc/examples/biomodels/BIOMD0000000793/Chen2011_1swapped.txt index 670d8814f..ff00152be 100644 --- a/doc/examples/biomodels/Chen2011_1swapped.txt +++ b/doc/examples/biomodels/BIOMD0000000793/Chen2011_1swapped.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Chen2011_1___bone_marrow_invasion_absolute_model() // Compartments and Species: @@ -39,7 +39,7 @@ model *Chen2011_1___bone_marrow_invasion_absolute_model() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-3 mole; unit unit_0 = 1 / dimensionless^-0; unit extent = substance; diff --git a/doc/examples/biomodels/Benary2019.txt b/doc/examples/biomodels/BIOMD0000000794/Benary2019.txt similarity index 99% rename from doc/examples/biomodels/Benary2019.txt rename to doc/examples/biomodels/BIOMD0000000794/Benary2019.txt index 0ad516fe2..1f4938288 100644 --- a/doc/examples/biomodels/Benary2019.txt +++ b/doc/examples/biomodels/BIOMD0000000794/Benary2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 // Warnings from automatic translation: // Layout error in model: unable to draw an arc between the species 'NFKB_nuc' and the reaction 'NFKB_export': 'NFKB_nuc' is not a participant in that reaction. @@ -153,7 +153,7 @@ model *benary2019___Controlling_NFKB_dynamics_by_B_TrCP() c1c is "k27"; c3c is "k28"; - # General layout options + // General layout options model.layout = on model.layout.size = {10, 10} model.layout.background = "#FFFFFFFF" @@ -232,7 +232,7 @@ model *benary2019___Controlling_NFKB_dynamics_by_B_TrCP() IkB_mRNA.font = Verdana IkB_mRNA.fontColor = black IkB_mRNA.fontSize = 12 - A20_mRNA.position = {84.52, 445.58} + A20_mRNA.position = {84.52, 445.58} A20_mRNA.size = {132, 28} A20_mRNA.font = Verdana A20_mRNA.fontColor = black diff --git a/doc/examples/biomodels/Chen2011_2.txt b/doc/examples/biomodels/BIOMD0000000795/Chen2011_2.txt similarity index 99% rename from doc/examples/biomodels/Chen2011_2.txt rename to doc/examples/biomodels/BIOMD0000000795/Chen2011_2.txt index d7b684818..0dec94aed 100644 --- a/doc/examples/biomodels/Chen2011_2.txt +++ b/doc/examples/biomodels/BIOMD0000000795/Chen2011_2.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Chen2011_2___bone_marrow_invasion_relative_model() // Compartments and Species: @@ -44,7 +44,7 @@ model *Chen2011_2___bone_marrow_invasion_relative_model() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-3 mole; unit unit_0 = 1 / dimensionless^-0; unit extent = substance; diff --git a/doc/examples/biomodels/Yang2012.txt b/doc/examples/biomodels/BIOMD0000000796/Yang2012.txt similarity index 99% rename from doc/examples/biomodels/Yang2012.txt rename to doc/examples/biomodels/BIOMD0000000796/Yang2012.txt index efd142e13..728d50333 100644 --- a/doc/examples/biomodels/Yang2012.txt +++ b/doc/examples/biomodels/BIOMD0000000796/Yang2012.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Yang2012___cancer_growth_with_angiogenesis() // Compartments and Species: @@ -103,7 +103,7 @@ model *Yang2012___cancer_growth_with_angiogenesis() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / 86400e-1 second; unit unit_1 = 1 / dimensionless^-0; diff --git a/doc/examples/biomodels/Hu2018.txt b/doc/examples/biomodels/BIOMD0000000797/Hu2018.txt similarity index 99% rename from doc/examples/biomodels/Hu2018.txt rename to doc/examples/biomodels/BIOMD0000000797/Hu2018.txt index fc0ddad85..72a15778d 100644 --- a/doc/examples/biomodels/Hu2018.txt +++ b/doc/examples/biomodels/BIOMD0000000797/Hu2018.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hu2018___Dynamics_of_tumor_CD4__cytokine_host_cells_interactions_with_treatments() // Compartments and Species: diff --git a/doc/examples/biomodels/Sharp2019.txt b/doc/examples/biomodels/BIOMD0000000798/Sharp2019.txt similarity index 99% rename from doc/examples/biomodels/Sharp2019.txt rename to doc/examples/biomodels/BIOMD0000000798/Sharp2019.txt index c974d5f7e..d291f9402 100644 --- a/doc/examples/biomodels/Sharp2019.txt +++ b/doc/examples/biomodels/BIOMD0000000798/Sharp2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Sharp2019___AML() // Compartments and Species: @@ -73,7 +73,7 @@ model *Sharp2019___AML() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-3 mole; unit unit_0 = 1 / dimensionless^-0; unit extent = substance; diff --git a/doc/examples/biomodels/Cucuianu2010.txt b/doc/examples/biomodels/BIOMD0000000799/Cucuianu2010.txt similarity index 98% rename from doc/examples/biomodels/Cucuianu2010.txt rename to doc/examples/biomodels/BIOMD0000000799/Cucuianu2010.txt index 7d08ccded..b75f1f3c6 100644 --- a/doc/examples/biomodels/Cucuianu2010.txt +++ b/doc/examples/biomodels/BIOMD0000000799/Cucuianu2010.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Cucuianu2010___A_hypothetical_mathematical_model_of_acute_myeloid_leukaemia_pathogenesis() // Compartments and Species: diff --git a/doc/examples/biomodels/Precup2012.txt b/doc/examples/biomodels/BIOMD0000000800/Precup2012.txt similarity index 99% rename from doc/examples/biomodels/Precup2012.txt rename to doc/examples/biomodels/BIOMD0000000800/Precup2012.txt index 88ba99033..4da075418 100644 --- a/doc/examples/biomodels/Precup2012.txt +++ b/doc/examples/biomodels/BIOMD0000000800/Precup2012.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Precup2012___Mathematical_modeling_of_cell_dynamics_after_allogeneic_bone_marrow_transplantation() // Compartments and Species: diff --git a/doc/examples/biomodels/Sturrock2015.txt b/doc/examples/biomodels/BIOMD0000000801/Sturrock2015.txt similarity index 99% rename from doc/examples/biomodels/Sturrock2015.txt rename to doc/examples/biomodels/BIOMD0000000801/Sturrock2015.txt index 6203c7cad..1b6979509 100644 --- a/doc/examples/biomodels/Sturrock2015.txt +++ b/doc/examples/biomodels/BIOMD0000000801/Sturrock2015.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Sturrock2015__glioma_growth() // Compartments and Species: @@ -80,7 +80,7 @@ model *Sturrock2015__glioma_growth() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / 86400e-1 second; unit unit_1 = 1 / dimensionless^-0; diff --git a/doc/examples/biomodels/Hoffman2017.txt b/doc/examples/biomodels/BIOMD0000000802/Hoffman2017.txt similarity index 99% rename from doc/examples/biomodels/Hoffman2017.txt rename to doc/examples/biomodels/BIOMD0000000802/Hoffman2017.txt index 6b77c7b6d..305f0409d 100644 --- a/doc/examples/biomodels/Hoffman2017.txt +++ b/doc/examples/biomodels/BIOMD0000000802/Hoffman2017.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hoffman2018__ADCC_against_cancer() // Compartments and Species: @@ -63,7 +63,7 @@ model *Hoffman2018__ADCC_against_cancer() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-3 mole; unit unit_0 = 1 / dimensionless^-0; unit extent = substance; diff --git a/doc/examples/biomodels/Park2019.txt b/doc/examples/biomodels/BIOMD0000000803/Park2019.txt similarity index 99% rename from doc/examples/biomodels/Park2019.txt rename to doc/examples/biomodels/BIOMD0000000803/Park2019.txt index 0b128ac17..d4c350550 100644 --- a/doc/examples/biomodels/Park2019.txt +++ b/doc/examples/biomodels/BIOMD0000000803/Park2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Park2019___IL7_receptor_signaling_in_T_cells() // Compartments and Species: diff --git a/doc/examples/biomodels/Koenders2015.txt b/doc/examples/biomodels/BIOMD0000000804/Koenders2015.txt similarity index 99% rename from doc/examples/biomodels/Koenders2015.txt rename to doc/examples/biomodels/BIOMD0000000804/Koenders2015.txt index b29dbfd00..f5d07b087 100644 --- a/doc/examples/biomodels/Koenders2015.txt +++ b/doc/examples/biomodels/BIOMD0000000804/Koenders2015.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Koenders2015___multiple_myeloma() // Compartments and Species: @@ -75,7 +75,7 @@ model *Koenders2015___multiple_myeloma() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit unit_0 = 1 / 86400e-1 second; unit unit_1 = 1 / dimensionless^-0; diff --git a/doc/examples/biomodels/Al-Husari2013.txt b/doc/examples/biomodels/BIOMD0000000805/Al-Husari2013.txt similarity index 99% rename from doc/examples/biomodels/Al-Husari2013.txt rename to doc/examples/biomodels/BIOMD0000000805/Al-Husari2013.txt index c895be9c3..4913681e6 100644 --- a/doc/examples/biomodels/Al-Husari2013.txt +++ b/doc/examples/biomodels/BIOMD0000000805/Al-Husari2013.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Al_Husari2013___pH_and_lactate_in_tumor() // Compartments and Species: @@ -69,7 +69,7 @@ model *Al_Husari2013___pH_and_lactate_in_tumor() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-3 mole; unit unit_0 = 1 / dimensionless^-0; unit extent = substance; diff --git a/doc/examples/biomodels/BIOMD0000000806/model.txt b/doc/examples/biomodels/BIOMD0000000806/model.txt new file mode 100644 index 000000000..9906b077c --- /dev/null +++ b/doc/examples/biomodels/BIOMD0000000806/model.txt @@ -0,0 +1,273 @@ +// Created by libAntimony v3.2.0 +model *Eftimie2019() + + // Compartments and Species: + compartment compartment_; + species UnInfected_Tumour_Cells_Xu in compartment_, Infected_Tumour_Cells_Xi in compartment_; + species Virus_Xv in compartment_, Effector_Cytotoxic_CD8_TCells__Xe in compartment_; + species M1_Macrophage_Xm1 in compartment_, M2_Macrophage_Xm2 in compartment_; + + // Reactions: + Uninfected_tumour_cell_logistic_growth: => UnInfected_Tumour_Cells_Xu; compartment_*(r*UnInfected_Tumour_Cells_Xu*(1 - UnInfected_Tumour_Cells_Xu/K)); + Uninfected_tumour_cell_infection: UnInfected_Tumour_Cells_Xu => Infected_Tumour_Cells_Xi; compartment_*(d_v*Virus_Xv*UnInfected_Tumour_Cells_Xu/(v_h_u + UnInfected_Tumour_Cells_Xu)); + Uninfected_tumour_cell_elimination_1: UnInfected_Tumour_Cells_Xu => ; compartment_*(d_u*UnInfected_Tumour_Cells_Xu*Effector_Cytotoxic_CD8_TCells__Xe/(h_e + Effector_Cytotoxic_CD8_TCells__Xe)); + Uninfected_tumour_cell_elimination_2: UnInfected_Tumour_Cells_Xu => ; compartment_*(d_m1*UnInfected_Tumour_Cells_Xu*M1_Macrophage_Xm1/(h_m + M2_Macrophage_Xm2)); + Uninfected_tumour_cell_growth_M2: => UnInfected_Tumour_Cells_Xu; compartment_*(d_m2*UnInfected_Tumour_Cells_Xu*M2_Macrophage_Xm2/(h_m + M2_Macrophage_Xm2)); + Infected_tumour_cell_death: Infected_Tumour_Cells_Xi => ; compartment_*delta_i*Infected_Tumour_Cells_Xi; + virus_growth: => Virus_Xv; compartment_*(delta_i*b*Infected_Tumour_Cells_Xi); + Infected_tumour_cell_elimination_1: Infected_Tumour_Cells_Xi => ; compartment_*(v_d_u*Infected_Tumour_Cells_Xi*Effector_Cytotoxic_CD8_TCells__Xe/(h_e + Effector_Cytotoxic_CD8_TCells__Xe)); + Infected_tumour_cell_elimination_2: Infected_Tumour_Cells_Xi => ; compartment_*(v_d_m1*Infected_Tumour_Cells_Xi*M1_Macrophage_Xm1/(h_m + M2_Macrophage_Xm2)); + virus_injection: => Virus_Xv; compartment_*H; + virus_death: Virus_Xv => ; compartment_*omega*Virus_Xv; + virus_clearance_1: Virus_Xv => ; compartment_*(v_d_m1*Virus_Xv*M1_Macrophage_Xm1/(h_m + M2_Macrophage_Xm2)); + virus_clearance_2: Virus_Xv => ; compartment_*(v_d_u*Virus_Xv*Effector_Cytotoxic_CD8_TCells__Xe/(h_e + Effector_Cytotoxic_CD8_TCells__Xe)); + M1_activation_1: => M1_Macrophage_Xm1; compartment_*(v_a_1*(Infected_Tumour_Cells_Xi + Virus_Xv)); + M1_activation_2: => M1_Macrophage_Xm1; compartment_*(u_a_1*UnInfected_Tumour_Cells_Xu); + M1_recruitment: => M1_Macrophage_Xm1; compartment_*(p_m1*M1_Macrophage_Xm1*(1 - (M1_Macrophage_Xm1 + M2_Macrophage_Xm2)/M)); + M1_to_M2_repolarisation: M1_Macrophage_Xm1 => M2_Macrophage_Xm2; compartment_*(M1_Macrophage_Xm1*(o_r_m1 + u_r_m1*UnInfected_Tumour_Cells_Xu/(h_u + UnInfected_Tumour_Cells_Xu))); + M2_to_M1_repolarisation: M2_Macrophage_Xm2 => M1_Macrophage_Xm1; compartment_*(M2_Macrophage_Xm2*(o_r_m2 + v_r_m2*Virus_Xv/(h_v + Virus_Xv))); + M1_death: M1_Macrophage_Xm1 => ; compartment_*d_em1*M1_Macrophage_Xm1; + M2_activation: => M2_Macrophage_Xm2; compartment_*(u_a_2*UnInfected_Tumour_Cells_Xu); + M2_growth: => M2_Macrophage_Xm2; compartment_*(p_m2*M2_Macrophage_Xm2*(1 - (M1_Macrophage_Xm1 + M2_Macrophage_Xm2)/M)); + M2_death: M2_Macrophage_Xm2 => ; compartment_*d_em2*M2_Macrophage_Xm2; + T_cells_activation: => Effector_Cytotoxic_CD8_TCells__Xe; compartment_*(p_e*M1_Macrophage_Xm1/(h_m + M2_Macrophage_Xm2)); + T_cells_death: Effector_Cytotoxic_CD8_TCells__Xe => ; compartment_*d_ee*Effector_Cytotoxic_CD8_TCells__Xe; + T_cells_inactivation: Effector_Cytotoxic_CD8_TCells__Xe => ; compartment_*(d_t*UnInfected_Tumour_Cells_Xu*Effector_Cytotoxic_CD8_TCells__Xe); + + // Events: + Heaviside_function_at_10: at time >= 10, t0=false, fromTrigger=false: H = H + 2*10^7; + Heaviside_function_at_11: at time >= 11, t0=false, fromTrigger=false: H = H - 2*10^7; + Heaviside_function_at_13: at time >= 13, t0=false, fromTrigger=false: H = H + 2*10^7; + Heaviside_function_at_14: at time >= 14, t0=false, fromTrigger=false: H = H - 2*10^7; + dm1_at_11: at time >= 11, t0=false, fromTrigger=false: d_m1 = d_m1 + 0.28; + du_at_15: at time >= 15, t0=false, fromTrigger=false: d_u = d_u + 0.41; + + // Species initializations: + UnInfected_Tumour_Cells_Xu = 500000; + UnInfected_Tumour_Cells_Xu has substance_per_volume; + Infected_Tumour_Cells_Xi = 0; + Infected_Tumour_Cells_Xi has substance_per_volume; + Virus_Xv = 0; + Virus_Xv has substance_per_volume; + Effector_Cytotoxic_CD8_TCells__Xe = 0; + Effector_Cytotoxic_CD8_TCells__Xe has substance_per_volume; + M1_Macrophage_Xm1 = 0; + M1_Macrophage_Xm1 has substance_per_volume; + M2_Macrophage_Xm2 = 0; + M2_Macrophage_Xm2 has substance_per_volume; + + // Compartment initializations: + compartment_ = 1; + compartment_ has volume; + + // Variable initializations: + H = 0; + d_m1 = 0.01; + d_u = 0.44; + r = 0.924; + r has unit_0; + K = 3300000000; + K has unit_1; + d_v = 0.011; + v_h_u = 100000; + h_e = 1; + h_m = 1000; + d_m2 = 0.4; + delta_i = 0.475; + delta_i has unit_0; + b = 2500; + v_d_u = 4.4; + v_d_u has unit_0; + v_d_m1 = 1.5; + v_d_m1 has unit_0; + omega = 2; + omega has unit_0; + d_em1 = 0.2; + v_a_1 = 1e-06; + v_a_1 has unit_0; + u_a_1 = 3e-06; + u_a_1 has unit_0; + p_m1 = 0.22; + p_m1 has unit_0; + M = 100000000; + o_r_m1 = 0.001; + o_r_m1 has unit_0; + o_r_m2 = 0.001; + o_r_m2 has unit_0; + u_r_m1 = 4; + u_r_m1 has unit_0; + v_r_m2 = 0.5; + v_r_m2 has unit_0; + p_m2 = 0.22; + p_m2 has unit_0; + h_u = 5000000000; + h_v = 0.105636; + d_em2 = 0.2; + d_em2 has unit_0; + u_a_2 = 4e-08; + u_a_2 has unit_0; + d_ee = 0.4; + d_ee has unit_0; + p_e = 2070; + p_e has unit_0; + d_t = 1e-10; + d_t has unit_0; + + // Other declarations: + var H, d_m1, d_u; + const compartment_, r, K, d_v, v_h_u, h_e, h_m, d_m2, delta_i, b, v_d_u; + const v_d_m1, omega, d_em1, v_a_1, u_a_1, p_m1, M, o_r_m1, o_r_m2, u_r_m1; + const v_r_m2, p_m2, h_u, h_v, d_em2, u_a_2, d_ee, p_e, d_t; + + // Unit definitions: + unit length = metre; + unit area = metre^2; + unit volume = 1e-3 litre; + unit time_unit = 86400 second; + unit substance = 1e-3 mole; + unit unit_0 = 1 / 1e-3 second; + unit unit_1 = 1 / dimensionless^-0; + unit extent = substance; + unit substance_per_volume = 1e-3 mole / 1e-3 litre; + + // Display Names: + time_unit is "time"; + unit_0 is "1/ms"; + unit_1 is "1"; + compartment_ is "compartment"; + UnInfected_Tumour_Cells_Xu is "UnInfected_Tumour_Cells(Xu)"; + Infected_Tumour_Cells_Xi is "Infected_Tumour_Cells(Xi)"; + Virus_Xv is "Virus(Xv)"; + Effector_Cytotoxic_CD8_TCells__Xe is "Effector_Cytotoxic_CD8_TCells (Xe)"; + M1_Macrophage_Xm1 is "M1_Macrophage(Xm1)"; + M2_Macrophage_Xm2 is "M2_Macrophage(Xm2)"; + Heaviside_function_at_10 is "Heaviside function at 10"; + Heaviside_function_at_11 is "Heaviside function at 11"; + Heaviside_function_at_13 is "Heaviside function at 13"; + Heaviside_function_at_14 is "Heaviside function at 14"; + dm1_at_11 is "dm1 at 11"; + du_at_15 is "du at 15"; + Uninfected_tumour_cell_logistic_growth is "Uninfected tumour cell logistic growth"; + Uninfected_tumour_cell_infection is "Uninfected tumour cell infection"; + Uninfected_tumour_cell_elimination_1 is "Uninfected tumour cell elimination 1"; + Uninfected_tumour_cell_elimination_2 is "Uninfected tumour cell elimination 2"; + Uninfected_tumour_cell_growth_M2 is "Uninfected tumour cell growth;M2"; + Infected_tumour_cell_death is "Infected tumour cell death"; + virus_growth is "virus growth"; + Infected_tumour_cell_elimination_1 is "Infected tumour cell elimination 1"; + Infected_tumour_cell_elimination_2 is "Infected tumour cell elimination 2"; + virus_injection is "virus injection"; + virus_death is "virus death"; + virus_clearance_1 is "virus clearance 1"; + virus_clearance_2 is "virus clearance 2"; + M1_activation_1 is "M1 activation 1"; + M1_activation_2 is "M1 activation 2"; + M1_recruitment is "M1 recruitment"; + M1_to_M2_repolarisation is "M1 to M2 repolarisation"; + M2_to_M1_repolarisation is "M2 to M1 repolarisation"; + M1_death is "M1 death"; + M2_activation is "M2 activation"; + M2_growth is "M2 growth"; + M2_death is "M2 death"; + T_cells_activation is "T cells activation"; + T_cells_death is "T cells death"; + T_cells_inactivation is "T cells inactivation"; + + // CV terms: + compartment_ isVersionOf "http://identifiers.org/ncit/C14424" + compartment_ isVersionOf "http://identifiers.org/ncit/C13413" + UnInfected_Tumour_Cells_Xu isVersionOf "http://identifiers.org/efo/0000311" + UnInfected_Tumour_Cells_Xu isVersionOf "http://identifiers.org/bto/BTO:0002014" + Infected_Tumour_Cells_Xi isVersionOf "http://identifiers.org/bto/BTO:0002014" + Infected_Tumour_Cells_Xi isVersionOf "http://identifiers.org/efo/EFO:0000311" + Infected_Tumour_Cells_Xi isVersionOf "http://identifiers.org/bto/BTO:0000152" + Virus_Xv isVersionOf "http://identifiers.org/taxonomy/11276" + Effector_Cytotoxic_CD8_TCells__Xe isVersionOf "http://identifiers.org/cl/CL:0000794" + M1_Macrophage_Xm1 isVersionOf "http://identifiers.org/ncit/C156004" + M2_Macrophage_Xm2 isVersionOf "http://identifiers.org/ncit/C123783" + K isVersionOf "http://identifiers.org/ncit/C25443" + omega isVersionOf "http://identifiers.org/sbo/SBO:0000356" + d_em1 isVersionOf "http://identifiers.org/sbo/SBO:0000356" + M isVersionOf "http://identifiers.org/ncit/C25443" + d_em2 isVersionOf "http://identifiers.org/sbo/SBO:0000356" + d_ee isVersionOf "http://identifiers.org/sbo/SBO:0000356" + Uninfected_tumour_cell_logistic_growth isVersionOf "http://identifiers.org/go/GO:0040007" + Uninfected_tumour_cell_infection isVersionOf "http://identifiers.org/go/GO:0019089" + Uninfected_tumour_cell_elimination_1 isVersionOf "http://identifiers.org/sbo/SBO:0000179" + Uninfected_tumour_cell_elimination_2 isVersionOf "http://identifiers.org/sbo/SBO:0000179" + Uninfected_tumour_cell_growth_M2 isVersionOf "http://identifiers.org/go/GO:0040007" + Infected_tumour_cell_death isVersionOf "http://identifiers.org/sbo/SBO:0000179" + virus_growth isVersionOf "http://identifiers.org/go/GO:0040007" + Infected_tumour_cell_elimination_1 isVersionOf "http://identifiers.org/sbo/SBO:0000179" + Infected_tumour_cell_elimination_2 isVersionOf "http://identifiers.org/sbo/SBO:0000179" + virus_injection isVersionOf "http://identifiers.org/go/GO:0035737" + virus_death isVersionOf "http://identifiers.org/sbo/SBO:0000179" + virus_clearance_1 isVersionOf "http://identifiers.org/sbo/SBO:0000179" + virus_clearance_2 isVersionOf "http://identifiers.org/sbo/SBO:0000179" + M1_activation_1 isVersionOf "http://identifiers.org/sbo/SBO:0000393" + M1_activation_2 isVersionOf "http://identifiers.org/sbo/SBO:0000393" + M1_recruitment isVersionOf "http://identifiers.org/go/GO:1905517" + M1_to_M2_repolarisation isPropertyOf "http://identifiers.org/go/GO:0048246" + M2_to_M1_repolarisation isPropertyOf "http://identifiers.org/go/GO:0048246" + M1_death isVersionOf "http://identifiers.org/sbo/SBO:0000179" + M2_activation isVersionOf "http://identifiers.org/go/GO:0042116" + M2_growth isVersionOf "http://identifiers.org/go/GO:0040007" + M2_death isVersionOf "http://identifiers.org/sbo/SBO:0000179" + T_cells_activation isVersionOf "http://identifiers.org/sbo/SBO:0000393" + T_cells_death isVersionOf "http://identifiers.org/sbo/SBO:0000179" + T_cells_inactivation isVersionOf "http://identifiers.org/go/GO:0002870" + + model model_source "http://identifiers.org/biomodels.db/MODEL1909050001", + "http://identifiers.org/biomodels.db/BIOMD0000000806" + model hasProperty "http://identifiers.org/doid/DOID:4159" + model hasProperty "http://identifiers.org/efo/0000311" + model hasProperty "http://identifiers.org/go/GO:0002837" + model hasProperty "http://identifiers.org/mamo/MAMO_0000046" + model hasProperty "http://identifiers.org/doid/DOID:162" + model hasProperty "http://identifiers.org/ncit/C62713" + model hasTaxon "http://identifiers.org/taxonomy/10090" + model hasTaxon "http://identifiers.org/taxonomy/11276" + model isDescribedBy "http://identifiers.org/pubmed/31410657" + model created "2019-08-20T16:28:35Z" + model modified "2019-08-20T16:28:35Z" + model creator1.givenName "Szeyi" + model creator1.familyName "Ng" + model creator1.organization "EMBL-EBI" + model creator1.email "muffet.ng@qq.com" + model creator2.givenName "Rahumans" + model creator2.familyName "Sheriff" + model creator2.organization "EMBL-EBI" + model creator2.email "sheriff@ebi.ac.uk" + + // Notes: + model notes ``` +This a model from the article: Investigating Macrophages Plasticity Following +Tumour–Immune Interactions During Oncolytic TherapiesR. Eftimie, G. Eftimie. Acta +Biotheoretica.Abstract: Over the last few years, oncolytic virus therapy has been +recognised as a promising approach in cancer treatment, due to the potential of these +viruses to induce systemic anti-tumour immunity and selectively killing tumour cells. +However, the effectiveness of these viruses depends significantly on their interactions +with the host immune responses, both innate (e.g., macrophages, which accumulate +in high numbers inside solid tumours) and adaptive (e.g., [Formula: see text] T cells). +In this article, we consider a mathematical approach to investigate the possible +outcomes of the complex interactions between two extreme types of macrophages (M1 +and M2 cells), effector [Formula: see text] T cells and an oncolytic Vesicular Stomatitis +Virus (VSV), on the growth/elimination of B16F10 melanoma. We discuss, in terms of +VSV, [Formula: see text] and macrophages levels, two different types of immune responses +which could ensure tumour control and eventual elimination. We show that both innate +and adaptive anti-tumour immune responses, as well as the oncolytic virus, could +be very important in delaying tumour relapse and eventually eliminating the tumour. +Overall this study supports the use mathematical modelling to increase our understanding +of the complex immune interaction following oncolytic virotherapies. However, the +complexity of the model combined with a lack of sufficient data for model parametrisation +has an impact on the possibility of making quantitative predictions. This model originates +from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). +It is copyright (c) 2005-2011 The BioModels.net Team.For more information see the +terms of use.To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez +N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka +M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated +resource for published quantitative kinetic models. BMC Syst Biol., 4:92. +``` +end + +Eftimie2019 is "Eftimie2019-Macrophages Plasticity" diff --git a/doc/examples/biomodels/BIOMD0000000807/model.txt b/doc/examples/biomodels/BIOMD0000000807/model.txt new file mode 100644 index 000000000..05fba509e --- /dev/null +++ b/doc/examples/biomodels/BIOMD0000000807/model.txt @@ -0,0 +1,228 @@ +// Created by libAntimony v3.2.0 +model *New_Model() + + // Compartments and Species: + compartment compartment_; + species normalized_normal_cell_n in compartment_, normalized_pre_cancer_cell_g in compartment_; + species normalized_cancer_cell_a in compartment_; + + // Assignment Rules: + n0 := N0/K; + g0 := G0/K; + a0 := A0/K; + A := normalized_cancer_cell_a*K; + G := normalized_pre_cancer_cell_g*K; + N := normalized_normal_cell_n*K; + N0 := r_N/mu_N - 1; + a := normalized_cancer_cell_a*10; + + // Reactions: + normal_cell_growth: => normalized_normal_cell_n; compartment_*(r_N/K); + normal_cell_death: normalized_normal_cell_n => ; compartment_*mu_N*normalized_normal_cell_n; + normal_cell_damage_A: normalized_normal_cell_n => ; compartment_*(beta_1*K*normalized_normal_cell_n*normalized_cancer_cell_a); + normal_cell_damage_G: normalized_normal_cell_n => ; compartment_*(beta_4*normalized_normal_cell_n*normalized_pre_cancer_cell_g); + pre_cancer_cell_logistic_growth: => normalized_pre_cancer_cell_g; compartment_*(r_G*normalized_pre_cancer_cell_g); + pre_cancer_cell_natural_death: normalized_pre_cancer_cell_g => ; compartment_*mu_G*normalized_pre_cancer_cell_g; + pre_cancer_cell_death_tissue_repair_system: normalized_pre_cancer_cell_g => ; compartment_*(beta_2*K*normalized_normal_cell_n*normalized_pre_cancer_cell_g); + pre_cancer_cell_death_apoptosis: normalized_pre_cancer_cell_g => ; compartment_*xi_G*normalized_pre_cancer_cell_g; + negative_effect_on_G_A: normalized_pre_cancer_cell_g => ; compartment_*(beta_5*normalized_cancer_cell_a*normalized_pre_cancer_cell_g); + negative_effect_on_A_G: normalized_cancer_cell_a => ; compartment_*(beta_6*normalized_cancer_cell_a*normalized_pre_cancer_cell_g); + cancer_cell_natural_death: normalized_cancer_cell_a => ; compartment_*mu_A*normalized_cancer_cell_a; + cancer_cell_logistic_growth: => normalized_cancer_cell_a; compartment_*(r_A*normalized_cancer_cell_a*(1 - normalized_cancer_cell_a/(K_A/K))); + cancer_cell_death_tissue_repair_system: normalized_cancer_cell_a => ; compartment_*(beta_3*K*normalized_normal_cell_n*normalized_cancer_cell_a); + cancer_cell_death_apoptosis: normalized_cancer_cell_a => ; compartment_*xi_A*normalized_cancer_cell_a; + transition_to_cancer_cell: normalized_pre_cancer_cell_g => normalized_cancer_cell_a; compartment_*(delta*normalized_pre_cancer_cell_g^2/(xi/K + normalized_pre_cancer_cell_g)); + + // Species initializations: + normalized_normal_cell_n = n0; + normalized_normal_cell_n has substance_per_volume; + normalized_pre_cancer_cell_g = g0; + normalized_pre_cancer_cell_g has substance_per_volume; + normalized_cancer_cell_a = a0; + normalized_cancer_cell_a has substance_per_volume; + + // Compartment initializations: + compartment_ = 1; + compartment_ has volume; + + // Variable initializations: + r_N = 1000000; + r_N has unit_2; + mu_N = 0.01; + mu_N has unit_2; + beta_1 = 3.5e-10; + beta_1 has unit_2; + beta_4 = 0; + beta_4 has unit_2; + r_G = 0.05; + r_G has unit_2; + mu_G = 0.01; + mu_G has unit_2; + xi_G = 0.01; + xi_G has unit_2; + beta_2 = 3.5e-10; + beta_2 has unit_2; + beta_5 = 0; + beta_5 has unit_2; + delta = 1e-05; + delta has unit_2; + xi = 1000; + xi has unit_1; + r_A = 0.05; + r_A has unit_2; + K_A = 10000000; + K_A has unit_1; + mu_A = 0.01; + mu_A has unit_2; + xi_A = 0.006; + xi_A has unit_2; + beta_3 = 3.5e-10; + beta_3 has unit_2; + beta_6 = 0; + beta_6 has unit_2; + K = 100000000; + G0 = 1; + A0 = 0; + + // Other declarations: + var n0, g0, a0, A, G, N, N0, a; + const compartment_, r_N, mu_N, beta_1, beta_4, r_G, mu_G, xi_G, beta_2; + const beta_5, delta, xi, r_A, K_A, mu_A, xi_A, beta_3, beta_6, K, G0, A0; + + // Unit definitions: + unit length = metre; + unit area = metre^2; + unit volume = 1e-3 litre; + unit time_unit = 86400 second; + unit substance = 1e-3 mole; + unit unit_0 = 1 / 86400e-1 second; + unit unit_1 = 1 / dimensionless^-0; + unit unit_2 = 1 / 1e-3 second; + unit extent = substance; + unit substance_per_volume = 1e-3 mole / 1e-3 litre; + + // Display Names: + time_unit is "time"; + unit_0 is "1/d"; + unit_1 is "1"; + unit_2 is "1/ms"; + compartment_ is "compartment"; + normalized_normal_cell_n is "normalized normal cell n"; + normalized_pre_cancer_cell_g is "normalized pre-cancer cell g"; + normalized_cancer_cell_a is "normalized cancer cell a"; + a is "a'"; + normal_cell_growth is "normal cell growth"; + normal_cell_death is "normal cell death"; + normal_cell_damage_A is "normal cell damage;A"; + normal_cell_damage_G is "normal cell damage;G"; + pre_cancer_cell_logistic_growth is "pre-cancer cell logistic growth"; + pre_cancer_cell_natural_death is "pre-cancer cell natural death"; + pre_cancer_cell_death_tissue_repair_system is "pre-cancer cell death;tissue repair system"; + pre_cancer_cell_death_apoptosis is "pre-cancer cell death;apoptosis"; + negative_effect_on_G_A is "negative effect on G;A"; + negative_effect_on_A_G is "negative effect on A;G"; + cancer_cell_natural_death is "cancer cell natural death"; + cancer_cell_logistic_growth is "cancer cell logistic growth"; + cancer_cell_death_tissue_repair_system is "cancer cell death;tissue repair system"; + cancer_cell_death_apoptosis is "cancer cell death;apoptosis"; + transition_to_cancer_cell is "transition to cancer cell"; + + // CV terms: + compartment_ isVersionOf "http://identifiers.org/ncit/C13413" + normalized_normal_cell_n hasProperty "http://identifiers.org/ncit/C12508" + normalized_normal_cell_n hasProperty "http://identifiers.org/ncit/C115935" + n0 hasProperty "http://identifiers.org/ncit/C115935" + n0 hasProperty "http://identifiers.org/ncit/C12508" + normalized_pre_cancer_cell_g hasProperty "http://identifiers.org/ncit/C12959" + normalized_pre_cancer_cell_g hasProperty "http://identifiers.org/ncit/C25629" + g0 hasProperty "http://identifiers.org/ncit/C12959" + g0 hasProperty "http://identifiers.org/ncit/C25629" + normalized_cancer_cell_a hasProperty "http://identifiers.org/ncit/C12959" + a0 hasProperty "http://identifiers.org/ncit/C12959" + r_N hasProperty "http://identifiers.org/sbo/SBO:0000610" + mu_N hasProperty "http://identifiers.org/ncit/C53346" + mu_N hasProperty "http://identifiers.org/ncit/C85060" + r_G hasProperty "http://identifiers.org/sbo/SBO:0000610" + mu_G hasProperty "http://identifiers.org/ncit/C85060" + mu_G hasProperty "http://identifiers.org/ncit/C53346" + xi_G hasProperty "http://identifiers.org/ncit/C53346" + delta hasProperty "http://identifiers.org/ncit/C25564" + delta hasProperty "http://identifiers.org/go/GO:0000492" + delta hasProperty "http://identifiers.org/ncit/C25636" + xi hasProperty "http://identifiers.org/ncit/C48228" + r_A hasProperty "http://identifiers.org/sbo/SBO:0000610" + K_A hasProperty "http://identifiers.org/sbo/SBO:0000661" + K_A hasProperty "http://identifiers.org/ncit/C81005" + mu_A hasProperty "http://identifiers.org/ncit/C53346" + mu_A hasProperty "http://identifiers.org/ncit/C85060" + xi_A hasProperty "http://identifiers.org/ncit/C53346" + A hasProperty "http://identifiers.org/ncit/C12959" + G hasProperty "http://identifiers.org/ncit/C12959" + G hasProperty "http://identifiers.org/ncit/C25629" + N hasProperty "http://identifiers.org/ncit/C12508" + N hasProperty "http://identifiers.org/ncit/C115935" + G0 hasProperty "http://identifiers.org/ncit/C25629" + G0 hasProperty "http://identifiers.org/ncit/C12959" + A0 hasProperty "http://identifiers.org/ncit/C12959" + N0 hasProperty "http://identifiers.org/ncit/C115935" + N0 hasProperty "http://identifiers.org/ncit/C12508" + a hasProperty "http://identifiers.org/ncit/C12959" + normal_cell_growth hasProperty "http://identifiers.org/sbo/SBO:0000629" + normal_cell_death hasProperty "http://identifiers.org/sbo/SBO:0000179" + normal_cell_damage_A hasProperty "http://identifiers.org/sbo/SBO:0000202" + normal_cell_damage_G hasProperty "http://identifiers.org/sbo/SBO:0000202" + pre_cancer_cell_logistic_growth hasProperty "http://identifiers.org/go/GO:0040007" + pre_cancer_cell_natural_death hasProperty "http://identifiers.org/sbo/SBO:0000179" + pre_cancer_cell_death_tissue_repair_system hasProperty "http://identifiers.org/sbo/SBO:0000179" + pre_cancer_cell_death_apoptosis hasProperty "http://identifiers.org/sbo/SBO:0000179" + negative_effect_on_G_A hasProperty "http://identifiers.org/sbo/SBO:0000202" + negative_effect_on_A_G hasProperty "http://identifiers.org/sbo/SBO:0000202" + cancer_cell_natural_death hasProperty "http://identifiers.org/sbo/SBO:0000179" + cancer_cell_logistic_growth hasProperty "http://identifiers.org/go/GO:0040007" + cancer_cell_death_tissue_repair_system hasProperty "http://identifiers.org/sbo/SBO:0000179" + cancer_cell_death_apoptosis hasProperty "http://identifiers.org/sbo/SBO:0000179" + transition_to_cancer_cell hasProperty "http://identifiers.org/sbo/SBO:0000181" + + model model_source "http://identifiers.org/biomodels.db/MODEL1909050003", + "http://identifiers.org/biomodels.db/BIOMD0000000807" + model hasProperty "http://identifiers.org/ncit/C18121" + model hasProperty "http://identifiers.org/ncit/C19320" + model hasProperty "http://identifiers.org/mamo/MAMO_0000046" + model hasProperty "http://identifiers.org/ncit/C17938" + model hasProperty "http://identifiers.org/ncit/C45576" + model hasProperty "http://identifiers.org/ncit/C16870" + model isDescribedBy "http://identifiers.org/pubmed/29947770" + model created "2019-08-22T15:35:24Z" + model modified "2019-08-22T15:35:24Z" + model creator1.givenName "Szeyi" + model creator1.familyName "Ng" + model creator1.organization "EMBL-EBI" + model creator1.email "muffet0307@gmail.com" + + // Notes: + model notes ``` +This model describes the multistep process that transform a normal cell and its descendants +into a malignant tumour by considering three populations: normal, premalignant and +cancer cells. Created by COPASI 4.24(Build 197)Abstract:Tumorigenesis has been described +as a multistep process, where each step is associated with a genetic alteration, +in the direction to progressively transform a normal cell and its descendants into +a malignant tumour. Into this work, we propose a mathematical model for cancer onset +and development, considering three populations: normal, premalignant and cancer cells. +The model takes into account three hallmarks of cancer: self-sufficiency on growth +signals, insensibility to anti-growth signals and evading apoptosis. By using a nonlinear +expression to describe the mutation from premalignant to cancer cells, the model +includes genetic instability as an enabling characteristic of tumour progression. +Mathematical analysis was performed in detail. Results indicate that apoptosis and +tissue repair system are the first barriers against tumour progression. One of these +mechanisms must be corrupted for cancer to develop from a single mutant cell. The +results also show that the presence of aggressive cancer cells opens way to survival +of less adapted premalignant cells. Numerical simulations were performed with parameter +values based on experimental data of breast cancer, and the necessary time taken +for cancer to reach a detectable size from a single mutant cell was estimated with +respect to some parameters. We find that the rates of apoptosis and mutations have +a large influence on the pace of tumour progression and on the time it takes to become +clinically detectable. +``` +end + +New_Model is "Fassoni2019 - Oncogenesis encompassing mutations and genetic instability" diff --git a/doc/examples/biomodels/Kronik2008.txt b/doc/examples/biomodels/BIOMD0000000808/Kronik2008.txt similarity index 99% rename from doc/examples/biomodels/Kronik2008.txt rename to doc/examples/biomodels/BIOMD0000000808/Kronik2008.txt index 2d5f155a8..fa4648f7b 100644 --- a/doc/examples/biomodels/Kronik2008.txt +++ b/doc/examples/biomodels/BIOMD0000000808/Kronik2008.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kronik2008___Improving_alloreactive_CTL_immunotherapy_for_malignant_gliomas_using_a_simulation_model_of_their_interactive_dynamics() // Compartments and Species: diff --git a/doc/examples/biomodels/Malinzi2018 - tumour-immune interaction model.txt b/doc/examples/biomodels/BIOMD0000000809/Malinzi2018 - tumour-immune interaction model.txt similarity index 99% rename from doc/examples/biomodels/Malinzi2018 - tumour-immune interaction model.txt rename to doc/examples/biomodels/BIOMD0000000809/Malinzi2018 - tumour-immune interaction model.txt index b3e15f7c4..440a7e956 100644 --- a/doc/examples/biomodels/Malinzi2018 - tumour-immune interaction model.txt +++ b/doc/examples/biomodels/BIOMD0000000809/Malinzi2018 - tumour-immune interaction model.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Ganguli2018-immuno regulatory mechanisms in tumor microenvironment.txt b/doc/examples/biomodels/BIOMD0000000810/Ganguli2018-immuno regulatory mechanisms in tumor microenvironment.txt similarity index 99% rename from doc/examples/biomodels/Ganguli2018-immuno regulatory mechanisms in tumor microenvironment.txt rename to doc/examples/biomodels/BIOMD0000000810/Ganguli2018-immuno regulatory mechanisms in tumor microenvironment.txt index 12aa3151d..94ab1c2bb 100644 --- a/doc/examples/biomodels/Ganguli2018-immuno regulatory mechanisms in tumor microenvironment.txt +++ b/doc/examples/biomodels/BIOMD0000000810/Ganguli2018-immuno regulatory mechanisms in tumor microenvironment.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/He2017.txt b/doc/examples/biomodels/BIOMD0000000811/He2017.txt similarity index 99% rename from doc/examples/biomodels/He2017.txt rename to doc/examples/biomodels/BIOMD0000000811/He2017.txt index a007f7828..a1f634e0a 100644 --- a/doc/examples/biomodels/He2017.txt +++ b/doc/examples/biomodels/BIOMD0000000811/He2017.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *He2017___A_mathematical_model_of_pancreatic_cancer_with_two_kinds_of_treatments() // Compartments and Species: diff --git a/doc/examples/biomodels/Galante2012.txt b/doc/examples/biomodels/BIOMD0000000812/Galante2012.txt similarity index 99% rename from doc/examples/biomodels/Galante2012.txt rename to doc/examples/biomodels/BIOMD0000000812/Galante2012.txt index 9787c16c2..f80425d83 100644 --- a/doc/examples/biomodels/Galante2012.txt +++ b/doc/examples/biomodels/BIOMD0000000812/Galante2012.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Galante2012___B7_H1_and_a_Mathematical_Model_for_Cytotoxic_T_Cell_and_Tumor_Cell_Interaction() // Compartments and Species: diff --git a/doc/examples/biomodels/Anderson2015.txt b/doc/examples/biomodels/BIOMD0000000813/Anderson2015.txt similarity index 99% rename from doc/examples/biomodels/Anderson2015.txt rename to doc/examples/biomodels/BIOMD0000000813/Anderson2015.txt index 82fac6c37..70e9b22ac 100644 --- a/doc/examples/biomodels/Anderson2015.txt +++ b/doc/examples/biomodels/BIOMD0000000813/Anderson2015.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Anderson2015___Qualitative_behavior_of_systems_of_tumor_CD4__cytokine_interactions_with_treatments() // Compartments and Species: diff --git a/doc/examples/biomodels/Perez-Garcia19 Computational design of improved standardized chemotherapy protocols for grade 2 oligodendrogliomas.txt b/doc/examples/biomodels/BIOMD0000000814/Perez-Garcia19 Computational design of improved standardized chemotherapy protocols for grade 2 oligodendrogliomas.txt similarity index 95% rename from doc/examples/biomodels/Perez-Garcia19 Computational design of improved standardized chemotherapy protocols for grade 2 oligodendrogliomas.txt rename to doc/examples/biomodels/BIOMD0000000814/Perez-Garcia19 Computational design of improved standardized chemotherapy protocols for grade 2 oligodendrogliomas.txt index a886cb549..9817fcc9c 100644 --- a/doc/examples/biomodels/Perez-Garcia19 Computational design of improved standardized chemotherapy protocols for grade 2 oligodendrogliomas.txt +++ b/doc/examples/biomodels/BIOMD0000000814/Perez-Garcia19 Computational design of improved standardized chemotherapy protocols for grade 2 oligodendrogliomas.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: @@ -14,11 +14,11 @@ model *New_Model() Elimination_of_Chemotherapy: Drug_Concentration_C => ; compartment_*(lambda*Drug_Concentration_C); // Events: - injection_1: at (((time%28) == 27) && (time > 54)) && (time < 608): Drug_Concentration_C = Drug_Concentration_C + beta*b*d, dose1 = dose1 + 1; - injection_2: at (((time%28) == 0) && (time > 54)) && (time < 608): dose2 = dose2 + 1, Drug_Concentration_C = Drug_Concentration_C + beta*d*b; - injection_3: at (((((((((((((((((((time == 57) || (time == 85)) || (time == 113)) || (time == 141)) || (time == 169)) || (time == 197)) || (time == 225)) || (time == 253)) || (time == 281)) || (time == 309)) || (time == 337)) || (time == 365)) || (time == 393)) || (time == 421)) || (time == 449)) || (time == 477)) || (time == 505)) || (time == 533)) || (time == 561)) || (time == 589): dose3 = dose3 + 1, Drug_Concentration_C = Drug_Concentration_C + beta*b*d; - injection_4: at (((((((((((((((((((time == 58) || (time == 86)) || (time == 114)) || (time == 142)) || (time == 170)) || (time == 198)) || (time == 226)) || (time == 254)) || (time == 282)) || (time == 310)) || (time == 338)) || (time == 366)) || (time == 394)) || (time == 422)) || (time == 450)) || (time == 478)) || (time == 506)) || (time == 534)) || (time == 562)) || (time == 590): dose_4 = dose_4 + 1, Drug_Concentration_C = Drug_Concentration_C + beta*b*d; - injection_5: at (((((((((((((((((((time == 59) || (time == 87)) || (time == 115)) || (time == 143)) || (time == 171)) || (time == 199)) || (time == 227)) || (time == 255)) || (time == 283)) || (time == 311)) || (time == 339)) || (time == 367)) || (time == 395)) || (time == 423)) || (time == 451)) || (time == 479)) || (time == 507)) || (time == 535)) || (time == 563)) || (time == 591): dose_5 = dose_5 + 1, Drug_Concentration_C = Drug_Concentration_C + beta*b*d; + injection_1: at (((time%28) == 27) && (time > 54)) && (time < 608): dose1 = dose1 + 1, Drug_Concentration_C = Drug_Concentration_C + beta*b*d; + injection_2: at (((time%28) == 0) && (time > 54)) && (time < 608): Drug_Concentration_C = Drug_Concentration_C + beta*d*b, dose2 = dose2 + 1; + injection_3: at (((((((((((((((((((time == 57) || (time == 85)) || (time == 113)) || (time == 141)) || (time == 169)) || (time == 197)) || (time == 225)) || (time == 253)) || (time == 281)) || (time == 309)) || (time == 337)) || (time == 365)) || (time == 393)) || (time == 421)) || (time == 449)) || (time == 477)) || (time == 505)) || (time == 533)) || (time == 561)) || (time == 589): Drug_Concentration_C = Drug_Concentration_C + beta*b*d, dose3 = dose3 + 1; + injection_4: at (((((((((((((((((((time == 58) || (time == 86)) || (time == 114)) || (time == 142)) || (time == 170)) || (time == 198)) || (time == 226)) || (time == 254)) || (time == 282)) || (time == 310)) || (time == 338)) || (time == 366)) || (time == 394)) || (time == 422)) || (time == 450)) || (time == 478)) || (time == 506)) || (time == 534)) || (time == 562)) || (time == 590): Drug_Concentration_C = Drug_Concentration_C + beta*b*d, dose_4 = dose_4 + 1; + injection_5: at (((((((((((((((((((time == 59) || (time == 87)) || (time == 115)) || (time == 143)) || (time == 171)) || (time == 199)) || (time == 227)) || (time == 255)) || (time == 283)) || (time == 311)) || (time == 339)) || (time == 367)) || (time == 395)) || (time == 423)) || (time == 451)) || (time == 479)) || (time == 507)) || (time == 535)) || (time == 563)) || (time == 591): Drug_Concentration_C = Drug_Concentration_C + beta*b*d, dose_5 = dose_5 + 1; // Species initializations: Drug_Concentration_C = 0; diff --git a/doc/examples/biomodels/Chrobak2011.txt b/doc/examples/biomodels/BIOMD0000000815/Chrobak2011.txt similarity index 98% rename from doc/examples/biomodels/Chrobak2011.txt rename to doc/examples/biomodels/BIOMD0000000815/Chrobak2011.txt index 4945c27e0..34b112e76 100644 --- a/doc/examples/biomodels/Chrobak2011.txt +++ b/doc/examples/biomodels/BIOMD0000000815/Chrobak2011.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Chrobak2011___A_mathematical_model_of_induced_cancer_adaptive_immune_system_competition() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000816/OV25.txt b/doc/examples/biomodels/BIOMD0000000816/OV25.txt new file mode 100644 index 000000000..df59027b9 --- /dev/null +++ b/doc/examples/biomodels/BIOMD0000000816/OV25.txt @@ -0,0 +1,194 @@ +// Created by libAntimony v3.2.0 +model *New_Model() + + // Compartments and Species: + compartment compartment_; + species Uninfected_Tumor_Cell_U in compartment_, Infected_Cancer_Cell_I in compartment_; + species Oncolytic_Adenovirus_V in compartment_, Tumor_targeting_T_cells_T in compartment_; + species Naive_T_cells_A in compartment_, Dendritic_Cells_D in compartment_; + species $Total_cells_N in compartment_, $total_tumor_cells in compartment_; + + // Assignment Rules: + Total_cells_N := Uninfected_Tumor_Cell_U + Infected_Cancer_Cell_I + Tumor_targeting_T_cells_T; + total_tumor_cells := Uninfected_Tumor_Cell_U + Infected_Cancer_Cell_I; + + // Reactions: + Tumor_cell_U_exponential_growth: => Uninfected_Tumor_Cell_U; compartment_*(r*Uninfected_Tumor_Cell_U); + Tumour_cell_U_elimination: Uninfected_Tumor_Cell_U => ; compartment_*((k0 + c_kill*Infected_Cancer_Cell_I)*Uninfected_Tumor_Cell_U*Tumor_targeting_T_cells_T/Total_cells_N); + Tumor_Cell_U_infection: Uninfected_Tumor_Cell_U => Infected_Cancer_Cell_I; compartment_*(beta*Uninfected_Tumor_Cell_U*Oncolytic_Adenovirus_V/Total_cells_N); + Infected_Tumor_Cell_I_death: Infected_Cancer_Cell_I => ; compartment_*(delta_I*Infected_Cancer_Cell_I); + Infected_Tumor_Cell_I_elimination: Infected_Cancer_Cell_I => ; compartment_*((k0 + c_kill*Infected_Cancer_Cell_I)*Infected_Cancer_Cell_I*Tumor_targeting_T_cells_T/Total_cells_N); + Treatment_with_virus: => Oncolytic_Adenovirus_V; compartment_*U_V; + Natural_decay_of_virus: Oncolytic_Adenovirus_V => ; compartment_*(delta_V*Oncolytic_Adenovirus_V); + Release_of_virus: => Oncolytic_Adenovirus_V; compartment_*(alpha*delta_I*Infected_Cancer_Cell_I); + Activation_of_T_Cells_IL12: => Tumor_targeting_T_cells_T; compartment_*(chi_A*Naive_T_cells_A); + Activation_of_naive_T_cells_IL12: => Naive_T_cells_A; compartment_*(C_A*Infected_Cancer_Cell_I); + Activation_of_T_cells_4_1BBL: => Tumor_targeting_T_cells_T; compartment_*(C_T*Infected_Cancer_Cell_I); + Production_of_T_cells: => Tumor_targeting_T_cells_T; compartment_*(chi_D*Dendritic_Cells_D); + natural_death_of_T_cells: Tumor_targeting_T_cells_T => ; compartment_*(delta_T*Tumor_targeting_T_cells_T); + natural_death_of_naive_T_cells: Naive_T_cells_A => ; compartment_*(delta_A*Naive_T_cells_A); + Treatment_with_Dendritic_Cells_D: => Dendritic_Cells_D; compartment_*U_D; + natural_decay_of_Dendritic_Cells_D: Dendritic_Cells_D => ; compartment_*(delta_D*Dendritic_Cells_D); + + // Events: + OV_1: at time == 0: Oncolytic_Adenovirus_V = Oncolytic_Adenovirus_V + OV_dose; + OV_2: at time == 2: Oncolytic_Adenovirus_V = Oncolytic_Adenovirus_V + OV_dose; + OV_3: at time == 4: Oncolytic_Adenovirus_V = Oncolytic_Adenovirus_V + OV_dose; + + // Species initializations: + Uninfected_Tumor_Cell_U = 41.277; + Infected_Cancer_Cell_I = 0; + Oncolytic_Adenovirus_V = 0; + Tumor_targeting_T_cells_T = 0; + Naive_T_cells_A = 0; + Dendritic_Cells_D = 0; + + // Compartment initializations: + compartment_ = 1; + + // Variable initializations: + OV_dose = 2.5; + r = 0.3198; + beta = 1.008538; + k0 = 2; + c_kill = 0.595397; + delta_I = 1; + U_V = 0; + alpha = 3; + delta_V = 2.3; + C_T = 1.698362; + chi_A = 1; + chi_D = 4.675397; + delta_T = 0.35; + C_A = 0.000517; + delta_A = 0.35; + U_D = 0; + delta_D = 0.35; + D0 = 1; + + // Other declarations: + const compartment_, OV_dose, r, beta, k0, c_kill, delta_I, U_V, alpha, delta_V; + const C_T, chi_A, chi_D, delta_T, C_A, delta_A, U_D, delta_D, D0; + + // Unit definitions: + unit volume = 1e-3 litre; + unit substance = 1e-3 mole; + + // Display Names: + compartment_ is "compartment"; + Uninfected_Tumor_Cell_U is "Uninfected Tumor Cell U"; + Infected_Cancer_Cell_I is "Infected Cancer Cell I"; + Oncolytic_Adenovirus_V is "Oncolytic Adenovirus V"; + Tumor_targeting_T_cells_T is "Tumor-targeting T cells T"; + Naive_T_cells_A is "Naive T cells A"; + Dendritic_Cells_D is "Dendritic Cells D"; + Total_cells_N is "Total cells N"; + total_tumor_cells is "total tumor cells"; + OV_1 is "OV 1"; + OV_dose is "OV dose"; + OV_2 is "OV 2"; + OV_3 is "OV 3"; + Tumor_cell_U_exponential_growth is "Tumor cell U exponential growth"; + Tumour_cell_U_elimination is "Tumour cell U elimination"; + Tumor_Cell_U_infection is "Tumor Cell U infection"; + Infected_Tumor_Cell_I_death is "Infected Tumor Cell I death"; + Infected_Tumor_Cell_I_elimination is "Infected Tumor Cell I elimination"; + Treatment_with_virus is "Treatment with virus"; + Natural_decay_of_virus is "Natural decay of virus"; + Release_of_virus is "Release of virus"; + Activation_of_T_Cells_IL12 is "Activation of T Cells;IL12"; + Activation_of_naive_T_cells_IL12 is "Activation of naive T cells;IL12"; + Activation_of_T_cells_4_1BBL is "Activation of T cells;4-1BBL"; + Production_of_T_cells is "Production of T cells"; + natural_death_of_T_cells is "natural death of T cells"; + natural_death_of_naive_T_cells is "natural death of naive T cells"; + Treatment_with_Dendritic_Cells_D is "Treatment with Dendritic Cells D"; + natural_decay_of_Dendritic_Cells_D is "natural decay of Dendritic Cells D"; + + // CV terms: + compartment_ hasProperty "http://identifiers.org/ncit/C13413" + compartment_ hasTaxon "http://identifiers.org/taxonomy/10090" + Uninfected_Tumor_Cell_U isVersionOf "http://identifiers.org/efo/0000311" + Uninfected_Tumor_Cell_U isVersionOf "http://identifiers.org/bto/BTO:0002014" + Infected_Cancer_Cell_I isVersionOf "http://identifiers.org/efo/0000311" + Infected_Cancer_Cell_I isVersionOf "http://identifiers.org/bto/BTO:0002014" + Infected_Cancer_Cell_I isPropertyOf "http://identifiers.org/ncit/C25401" + Oncolytic_Adenovirus_V isVersionOf "http://identifiers.org/ncit/C14179" + Oncolytic_Adenovirus_V isVersionOf "http://identifiers.org/ncit/C28373" + Tumor_targeting_T_cells_T isVersionOf "http://identifiers.org/ncit/C129906" + Tumor_targeting_T_cells_T isPropertyOf "http://identifiers.org/ncit/C64542" + Naive_T_cells_A isVersionOf "http://identifiers.org/ncit/C129906" + Dendritic_Cells_D isVersionOf "http://identifiers.org/ncit/C12583" + Dendritic_Cells_D isVersionOf "http://identifiers.org/bto/BTO:0002042" + Total_cells_N isPartOf "http://identifiers.org/efo/0000311" + Total_cells_N isPartOf "http://identifiers.org/bto/BTO:0002014" + Total_cells_N isPartOf "http://identifiers.org/ncit/C129906" + total_tumor_cells isVersionOf "http://identifiers.org/efo/0000311" + total_tumor_cells isVersionOf "http://identifiers.org/bto/BTO:0002014" + r isVersionOf "http://identifiers.org/sbo/SBO:0000610" + delta_I isVersionOf "http://identifiers.org/sbo/SBO:0000356" + delta_V isVersionOf "http://identifiers.org/sbo/SBO:0000356" + C_T isVersionOf "http://identifiers.org/sbo/SBO:0000610" + chi_A isVersionOf "http://identifiers.org/sbo/SBO:0000610" + chi_D isVersionOf "http://identifiers.org/sbo/SBO:0000610" + delta_T isVersionOf "http://identifiers.org/sbo/SBO:0000356" + C_A isVersionOf "http://identifiers.org/sbo/SBO:0000610" + delta_A isVersionOf "http://identifiers.org/sbo/SBO:0000356" + delta_D isVersionOf "http://identifiers.org/sbo/SBO:0000356" + Tumor_cell_U_exponential_growth isVersionOf "http://identifiers.org/go/GO:0040007" + Tumour_cell_U_elimination isVersionOf "http://identifiers.org/sbo/SBO:0000179" + Tumor_Cell_U_infection isVersionOf "http://identifiers.org/go/GO:0019089" + Infected_Tumor_Cell_I_death isVersionOf "http://identifiers.org/sbo/SBO:0000179" + Infected_Tumor_Cell_I_elimination isVersionOf "http://identifiers.org/sbo/SBO:0000179" + Treatment_with_virus isVersionOf "http://identifiers.org/go/GO:0035737" + Natural_decay_of_virus isVersionOf "http://identifiers.org/sbo/SBO:0000179" + Release_of_virus isVersionOf "http://identifiers.org/sbo/SBO:0000393" + Activation_of_T_Cells_IL12 isVersionOf "http://identifiers.org/go/GO:0051132" + Activation_of_naive_T_cells_IL12 isVersionOf "http://identifiers.org/go/GO:0051132" + Activation_of_T_cells_4_1BBL isVersionOf "http://identifiers.org/go/GO:0051132" + Production_of_T_cells isVersionOf "http://identifiers.org/sbo/SBO:0000393" + natural_death_of_T_cells isVersionOf "http://identifiers.org/sbo/SBO:0000179" + natural_death_of_naive_T_cells isVersionOf "http://identifiers.org/sbo/SBO:0000179" + Treatment_with_Dendritic_Cells_D isVersionOf "http://identifiers.org/go/GO:0035737" + natural_decay_of_Dendritic_Cells_D isVersionOf "http://identifiers.org/sbo/SBO:0000179" + + model hasProperty "http://identifiers.org/ncit/C62713" + model hasProperty "http://identifiers.org/doid/DOID:1909" + model hasProperty "http://identifiers.org/efo/0000311" + model hasProperty "http://identifiers.org/bto/BTO:0002014" + model hasProperty "http://identifiers.org/mamo/MAMO_0000046" + model hasProperty "http://identifiers.org/efo/0000756" + model hasTaxon "http://identifiers.org/taxonomy/10090" + model isDescribedBy "http://identifiers.org/pubmed/30510594" + model created "2019-09-06T14:44:44Z" + model modified "2019-09-06T14:44:44Z" + model creator1.givenName "Szeyi" + model creator1.familyName "Ng" + model creator1.organization "EMBL-EBI" + model creator1.email "muffet0307@gmail.com" + + // Notes: + model notes ``` +The model is based on 'Developing a Minimally Structured Mathematical Model +of Cancer Treatment with Oncolytic Viruses and Dendritic Cell Injections', PMID:30510594. +Author:Jana L.Gevertz and Joanna R.Wares. This model describes the original mathematical +model described in section 2.1. Built by COPASI 4.24( Build 197)Abstract:Mathematical +models of biological systems must strike a balance between being sufficiently complex +to capture important biological features, while being simple enough that they remain +tractable through analysis or simulation. In this work, we rigorously explore how +to balance these competing interests when modeling murine melanoma treatment with +oncolytic viruses and dendritic cell injections. Previously, we developed a system +of six ordinary differential equations containing fourteen parameters that well describes +experimental data on the efficacy of these treatments. Here, we explore whether this +previously developed model is the minimal model needed to accurately describe the +data. Using a variety of techniques, including sensitivity analyses and a parameter +sloppiness analysis, we find that our model can be reduced by one variable and three +parameters and still give excellent fits to the data. We also argue that our model +is not too simple to capture the dynamics of the data, and that the original and +minimal models make similar predictions about the efficacy and robustness of protocols +not considered in experiments. Reducing the model to its minimal form allows us to +increase the tractability of the system in the face of parametric uncertainty. +``` +end + +New_Model is "New Model" diff --git a/doc/examples/biomodels/BIOMD0000000816/OV5.txt b/doc/examples/biomodels/BIOMD0000000816/OV5.txt new file mode 100644 index 000000000..ba886ee40 --- /dev/null +++ b/doc/examples/biomodels/BIOMD0000000816/OV5.txt @@ -0,0 +1,194 @@ +// Created by libAntimony v3.2.0 +model *New_Model() + + // Compartments and Species: + compartment compartment_; + species Uninfected_Tumor_Cell_U in compartment_, Infected_Cancer_Cell_I in compartment_; + species Oncolytic_Adenovirus_V in compartment_, Tumor_targeting_T_cells_T in compartment_; + species Naive_T_cells_A in compartment_, Dendritic_Cells_D in compartment_; + species $Total_cells_N in compartment_, $total_tumor_cells in compartment_; + + // Assignment Rules: + Total_cells_N := Uninfected_Tumor_Cell_U + Infected_Cancer_Cell_I + Tumor_targeting_T_cells_T; + total_tumor_cells := Uninfected_Tumor_Cell_U + Infected_Cancer_Cell_I; + + // Reactions: + Tumor_cell_U_exponential_growth: => Uninfected_Tumor_Cell_U; compartment_*(r*Uninfected_Tumor_Cell_U); + Tumour_cell_U_elimination: Uninfected_Tumor_Cell_U => ; compartment_*((k0 + c_kill*Infected_Cancer_Cell_I)*Uninfected_Tumor_Cell_U*Tumor_targeting_T_cells_T/Total_cells_N); + Tumor_Cell_U_infection: Uninfected_Tumor_Cell_U => Infected_Cancer_Cell_I; compartment_*(beta*Uninfected_Tumor_Cell_U*Oncolytic_Adenovirus_V/Total_cells_N); + Infected_Tumor_Cell_I_death: Infected_Cancer_Cell_I => ; compartment_*(delta_I*Infected_Cancer_Cell_I); + Infected_Tumor_Cell_I_elimination: Infected_Cancer_Cell_I => ; compartment_*((k0 + c_kill*Infected_Cancer_Cell_I)*Infected_Cancer_Cell_I*Tumor_targeting_T_cells_T/Total_cells_N); + Treatment_with_virus: => Oncolytic_Adenovirus_V; compartment_*U_V; + Natural_decay_of_virus: Oncolytic_Adenovirus_V => ; compartment_*(delta_V*Oncolytic_Adenovirus_V); + Release_of_virus: => Oncolytic_Adenovirus_V; compartment_*(alpha*delta_I*Infected_Cancer_Cell_I); + Activation_of_T_Cells_IL12: => Tumor_targeting_T_cells_T; compartment_*(chi_A*Naive_T_cells_A); + Activation_of_naive_T_cells_IL12: => Naive_T_cells_A; compartment_*(C_A*Infected_Cancer_Cell_I); + Activation_of_T_cells_4_1BBL: => Tumor_targeting_T_cells_T; compartment_*(C_T*Infected_Cancer_Cell_I); + Production_of_T_cells: => Tumor_targeting_T_cells_T; compartment_*(chi_D*Dendritic_Cells_D); + natural_death_of_T_cells: Tumor_targeting_T_cells_T => ; compartment_*(delta_T*Tumor_targeting_T_cells_T); + natural_death_of_naive_T_cells: Naive_T_cells_A => ; compartment_*(delta_A*Naive_T_cells_A); + Treatment_with_Dendritic_Cells_D: => Dendritic_Cells_D; compartment_*U_D; + natural_decay_of_Dendritic_Cells_D: Dendritic_Cells_D => ; compartment_*(delta_D*Dendritic_Cells_D); + + // Events: + OV_1: at time == 0: Oncolytic_Adenovirus_V = Oncolytic_Adenovirus_V + OV_dose; + OV_2: at time == 2: Oncolytic_Adenovirus_V = Oncolytic_Adenovirus_V + OV_dose; + OV_3: at time == 4: Oncolytic_Adenovirus_V = Oncolytic_Adenovirus_V + OV_dose; + + // Species initializations: + Uninfected_Tumor_Cell_U = 83.9463; + Infected_Cancer_Cell_I = 0; + Oncolytic_Adenovirus_V = 0; + Tumor_targeting_T_cells_T = 0; + Naive_T_cells_A = 0; + Dendritic_Cells_D = 0; + + // Compartment initializations: + compartment_ = 1; + + // Variable initializations: + OV_dose = 5; + r = 0.3198; + beta = 1.008538; + k0 = 2; + c_kill = 0.595397; + delta_I = 1; + U_V = 0; + alpha = 3; + delta_V = 2.3; + C_T = 1.698362; + chi_A = 1; + chi_D = 4.675397; + delta_T = 0.35; + C_A = 0.000517; + delta_A = 0.35; + U_D = 0; + delta_D = 0.35; + D0 = 1; + + // Other declarations: + const compartment_, OV_dose, r, beta, k0, c_kill, delta_I, U_V, alpha, delta_V; + const C_T, chi_A, chi_D, delta_T, C_A, delta_A, U_D, delta_D, D0; + + // Unit definitions: + unit volume = 1e-3 litre; + unit substance = 1e-3 mole; + + // Display Names: + compartment_ is "compartment"; + Uninfected_Tumor_Cell_U is "Uninfected Tumor Cell U"; + Infected_Cancer_Cell_I is "Infected Cancer Cell I"; + Oncolytic_Adenovirus_V is "Oncolytic Adenovirus V"; + Tumor_targeting_T_cells_T is "Tumor-targeting T cells T"; + Naive_T_cells_A is "Naive T cells A"; + Dendritic_Cells_D is "Dendritic Cells D"; + Total_cells_N is "Total cells N"; + total_tumor_cells is "total tumor cells"; + OV_1 is "OV 1"; + OV_dose is "OV dose"; + OV_2 is "OV 2"; + OV_3 is "OV 3"; + Tumor_cell_U_exponential_growth is "Tumor cell U exponential growth"; + Tumour_cell_U_elimination is "Tumour cell U elimination"; + Tumor_Cell_U_infection is "Tumor Cell U infection"; + Infected_Tumor_Cell_I_death is "Infected Tumor Cell I death"; + Infected_Tumor_Cell_I_elimination is "Infected Tumor Cell I elimination"; + Treatment_with_virus is "Treatment with virus"; + Natural_decay_of_virus is "Natural decay of virus"; + Release_of_virus is "Release of virus"; + Activation_of_T_Cells_IL12 is "Activation of T Cells;IL12"; + Activation_of_naive_T_cells_IL12 is "Activation of naive T cells;IL12"; + Activation_of_T_cells_4_1BBL is "Activation of T cells;4-1BBL"; + Production_of_T_cells is "Production of T cells"; + natural_death_of_T_cells is "natural death of T cells"; + natural_death_of_naive_T_cells is "natural death of naive T cells"; + Treatment_with_Dendritic_Cells_D is "Treatment with Dendritic Cells D"; + natural_decay_of_Dendritic_Cells_D is "natural decay of Dendritic Cells D"; + + // CV terms: + compartment_ hasProperty "http://identifiers.org/ncit/C13413" + compartment_ hasTaxon "http://identifiers.org/taxonomy/10090" + Uninfected_Tumor_Cell_U isVersionOf "http://identifiers.org/bto/BTO:0002014" + Uninfected_Tumor_Cell_U isVersionOf "http://identifiers.org/efo/0000311" + Infected_Cancer_Cell_I isVersionOf "http://identifiers.org/bto/BTO:0002014" + Infected_Cancer_Cell_I isVersionOf "http://identifiers.org/efo/0000311" + Infected_Cancer_Cell_I isPropertyOf "http://identifiers.org/ncit/C25401" + Oncolytic_Adenovirus_V isVersionOf "http://identifiers.org/ncit/C28373" + Oncolytic_Adenovirus_V isVersionOf "http://identifiers.org/ncit/C14179" + Tumor_targeting_T_cells_T isVersionOf "http://identifiers.org/ncit/C129906" + Tumor_targeting_T_cells_T isPropertyOf "http://identifiers.org/ncit/C64542" + Naive_T_cells_A isVersionOf "http://identifiers.org/ncit/C129906" + Dendritic_Cells_D isVersionOf "http://identifiers.org/bto/BTO:0002042" + Dendritic_Cells_D isVersionOf "http://identifiers.org/ncit/C12583" + Total_cells_N isPartOf "http://identifiers.org/bto/BTO:0002014" + Total_cells_N isPartOf "http://identifiers.org/ncit/C129906" + Total_cells_N isPartOf "http://identifiers.org/efo/0000311" + total_tumor_cells isVersionOf "http://identifiers.org/efo/0000311" + total_tumor_cells isVersionOf "http://identifiers.org/bto/BTO:0002014" + r isVersionOf "http://identifiers.org/sbo/SBO:0000610" + delta_I isVersionOf "http://identifiers.org/sbo/SBO:0000356" + delta_V isVersionOf "http://identifiers.org/sbo/SBO:0000356" + C_T isVersionOf "http://identifiers.org/sbo/SBO:0000610" + chi_A isVersionOf "http://identifiers.org/sbo/SBO:0000610" + chi_D isVersionOf "http://identifiers.org/sbo/SBO:0000610" + delta_T isVersionOf "http://identifiers.org/sbo/SBO:0000356" + C_A isVersionOf "http://identifiers.org/sbo/SBO:0000610" + delta_A isVersionOf "http://identifiers.org/sbo/SBO:0000356" + delta_D isVersionOf "http://identifiers.org/sbo/SBO:0000356" + Tumor_cell_U_exponential_growth isVersionOf "http://identifiers.org/go/GO:0040007" + Tumour_cell_U_elimination isVersionOf "http://identifiers.org/sbo/SBO:0000179" + Tumor_Cell_U_infection isVersionOf "http://identifiers.org/go/GO:0019089" + Infected_Tumor_Cell_I_death isVersionOf "http://identifiers.org/sbo/SBO:0000179" + Infected_Tumor_Cell_I_elimination isVersionOf "http://identifiers.org/sbo/SBO:0000179" + Treatment_with_virus isVersionOf "http://identifiers.org/go/GO:0035737" + Natural_decay_of_virus isVersionOf "http://identifiers.org/sbo/SBO:0000179" + Release_of_virus isVersionOf "http://identifiers.org/sbo/SBO:0000393" + Activation_of_T_Cells_IL12 isVersionOf "http://identifiers.org/go/GO:0051132" + Activation_of_naive_T_cells_IL12 isVersionOf "http://identifiers.org/go/GO:0051132" + Activation_of_T_cells_4_1BBL isVersionOf "http://identifiers.org/go/GO:0051132" + Production_of_T_cells isVersionOf "http://identifiers.org/sbo/SBO:0000393" + natural_death_of_T_cells isVersionOf "http://identifiers.org/sbo/SBO:0000179" + natural_death_of_naive_T_cells isVersionOf "http://identifiers.org/sbo/SBO:0000179" + Treatment_with_Dendritic_Cells_D isVersionOf "http://identifiers.org/go/GO:0035737" + natural_decay_of_Dendritic_Cells_D isVersionOf "http://identifiers.org/sbo/SBO:0000179" + + model hasProperty "http://identifiers.org/doid/DOID:1909" + model hasProperty "http://identifiers.org/bto/BTO:0002014" + model hasProperty "http://identifiers.org/mamo/MAMO_0000046" + model hasProperty "http://identifiers.org/efo/0000756" + model hasProperty "http://identifiers.org/ncit/C62713" + model hasProperty "http://identifiers.org/efo/0000311" + model hasTaxon "http://identifiers.org/taxonomy/10090" + model isDescribedBy "http://identifiers.org/pubmed/30510594" + model created "2019-09-06T14:44:44Z" + model modified "2019-09-06T14:44:44Z" + model creator1.givenName "Szeyi" + model creator1.familyName "Ng" + model creator1.organization "EMBL-EBI" + model creator1.email "muffet0307@gmail.com" + + // Notes: + model notes ``` +The model is based on 'Developing a Minimally Structured Mathematical Model +of Cancer Treatment with Oncolytic Viruses and Dendritic Cell Injections', PMID:30510594. +Author:Jana L.Gevertz and Joanna R.Wares. This model describes the original mathematical +model described in section 2.1. Built by COPASI 4.24( Build 197)Abstract:Mathematical +models of biological systems must strike a balance between being sufficiently complex +to capture important biological features, while being simple enough that they remain +tractable through analysis or simulation. In this work, we rigorously explore how +to balance these competing interests when modeling murine melanoma treatment with +oncolytic viruses and dendritic cell injections. Previously, we developed a system +of six ordinary differential equations containing fourteen parameters that well describes +experimental data on the efficacy of these treatments. Here, we explore whether this +previously developed model is the minimal model needed to accurately describe the +data. Using a variety of techniques, including sensitivity analyses and a parameter +sloppiness analysis, we find that our model can be reduced by one variable and three +parameters and still give excellent fits to the data. We also argue that our model +is not too simple to capture the dynamics of the data, and that the original and +minimal models make similar predictions about the efficacy and robustness of protocols +not considered in experiments. Reducing the model to its minimal form allows us to +increase the tractability of the system in the face of parametric uncertainty. +``` +end + +New_Model is "New Model" diff --git a/doc/examples/biomodels/BIOMD0000000816/model.txt b/doc/examples/biomodels/BIOMD0000000816/model.txt new file mode 100644 index 000000000..b25f703c9 --- /dev/null +++ b/doc/examples/biomodels/BIOMD0000000816/model.txt @@ -0,0 +1,202 @@ +// Created by libAntimony v3.2.0 +model *New_Model() + + // Compartments and Species: + compartment compartment_; + species Uninfected_Tumor_Cell_U in compartment_, Infected_Cancer_Cell_I in compartment_; + species Oncolytic_Adenovirus_V in compartment_, Tumor_targeting_T_cells_T in compartment_; + species Naive_T_cells_A in compartment_, Dendritic_Cells_D in compartment_; + species $Total_cells_N in compartment_, $total_tumor_cells in compartment_; + + // Assignment Rules: + Total_cells_N := Uninfected_Tumor_Cell_U + Infected_Cancer_Cell_I + Tumor_targeting_T_cells_T; + total_tumor_cells := Uninfected_Tumor_Cell_U + Infected_Cancer_Cell_I; + + // Reactions: + Tumor_cell_U_exponential_growth: => Uninfected_Tumor_Cell_U; compartment_*(r*Uninfected_Tumor_Cell_U); + Tumour_cell_U_elimination: Uninfected_Tumor_Cell_U => ; compartment_*((k0 + c_kill*Infected_Cancer_Cell_I)*Uninfected_Tumor_Cell_U*Tumor_targeting_T_cells_T/Total_cells_N); + Tumor_Cell_U_infection: Uninfected_Tumor_Cell_U => Infected_Cancer_Cell_I; compartment_*(beta*Uninfected_Tumor_Cell_U*Oncolytic_Adenovirus_V/Total_cells_N); + Infected_Tumor_Cell_I_death: Infected_Cancer_Cell_I => ; compartment_*(delta_I*Infected_Cancer_Cell_I); + Infected_Tumor_Cell_I_elimination: Infected_Cancer_Cell_I => ; compartment_*((k0 + c_kill*Infected_Cancer_Cell_I)*Infected_Cancer_Cell_I*Tumor_targeting_T_cells_T/Total_cells_N); + Treatment_with_virus: => Oncolytic_Adenovirus_V; compartment_*U_V; + Natural_decay_of_virus: Oncolytic_Adenovirus_V => ; compartment_*(delta_V*Oncolytic_Adenovirus_V); + Release_of_virus: => Oncolytic_Adenovirus_V; compartment_*(alpha*delta_I*Infected_Cancer_Cell_I); + Activation_of_T_Cells_IL12: => Tumor_targeting_T_cells_T; compartment_*(chi_A*Naive_T_cells_A); + Activation_of_naive_T_cells_IL12: => Naive_T_cells_A; compartment_*(C_A*Infected_Cancer_Cell_I); + Activation_of_T_cells_4_1BBL: => Tumor_targeting_T_cells_T; compartment_*(C_T*Infected_Cancer_Cell_I); + Production_of_T_cells: => Tumor_targeting_T_cells_T; compartment_*(chi_D*Dendritic_Cells_D); + natural_death_of_T_cells: Tumor_targeting_T_cells_T => ; compartment_*(delta_T*Tumor_targeting_T_cells_T); + natural_death_of_naive_T_cells: Naive_T_cells_A => ; compartment_*(delta_A*Naive_T_cells_A); + Treatment_with_Dendritic_Cells_D: => Dendritic_Cells_D; compartment_*U_D; + natural_decay_of_Dendritic_Cells_D: Dendritic_Cells_D => ; compartment_*(delta_D*Dendritic_Cells_D); + + // Events: + OV_1: at time == 0: Oncolytic_Adenovirus_V = Oncolytic_Adenovirus_V + OV_dose; + OV_2: at time == 2: Oncolytic_Adenovirus_V = Oncolytic_Adenovirus_V + OV_dose; + OV_3: at time == 4: Oncolytic_Adenovirus_V = Oncolytic_Adenovirus_V + OV_dose; + AD_1: at time == 1: Dendritic_Cells_D = Dendritic_Cells_D + D0; + AD_2: at time == 3: Dendritic_Cells_D = Dendritic_Cells_D + D0; + AD_3: at time == 5: Dendritic_Cells_D = D0 + Dendritic_Cells_D; + + // Species initializations: + Uninfected_Tumor_Cell_U = 58.020755; + Infected_Cancer_Cell_I = 0; + Oncolytic_Adenovirus_V = 0; + Tumor_targeting_T_cells_T = 0; + Naive_T_cells_A = 0; + Dendritic_Cells_D = 0; + + // Compartment initializations: + compartment_ = 1; + + // Variable initializations: + OV_dose = 2.5; + D0 = 1; + r = 0.3198; + beta = 1.008538; + k0 = 2; + c_kill = 0.595397; + delta_I = 1; + U_V = 0; + alpha = 3; + delta_V = 2.3; + C_T = 1.698362; + chi_A = 1; + chi_D = 4.675397; + delta_T = 0.35; + C_A = 0.000517; + delta_A = 0.35; + U_D = 0; + delta_D = 0.35; + + // Other declarations: + const compartment_, OV_dose, D0, r, beta, k0, c_kill, delta_I, U_V, alpha; + const delta_V, C_T, chi_A, chi_D, delta_T, C_A, delta_A, U_D, delta_D; + + // Unit definitions: + unit volume = 1e-3 litre; + unit substance = 1e-3 mole; + + // Display Names: + compartment_ is "compartment"; + Uninfected_Tumor_Cell_U is "Uninfected Tumor Cell U"; + Infected_Cancer_Cell_I is "Infected Cancer Cell I"; + Oncolytic_Adenovirus_V is "Oncolytic Adenovirus V"; + Tumor_targeting_T_cells_T is "Tumor-targeting T cells T"; + Naive_T_cells_A is "Naive T cells A"; + Dendritic_Cells_D is "Dendritic Cells D"; + Total_cells_N is "Total cells N"; + total_tumor_cells is "total tumor cells"; + OV_1 is "OV 1"; + OV_dose is "OV dose"; + OV_2 is "OV 2"; + OV_3 is "OV 3"; + AD_1 is "AD 1"; + AD_2 is "AD 2"; + AD_3 is "AD 3"; + Tumor_cell_U_exponential_growth is "Tumor cell U exponential growth"; + Tumour_cell_U_elimination is "Tumour cell U elimination"; + Tumor_Cell_U_infection is "Tumor Cell U infection"; + Infected_Tumor_Cell_I_death is "Infected Tumor Cell I death"; + Infected_Tumor_Cell_I_elimination is "Infected Tumor Cell I elimination"; + Treatment_with_virus is "Treatment with virus"; + Natural_decay_of_virus is "Natural decay of virus"; + Release_of_virus is "Release of virus"; + Activation_of_T_Cells_IL12 is "Activation of T Cells;IL12"; + Activation_of_naive_T_cells_IL12 is "Activation of naive T cells;IL12"; + Activation_of_T_cells_4_1BBL is "Activation of T cells;4-1BBL"; + Production_of_T_cells is "Production of T cells"; + natural_death_of_T_cells is "natural death of T cells"; + natural_death_of_naive_T_cells is "natural death of naive T cells"; + Treatment_with_Dendritic_Cells_D is "Treatment with Dendritic Cells D"; + natural_decay_of_Dendritic_Cells_D is "natural decay of Dendritic Cells D"; + + // CV terms: + compartment_ hasProperty "http://identifiers.org/ncit/C13413" + compartment_ hasTaxon "http://identifiers.org/taxonomy/10090" + Uninfected_Tumor_Cell_U isVersionOf "http://identifiers.org/efo/0000311" + Uninfected_Tumor_Cell_U isVersionOf "http://identifiers.org/bto/BTO:0002014" + Infected_Cancer_Cell_I isVersionOf "http://identifiers.org/efo/0000311" + Infected_Cancer_Cell_I isVersionOf "http://identifiers.org/bto/BTO:0002014" + Infected_Cancer_Cell_I isPropertyOf "http://identifiers.org/ncit/C25401" + Oncolytic_Adenovirus_V isVersionOf "http://identifiers.org/ncit/C14179" + Oncolytic_Adenovirus_V isVersionOf "http://identifiers.org/ncit/C28373" + Tumor_targeting_T_cells_T isVersionOf "http://identifiers.org/ncit/C129906" + Tumor_targeting_T_cells_T isPropertyOf "http://identifiers.org/ncit/C64542" + Naive_T_cells_A isVersionOf "http://identifiers.org/ncit/C129906" + Dendritic_Cells_D isVersionOf "http://identifiers.org/ncit/C12583" + Dendritic_Cells_D isVersionOf "http://identifiers.org/bto/BTO:0002042" + Total_cells_N isPartOf "http://identifiers.org/efo/0000311" + Total_cells_N isPartOf "http://identifiers.org/bto/BTO:0002014" + Total_cells_N isPartOf "http://identifiers.org/ncit/C129906" + total_tumor_cells isVersionOf "http://identifiers.org/bto/BTO:0002014" + total_tumor_cells isVersionOf "http://identifiers.org/efo/0000311" + r isVersionOf "http://identifiers.org/sbo/SBO:0000610" + delta_I isVersionOf "http://identifiers.org/sbo/SBO:0000356" + delta_V isVersionOf "http://identifiers.org/sbo/SBO:0000356" + C_T isVersionOf "http://identifiers.org/sbo/SBO:0000610" + chi_A isVersionOf "http://identifiers.org/sbo/SBO:0000610" + chi_D isVersionOf "http://identifiers.org/sbo/SBO:0000610" + delta_T isVersionOf "http://identifiers.org/sbo/SBO:0000356" + C_A isVersionOf "http://identifiers.org/sbo/SBO:0000610" + delta_A isVersionOf "http://identifiers.org/sbo/SBO:0000356" + delta_D isVersionOf "http://identifiers.org/sbo/SBO:0000356" + Tumor_cell_U_exponential_growth isVersionOf "http://identifiers.org/go/GO:0040007" + Tumour_cell_U_elimination isVersionOf "http://identifiers.org/sbo/SBO:0000179" + Tumor_Cell_U_infection isVersionOf "http://identifiers.org/go/GO:0019089" + Infected_Tumor_Cell_I_death isVersionOf "http://identifiers.org/sbo/SBO:0000179" + Infected_Tumor_Cell_I_elimination isVersionOf "http://identifiers.org/sbo/SBO:0000179" + Treatment_with_virus isVersionOf "http://identifiers.org/go/GO:0035737" + Natural_decay_of_virus isVersionOf "http://identifiers.org/sbo/SBO:0000179" + Release_of_virus isVersionOf "http://identifiers.org/sbo/SBO:0000393" + Activation_of_T_Cells_IL12 isVersionOf "http://identifiers.org/go/GO:0051132" + Activation_of_naive_T_cells_IL12 isVersionOf "http://identifiers.org/go/GO:0051132" + Activation_of_T_cells_4_1BBL isVersionOf "http://identifiers.org/go/GO:0051132" + Production_of_T_cells isVersionOf "http://identifiers.org/sbo/SBO:0000393" + natural_death_of_T_cells isVersionOf "http://identifiers.org/sbo/SBO:0000179" + natural_death_of_naive_T_cells isVersionOf "http://identifiers.org/sbo/SBO:0000179" + Treatment_with_Dendritic_Cells_D isVersionOf "http://identifiers.org/go/GO:0035737" + natural_decay_of_Dendritic_Cells_D isVersionOf "http://identifiers.org/sbo/SBO:0000179" + + model model_source "http://identifiers.org/biomodels.db/MODEL1909180001", + "http://identifiers.org/biomodels.db/BIOMD0000000816" + model hasProperty "http://identifiers.org/doid/DOID:1909" + model hasProperty "http://identifiers.org/mamo/MAMO_0000046" + model hasProperty "http://identifiers.org/efo/0000756" + model hasProperty "http://identifiers.org/efo/0000311" + model hasProperty "http://identifiers.org/ncit/C62713" + model hasProperty "http://identifiers.org/bto/BTO:0002014" + model hasTaxon "http://identifiers.org/taxonomy/10090" + model isDescribedBy "http://identifiers.org/pubmed/30510594" + model created "2019-09-06T14:44:44Z" + model modified "2019-09-06T14:44:44Z" + model creator1.givenName "Szeyi" + model creator1.familyName "Ng" + model creator1.organization "EMBL-EBI" + model creator1.email "muffet0307@gmail.com" + + // Notes: + model notes ``` +The model is based on 'Developing a Minimally Structured Mathematical Model +of Cancer Treatment with Oncolytic Viruses and Dendritic Cell Injections', PMID:30510594. +Author:Jana L.Gevertz and Joanna R.Wares. This model describes the original mathematical +model described in section 2.1. Built by COPASI 4.24( Build 197)Abstract:Mathematical +models of biological systems must strike a balance between being sufficiently complex +to capture important biological features, while being simple enough that they remain +tractable through analysis or simulation. In this work, we rigorously explore how +to balance these competing interests when modeling murine melanoma treatment with +oncolytic viruses and dendritic cell injections. Previously, we developed a system +of six ordinary differential equations containing fourteen parameters that well describes +experimental data on the efficacy of these treatments. Here, we explore whether this +previously developed model is the minimal model needed to accurately describe the +data. Using a variety of techniques, including sensitivity analyses and a parameter +sloppiness analysis, we find that our model can be reduced by one variable and three +parameters and still give excellent fits to the data. We also argue that our model +is not too simple to capture the dynamics of the data, and that the original and +minimal models make similar predictions about the efficacy and robustness of protocols +not considered in experiments. Reducing the model to its minimal form allows us to +increase the tractability of the system in the face of parametric uncertainty. +``` +end + +New_Model is "Gevertz2018 - Cancer Treatment with Oncolytic Viruses and Dendritic Cell injections original model" diff --git a/doc/examples/biomodels/OV25.txt b/doc/examples/biomodels/BIOMD0000000817/OV25.txt similarity index 99% rename from doc/examples/biomodels/OV25.txt rename to doc/examples/biomodels/BIOMD0000000817/OV25.txt index b09ff6c42..cb16f9bd1 100644 --- a/doc/examples/biomodels/OV25.txt +++ b/doc/examples/biomodels/BIOMD0000000817/OV25.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/OV5.txt b/doc/examples/biomodels/BIOMD0000000817/OV5.txt similarity index 99% rename from doc/examples/biomodels/OV5.txt rename to doc/examples/biomodels/BIOMD0000000817/OV5.txt index b03693109..7243e84ee 100644 --- a/doc/examples/biomodels/OV5.txt +++ b/doc/examples/biomodels/BIOMD0000000817/OV5.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Model.txt b/doc/examples/biomodels/BIOMD0000000817/model.txt similarity index 99% rename from doc/examples/biomodels/Model.txt rename to doc/examples/biomodels/BIOMD0000000817/model.txt index 07c8c14f4..d43d8cf3a 100644 --- a/doc/examples/biomodels/Model.txt +++ b/doc/examples/biomodels/BIOMD0000000817/model.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: @@ -80,7 +80,7 @@ model *New_Model() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-3 mole; unit extent = substance; unit substance_per_volume = 1e-3 mole / 1e-3 litre; diff --git a/doc/examples/biomodels/Lee2008.txt b/doc/examples/biomodels/BIOMD0000000818/Lee2008.txt similarity index 99% rename from doc/examples/biomodels/Lee2008.txt rename to doc/examples/biomodels/BIOMD0000000818/Lee2008.txt index 239e31bfb..23c365391 100644 --- a/doc/examples/biomodels/Lee2008.txt +++ b/doc/examples/biomodels/BIOMD0000000818/Lee2008.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Lee2008___ERK_and_PI3K_signal_integration_by_Myc() // Compartments and Species: diff --git a/doc/examples/biomodels/Nazari2018 - IL6 mediated stem cell driven tumor growth and targeted treatment.txt b/doc/examples/biomodels/BIOMD0000000819/Nazari2018 - IL6 mediated stem cell driven tumor growth and targeted treatment.txt similarity index 99% rename from doc/examples/biomodels/Nazari2018 - IL6 mediated stem cell driven tumor growth and targeted treatment.txt rename to doc/examples/biomodels/BIOMD0000000819/Nazari2018 - IL6 mediated stem cell driven tumor growth and targeted treatment.txt index 6dd0d3b0d..8b5b10914 100644 --- a/doc/examples/biomodels/Nazari2018 - IL6 mediated stem cell driven tumor growth and targeted treatment.txt +++ b/doc/examples/biomodels/BIOMD0000000819/Nazari2018 - IL6 mediated stem cell driven tumor growth and targeted treatment.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/West2019 - Cellular interactions constrain tumor growth.txt b/doc/examples/biomodels/BIOMD0000000820/West2019 - Cellular interactions constrain tumor growth.txt similarity index 97% rename from doc/examples/biomodels/West2019 - Cellular interactions constrain tumor growth.txt rename to doc/examples/biomodels/BIOMD0000000820/West2019 - Cellular interactions constrain tumor growth.txt index 71ca8b67a..d2a9effe4 100644 --- a/doc/examples/biomodels/West2019 - Cellular interactions constrain tumor growth.txt +++ b/doc/examples/biomodels/BIOMD0000000820/West2019 - Cellular interactions constrain tumor growth.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: @@ -21,7 +21,7 @@ model *New_Model() logistic_growth: => tumor_at_Logistic_growth; compartment_*(alpha*tumor_at_Logistic_growth*(1 - tumor_at_Logistic_growth/K)); // Events: - exponential_model_switch: at time > tau: alpha_0_variable = alpha_0_variable - alpha_0, alpha_1_variable = alpha_1_variable + alpha_1; + exponential_model_switch: at time > tau: alpha_1_variable = alpha_1_variable + alpha_1, alpha_0_variable = alpha_0_variable - alpha_0; // Species initializations: tumor_at_Exp_Lin_growth = 1; diff --git a/doc/examples/biomodels/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.txt b/doc/examples/biomodels/BIOMD0000000821/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.txt similarity index 99% rename from doc/examples/biomodels/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.txt rename to doc/examples/biomodels/BIOMD0000000821/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.txt index ba6dbc144..23e080b42 100644 --- a/doc/examples/biomodels/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.txt +++ b/doc/examples/biomodels/BIOMD0000000821/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Dorvash2019 - Dynamic modeling of signal transduction by mTOR complexes in cancer.txt b/doc/examples/biomodels/BIOMD0000000822/Dorvash2019 - Dynamic modeling of signal transduction by mTOR complexes in cancer.txt similarity index 99% rename from doc/examples/biomodels/Dorvash2019 - Dynamic modeling of signal transduction by mTOR complexes in cancer.txt rename to doc/examples/biomodels/BIOMD0000000822/Dorvash2019 - Dynamic modeling of signal transduction by mTOR complexes in cancer.txt index aed87a209..375cf4a26 100644 --- a/doc/examples/biomodels/Dorvash2019 - Dynamic modeling of signal transduction by mTOR complexes in cancer.txt +++ b/doc/examples/biomodels/BIOMD0000000822/Dorvash2019 - Dynamic modeling of signal transduction by mTOR complexes in cancer.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Varusai2018.txt b/doc/examples/biomodels/BIOMD0000000823/Varusai2018.txt similarity index 99% rename from doc/examples/biomodels/Varusai2018.txt rename to doc/examples/biomodels/BIOMD0000000823/Varusai2018.txt index b5308ca84..97fa030de 100644 --- a/doc/examples/biomodels/Varusai2018.txt +++ b/doc/examples/biomodels/BIOMD0000000823/Varusai2018.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Varusai2018___Dynamic_modelling_of_the_mTOR_signalling_network_reveals_complex_emergent_behaviours_conferred_by_DEPTOR() // Compartments and Species: diff --git a/doc/examples/biomodels/Lewkiewics2019 - effects of aging on naive T cell populations and diversity.txt b/doc/examples/biomodels/BIOMD0000000824/Lewkiewics2019 - effects of aging on naive T cell populations and diversity.txt similarity index 99% rename from doc/examples/biomodels/Lewkiewics2019 - effects of aging on naive T cell populations and diversity.txt rename to doc/examples/biomodels/BIOMD0000000824/Lewkiewics2019 - effects of aging on naive T cell populations and diversity.txt index 438752c71..ec19c1c1c 100644 --- a/doc/examples/biomodels/Lewkiewics2019 - effects of aging on naive T cell populations and diversity.txt +++ b/doc/examples/biomodels/BIOMD0000000824/Lewkiewics2019 - effects of aging on naive T cell populations and diversity.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Greene2019 - Differentiate Spontaneous and Induced Evolution to Drug Resistance During Cancer Treatment.txt b/doc/examples/biomodels/BIOMD0000000825/Greene2019 - Differentiate Spontaneous and Induced Evolution to Drug Resistance During Cancer Treatment.txt similarity index 98% rename from doc/examples/biomodels/Greene2019 - Differentiate Spontaneous and Induced Evolution to Drug Resistance During Cancer Treatment.txt rename to doc/examples/biomodels/BIOMD0000000825/Greene2019 - Differentiate Spontaneous and Induced Evolution to Drug Resistance During Cancer Treatment.txt index f1331326f..364129342 100644 --- a/doc/examples/biomodels/Greene2019 - Differentiate Spontaneous and Induced Evolution to Drug Resistance During Cancer Treatment.txt +++ b/doc/examples/biomodels/BIOMD0000000825/Greene2019 - Differentiate Spontaneous and Induced Evolution to Drug Resistance During Cancer Treatment.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: @@ -52,7 +52,7 @@ model *New_Model() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-3 mole; unit extent = substance; unit substance_per_volume = 1e-3 mole / 1e-3 litre; diff --git a/doc/examples/biomodels/Shin2018.txt b/doc/examples/biomodels/BIOMD0000000826/Shin2018.txt similarity index 99% rename from doc/examples/biomodels/Shin2018.txt rename to doc/examples/biomodels/BIOMD0000000826/Shin2018.txt index 9bb977fe6..0bd2cf71b 100644 --- a/doc/examples/biomodels/Shin2018.txt +++ b/doc/examples/biomodels/BIOMD0000000826/Shin2018.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Shin_2018_EGFR_PYK2_c_Met_interaction_network_model() // Compartments and Species: diff --git a/doc/examples/biomodels/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.txt b/doc/examples/biomodels/BIOMD0000000827/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.txt similarity index 99% rename from doc/examples/biomodels/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.txt rename to doc/examples/biomodels/BIOMD0000000827/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.txt index bf9133fcc..6a632314f 100644 --- a/doc/examples/biomodels/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.txt +++ b/doc/examples/biomodels/BIOMD0000000827/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Jung2019 model.txt b/doc/examples/biomodels/BIOMD0000000828/Jung2019 model.txt similarity index 97% rename from doc/examples/biomodels/Jung2019 model.txt rename to doc/examples/biomodels/BIOMD0000000828/Jung2019 model.txt index 6ba682901..28438766f 100644 --- a/doc/examples/biomodels/Jung2019 model.txt +++ b/doc/examples/biomodels/BIOMD0000000828/Jung2019 model.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: @@ -24,8 +24,8 @@ model *New_Model() loss_of_mTOR: mTOR_R => ; compartment_*(mTOR_R/epsilon_2); // Events: - event_: at (time%12) == 0, t0=false, fromTrigger=false: u_2 = u_2 + 1, u_1 = u_1 + 1; - event_2: at (((((((((time == 3) || (time == 15)) || (time == 27)) || (time == 39)) || (time == 51)) || (time == 63)) || (time == 75)) || (time == 87)) || (time == 99)) || (time == 111), t0=false, fromTrigger=false: u_2 = u_2 - 1, u_1 = u_1 - 1; + event_: at (time%12) == 0, t0=false, fromTrigger=false: u_1 = u_1 + 1, u_2 = u_2 + 1; + event_2: at (((((((((time == 3) || (time == 15)) || (time == 27)) || (time == 39)) || (time == 51)) || (time == 63)) || (time == 75)) || (time == 87)) || (time == 99)) || (time == 111), t0=false, fromTrigger=false: u_1 = u_1 - 1, u_2 = u_2 - 1; // Species initializations: Glucose_G = 6.64215616170866e-22; @@ -72,7 +72,7 @@ model *New_Model() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-3 mole; unit extent = substance; unit substance_per_volume = 1e-3 mole / 1e-3 litre; diff --git a/doc/examples/biomodels/Jung2019 - egulating glioblastoma signaling pathways and anti-invasion therapy cell cycle dynamics model.txt b/doc/examples/biomodels/BIOMD0000000829/Jung2019 - egulating glioblastoma signaling pathways and anti-invasion therapy cell cycle dynamics model.txt similarity index 98% rename from doc/examples/biomodels/Jung2019 - egulating glioblastoma signaling pathways and anti-invasion therapy cell cycle dynamics model.txt rename to doc/examples/biomodels/BIOMD0000000829/Jung2019 - egulating glioblastoma signaling pathways and anti-invasion therapy cell cycle dynamics model.txt index 23e74d158..8152768ea 100644 --- a/doc/examples/biomodels/Jung2019 - egulating glioblastoma signaling pathways and anti-invasion therapy cell cycle dynamics model.txt +++ b/doc/examples/biomodels/BIOMD0000000829/Jung2019 - egulating glioblastoma signaling pathways and anti-invasion therapy cell cycle dynamics model.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: @@ -46,8 +46,8 @@ model *New_Model() grow_of_mass: => mass; compartment_*(myu_0*mass*(1 - mass/m)); // Events: - event_: at (time%12) == 0: u_2 = u_2 + 1, u_1 = u_1 + 1; - event_2: at (((((((((((((time == 3) || (time == 15)) || (time == 27)) || (time == 39)) || (time == 51)) || (time == 63)) || (time == 75)) || (time == 87)) || (time == 99)) || (time == 111)) || (time == 123)) || (time == 135)) || (time == 147)) || (time == 159): u_2 = u_2 - 1, u_1 = u_1 - 1; + event_: at (time%12) == 0: u_1 = u_1 + 1, u_2 = u_2 + 1; + event_2: at (((((((((((((time == 3) || (time == 15)) || (time == 27)) || (time == 39)) || (time == 51)) || (time == 63)) || (time == 75)) || (time == 87)) || (time == 99)) || (time == 111)) || (time == 123)) || (time == 135)) || (time == 147)) || (time == 159): u_1 = u_1 - 1, u_2 = u_2 - 1; // Species initializations: Glucose_G = 6.64215616170866e-22; diff --git a/doc/examples/biomodels/Giantsos-Adams2013.txt b/doc/examples/biomodels/BIOMD0000000830/Giantsos-Adams2013.txt similarity index 97% rename from doc/examples/biomodels/Giantsos-Adams2013.txt rename to doc/examples/biomodels/BIOMD0000000830/Giantsos-Adams2013.txt index 6a519b239..107b1eadc 100644 --- a/doc/examples/biomodels/Giantsos-Adams2013.txt +++ b/doc/examples/biomodels/BIOMD0000000830/Giantsos-Adams2013.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 // Warnings from automatic translation: // Layout error in model: unable to draw an arc between the species '' and the reaction 'k_deg': '' is not a participant in that reaction. -// Attempted to set a source/sink for the reaction k_deg, but that reaction has both reactants and products. +// Unable to set layout_glyph_3.position to {668,240}. // Layout error in model: unable to draw an arc between the species '' and the reaction 'k_shed': '' is not a participant in that reaction. -// Attempted to set a source/sink for the reaction k_shed, but that reaction has both reactants and products. +// Unable to set layout_glyph_5.position to {372,61}. model *Giantsos_Adams2013___Growth_of_glycocalyx_under_static_conditions() @@ -64,7 +64,7 @@ model *Giantsos_Adams2013___Growth_of_glycocalyx_under_static_conditions() k_deg is "HS release from lysosome"; k_shed is "HS cell surface shedding"; - # General layout options + // General layout options model.layout = on model.layout.size = {800, 600} model.layout.background = "#FFFFFFFF" diff --git a/doc/examples/biomodels/MODEL1609100000_url.txt b/doc/examples/biomodels/BIOMD0000000830/MODEL1609100000_url.txt similarity index 99% rename from doc/examples/biomodels/MODEL1609100000_url.txt rename to doc/examples/biomodels/BIOMD0000000830/MODEL1609100000_url.txt index fed76885d..c6338545e 100644 --- a/doc/examples/biomodels/MODEL1609100000_url.txt +++ b/doc/examples/biomodels/BIOMD0000000830/MODEL1609100000_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1609100000() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL7898438988_url.txt b/doc/examples/biomodels/BIOMD0000000831/MODEL7898438988_url.txt similarity index 99% rename from doc/examples/biomodels/MODEL7898438988_url.txt rename to doc/examples/biomodels/BIOMD0000000831/MODEL7898438988_url.txt index 165b7b6d7..ba5a8abf7 100644 --- a/doc/examples/biomodels/MODEL7898438988_url.txt +++ b/doc/examples/biomodels/BIOMD0000000831/MODEL7898438988_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Smith1980_HypothalamicRegulation() // Compartments and Species: diff --git a/doc/examples/biomodels/Smith1980_HypothalamicRegulation.txt b/doc/examples/biomodels/BIOMD0000000831/Smith1980_HypothalamicRegulation.txt similarity index 99% rename from doc/examples/biomodels/Smith1980_HypothalamicRegulation.txt rename to doc/examples/biomodels/BIOMD0000000831/Smith1980_HypothalamicRegulation.txt index 6f9ca6b57..06d50a804 100644 --- a/doc/examples/biomodels/Smith1980_HypothalamicRegulation.txt +++ b/doc/examples/biomodels/BIOMD0000000831/Smith1980_HypothalamicRegulation.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Smith1980_HypothalamicRegulation() // Compartments and Species: diff --git a/doc/examples/biomodels/Shin2016.txt b/doc/examples/biomodels/BIOMD0000000832/Shin2016.txt similarity index 99% rename from doc/examples/biomodels/Shin2016.txt rename to doc/examples/biomodels/BIOMD0000000832/Shin2016.txt index 832faac51..192958bf1 100644 --- a/doc/examples/biomodels/Shin2016.txt +++ b/doc/examples/biomodels/BIOMD0000000832/Shin2016.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Shin2016___Unveiling_Hidden_Dynamics_of_Hippo_Signalling() // Compartments and Species: diff --git a/doc/examples/biomodels/DiCamillo2016.txt b/doc/examples/biomodels/BIOMD0000000833/DiCamillo2016.txt similarity index 99% rename from doc/examples/biomodels/DiCamillo2016.txt rename to doc/examples/biomodels/BIOMD0000000833/DiCamillo2016.txt index e0418c8a4..90d187c81 100644 --- a/doc/examples/biomodels/DiCamillo2016.txt +++ b/doc/examples/biomodels/BIOMD0000000833/DiCamillo2016.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *DiCamillo2016___Insulin_signalling_pathway___Rule_based_model() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1604100005_url.txt b/doc/examples/biomodels/BIOMD0000000833/MODEL1604100005_url.txt similarity index 99% rename from doc/examples/biomodels/MODEL1604100005_url.txt rename to doc/examples/biomodels/BIOMD0000000833/MODEL1604100005_url.txt index 588fe2a42..2150a4878 100644 --- a/doc/examples/biomodels/MODEL1604100005_url.txt +++ b/doc/examples/biomodels/BIOMD0000000833/MODEL1604100005_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1604100005() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1603110003_url.txt b/doc/examples/biomodels/BIOMD0000000834/MODEL1603110003_url.txt similarity index 99% rename from doc/examples/biomodels/MODEL1603110003_url.txt rename to doc/examples/biomodels/BIOMD0000000834/MODEL1603110003_url.txt index b5ec26ec8..a99f3ab83 100644 --- a/doc/examples/biomodels/MODEL1603110003_url.txt +++ b/doc/examples/biomodels/BIOMD0000000834/MODEL1603110003_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1603110003() // Compartments and Species: diff --git a/doc/examples/biomodels/Verma2016.txt b/doc/examples/biomodels/BIOMD0000000834/Verma2016.txt similarity index 99% rename from doc/examples/biomodels/Verma2016.txt rename to doc/examples/biomodels/BIOMD0000000834/Verma2016.txt index 587363597..5ffbcd0a2 100644 --- a/doc/examples/biomodels/Verma2016.txt +++ b/doc/examples/biomodels/BIOMD0000000834/Verma2016.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Verma2016___Ca_2___Signal_Propagation_Along_Hepatocyte_Cords() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1403250000_url-1.txt b/doc/examples/biomodels/BIOMD0000000835/MODEL1403250000_url-1.txt similarity index 99% rename from doc/examples/biomodels/MODEL1403250000_url-1.txt rename to doc/examples/biomodels/BIOMD0000000835/MODEL1403250000_url-1.txt index 3ea6e23c2..2fd7989a3 100644 --- a/doc/examples/biomodels/MODEL1403250000_url-1.txt +++ b/doc/examples/biomodels/BIOMD0000000835/MODEL1403250000_url-1.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1403250000() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1403250000_urn.txt b/doc/examples/biomodels/BIOMD0000000835/MODEL1403250000_urn.txt similarity index 99% rename from doc/examples/biomodels/MODEL1403250000_urn.txt rename to doc/examples/biomodels/BIOMD0000000835/MODEL1403250000_urn.txt index 1467c8369..02a08f701 100644 --- a/doc/examples/biomodels/MODEL1403250000_urn.txt +++ b/doc/examples/biomodels/BIOMD0000000835/MODEL1403250000_urn.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1403250000() // Compartments and Species: diff --git a/doc/examples/biomodels/Rao2014.txt b/doc/examples/biomodels/BIOMD0000000835/Rao2014.txt similarity index 99% rename from doc/examples/biomodels/Rao2014.txt rename to doc/examples/biomodels/BIOMD0000000835/Rao2014.txt index cf5178831..853ff55e8 100644 --- a/doc/examples/biomodels/Rao2014.txt +++ b/doc/examples/biomodels/BIOMD0000000835/Rao2014.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Rao2014___Fatty_acid_beta_oxidation__reduced_model() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1203070000_url.txt b/doc/examples/biomodels/BIOMD0000000836/MODEL1203070000_url.txt similarity index 97% rename from doc/examples/biomodels/MODEL1203070000_url.txt rename to doc/examples/biomodels/BIOMD0000000836/MODEL1203070000_url.txt index 0cf631393..9843f6d79 100644 --- a/doc/examples/biomodels/MODEL1203070000_url.txt +++ b/doc/examples/biomodels/BIOMD0000000836/MODEL1203070000_url.txt @@ -1,9 +1,9 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model01() // Compartments and Species: compartment compartment_; - species $S in compartment_, $P in compartment_; + species S in compartment_, P in compartment_; // Rate Rules: S' = (alpha*(1 - S/C) - beta*P)*S; diff --git a/doc/examples/biomodels/Radosavljevic2009.txt b/doc/examples/biomodels/BIOMD0000000836/Radosavljevic2009.txt similarity index 99% rename from doc/examples/biomodels/Radosavljevic2009.txt rename to doc/examples/biomodels/BIOMD0000000836/Radosavljevic2009.txt index dbb4a0c0b..0d6bf40c6 100644 --- a/doc/examples/biomodels/Radosavljevic2009.txt +++ b/doc/examples/biomodels/BIOMD0000000836/Radosavljevic2009.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Radosavljevic2009_BioterroristAttack_PanicProtection_1() // Compartments and Species: diff --git a/doc/examples/biomodels/Hanson2016.txt b/doc/examples/biomodels/BIOMD0000000837/Hanson2016.txt similarity index 99% rename from doc/examples/biomodels/Hanson2016.txt rename to doc/examples/biomodels/BIOMD0000000837/Hanson2016.txt index 128829ebb..59e8986d0 100644 --- a/doc/examples/biomodels/Hanson2016.txt +++ b/doc/examples/biomodels/BIOMD0000000837/Hanson2016.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hanson2016___Toxicity_Management_in_CAR_T_cell_therapy_for_B_ALL() // Compartments and Species: diff --git a/doc/examples/biomodels/Tsur2019.txt b/doc/examples/biomodels/BIOMD0000000838/Tsur2019.txt similarity index 98% rename from doc/examples/biomodels/Tsur2019.txt rename to doc/examples/biomodels/BIOMD0000000838/Tsur2019.txt index 7e597a362..10bcc634d 100644 --- a/doc/examples/biomodels/Tsur2019.txt +++ b/doc/examples/biomodels/BIOMD0000000838/Tsur2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Tsur2019___Response_of_patients_with_melanoma_to_immune_checkpoint_blockade() // Compartments and Species: diff --git a/doc/examples/biomodels/Almeida2019.txt b/doc/examples/biomodels/BIOMD0000000839/Almeida2019.txt similarity index 99% rename from doc/examples/biomodels/Almeida2019.txt rename to doc/examples/biomodels/BIOMD0000000839/Almeida2019.txt index 3e15630a7..e20fff42b 100644 --- a/doc/examples/biomodels/Almeida2019.txt +++ b/doc/examples/biomodels/BIOMD0000000839/Almeida2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Almeida2019___Transcription_based_circadian_mechanism_controls_the_duration_of_molecular_clock_states_in_response_to_signaling_inputs() // Compartments and Species: diff --git a/doc/examples/biomodels/Caldwell2019.txt b/doc/examples/biomodels/BIOMD0000000840/Caldwell2019.txt similarity index 99% rename from doc/examples/biomodels/Caldwell2019.txt rename to doc/examples/biomodels/BIOMD0000000840/Caldwell2019.txt index d6c28a376..c007b2339 100644 --- a/doc/examples/biomodels/Caldwell2019.txt +++ b/doc/examples/biomodels/BIOMD0000000840/Caldwell2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Caldwell2019___The_Vicodin_abuse_problem() // Compartments and Species: diff --git a/doc/examples/biomodels/Dhawan2019.txt b/doc/examples/biomodels/BIOMD0000000841/Dhawan2019.txt similarity index 99% rename from doc/examples/biomodels/Dhawan2019.txt rename to doc/examples/biomodels/BIOMD0000000841/Dhawan2019.txt index ff1db219e..2ef86906b 100644 --- a/doc/examples/biomodels/Dhawan2019.txt +++ b/doc/examples/biomodels/BIOMD0000000841/Dhawan2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Dhawan2019___Endogenous_miRNA_sponges_mediate_the_generation_of_oscillatory_dynamics_for_a_non_coding_RNA_network() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1012080000.txt b/doc/examples/biomodels/BIOMD0000000842/MODEL1012080000.txt similarity index 99% rename from doc/examples/biomodels/MODEL1012080000.txt rename to doc/examples/biomodels/BIOMD0000000842/MODEL1012080000.txt index 1e6d9d6f2..76b131f13 100644 --- a/doc/examples/biomodels/MODEL1012080000.txt +++ b/doc/examples/biomodels/BIOMD0000000842/MODEL1012080000.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Heitzler2012_GPCRsignalling() // Compartments and Species: diff --git a/doc/examples/biomodels/Dudziuk2019.txt b/doc/examples/biomodels/BIOMD0000000843/Dudziuk2019.txt similarity index 99% rename from doc/examples/biomodels/Dudziuk2019.txt rename to doc/examples/biomodels/BIOMD0000000843/Dudziuk2019.txt index 38a4a3944..6207bcc1d 100644 --- a/doc/examples/biomodels/Dudziuk2019.txt +++ b/doc/examples/biomodels/BIOMD0000000843/Dudziuk2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Dudziuk2019___Biologically_sound_formal_model_of_Hsp70_heat_induction() // Compartments and Species: diff --git a/doc/examples/biomodels/Viertel2019.txt b/doc/examples/biomodels/BIOMD0000000844/Viertel2019.txt similarity index 99% rename from doc/examples/biomodels/Viertel2019.txt rename to doc/examples/biomodels/BIOMD0000000844/Viertel2019.txt index d1ad14fc5..195cc76ef 100644 --- a/doc/examples/biomodels/Viertel2019.txt +++ b/doc/examples/biomodels/BIOMD0000000844/Viertel2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Viertel2019___A_Computational_model_of_the_mammalian_external_tufted_cell() // Compartments and Species: diff --git a/doc/examples/biomodels/Gulbudak2019.1.Lytic.txt b/doc/examples/biomodels/BIOMD0000000845/Gulbudak2019.1.Lytic.txt similarity index 98% rename from doc/examples/biomodels/Gulbudak2019.1.Lytic.txt rename to doc/examples/biomodels/BIOMD0000000845/Gulbudak2019.1.Lytic.txt index bdb86383a..9358e4064 100644 --- a/doc/examples/biomodels/Gulbudak2019.1.Lytic.txt +++ b/doc/examples/biomodels/BIOMD0000000845/Gulbudak2019.1.Lytic.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Gulbudak2019___Heterogeneous_viral_strategies_promote_coexistence_in_virus_microbe_systems() // Compartments and Species: diff --git a/doc/examples/biomodels/Gulbudak2019.2.Chronic.txt b/doc/examples/biomodels/BIOMD0000000846/Gulbudak2019.2.Chronic.txt similarity index 98% rename from doc/examples/biomodels/Gulbudak2019.2.Chronic.txt rename to doc/examples/biomodels/BIOMD0000000846/Gulbudak2019.2.Chronic.txt index 86f5f3ec1..ec624ab21 100644 --- a/doc/examples/biomodels/Gulbudak2019.2.Chronic.txt +++ b/doc/examples/biomodels/BIOMD0000000846/Gulbudak2019.2.Chronic.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Gulbudak2019_2___Heterogeneous_viral_strategies_promote_coexistence_in_virus_microbe_systems__Chronic() // Compartments and Species: diff --git a/doc/examples/biomodels/Adams2019.txt b/doc/examples/biomodels/BIOMD0000000847/Adams2019.txt similarity index 99% rename from doc/examples/biomodels/Adams2019.txt rename to doc/examples/biomodels/BIOMD0000000847/Adams2019.txt index 8bbc31175..32cb093a5 100644 --- a/doc/examples/biomodels/Adams2019.txt +++ b/doc/examples/biomodels/BIOMD0000000847/Adams2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Adams2019___The_regulatory_role_of_shikimate_in_plant_phenylalanine_metabolism() // Compartments and Species: diff --git a/doc/examples/biomodels/FatehiChenar2018.txt b/doc/examples/biomodels/BIOMD0000000848/FatehiChenar2018.txt similarity index 99% rename from doc/examples/biomodels/FatehiChenar2018.txt rename to doc/examples/biomodels/BIOMD0000000848/FatehiChenar2018.txt index 767f59611..dea879276 100644 --- a/doc/examples/biomodels/FatehiChenar2018.txt +++ b/doc/examples/biomodels/BIOMD0000000848/FatehiChenar2018.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *FatehiChenar2018___Mathematical_model_of_immune_response_to_hepatitis_B() // Compartments and Species: diff --git a/doc/examples/biomodels/Berg2017.txt b/doc/examples/biomodels/BIOMD0000000849/Berg2017.txt similarity index 99% rename from doc/examples/biomodels/Berg2017.txt rename to doc/examples/biomodels/BIOMD0000000849/Berg2017.txt index 2396ee8ea..596f5cd5d 100644 --- a/doc/examples/biomodels/Berg2017.txt +++ b/doc/examples/biomodels/BIOMD0000000849/Berg2017.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1710230000() // Compartments and Species: @@ -327,7 +327,7 @@ model *MODEL1710230000() re36 is "SrcGp"; re31 is "SrcIn"; - # General layout options + // General layout options model.layout = on model.layout.size = {1081, 940} model.layout.background = "#FFFFFFFF" diff --git a/doc/examples/biomodels/MODEL1710230000_url.txt b/doc/examples/biomodels/BIOMD0000000849/MODEL1710230000_url.txt similarity index 97% rename from doc/examples/biomodels/MODEL1710230000_url.txt rename to doc/examples/biomodels/BIOMD0000000849/MODEL1710230000_url.txt index cf74db8b6..949d14d75 100644 --- a/doc/examples/biomodels/MODEL1710230000_url.txt +++ b/doc/examples/biomodels/BIOMD0000000849/MODEL1710230000_url.txt @@ -1,10 +1,10 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1710230000() // Compartments and Species: compartment default, c1, c2; - species K_ECF in c2, K_ICF in c1, K_urin in default, $K_ECF_mmol in c2; - species $K_ICF_mmol in c1, Gluc_b in c2, ins_b in c2, s24 in default; + species K_ECF in c2, K_ICF in c1, K_urin in default, K_ECF_mmol in c2, K_ICF_mmol in c1; + species Gluc_b in c2, ins_b in c2, s24 in default; substanceOnly species K_tiss in default, K_sal in default, met_act in default; substanceOnly species K_milk in default, K_git in default, Gluc_stor in default; substanceOnly species Gluc_prod in default, $src_metact in default, $snk_metact in default; diff --git a/doc/examples/biomodels/Jenner2019.txt b/doc/examples/biomodels/BIOMD0000000850/Jenner2019.txt similarity index 98% rename from doc/examples/biomodels/Jenner2019.txt rename to doc/examples/biomodels/BIOMD0000000850/Jenner2019.txt index 008aff92e..dab65346f 100644 --- a/doc/examples/biomodels/Jenner2019.txt +++ b/doc/examples/biomodels/BIOMD0000000850/Jenner2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Jenner2019___Oncolytic_virotherapy_for_tumours_following_a_Gompertz_growth_law() // Compartments and Species: diff --git a/doc/examples/biomodels/Ho2019.txt b/doc/examples/biomodels/BIOMD0000000851/Ho2019.txt similarity index 99% rename from doc/examples/biomodels/Ho2019.txt rename to doc/examples/biomodels/BIOMD0000000851/Ho2019.txt index 2952951d7..b4f525889 100644 --- a/doc/examples/biomodels/Ho2019.txt +++ b/doc/examples/biomodels/BIOMD0000000851/Ho2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ho2019___Mathematical_models_of_transmission_dynamics_and_vaccine_strategies_in_Hong_Kong_during_the_2017_2018_winter_influenza_season__Simple() // Compartments and Species: diff --git a/doc/examples/biomodels/Andersen2017.txt b/doc/examples/biomodels/BIOMD0000000852/Andersen2017.txt similarity index 99% rename from doc/examples/biomodels/Andersen2017.txt rename to doc/examples/biomodels/BIOMD0000000852/Andersen2017.txt index 2a45f025e..bb5463f19 100644 --- a/doc/examples/biomodels/Andersen2017.txt +++ b/doc/examples/biomodels/BIOMD0000000852/Andersen2017.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Andersen2017___Mathematical_modelling_as_a_proof_of_concept_for_MPNs_as_a_human_inflammation_model_for_cancer_development() // Compartments and Species: diff --git a/doc/examples/biomodels/Smolen2018.txt b/doc/examples/biomodels/BIOMD0000000853/Smolen2018.txt similarity index 99% rename from doc/examples/biomodels/Smolen2018.txt rename to doc/examples/biomodels/BIOMD0000000853/Smolen2018.txt index 43f18bcc2..9ab28c40b 100644 --- a/doc/examples/biomodels/Smolen2018.txt +++ b/doc/examples/biomodels/BIOMD0000000853/Smolen2018.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Smolen2018___Paradoxical_LTP_maintenance_with_inhibition_of_protein_synthesis_and_the_proteasome() // Compartments and Species: diff --git a/doc/examples/biomodels/Gray2016.txt b/doc/examples/biomodels/BIOMD0000000854/Gray2016.txt similarity index 99% rename from doc/examples/biomodels/Gray2016.txt rename to doc/examples/biomodels/BIOMD0000000854/Gray2016.txt index 2d6257ed5..8fd12a00e 100644 --- a/doc/examples/biomodels/Gray2016.txt +++ b/doc/examples/biomodels/BIOMD0000000854/Gray2016.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Gray2016___The_Akt_switch_model() // Compartments and Species: diff --git a/doc/examples/biomodels/Cooper2015.txt b/doc/examples/biomodels/BIOMD0000000855/Cooper2015.txt similarity index 99% rename from doc/examples/biomodels/Cooper2015.txt rename to doc/examples/biomodels/BIOMD0000000855/Cooper2015.txt index 0c25467e7..bf601a1cd 100644 --- a/doc/examples/biomodels/Cooper2015.txt +++ b/doc/examples/biomodels/BIOMD0000000855/Cooper2015.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Cooper2015___Modeling_the_effects_of_systemic_mediators_on_the_inflammatory_phase_of_wound_healing() // Compartments and Species: diff --git a/doc/examples/biomodels/Heldt2018.txt b/doc/examples/biomodels/BIOMD0000000856/Heldt2018.txt similarity index 95% rename from doc/examples/biomodels/Heldt2018.txt rename to doc/examples/biomodels/BIOMD0000000856/Heldt2018.txt index 34894734a..6d730f1f6 100644 --- a/doc/examples/biomodels/Heldt2018.txt +++ b/doc/examples/biomodels/BIOMD0000000856/Heldt2018.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Budding_yeast_size_control_by_titration_of_nuclear_sites() // Compartments and Species: @@ -58,8 +58,8 @@ model *Budding_yeast_size_control_by_titration_of_nuclear_sites() Hyper_phosphorylation_of_Whi5_in_hypo_phosphorylated_Whi5_SBF_complexes: WHIpSBF => $SBF + WHIp; tV*((kPhWhipCln3*(CLN3/tV) + kPhWhipCln*(CLN/tV))*(WHIpSBF/tV)); // Events: - Start: at (CLN/tV) >= StartThr: SBFu = (SBFu/tV)*2*tV, SBFp = (SBFp/tV)*2*tV, NSt = NSt*2, GDt = GDt*2, GIt = GIt*2, GWt = GWt*2, GCt = GCt*2, GCN = GCN*2, GRd = 1, GRm = 0; - Division: at (CLN/tV + CLB/tV) <= MitosisThr: WHIpSBF = (WHIpSBF/tV)*rV*tV, CLN3WHISBF = (CLN3WHISBF/tV)*rV*tV, NSt = NSt/2, CDHi = (CDHi/tV)*rV*tV, CDHa = (CDHa/tV)*rV*tV, CDCi = (CDCi/tV)*rV*tV, CDCa = (CDCa/tV)*rV*tV, SBFu = (SBFu/tV/2)*tV, SBFp = (SBFp/tV/2)*tV, WHIn = 0*tV, WHISBF = (WHISBF/tV)*rV*tV, WHIp = (WHIp/tV)*rV*tV, WHI = ((WHI/tV)*rV + WHIn/tV)*tV, TM = (TM/tV)*rV*tV, GIt = GIt/2, GITM = (GITM/tV)*rV*tV, GDt = GDt/2, GDTM = (GDTM/tV)*rV*tV, dV = 0, CLN3 = (CLN3/tV)*rV*tV, CLB = (CLB/tV)*rV*tV, CLN = (CLN/tV)*rV*tV, mV = dV, GWt = GWt/2, GCt = GCt/2, GCN = GCN/2, GRd = 0, GRm = 1; + Start: at (CLN/tV) >= StartThr: GRm = 0, GRd = 1, GCN = GCN*2, GCt = GCt*2, GWt = GWt*2, GIt = GIt*2, GDt = GDt*2, NSt = NSt*2, SBFp = (SBFp/tV)*2*tV, SBFu = (SBFu/tV)*2*tV; + Division: at (CLN/tV + CLB/tV) <= MitosisThr: GRm = 1, GRd = 0, GCN = GCN/2, GCt = GCt/2, GWt = GWt/2, mV = dV, CLN = (CLN/tV)*rV*tV, CLB = (CLB/tV)*rV*tV, CLN3 = (CLN3/tV)*rV*tV, dV = 0, GDTM = (GDTM/tV)*rV*tV, GDt = GDt/2, GITM = (GITM/tV)*rV*tV, GIt = GIt/2, TM = (TM/tV)*rV*tV, WHI = ((WHI/tV)*rV + WHIn/tV)*tV, WHIp = (WHIp/tV)*rV*tV, WHISBF = (WHISBF/tV)*rV*tV, WHIn = 0*tV, SBFp = (SBFp/tV/2)*tV, SBFu = (SBFu/tV/2)*tV, CDCa = (CDCa/tV)*rV*tV, CDCi = (CDCi/tV)*rV*tV, CDHa = (CDHa/tV)*rV*tV, CDHi = (CDHi/tV)*rV*tV, NSt = NSt/2, CLN3WHISBF = (CLN3WHISBF/tV)*rV*tV, WHIpSBF = (WHIpSBF/tV)*rV*tV; // Species initializations: GDTM = 60; diff --git a/doc/examples/biomodels/Heldt2018_YeastSizeControl_TitrationOfNuclearSites.txt b/doc/examples/biomodels/BIOMD0000000856/Heldt2018_YeastSizeControl_TitrationOfNuclearSites.txt similarity index 95% rename from doc/examples/biomodels/Heldt2018_YeastSizeControl_TitrationOfNuclearSites.txt rename to doc/examples/biomodels/BIOMD0000000856/Heldt2018_YeastSizeControl_TitrationOfNuclearSites.txt index af320936f..0a6b594c4 100644 --- a/doc/examples/biomodels/Heldt2018_YeastSizeControl_TitrationOfNuclearSites.txt +++ b/doc/examples/biomodels/BIOMD0000000856/Heldt2018_YeastSizeControl_TitrationOfNuclearSites.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Budding_yeast_size_control_by_titration_of_nuclear_sites() // Compartments and Species: @@ -58,8 +58,8 @@ model *Budding_yeast_size_control_by_titration_of_nuclear_sites() Hyper_phosphorylation_of_Whi5_in_hypo_phosphorylated_Whi5_SBF_complexes: WHIpSBF => $SBF + WHIp; tV*((kPhWhipCln3*(CLN3/tV) + kPhWhipCln*(CLN/tV))*(WHIpSBF/tV)); // Events: - Start: at (CLN/tV) >= StartThr: SBFu = (SBFu/tV)*2*tV, SBFp = (SBFp/tV)*2*tV, NSt = NSt*2, GDt = GDt*2, GIt = GIt*2, GWt = GWt*2, GCt = GCt*2, GCN = GCN*2, GRd = 1, GRm = 0; - Division: at (CLN/tV + CLB/tV) <= MitosisThr: WHIpSBF = (WHIpSBF/tV)*rV*tV, CLN3WHISBF = (CLN3WHISBF/tV)*rV*tV, NSt = NSt/2, CDHi = (CDHi/tV)*rV*tV, CDHa = (CDHa/tV)*rV*tV, CDCi = (CDCi/tV)*rV*tV, CDCa = (CDCa/tV)*rV*tV, SBFu = (SBFu/tV/2)*tV, SBFp = (SBFp/tV/2)*tV, WHIn = 0*tV, WHISBF = (WHISBF/tV)*rV*tV, WHIp = (WHIp/tV)*rV*tV, WHI = ((WHI/tV)*rV + WHIn/tV)*tV, TM = (TM/tV)*rV*tV, GIt = GIt/2, GITM = (GITM/tV)*rV*tV, GDt = GDt/2, GDTM = (GDTM/tV)*rV*tV, dV = 0, CLN3 = (CLN3/tV)*rV*tV, CLB = (CLB/tV)*rV*tV, CLN = (CLN/tV)*rV*tV, mV = dV, GWt = GWt/2, GCt = GCt/2, GCN = GCN/2, GRd = 0, GRm = 1; + Start: at (CLN/tV) >= StartThr: GRm = 0, GRd = 1, GCN = GCN*2, GCt = GCt*2, GWt = GWt*2, GIt = GIt*2, GDt = GDt*2, NSt = NSt*2, SBFp = (SBFp/tV)*2*tV, SBFu = (SBFu/tV)*2*tV; + Division: at (CLN/tV + CLB/tV) <= MitosisThr: GRm = 1, GRd = 0, GCN = GCN/2, GCt = GCt/2, GWt = GWt/2, mV = dV, CLN = (CLN/tV)*rV*tV, CLB = (CLB/tV)*rV*tV, CLN3 = (CLN3/tV)*rV*tV, dV = 0, GDTM = (GDTM/tV)*rV*tV, GDt = GDt/2, GITM = (GITM/tV)*rV*tV, GIt = GIt/2, TM = (TM/tV)*rV*tV, WHI = ((WHI/tV)*rV + WHIn/tV)*tV, WHIp = (WHIp/tV)*rV*tV, WHISBF = (WHISBF/tV)*rV*tV, WHIn = 0*tV, SBFp = (SBFp/tV/2)*tV, SBFu = (SBFu/tV/2)*tV, CDCa = (CDCa/tV)*rV*tV, CDCi = (CDCi/tV)*rV*tV, CDHa = (CDHa/tV)*rV*tV, CDHi = (CDHi/tV)*rV*tV, NSt = NSt/2, CLN3WHISBF = (CLN3WHISBF/tV)*rV*tV, WHIpSBF = (WHIpSBF/tV)*rV*tV; // Species initializations: GDTM = 60; diff --git a/doc/examples/biomodels/Larbat2016.1.txt b/doc/examples/biomodels/BIOMD0000000857/Larbat2016.1.txt similarity index 99% rename from doc/examples/biomodels/Larbat2016.1.txt rename to doc/examples/biomodels/BIOMD0000000857/Larbat2016.1.txt index e7c5438cc..4e87bd402 100644 --- a/doc/examples/biomodels/Larbat2016.1.txt +++ b/doc/examples/biomodels/BIOMD0000000857/Larbat2016.1.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Larbat2016_1___Modeling_the_diversion_of_primary_carbon_flux_into_secondary_metabolism_under_variable_nitrate_and_light_or_dark_conditions__Base_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Larbat2016.2.txt b/doc/examples/biomodels/BIOMD0000000858/Larbat2016.2.txt similarity index 99% rename from doc/examples/biomodels/Larbat2016.2.txt rename to doc/examples/biomodels/BIOMD0000000858/Larbat2016.2.txt index 9a0b5b4dc..073f9ef8c 100644 --- a/doc/examples/biomodels/Larbat2016.2.txt +++ b/doc/examples/biomodels/BIOMD0000000858/Larbat2016.2.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Larbat2016_2___Modeling_the_diversion_of_primary_carbon_flux_into_secondary_metabolism_under_variable_nitrate_and_light_or_dark_conditions__Light_Dark_Cycles() // Compartments and Species: diff --git a/doc/examples/biomodels/Larbat2016.3.txt b/doc/examples/biomodels/BIOMD0000000859/Larbat2016.3.txt similarity index 99% rename from doc/examples/biomodels/Larbat2016.3.txt rename to doc/examples/biomodels/BIOMD0000000859/Larbat2016.3.txt index 6aa26b62c..a0b845c13 100644 --- a/doc/examples/biomodels/Larbat2016.3.txt +++ b/doc/examples/biomodels/BIOMD0000000859/Larbat2016.3.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Larbat2016_3___Modeling_the_diversion_of_primary_carbon_flux_into_secondary_metabolism_under_variable_nitrate_and_light_or_dark_conditions__Light_Dark_Cycles_with_Minimum_Starch_Adaption() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1610100004_url.txt b/doc/examples/biomodels/BIOMD0000000860/MODEL1610100004_url.txt similarity index 99% rename from doc/examples/biomodels/MODEL1610100004_url.txt rename to doc/examples/biomodels/BIOMD0000000860/MODEL1610100004_url.txt index 4c3199ede..1dc3d0653 100644 --- a/doc/examples/biomodels/MODEL1610100004_url.txt +++ b/doc/examples/biomodels/BIOMD0000000860/MODEL1610100004_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1610100004() // Compartments and Species: diff --git a/doc/examples/biomodels/proctor2017_model4.txt b/doc/examples/biomodels/BIOMD0000000860/proctor2017_model4.txt similarity index 99% rename from doc/examples/biomodels/proctor2017_model4.txt rename to doc/examples/biomodels/BIOMD0000000860/proctor2017_model4.txt index 63af0ebf6..260a3993a 100644 --- a/doc/examples/biomodels/proctor2017_model4.txt +++ b/doc/examples/biomodels/BIOMD0000000860/proctor2017_model4.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1610100004() // Compartments and Species: diff --git a/doc/examples/biomodels/Bachmann2011.txt b/doc/examples/biomodels/BIOMD0000000861/Bachmann2011.txt similarity index 99% rename from doc/examples/biomodels/Bachmann2011.txt rename to doc/examples/biomodels/BIOMD0000000861/Bachmann2011.txt index 1aefe40c5..c4aee90a3 100644 --- a/doc/examples/biomodels/Bachmann2011.txt +++ b/doc/examples/biomodels/BIOMD0000000861/Bachmann2011.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *jak2_stat5_feedbacks() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1610100000_url.txt b/doc/examples/biomodels/BIOMD0000000862/MODEL1610100000_url.txt similarity index 99% rename from doc/examples/biomodels/MODEL1610100000_url.txt rename to doc/examples/biomodels/BIOMD0000000862/MODEL1610100000_url.txt index 9e2202d81..974af67c5 100644 --- a/doc/examples/biomodels/MODEL1610100000_url.txt +++ b/doc/examples/biomodels/BIOMD0000000862/MODEL1610100000_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1610100000() // Compartments and Species: diff --git a/doc/examples/biomodels/Proctor2017_model0.txt b/doc/examples/biomodels/BIOMD0000000862/Proctor2017_model0.txt similarity index 99% rename from doc/examples/biomodels/Proctor2017_model0.txt rename to doc/examples/biomodels/BIOMD0000000862/Proctor2017_model0.txt index 3b0c70901..464d14a24 100644 --- a/doc/examples/biomodels/Proctor2017_model0.txt +++ b/doc/examples/biomodels/BIOMD0000000862/Proctor2017_model0.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1610100000() // Compartments and Species: diff --git a/doc/examples/biomodels/Kosinsky2018.txt b/doc/examples/biomodels/BIOMD0000000863/Kosinsky2018.txt similarity index 99% rename from doc/examples/biomodels/Kosinsky2018.txt rename to doc/examples/biomodels/BIOMD0000000863/Kosinsky2018.txt index f9ca1a2fb..299b0304c 100644 --- a/doc/examples/biomodels/Kosinsky2018.txt +++ b/doc/examples/biomodels/BIOMD0000000863/Kosinsky2018.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1610100001_url.txt b/doc/examples/biomodels/BIOMD0000000864/MODEL1610100001_url.txt similarity index 99% rename from doc/examples/biomodels/MODEL1610100001_url.txt rename to doc/examples/biomodels/BIOMD0000000864/MODEL1610100001_url.txt index a083b4a97..2f1ab8d6c 100644 --- a/doc/examples/biomodels/MODEL1610100001_url.txt +++ b/doc/examples/biomodels/BIOMD0000000864/MODEL1610100001_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1610100001() // Compartments and Species: diff --git a/doc/examples/biomodels/Proctor2017_model1.txt b/doc/examples/biomodels/BIOMD0000000864/Proctor2017_model1.txt similarity index 99% rename from doc/examples/biomodels/Proctor2017_model1.txt rename to doc/examples/biomodels/BIOMD0000000864/Proctor2017_model1.txt index 2db73f046..efd050200 100644 --- a/doc/examples/biomodels/Proctor2017_model1.txt +++ b/doc/examples/biomodels/BIOMD0000000864/Proctor2017_model1.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1610100001() // Compartments and Species: diff --git a/doc/examples/biomodels/Nikolaev2019.txt b/doc/examples/biomodels/BIOMD0000000865/Nikolaev2019.txt similarity index 99% rename from doc/examples/biomodels/Nikolaev2019.txt rename to doc/examples/biomodels/BIOMD0000000865/Nikolaev2019.txt index a5a974f8f..0b575d8bb 100644 --- a/doc/examples/biomodels/Nikolaev2019.txt +++ b/doc/examples/biomodels/BIOMD0000000865/Nikolaev2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Nikolaev2019___Immunobiochemical_reconstruction_of_influenza_lung_infection_melanoma_skin_cancer_interactions() // Compartments and Species: diff --git a/doc/examples/biomodels/MM-p52.txt b/doc/examples/biomodels/BIOMD0000000866/MM-p52.txt similarity index 98% rename from doc/examples/biomodels/MM-p52.txt rename to doc/examples/biomodels/BIOMD0000000866/MM-p52.txt index 6e00d53e0..a2b700a05 100644 --- a/doc/examples/biomodels/MM-p52.txt +++ b/doc/examples/biomodels/BIOMD0000000866/MM-p52.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Simon2019.txt b/doc/examples/biomodels/BIOMD0000000866/Simon2019.txt similarity index 98% rename from doc/examples/biomodels/Simon2019.txt rename to doc/examples/biomodels/BIOMD0000000866/Simon2019.txt index b791af5ac..8a40744c7 100644 --- a/doc/examples/biomodels/Simon2019.txt +++ b/doc/examples/biomodels/BIOMD0000000866/Simon2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Coulibaly2019.txt b/doc/examples/biomodels/BIOMD0000000867/Coulibaly2019.txt similarity index 99% rename from doc/examples/biomodels/Coulibaly2019.txt rename to doc/examples/biomodels/BIOMD0000000867/Coulibaly2019.txt index 9e334fdb9..b7e852bf0 100644 --- a/doc/examples/biomodels/Coulibaly2019.txt +++ b/doc/examples/biomodels/BIOMD0000000867/Coulibaly2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Coulibaly2019___Interleukin_15_Signaling_in_HIF_1a_Regulation_in_Natural_Killer_Cells() // Compartments and Species: diff --git a/doc/examples/biomodels/MA-p52.txt b/doc/examples/biomodels/BIOMD0000000868/MA-p52.txt similarity index 98% rename from doc/examples/biomodels/MA-p52.txt rename to doc/examples/biomodels/BIOMD0000000868/MA-p52.txt index 9892a7d83..4f9b245c2 100644 --- a/doc/examples/biomodels/MA-p52.txt +++ b/doc/examples/biomodels/BIOMD0000000868/MA-p52.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/simon2019_model2.txt b/doc/examples/biomodels/BIOMD0000000868/simon2019_model2.txt similarity index 99% rename from doc/examples/biomodels/simon2019_model2.txt rename to doc/examples/biomodels/BIOMD0000000868/simon2019_model2.txt index 7f22e307e..150f2f1c3 100644 --- a/doc/examples/biomodels/simon2019_model2.txt +++ b/doc/examples/biomodels/BIOMD0000000868/simon2019_model2.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/MM-p52-IkBd.txt b/doc/examples/biomodels/BIOMD0000000869/MM-p52-IkBd.txt similarity index 98% rename from doc/examples/biomodels/MM-p52-IkBd.txt rename to doc/examples/biomodels/BIOMD0000000869/MM-p52-IkBd.txt index 876314dd5..a8b1592f9 100644 --- a/doc/examples/biomodels/MM-p52-IkBd.txt +++ b/doc/examples/biomodels/BIOMD0000000869/MM-p52-IkBd.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Simon2019_model3.txt b/doc/examples/biomodels/BIOMD0000000869/Simon2019_model3.txt similarity index 99% rename from doc/examples/biomodels/Simon2019_model3.txt rename to doc/examples/biomodels/BIOMD0000000869/Simon2019_model3.txt index df680e746..c7b536331 100644 --- a/doc/examples/biomodels/Simon2019_model3.txt +++ b/doc/examples/biomodels/BIOMD0000000869/Simon2019_model3.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/MA-p52-IkBd.txt b/doc/examples/biomodels/BIOMD0000000870/MA-p52-IkBd.txt similarity index 99% rename from doc/examples/biomodels/MA-p52-IkBd.txt rename to doc/examples/biomodels/BIOMD0000000870/MA-p52-IkBd.txt index 314b5f5d6..a79469eda 100644 --- a/doc/examples/biomodels/MA-p52-IkBd.txt +++ b/doc/examples/biomodels/BIOMD0000000870/MA-p52-IkBd.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Simon2019_model4.txt b/doc/examples/biomodels/BIOMD0000000870/Simon2019_model4.txt similarity index 99% rename from doc/examples/biomodels/Simon2019_model4.txt rename to doc/examples/biomodels/BIOMD0000000870/Simon2019_model4.txt index a7bfd36ca..00c35413a 100644 --- a/doc/examples/biomodels/Simon2019_model4.txt +++ b/doc/examples/biomodels/BIOMD0000000870/Simon2019_model4.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/MA-p52-IkBd-Fig3B.txt b/doc/examples/biomodels/BIOMD0000000871/MA-p52-IkBd-Fig3B.txt similarity index 99% rename from doc/examples/biomodels/MA-p52-IkBd-Fig3B.txt rename to doc/examples/biomodels/BIOMD0000000871/MA-p52-IkBd-Fig3B.txt index 06c50a9ce..93fc84c3f 100644 --- a/doc/examples/biomodels/MA-p52-IkBd-Fig3B.txt +++ b/doc/examples/biomodels/BIOMD0000000871/MA-p52-IkBd-Fig3B.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Simon2019_Figure3b.txt b/doc/examples/biomodels/BIOMD0000000871/Simon2019_Figure3b.txt similarity index 99% rename from doc/examples/biomodels/Simon2019_Figure3b.txt rename to doc/examples/biomodels/BIOMD0000000871/Simon2019_Figure3b.txt index c7cbf33e2..4f9653f35 100644 --- a/doc/examples/biomodels/Simon2019_Figure3b.txt +++ b/doc/examples/biomodels/BIOMD0000000871/Simon2019_Figure3b.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *NIK_dependent_p100_processing_into_p52_with_RelB_binding_and_IkBd_degradation__mass_action__SBML_2v4() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1605030001_url.txt b/doc/examples/biomodels/BIOMD0000000872/MODEL1605030001_url.txt similarity index 99% rename from doc/examples/biomodels/MODEL1605030001_url.txt rename to doc/examples/biomodels/BIOMD0000000872/MODEL1605030001_url.txt index 1bc3bf099..edf4034f8 100644 --- a/doc/examples/biomodels/MODEL1605030001_url.txt +++ b/doc/examples/biomodels/BIOMD0000000872/MODEL1605030001_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 // Warnings from automatic translation: // The alias node 1 for species s13 does not connect to the reaction(s) re24, but instead connects to re17, re24 @@ -109,7 +109,7 @@ model *MODEL1605030001() re26 is "Production of Effector cell"; Production_of_HPV_due_to_HPV_self_proliferating is "Production of HPV due to HPV self proliferating"; - # General layout options + // General layout options model.layout = on model.layout.size = {694.67, 563.7} model.layout.background = "#FFFFFFFF" diff --git a/doc/examples/biomodels/verma2017.txt b/doc/examples/biomodels/BIOMD0000000872/verma2017.txt similarity index 99% rename from doc/examples/biomodels/verma2017.txt rename to doc/examples/biomodels/BIOMD0000000872/verma2017.txt index 7d447fae5..ee0de303a 100644 --- a/doc/examples/biomodels/verma2017.txt +++ b/doc/examples/biomodels/BIOMD0000000872/verma2017.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 // Warnings from automatic translation: // The alias node 1 for species s13 does not connect to the reaction(s) re24, but instead connects to re17, re24 @@ -109,9 +109,9 @@ model *Verma2016___HIV_and_HPV_co_infection__T_cell_response() re26 is "Production of Effector cell"; Production_of_HPV_due_to_HPV_self_proliferating is "Production of HPV due to HPV self proliferating"; - # General layout options + // General layout options model.layout = on - model.layout.size = {2000, 1000} + model.layout.size = {2000, 1000} model.layout.background = "#FFFFFFFF" // Species layout defaults diff --git a/doc/examples/biomodels/M2 Phenotype.txt b/doc/examples/biomodels/BIOMD0000000873/M2 Phenotype.txt similarity index 99% rename from doc/examples/biomodels/M2 Phenotype.txt rename to doc/examples/biomodels/BIOMD0000000873/M2 Phenotype.txt index 824c96643..3a0618712 100644 --- a/doc/examples/biomodels/M2 Phenotype.txt +++ b/doc/examples/biomodels/BIOMD0000000873/M2 Phenotype.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *mw544bb737_3306_4dd3_8b42_857e3d8a4062() // Compartments and Species: diff --git a/doc/examples/biomodels/Soni2018.txt b/doc/examples/biomodels/BIOMD0000000873/Soni2018.txt similarity index 99% rename from doc/examples/biomodels/Soni2018.txt rename to doc/examples/biomodels/BIOMD0000000873/Soni2018.txt index 0f9c03786..bf0e031a8 100644 --- a/doc/examples/biomodels/Soni2018.txt +++ b/doc/examples/biomodels/BIOMD0000000873/Soni2018.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Soni2018___IL6_induced_M2_Phenotype_in_Leishmania_major_infected_macrophage() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1006230079_url.txt b/doc/examples/biomodels/BIOMD0000000874/MODEL1006230079_url.txt similarity index 99% rename from doc/examples/biomodels/MODEL1006230079_url.txt rename to doc/examples/biomodels/BIOMD0000000874/MODEL1006230079_url.txt index c30110ace..888827864 100644 --- a/doc/examples/biomodels/MODEL1006230079_url.txt +++ b/doc/examples/biomodels/BIOMD0000000874/MODEL1006230079_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Perelson1993_HIVinfection_CD4Tcells_ModelA() // Compartments and Species: diff --git a/doc/examples/biomodels/Perelson1993.txt b/doc/examples/biomodels/BIOMD0000000874/Perelson1993.txt similarity index 99% rename from doc/examples/biomodels/Perelson1993.txt rename to doc/examples/biomodels/BIOMD0000000874/Perelson1993.txt index a994b0139..e3bdc66f9 100644 --- a/doc/examples/biomodels/Perelson1993.txt +++ b/doc/examples/biomodels/BIOMD0000000874/Perelson1993.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Perelson1993_HIVinfection_CD4Tcells_ModelA() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL8268650277_url.txt b/doc/examples/biomodels/BIOMD0000000875/MODEL8268650277_url.txt similarity index 99% rename from doc/examples/biomodels/MODEL8268650277_url.txt rename to doc/examples/biomodels/BIOMD0000000875/MODEL8268650277_url.txt index 60bfe3ccd..b885b0f97 100644 --- a/doc/examples/biomodels/MODEL8268650277_url.txt +++ b/doc/examples/biomodels/BIOMD0000000875/MODEL8268650277_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_0000001() // Compartments and Species: diff --git a/doc/examples/biomodels/Nelson2000.txt b/doc/examples/biomodels/BIOMD0000000875/Nelson2000.txt similarity index 99% rename from doc/examples/biomodels/Nelson2000.txt rename to doc/examples/biomodels/BIOMD0000000875/Nelson2000.txt index 707077072..e71c08cf0 100644 --- a/doc/examples/biomodels/Nelson2000.txt +++ b/doc/examples/biomodels/BIOMD0000000875/Nelson2000.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Nelson2000_HIV_1_general_model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/Aavani2019.txt b/doc/examples/biomodels/BIOMD0000000876/Aavani2019.txt similarity index 99% rename from doc/examples/biomodels/Aavani2019.txt rename to doc/examples/biomodels/BIOMD0000000876/Aavani2019.txt index 2b7eb7a2b..80060431d 100644 --- a/doc/examples/biomodels/Aavani2019.txt +++ b/doc/examples/biomodels/BIOMD0000000876/Aavani2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Aavani2019___The_role_of_CD4_T_cells_in_immune_system_activation_and_viral_reproduction_in_a_simple_model_for_HIV_infection() // Compartments and Species: diff --git a/doc/examples/biomodels/Ontah2019.txt b/doc/examples/biomodels/BIOMD0000000877/Ontah2019.txt similarity index 99% rename from doc/examples/biomodels/Ontah2019.txt rename to doc/examples/biomodels/BIOMD0000000877/Ontah2019.txt index f6ea1ef20..f09f0bdef 100644 --- a/doc/examples/biomodels/Ontah2019.txt +++ b/doc/examples/biomodels/BIOMD0000000877/Ontah2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ontah2019___Dynamic_analysis_of_a_tumor_treatment_model_using_oncolytic_virus_and_chemotherapy_with_saturated_infection_rate() // Compartments and Species: diff --git a/doc/examples/biomodels/Lenbury2001.txt b/doc/examples/biomodels/BIOMD0000000878/Lenbury2001.txt similarity index 99% rename from doc/examples/biomodels/Lenbury2001.txt rename to doc/examples/biomodels/BIOMD0000000878/Lenbury2001.txt index e9308e2bb..9613a92dd 100644 --- a/doc/examples/biomodels/Lenbury2001.txt +++ b/doc/examples/biomodels/BIOMD0000000878/Lenbury2001.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Lenbury2001_InsulinKineticsModel_A() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1201140002_url.txt b/doc/examples/biomodels/BIOMD0000000878/MODEL1201140002_url.txt similarity index 99% rename from doc/examples/biomodels/MODEL1201140002_url.txt rename to doc/examples/biomodels/BIOMD0000000878/MODEL1201140002_url.txt index 07c545b6a..ca3a612b0 100644 --- a/doc/examples/biomodels/MODEL1201140002_url.txt +++ b/doc/examples/biomodels/BIOMD0000000878/MODEL1201140002_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Lenbury2001_InsulinKineticsModel_A() // Compartments and Species: diff --git a/doc/examples/biomodels/Rodrigues2019.txt b/doc/examples/biomodels/BIOMD0000000879/Rodrigues2019.txt similarity index 99% rename from doc/examples/biomodels/Rodrigues2019.txt rename to doc/examples/biomodels/BIOMD0000000879/Rodrigues2019.txt index e690c1f7d..c6e2b235f 100644 --- a/doc/examples/biomodels/Rodrigues2019.txt +++ b/doc/examples/biomodels/BIOMD0000000879/Rodrigues2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Rodrigues2019___A_mathematical_model_for_chemoimmunotherapy_of_chronic_lymphocytic_leukemia() // Compartments and Species: diff --git a/doc/examples/biomodels/Trisilowati2018.txt b/doc/examples/biomodels/BIOMD0000000880/Trisilowati2018.txt similarity index 99% rename from doc/examples/biomodels/Trisilowati2018.txt rename to doc/examples/biomodels/BIOMD0000000880/Trisilowati2018.txt index acd41ab41..269cb948a 100644 --- a/doc/examples/biomodels/Trisilowati2018.txt +++ b/doc/examples/biomodels/BIOMD0000000880/Trisilowati2018.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Trisilowati2018___Optimal_control_of_tumor_immune_system_interaction_with_treatment() // Compartments and Species: diff --git a/doc/examples/biomodels/Kogan2013.txt b/doc/examples/biomodels/BIOMD0000000881/Kogan2013.txt similarity index 99% rename from doc/examples/biomodels/Kogan2013.txt rename to doc/examples/biomodels/BIOMD0000000881/Kogan2013.txt index 9cf3bade8..30dc696f8 100644 --- a/doc/examples/biomodels/Kogan2013.txt +++ b/doc/examples/biomodels/BIOMD0000000881/Kogan2013.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kogan2013___A_mathematical_model_for_the_immunotherapeutic_control_of_the_TH1_TH2_imbalance_in_melanoma() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1008060001_url.txt b/doc/examples/biomodels/BIOMD0000000882/MODEL1008060001_url.txt similarity index 98% rename from doc/examples/biomodels/MODEL1008060001_url.txt rename to doc/examples/biomodels/BIOMD0000000882/MODEL1008060001_url.txt index c99b09ca7..ff871f7f4 100644 --- a/doc/examples/biomodels/MODEL1008060001_url.txt +++ b/doc/examples/biomodels/BIOMD0000000882/MODEL1008060001_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1008060001() // Compartments and Species: @@ -21,7 +21,7 @@ model *MODEL1008060001() // Species initializations: S = N; I = 0; - Z = 1/env; + Z = 1*env; R = 0; // Compartment initializations: diff --git a/doc/examples/biomodels/munz2000.txt b/doc/examples/biomodels/BIOMD0000000882/munz2000.txt similarity index 99% rename from doc/examples/biomodels/munz2000.txt rename to doc/examples/biomodels/BIOMD0000000882/munz2000.txt index 99fc3fea1..55a36fd97 100644 --- a/doc/examples/biomodels/munz2000.txt +++ b/doc/examples/biomodels/BIOMD0000000882/munz2000.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Giani2019.txt b/doc/examples/biomodels/BIOMD0000000883/Giani2019.txt similarity index 99% rename from doc/examples/biomodels/Giani2019.txt rename to doc/examples/biomodels/BIOMD0000000883/Giani2019.txt index c45e77d06..b7d4c4ba4 100644 --- a/doc/examples/biomodels/Giani2019.txt +++ b/doc/examples/biomodels/BIOMD0000000883/Giani2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Giani2019___Computational_modeling_to_predict_MAP3K8_effects_as_mediator_of_resistance_to_vemurafenib_in_thyroid_cancer_stem_cells() // Compartments and Species: diff --git a/doc/examples/biomodels/Cortes2019.txt b/doc/examples/biomodels/BIOMD0000000884/Cortes2019.txt similarity index 99% rename from doc/examples/biomodels/Cortes2019.txt rename to doc/examples/biomodels/BIOMD0000000884/Cortes2019.txt index ece56790a..266755057 100644 --- a/doc/examples/biomodels/Cortes2019.txt +++ b/doc/examples/biomodels/BIOMD0000000884/Cortes2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Sumana2018.txt b/doc/examples/biomodels/BIOMD0000000885/Sumana2018.txt similarity index 99% rename from doc/examples/biomodels/Sumana2018.txt rename to doc/examples/biomodels/BIOMD0000000885/Sumana2018.txt index f759a18db..bc2645d0f 100644 --- a/doc/examples/biomodels/Sumana2018.txt +++ b/doc/examples/biomodels/BIOMD0000000885/Sumana2018.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Sumana2018___Mathematical_modeling_of_cancer_immune_system__considering_the_role_of_antibodies() // Compartments and Species: diff --git a/doc/examples/biomodels/Dubey2008.txt b/doc/examples/biomodels/BIOMD0000000886/Dubey2008.txt similarity index 99% rename from doc/examples/biomodels/Dubey2008.txt rename to doc/examples/biomodels/BIOMD0000000886/Dubey2008.txt index 3588d3c79..443479776 100644 --- a/doc/examples/biomodels/Dubey2008.txt +++ b/doc/examples/biomodels/BIOMD0000000886/Dubey2008.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Lim2014.txt b/doc/examples/biomodels/BIOMD0000000887/Lim2014.txt similarity index 99% rename from doc/examples/biomodels/Lim2014.txt rename to doc/examples/biomodels/BIOMD0000000887/Lim2014.txt index 03994810f..fc7090270 100644 --- a/doc/examples/biomodels/Lim2014.txt +++ b/doc/examples/biomodels/BIOMD0000000887/Lim2014.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Lim2014___HTLV_I_infection_A_dynamic_struggle_between_viral_persistence_and_host_immunity() // Compartments and Species: diff --git a/doc/examples/biomodels/unni2019.txt b/doc/examples/biomodels/BIOMD0000000888/unni2019.txt similarity index 99% rename from doc/examples/biomodels/unni2019.txt rename to doc/examples/biomodels/BIOMD0000000888/unni2019.txt index f6adf4cac..150158303 100644 --- a/doc/examples/biomodels/unni2019.txt +++ b/doc/examples/biomodels/BIOMD0000000888/unni2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Fribourg2014.txt b/doc/examples/biomodels/BIOMD0000000889/Fribourg2014.txt similarity index 99% rename from doc/examples/biomodels/Fribourg2014.txt rename to doc/examples/biomodels/BIOMD0000000889/Fribourg2014.txt index bde78cdaf..7ef103f8d 100644 --- a/doc/examples/biomodels/Fribourg2014.txt +++ b/doc/examples/biomodels/BIOMD0000000889/Fribourg2014.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Fribourg2014___Model_of_influenza_A_virus_infection_dynamics_of_viral_antagonism_and_innate_immune_response() // Compartments and Species: diff --git a/doc/examples/biomodels/Bhattacharya2014.txt b/doc/examples/biomodels/BIOMD0000000890/Bhattacharya2014.txt similarity index 99% rename from doc/examples/biomodels/Bhattacharya2014.txt rename to doc/examples/biomodels/BIOMD0000000890/Bhattacharya2014.txt index 476443c5f..9e2c638b3 100644 --- a/doc/examples/biomodels/Bhattacharya2014.txt +++ b/doc/examples/biomodels/BIOMD0000000890/Bhattacharya2014.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bhattacharya2014___A_mathematical_model_of_the_sterol_regulatory_element_binding_protein_2_cholesterol_biosynthesis_pathway() // Compartments and Species: diff --git a/doc/examples/biomodels/Khajanchi2019.txt b/doc/examples/biomodels/BIOMD0000000891/Khajanchi2019.txt similarity index 99% rename from doc/examples/biomodels/Khajanchi2019.txt rename to doc/examples/biomodels/BIOMD0000000891/Khajanchi2019.txt index ffcf77472..562f0d4b4 100644 --- a/doc/examples/biomodels/Khajanchi2019.txt +++ b/doc/examples/biomodels/BIOMD0000000891/Khajanchi2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Sandip2013.txt b/doc/examples/biomodels/BIOMD0000000892/Sandip2013.txt similarity index 99% rename from doc/examples/biomodels/Sandip2013.txt rename to doc/examples/biomodels/BIOMD0000000892/Sandip2013.txt index d7b4f5722..a6395b81b 100644 --- a/doc/examples/biomodels/Sandip2013.txt +++ b/doc/examples/biomodels/BIOMD0000000892/Sandip2013.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Sandip2013___Modeling_the_dynamics_of_hepatitis_C_virus_with_combined_antiviral_drug_therapy__interferon_and_ribavirin() // Compartments and Species: diff --git a/doc/examples/biomodels/GonzalezMiranda2013.txt b/doc/examples/biomodels/BIOMD0000000893/GonzalezMiranda2013.txt similarity index 98% rename from doc/examples/biomodels/GonzalezMiranda2013.txt rename to doc/examples/biomodels/BIOMD0000000893/GonzalezMiranda2013.txt index f5c669bdb..ff3fb3448 100644 --- a/doc/examples/biomodels/GonzalezMiranda2013.txt +++ b/doc/examples/biomodels/BIOMD0000000893/GonzalezMiranda2013.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *GonzalezMiranda2013___The_effect_of_circadian_oscillations_on_biochemical_cell_signaling_by_NF__B() // Compartments and Species: diff --git a/doc/examples/biomodels/Bose2011.txt b/doc/examples/biomodels/BIOMD0000000894/Bose2011.txt similarity index 99% rename from doc/examples/biomodels/Bose2011.txt rename to doc/examples/biomodels/BIOMD0000000894/Bose2011.txt index 248126be3..a1a1364bc 100644 --- a/doc/examples/biomodels/Bose2011.txt +++ b/doc/examples/biomodels/BIOMD0000000894/Bose2011.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bose2011___Noise_assisted_interactions_of_tumor_and_immune_cells() // Compartments and Species: diff --git a/doc/examples/biomodels/Schokker2013.txt b/doc/examples/biomodels/BIOMD0000000895/Schokker2013.txt similarity index 99% rename from doc/examples/biomodels/Schokker2013.txt rename to doc/examples/biomodels/BIOMD0000000895/Schokker2013.txt index d7ea6fb83..2111178f0 100644 --- a/doc/examples/biomodels/Schokker2013.txt +++ b/doc/examples/biomodels/BIOMD0000000895/Schokker2013.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Schokker2013___A_mathematical_model_representing_cellular_immune_development_and_response_to_Salmonella_of_chicken_intestinal_tissue() // Compartments and Species: diff --git a/doc/examples/biomodels/Szymanska2009.txt b/doc/examples/biomodels/BIOMD0000000896/Szymanska2009.txt similarity index 99% rename from doc/examples/biomodels/Szymanska2009.txt rename to doc/examples/biomodels/BIOMD0000000896/Szymanska2009.txt index 3aa15915e..76d812dbc 100644 --- a/doc/examples/biomodels/Szymanska2009.txt +++ b/doc/examples/biomodels/BIOMD0000000896/Szymanska2009.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Szymanska2009___Mathematical_modeling_of_heat_shock_protein_synthesis_in_response_to_temperature_change() // Compartments and Species: diff --git a/doc/examples/biomodels/Khajanchi2015.txt b/doc/examples/biomodels/BIOMD0000000897/Khajanchi2015.txt similarity index 99% rename from doc/examples/biomodels/Khajanchi2015.txt rename to doc/examples/biomodels/BIOMD0000000897/Khajanchi2015.txt index 019040414..3326b08c0 100644 --- a/doc/examples/biomodels/Khajanchi2015.txt +++ b/doc/examples/biomodels/BIOMD0000000897/Khajanchi2015.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Jiao2018.txt b/doc/examples/biomodels/BIOMD0000000898/Jiao2018.txt similarity index 99% rename from doc/examples/biomodels/Jiao2018.txt rename to doc/examples/biomodels/BIOMD0000000898/Jiao2018.txt index bfe466f58..5867066e6 100644 --- a/doc/examples/biomodels/Jiao2018.txt +++ b/doc/examples/biomodels/BIOMD0000000898/Jiao2018.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Jiao2018___Feedback_regulation_in_a_stem_cell_model_with_acute_myeloid_leukaemia() // Compartments and Species: diff --git a/doc/examples/biomodels/Ota2015_GDI-integrated.txt b/doc/examples/biomodels/BIOMD0000000899/Ota2015_GDI-integrated.txt similarity index 99% rename from doc/examples/biomodels/Ota2015_GDI-integrated.txt rename to doc/examples/biomodels/BIOMD0000000899/Ota2015_GDI-integrated.txt index c550acaa2..22ee4b460 100644 --- a/doc/examples/biomodels/Ota2015_GDI-integrated.txt +++ b/doc/examples/biomodels/BIOMD0000000899/Ota2015_GDI-integrated.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *NoName() // Compartments and Species: @@ -73,7 +73,7 @@ model *NoName() s13 is "GDI·GTP-Rho"; s16 is "Effector·GTP-Rho"; - # General layout options + // General layout options model.layout = on model.layout.size = {1200, 800} model.layout.background = "#FFFFFFFF" diff --git a/doc/examples/biomodels/Bianca2013.txt b/doc/examples/biomodels/BIOMD0000000900/Bianca2013.txt similarity index 99% rename from doc/examples/biomodels/Bianca2013.txt rename to doc/examples/biomodels/BIOMD0000000900/Bianca2013.txt index 9dc0d9e4b..0e4437acb 100644 --- a/doc/examples/biomodels/Bianca2013.txt +++ b/doc/examples/biomodels/BIOMD0000000900/Bianca2013.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/ChowHall2008 - Dynamics of Human Weight Change.txt b/doc/examples/biomodels/BIOMD0000000901/ChowHall2008 - Dynamics of Human Weight Change.txt similarity index 98% rename from doc/examples/biomodels/ChowHall2008 - Dynamics of Human Weight Change.txt rename to doc/examples/biomodels/BIOMD0000000901/ChowHall2008 - Dynamics of Human Weight Change.txt index c81b8c506..948ca8bec 100644 --- a/doc/examples/biomodels/ChowHall2008 - Dynamics of Human Weight Change.txt +++ b/doc/examples/biomodels/BIOMD0000000901/ChowHall2008 - Dynamics of Human Weight Change.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *ChowHall2008_Dynamics_of_Human_Weight_Change_1() // Compartments and Species: @@ -43,7 +43,7 @@ model *ChowHall2008_Dynamics_of_Human_Weight_Change_1() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = 1e-3 mole; unit extent = substance; unit substance_per_volume = 1e-3 mole / 1e-3 litre; diff --git a/doc/examples/biomodels/Wang2019.txt b/doc/examples/biomodels/BIOMD0000000902/Wang2019.txt similarity index 98% rename from doc/examples/biomodels/Wang2019.txt rename to doc/examples/biomodels/BIOMD0000000902/Wang2019.txt index 89ac7deee..724300fc2 100644 --- a/doc/examples/biomodels/Wang2019.txt +++ b/doc/examples/biomodels/BIOMD0000000902/Wang2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wang2019___A_mathematical_model_of_oncolytic_virotherapy_with_time_delay() // Compartments and Species: diff --git a/doc/examples/biomodels/Solis-perez2019.txt b/doc/examples/biomodels/BIOMD0000000903/Solis-perez2019.txt similarity index 99% rename from doc/examples/biomodels/Solis-perez2019.txt rename to doc/examples/biomodels/BIOMD0000000903/Solis-perez2019.txt index ee25b930c..cbfbc6969 100644 --- a/doc/examples/biomodels/Solis-perez2019.txt +++ b/doc/examples/biomodels/BIOMD0000000903/Solis-perez2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Solis_perez2019___A_fractional_mathematical_model_of_breast_cancer_competition_model() // Compartments and Species: diff --git a/doc/examples/biomodels/Admon2017.txt b/doc/examples/biomodels/BIOMD0000000904/Admon2017.txt similarity index 99% rename from doc/examples/biomodels/Admon2017.txt rename to doc/examples/biomodels/BIOMD0000000904/Admon2017.txt index adc992ac1..50b45c945 100644 --- a/doc/examples/biomodels/Admon2017.txt +++ b/doc/examples/biomodels/BIOMD0000000904/Admon2017.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Admon2017___Modelling_tumor_growth_with_immune_response_and_drug_using_ordinary_differential_equations() // Compartments and Species: diff --git a/doc/examples/biomodels/Dubey2007_model2.txt b/doc/examples/biomodels/BIOMD0000000905/Dubey2007_model2.txt similarity index 99% rename from doc/examples/biomodels/Dubey2007_model2.txt rename to doc/examples/biomodels/BIOMD0000000905/Dubey2007_model2.txt index dad3b3a22..f19bde94f 100644 --- a/doc/examples/biomodels/Dubey2007_model2.txt +++ b/doc/examples/biomodels/BIOMD0000000905/Dubey2007_model2.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Dubey2007___A_mathematical_model_for_the_effect_of_toxicant_on_the_immune_system__without_toxicant_effect__Model1() // Compartments and Species: diff --git a/doc/examples/biomodels/Dubey2007_model1.txt b/doc/examples/biomodels/BIOMD0000000906/Dubey2007_model1.txt similarity index 99% rename from doc/examples/biomodels/Dubey2007_model1.txt rename to doc/examples/biomodels/BIOMD0000000906/Dubey2007_model1.txt index 2a2b55ee1..8dca4aa57 100644 --- a/doc/examples/biomodels/Dubey2007_model1.txt +++ b/doc/examples/biomodels/BIOMD0000000906/Dubey2007_model1.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Dubey2007___A_mathematical_model_for_the_effect_of_toxicant_on_the_immune_system__without_toxicant_effect__Model1() // Compartments and Species: diff --git a/doc/examples/biomodels/Navas2019_model3.txt b/doc/examples/biomodels/BIOMD0000000907/Navas2019_model3.txt similarity index 99% rename from doc/examples/biomodels/Navas2019_model3.txt rename to doc/examples/biomodels/BIOMD0000000907/Navas2019_model3.txt index d72151ef9..accc7ba0e 100644 --- a/doc/examples/biomodels/Navas2019_model3.txt +++ b/doc/examples/biomodels/BIOMD0000000907/Navas2019_model3.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *HeberleRazquinNavas2019___The_PI3K_and_MAPK_p38_pathways_control_stress_granuleassembly_in_a_hierarchical_manner_model_3() // Compartments and Species: diff --git a/doc/examples/biomodels/dePillis2013.txt b/doc/examples/biomodels/BIOMD0000000908/dePillis2013.txt similarity index 99% rename from doc/examples/biomodels/dePillis2013.txt rename to doc/examples/biomodels/BIOMD0000000908/dePillis2013.txt index 573482079..f1c4055c9 100644 --- a/doc/examples/biomodels/dePillis2013.txt +++ b/doc/examples/biomodels/BIOMD0000000908/dePillis2013.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *dePillis2013___Mathematical_modeling_of_regulatory_T_cell_effects_on_renal_cell_carcinoma_treatment() // Compartments and Species: diff --git a/doc/examples/biomodels/dePillis2003.txt b/doc/examples/biomodels/BIOMD0000000909/dePillis2003.txt similarity index 99% rename from doc/examples/biomodels/dePillis2003.txt rename to doc/examples/biomodels/BIOMD0000000909/dePillis2003.txt index a4aed7c45..1dd5e9a8e 100644 --- a/doc/examples/biomodels/dePillis2003.txt +++ b/doc/examples/biomodels/BIOMD0000000909/dePillis2003.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *dePillis2003___The_dynamics_of_an_optimally_controlled_tumor_model__A_case_study() // Compartments and Species: diff --git a/doc/examples/biomodels/Isaeva2008.txt b/doc/examples/biomodels/BIOMD0000000910/Isaeva2008.txt similarity index 99% rename from doc/examples/biomodels/Isaeva2008.txt rename to doc/examples/biomodels/BIOMD0000000910/Isaeva2008.txt index 78510fb5c..62ea556b5 100644 --- a/doc/examples/biomodels/Isaeva2008.txt +++ b/doc/examples/biomodels/BIOMD0000000910/Isaeva2008.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Isaeva2008___Modelling_of_Anti_Tumour_Immune_Response_Immunocorrective_Effect_of_Weak_Centimetre_Electromagnetic_Waves() // Compartments and Species: diff --git a/doc/examples/biomodels/Merola2008.txt b/doc/examples/biomodels/BIOMD0000000911/Merola2008.txt similarity index 99% rename from doc/examples/biomodels/Merola2008.txt rename to doc/examples/biomodels/BIOMD0000000911/Merola2008.txt index 89b648c14..898c7bd19 100644 --- a/doc/examples/biomodels/Merola2008.txt +++ b/doc/examples/biomodels/BIOMD0000000911/Merola2008.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Merola2008___An_insight_into_tumor_dormancy_equilibrium_via_the_analysis_of_its_domain_of_attraction() // Compartments and Species: diff --git a/doc/examples/biomodels/Caravagna2010.txt b/doc/examples/biomodels/BIOMD0000000912/Caravagna2010.txt similarity index 99% rename from doc/examples/biomodels/Caravagna2010.txt rename to doc/examples/biomodels/BIOMD0000000912/Caravagna2010.txt index bc550da10..b8427b8e3 100644 --- a/doc/examples/biomodels/Caravagna2010.txt +++ b/doc/examples/biomodels/BIOMD0000000912/Caravagna2010.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Caravagna2010___Tumour_suppression_by_immune_system() // Compartments and Species: diff --git a/doc/examples/biomodels/dePillis2008.txt b/doc/examples/biomodels/BIOMD0000000913/dePillis2008.txt similarity index 99% rename from doc/examples/biomodels/dePillis2008.txt rename to doc/examples/biomodels/BIOMD0000000913/dePillis2008.txt index 7669db0d1..a28c7057b 100644 --- a/doc/examples/biomodels/dePillis2008.txt +++ b/doc/examples/biomodels/BIOMD0000000913/dePillis2008.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *dePillis2008___Optimal_control_of_mixed_immunotherapy_and_chemotherapy_of_tumors() // Compartments and Species: diff --git a/doc/examples/biomodels/Parra_Guillen2013.txt b/doc/examples/biomodels/BIOMD0000000914/Parra_Guillen2013.txt similarity index 99% rename from doc/examples/biomodels/Parra_Guillen2013.txt rename to doc/examples/biomodels/BIOMD0000000914/Parra_Guillen2013.txt index b89c2c8bc..a5837a44c 100644 --- a/doc/examples/biomodels/Parra_Guillen2013.txt +++ b/doc/examples/biomodels/BIOMD0000000914/Parra_Guillen2013.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Parra_Guillen2013____Mathematical_model_approach_to_describe_tumour_response_in_mice_after_vaccine_administration_model1() // Compartments and Species: diff --git a/doc/examples/biomodels/Sun2018 - Instantaneous mutation rate in cancer initiation and progression.txt b/doc/examples/biomodels/BIOMD0000000915/Sun2018 - Instantaneous mutation rate in cancer initiation and progression.txt similarity index 99% rename from doc/examples/biomodels/Sun2018 - Instantaneous mutation rate in cancer initiation and progression.txt rename to doc/examples/biomodels/BIOMD0000000915/Sun2018 - Instantaneous mutation rate in cancer initiation and progression.txt index b42a1236c..ee891d6df 100644 --- a/doc/examples/biomodels/Sun2018 - Instantaneous mutation rate in cancer initiation and progression.txt +++ b/doc/examples/biomodels/BIOMD0000000915/Sun2018 - Instantaneous mutation rate in cancer initiation and progression.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Sun2018.txt b/doc/examples/biomodels/BIOMD0000000915/Sun2018.txt similarity index 99% rename from doc/examples/biomodels/Sun2018.txt rename to doc/examples/biomodels/BIOMD0000000915/Sun2018.txt index a202c2ae8..d39b0625f 100644 --- a/doc/examples/biomodels/Sun2018.txt +++ b/doc/examples/biomodels/BIOMD0000000915/Sun2018.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Sun2018___Instantaneous_mutation_rate_in_cancer_initiation_and_progression_1() // Compartments and Species: diff --git a/doc/examples/biomodels/Kraan1992.txt b/doc/examples/biomodels/BIOMD0000000916/Kraan1992.txt similarity index 99% rename from doc/examples/biomodels/Kraan1992.txt rename to doc/examples/biomodels/BIOMD0000000916/Kraan1992.txt index 2a4146f34..c6f78ecc1 100644 --- a/doc/examples/biomodels/Kraan1992.txt +++ b/doc/examples/biomodels/BIOMD0000000916/Kraan1992.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Phillips2007_Curated.txt b/doc/examples/biomodels/BIOMD0000000917/Phillips2007_Curated.txt similarity index 99% rename from doc/examples/biomodels/Phillips2007_Curated.txt rename to doc/examples/biomodels/BIOMD0000000917/Phillips2007_Curated.txt index 1db4679e0..57d1371a3 100644 --- a/doc/examples/biomodels/Phillips2007_Curated.txt +++ b/doc/examples/biomodels/BIOMD0000000917/Phillips2007_Curated.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Phillips2007_AscendingArousalSystem_SleepWakeDynamics() // Compartments and Species: @@ -57,7 +57,7 @@ model *Phillips2007_AscendingArousalSystem_SleepWakeDynamics() unit length = metre; unit area = metre^2; unit volume = litre; - unit time_unit = time_unit; + unit time_unit = 3600 second; unit substance = mole; unit extent = substance; unit substance_per_volume = mole / litre; diff --git a/doc/examples/biomodels/Phillips2007_Original.txt b/doc/examples/biomodels/BIOMD0000000917/Phillips2007_Original.txt similarity index 99% rename from doc/examples/biomodels/Phillips2007_Original.txt rename to doc/examples/biomodels/BIOMD0000000917/Phillips2007_Original.txt index 490346b95..46798799f 100644 --- a/doc/examples/biomodels/Phillips2007_Original.txt +++ b/doc/examples/biomodels/BIOMD0000000917/Phillips2007_Original.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Phillips2007_AscendingArousalSystem_SleepWakeDynamics() // Compartments and Species: diff --git a/doc/examples/biomodels/Schwarz2018.txt b/doc/examples/biomodels/BIOMD0000000918/Schwarz2018.txt similarity index 99% rename from doc/examples/biomodels/Schwarz2018.txt rename to doc/examples/biomodels/BIOMD0000000918/Schwarz2018.txt index fb873d157..a3af18afc 100644 --- a/doc/examples/biomodels/Schwarz2018.txt +++ b/doc/examples/biomodels/BIOMD0000000918/Schwarz2018.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Schwarz2018_Cdk_Activity_Threshold_Determines_Passage_through_the_Restriction_Point() // Compartments and Species: diff --git a/doc/examples/biomodels/Schwarz2018_orignal.txt b/doc/examples/biomodels/BIOMD0000000918/Schwarz2018_orignal.txt similarity index 99% rename from doc/examples/biomodels/Schwarz2018_orignal.txt rename to doc/examples/biomodels/BIOMD0000000918/Schwarz2018_orignal.txt index 0f7fec8bf..1b3effc8d 100644 --- a/doc/examples/biomodels/Schwarz2018_orignal.txt +++ b/doc/examples/biomodels/BIOMD0000000918/Schwarz2018_orignal.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Schwarz2018_Cdk_Activity_Threshold_Determines_Passage_through_the_Restriction_Point() // Compartments and Species: diff --git a/doc/examples/biomodels/Ledzewicz2013.txt b/doc/examples/biomodels/BIOMD0000000919/Ledzewicz2013.txt similarity index 99% rename from doc/examples/biomodels/Ledzewicz2013.txt rename to doc/examples/biomodels/BIOMD0000000919/Ledzewicz2013.txt index 659ecc4e5..04d383127 100644 --- a/doc/examples/biomodels/Ledzewicz2013.txt +++ b/doc/examples/biomodels/BIOMD0000000919/Ledzewicz2013.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ledzewicz2013___On_optimal_chemotherapy_with_a_strongly_targeted_agent_for_a_model_of_tumor_immune_system_interactions_with_generalized_logistic_growth() // Compartments and Species: diff --git a/doc/examples/biomodels/Jarrett2015.txt b/doc/examples/biomodels/BIOMD0000000920/Jarrett2015.txt similarity index 99% rename from doc/examples/biomodels/Jarrett2015.txt rename to doc/examples/biomodels/BIOMD0000000920/Jarrett2015.txt index d1db11aac..980475f42 100644 --- a/doc/examples/biomodels/Jarrett2015.txt +++ b/doc/examples/biomodels/BIOMD0000000920/Jarrett2015.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Jarrett2015___Modelling_the_interaction_between_immune_response__bacterial_dynamics_and_inflammatory_damage() // Compartments and Species: diff --git a/doc/examples/biomodels/Jarrett2015_orignal.txt b/doc/examples/biomodels/BIOMD0000000920/Jarrett2015_orignal.txt similarity index 98% rename from doc/examples/biomodels/Jarrett2015_orignal.txt rename to doc/examples/biomodels/BIOMD0000000920/Jarrett2015_orignal.txt index edcf8d4f2..d9fd7effd 100644 --- a/doc/examples/biomodels/Jarrett2015_orignal.txt +++ b/doc/examples/biomodels/BIOMD0000000920/Jarrett2015_orignal.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Jarrett2015___Modelling_the_interaction_between_immune_response__bacterial_dynamics_and_inflammatory_damage() // Compartments and Species: diff --git a/doc/examples/biomodels/khajanchi2017.txt b/doc/examples/biomodels/BIOMD0000000921/khajanchi2017.txt similarity index 99% rename from doc/examples/biomodels/khajanchi2017.txt rename to doc/examples/biomodels/BIOMD0000000921/khajanchi2017.txt index 8ae57d12b..a901fa8c9 100644 --- a/doc/examples/biomodels/khajanchi2017.txt +++ b/doc/examples/biomodels/BIOMD0000000921/khajanchi2017.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Khajanchi2017___Uniform_Persistence_and_Global_Stability_for_a_Brain_Tumor_and_Immune_System_Interaction() // Compartments and Species: diff --git a/doc/examples/biomodels/Turner2015_ELP.txt b/doc/examples/biomodels/BIOMD0000000922/Turner2015_ELP.txt similarity index 98% rename from doc/examples/biomodels/Turner2015_ELP.txt rename to doc/examples/biomodels/BIOMD0000000922/Turner2015_ELP.txt index 383ad6563..aba0cf4a9 100644 --- a/doc/examples/biomodels/Turner2015_ELP.txt +++ b/doc/examples/biomodels/BIOMD0000000922/Turner2015_ELP.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Turner2015_Human_Mosquito_ELP_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Lio2012_Modelling osteomyelitis_Control Model.txt b/doc/examples/biomodels/BIOMD0000000923/Lio2012_Modelling osteomyelitis_Control Model.txt similarity index 99% rename from doc/examples/biomodels/Lio2012_Modelling osteomyelitis_Control Model.txt rename to doc/examples/biomodels/BIOMD0000000923/Lio2012_Modelling osteomyelitis_Control Model.txt index 0f2b2f11c..9e5a4fbe0 100644 --- a/doc/examples/biomodels/Lio2012_Modelling osteomyelitis_Control Model.txt +++ b/doc/examples/biomodels/BIOMD0000000923/Lio2012_Modelling osteomyelitis_Control Model.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Li_2012_Modelling_osteomyelitis_Control_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Final Version (7).txt b/doc/examples/biomodels/BIOMD0000000924/Final Version (7).txt similarity index 98% rename from doc/examples/biomodels/Final Version (7).txt rename to doc/examples/biomodels/BIOMD0000000924/Final Version (7).txt index 5eecd0f6d..883886a4e 100644 --- a/doc/examples/biomodels/Final Version (7).txt +++ b/doc/examples/biomodels/BIOMD0000000924/Final Version (7).txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Smith2011_V1.txt b/doc/examples/biomodels/BIOMD0000000924/Smith2011_V1.txt similarity index 99% rename from doc/examples/biomodels/Smith2011_V1.txt rename to doc/examples/biomodels/BIOMD0000000924/Smith2011_V1.txt index 272d53d96..bc55bb03c 100644 --- a/doc/examples/biomodels/Smith2011_V1.txt +++ b/doc/examples/biomodels/BIOMD0000000924/Smith2011_V1.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Smith2011___Three_Stage_Innate_Immune_Response_to_a_Pneumococcal_Lung_Infection() // Compartments and Species: @@ -78,7 +78,7 @@ model *Smith2011___Three_Stage_Innate_Immune_Response_to_a_Pneumococcal_Lung_Inf // Unit definitions: unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 3600 second; unit substance = 1e-3 mole; unit area = metre^2; unit length = metre; diff --git a/doc/examples/biomodels/Dunster2016_Nondimensional_Model (1).txt b/doc/examples/biomodels/BIOMD0000000925/Dunster2016_Nondimensional_Model (1).txt similarity index 99% rename from doc/examples/biomodels/Dunster2016_Nondimensional_Model (1).txt rename to doc/examples/biomodels/BIOMD0000000925/Dunster2016_Nondimensional_Model (1).txt index 7a62b703c..172264f56 100644 --- a/doc/examples/biomodels/Dunster2016_Nondimensional_Model (1).txt +++ b/doc/examples/biomodels/BIOMD0000000925/Dunster2016_Nondimensional_Model (1).txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Dunster2016___Nondimensional_Coagulation_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Dunster2016_Nondimensional_Model_Curated.txt b/doc/examples/biomodels/BIOMD0000000925/Dunster2016_Nondimensional_Model_Curated.txt similarity index 99% rename from doc/examples/biomodels/Dunster2016_Nondimensional_Model_Curated.txt rename to doc/examples/biomodels/BIOMD0000000925/Dunster2016_Nondimensional_Model_Curated.txt index 8c2166b43..05497b734 100644 --- a/doc/examples/biomodels/Dunster2016_Nondimensional_Model_Curated.txt +++ b/doc/examples/biomodels/BIOMD0000000925/Dunster2016_Nondimensional_Model_Curated.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 // Warnings from automatic translation: // Layout error in model: unable to draw an arc between the species 'Factor_Xa' and the reaction 'reaction_for_Inactivation_of_prothrombinase_2': 'Factor_Xa' is not a participant in that reaction. @@ -121,7 +121,7 @@ model *Dunster2016___Nondimensional_Coagulation_Model() Reaction_for_Prothrombin_inactivation is "Reaction for Prothrombin inactivation"; Reaction_for_Inactive_Xa is "Reaction for Inactive Xa production"; - # General layout options + // General layout options model.layout = on model.layout.size = {10, 10} model.layout.background = "#FFFFFFFF" diff --git a/doc/examples/biomodels/Rhodes2019-Immune-Mediated theory of Metastasis.txt b/doc/examples/biomodels/BIOMD0000000926/Rhodes2019-Immune-Mediated theory of Metastasis.txt similarity index 99% rename from doc/examples/biomodels/Rhodes2019-Immune-Mediated theory of Metastasis.txt rename to doc/examples/biomodels/BIOMD0000000926/Rhodes2019-Immune-Mediated theory of Metastasis.txt index 9ef6adea2..f1e1874ff 100644 --- a/doc/examples/biomodels/Rhodes2019-Immune-Mediated theory of Metastasis.txt +++ b/doc/examples/biomodels/BIOMD0000000926/Rhodes2019-Immune-Mediated theory of Metastasis.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Rhodes2019-Immune-Mediated theory of Metastasis_V1.txt b/doc/examples/biomodels/BIOMD0000000926/Rhodes2019-Immune-Mediated theory of Metastasis_V1.txt similarity index 99% rename from doc/examples/biomodels/Rhodes2019-Immune-Mediated theory of Metastasis_V1.txt rename to doc/examples/biomodels/BIOMD0000000926/Rhodes2019-Immune-Mediated theory of Metastasis_V1.txt index 002a79948..b363f69c0 100644 --- a/doc/examples/biomodels/Rhodes2019-Immune-Mediated theory of Metastasis_V1.txt +++ b/doc/examples/biomodels/BIOMD0000000926/Rhodes2019-Immune-Mediated theory of Metastasis_V1.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *New_Model() // Compartments and Species: diff --git a/doc/examples/biomodels/Grigolon2018_fig1b.txt b/doc/examples/biomodels/BIOMD0000000927/Grigolon2018_fig1b.txt similarity index 99% rename from doc/examples/biomodels/Grigolon2018_fig1b.txt rename to doc/examples/biomodels/BIOMD0000000927/Grigolon2018_fig1b.txt index 22df04d77..0840017f2 100644 --- a/doc/examples/biomodels/Grigolon2018_fig1b.txt +++ b/doc/examples/biomodels/BIOMD0000000927/Grigolon2018_fig1b.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Grigolon2018_Responses_to_auxin_signals() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1706070000_url.txt b/doc/examples/biomodels/BIOMD0000000927/MODEL1706070000_url.txt similarity index 99% rename from doc/examples/biomodels/MODEL1706070000_url.txt rename to doc/examples/biomodels/BIOMD0000000927/MODEL1706070000_url.txt index b0d4657d7..79ed9cff4 100644 --- a/doc/examples/biomodels/MODEL1706070000_url.txt +++ b/doc/examples/biomodels/BIOMD0000000927/MODEL1706070000_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1706070000() // Compartments and Species: diff --git a/doc/examples/biomodels/Baker2017_Fig14.txt b/doc/examples/biomodels/BIOMD0000000928/Baker2017_Fig14.txt similarity index 99% rename from doc/examples/biomodels/Baker2017_Fig14.txt rename to doc/examples/biomodels/BIOMD0000000928/Baker2017_Fig14.txt index 8c16cf63a..407516521 100644 --- a/doc/examples/biomodels/Baker2017_Fig14.txt +++ b/doc/examples/biomodels/BIOMD0000000928/Baker2017_Fig14.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Baker2017___The_role_of_cytokines__MMPs_and_fibronectin_fragments_osteoarthritis() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1704120000_url.txt b/doc/examples/biomodels/BIOMD0000000928/MODEL1704120000_url.txt similarity index 99% rename from doc/examples/biomodels/MODEL1704120000_url.txt rename to doc/examples/biomodels/BIOMD0000000928/MODEL1704120000_url.txt index 184afcaf8..ed2214e80 100644 --- a/doc/examples/biomodels/MODEL1704120000_url.txt +++ b/doc/examples/biomodels/BIOMD0000000928/MODEL1704120000_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL1704120000() // Compartments and Species: diff --git a/doc/examples/biomodels/Li2016.txt b/doc/examples/biomodels/BIOMD0000000929/Li2016.txt similarity index 99% rename from doc/examples/biomodels/Li2016.txt rename to doc/examples/biomodels/BIOMD0000000929/Li2016.txt index 0e292d7a8..76af7d8b1 100644 --- a/doc/examples/biomodels/Li2016.txt +++ b/doc/examples/biomodels/BIOMD0000000929/Li2016.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Li2016___Model_for_pancreatic_cancer_patients_receiving_immunotherapy() // Compartments and Species: diff --git a/doc/examples/biomodels/Liu2017.txt b/doc/examples/biomodels/BIOMD0000000930/Liu2017.txt similarity index 99% rename from doc/examples/biomodels/Liu2017.txt rename to doc/examples/biomodels/BIOMD0000000930/Liu2017.txt index 74d824915..047f798bc 100644 --- a/doc/examples/biomodels/Liu2017.txt +++ b/doc/examples/biomodels/BIOMD0000000930/Liu2017.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Liu2017___chemotherapy_targeted_model_of_tumor_immune_system() // Compartments and Species: diff --git a/doc/examples/biomodels/Voliotis2019-original.txt b/doc/examples/biomodels/BIOMD0000000931/Voliotis2019-original.txt similarity index 99% rename from doc/examples/biomodels/Voliotis2019-original.txt rename to doc/examples/biomodels/BIOMD0000000931/Voliotis2019-original.txt index e011aa506..5af756f42 100644 --- a/doc/examples/biomodels/Voliotis2019-original.txt +++ b/doc/examples/biomodels/BIOMD0000000931/Voliotis2019-original.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Voliotis2019_GnRH_Pulse_Generation() // Compartments and Species: diff --git a/doc/examples/biomodels/Voliotis2019.txt b/doc/examples/biomodels/BIOMD0000000931/Voliotis2019.txt similarity index 99% rename from doc/examples/biomodels/Voliotis2019.txt rename to doc/examples/biomodels/BIOMD0000000931/Voliotis2019.txt index e011aa506..5af756f42 100644 --- a/doc/examples/biomodels/Voliotis2019.txt +++ b/doc/examples/biomodels/BIOMD0000000931/Voliotis2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Voliotis2019_GnRH_Pulse_Generation() // Compartments and Species: diff --git a/doc/examples/biomodels/BIOMD0000000932/Garde2020.txt b/doc/examples/biomodels/BIOMD0000000932/Garde2020.txt new file mode 100644 index 000000000..d5df0ed5e --- /dev/null +++ b/doc/examples/biomodels/BIOMD0000000932/Garde2020.txt @@ -0,0 +1,104 @@ +// Created by libAntimony v3.2.0 +model *Garde2020_Minimal_model_describing_metabolic_oscillations_in_Bacillus_subtilis_biofilms() + + // Compartments and Species: + compartment compartment_; + species Gp in compartment_, Gi in compartment_, A in compartment_, B in compartment_; + + // Reactions: + The_uptake_of_glutamate_and_Consumption_of_glutamate_and_ammonia: => Gp; compartment_*(k1*GE*Gp - k2*A*Gp); + Diffusion_of_glutamate: Gp => Gi; compartment_*(k4*Gp); + Consumption_of_glutamate_to_produce_ammonia: Gi => A; compartment_*(k5*Gi); + Diffusion_of_ammonia: A => ; compartment_*(k3*A); + The_synthesis_of_biomass_from_ammonia_and_glutamate: => B; compartment_*(b*A*Gp*B); + + // Species initializations: + Gp = 1; + Gi = 1; + A = 1; + B = 100000000000; + + // Compartment initializations: + compartment_ = 1; + + // Variable initializations: + k1 = 0.3426; + k2 = 5.3; + k3 = 4; + k4 = 2; + k5 = 2.3; + GE = 30; + b = 0.1; + + // Other declarations: + const compartment_, k1, k2, k3, k4, k5, GE, b; + + // Unit definitions: + unit time_unit = 3600 second; + unit substance = 1e-3 mole; + + // Display Names: + time_unit is "time"; + compartment_ is "compartment"; + The_uptake_of_glutamate_and_Consumption_of_glutamate_and_ammonia is "The uptake of glutamate and Consumption of glutamate and ammonia"; + Diffusion_of_glutamate is "Diffusion of glutamate"; + Consumption_of_glutamate_to_produce_ammonia is "Consumption of glutamate to produce ammonia"; + Diffusion_of_ammonia is "Diffusion of ammonia"; + The_synthesis_of_biomass_from_ammonia_and_glutamate is "The synthesis of biomass from ammonia and glutamate"; + + // CV terms: + Gp hasProperty "http://identifiers.org/chebi/CHEBI:32484" + Gp hasProperty "http://identifiers.org/ncit/C25233" + Gi hasProperty "http://identifiers.org/chebi/CHEBI:32484" + Gi hasProperty "http://identifiers.org/ncit/C25234" + A hasProperty "http://identifiers.org/chebi/CHEBI:16134" + B hasProperty "http://identifiers.org/sbo/SBO:0000629" + The_uptake_of_glutamate_and_Consumption_of_glutamate_and_ammonia hasProperty "http://identifiers.org/ncit/C71688" + The_uptake_of_glutamate_and_Consumption_of_glutamate_and_ammonia hasProperty "http://identifiers.org/sbo/SBO:0000394" + Diffusion_of_glutamate hasProperty "http://identifiers.org/ncit/C82333" + Consumption_of_glutamate_to_produce_ammonia hasProperty "http://identifiers.org/sbo/SBO:0000394" + Diffusion_of_ammonia hasProperty "http://identifiers.org/ncit/C82333" + The_synthesis_of_biomass_from_ammonia_and_glutamate hasProperty "http://identifiers.org/ncit/C61408" + + model origin "http://identifiers.org/go/GO:0006536", + "http://identifiers.org/envo/ENVO:00002034", + "http://identifiers.org/mamo/MAMO_0000046", + "http://identifiers.org/ncit/C28240", + "http://identifiers.org/biomodels.teddy/TEDDY_0000072", + "http://identifiers.org/taxonomy/1423", + "urn:miriam:doi:10.1007/BF01165134" + model model_source "http://identifiers.org/biomodels.db/MODEL2004140001", + "http://identifiers.org/biomodels.db/BIOMD0000000932" + model hasTaxon "http://identifiers.org/taxonomy/1423" + model isDescribedBy "urn:miriam:doi:10.1007/BF01165134", + "http://identifiers.org/pubmed/32257302" + model hasProperty "http://identifiers.org/go/GO:0006536", + "http://identifiers.org/envo/ENVO:00002034", + "http://identifiers.org/ncit/C28240", + "http://identifiers.org/biomodels.teddy/TEDDY_0000072", + "http://identifiers.org/mamo/MAMO_0000046" + model created "2020-04-14T10:47:12Z" + model modified "2020-04-14T15:02:34Z" + model creator1.givenName "Ahmad" + model creator1.familyName "Zyoud" + model creator1.organization "EMBL-EBI" + model creator1.email "ahmad.azd@hotmail.com" + + // Notes: + model notes ``` +Biofilms offer an excellent example of ecological interaction among bacteria. +Temporal and spatial oscillations in biofilms are an emerging topic. In this paper, +we describe the metabolic oscillations in Bacillus subtilis biofilms by applying +the smallest theoretical chemical reaction system showing Hopf bifurcation proposed +by Wilhelm and Heinrich in 1995. The system involves three differential equations +and a single bilinear term. We specifically select parameters that are suitable for +the biological scenario of biofilm oscillations. We perform computer simulations +and a detailed analysis of the system including bifurcation analysis and quasi-steady-state +approximation. We also discuss the feedback structure of the system and the correspondence +of the simulations to biological observations. Our theoretical work suggests potential +scenarios about the oscillatory behaviour of biofilms and also serves as an application +of a previously described chemical oscillator to a biological system. +``` +end + +Garde2020_Minimal_model_describing_metabolic_oscillations_in_Bacillus_subtilis_biofilms is "Garde2020-Minimal model describing metabolic oscillations in Bacillus subtilis biofilms" diff --git a/doc/examples/biomodels/Kosiuk2015.txt b/doc/examples/biomodels/BIOMD0000000933/Kosiuk2015.txt similarity index 99% rename from doc/examples/biomodels/Kosiuk2015.txt rename to doc/examples/biomodels/BIOMD0000000933/Kosiuk2015.txt index 9df986bdd..1c129e9c1 100644 --- a/doc/examples/biomodels/Kosiuk2015.txt +++ b/doc/examples/biomodels/BIOMD0000000933/Kosiuk2015.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kosiuk2015_Geometric_analysis_of_the_Goldbeter_minimal_model_for_the_embryonic_cell_cycle() // Compartments and Species: diff --git a/doc/examples/biomodels/Linke2017.txt b/doc/examples/biomodels/BIOMD0000000934/Linke2017.txt similarity index 99% rename from doc/examples/biomodels/Linke2017.txt rename to doc/examples/biomodels/BIOMD0000000934/Linke2017.txt index 9f05d4cef..833792ffa 100644 --- a/doc/examples/biomodels/Linke2017.txt +++ b/doc/examples/biomodels/BIOMD0000000934/Linke2017.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Linke2017___Synchronization_of_Cyclins__expression_by_the_Fkh2_transcription_factor_in_the_budding_yeast_cell_cycle() // Compartments and Species: diff --git a/doc/examples/biomodels/Ferrel2011.txt b/doc/examples/biomodels/BIOMD0000000935/Ferrel2011.txt similarity index 98% rename from doc/examples/biomodels/Ferrel2011.txt rename to doc/examples/biomodels/BIOMD0000000935/Ferrel2011.txt index 68d1617d0..8edf188dd 100644 --- a/doc/examples/biomodels/Ferrel2011.txt +++ b/doc/examples/biomodels/BIOMD0000000935/Ferrel2011.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ferrel2011___Cdk1_and_APC_regulation_in_cell_cycle_in_Xenopus_laevis() // Compartments and Species: diff --git a/doc/examples/biomodels/Ferrel2011_V2.txt b/doc/examples/biomodels/BIOMD0000000936/Ferrel2011_V2.txt similarity index 98% rename from doc/examples/biomodels/Ferrel2011_V2.txt rename to doc/examples/biomodels/BIOMD0000000936/Ferrel2011_V2.txt index fbad3a049..0769774c8 100644 --- a/doc/examples/biomodels/Ferrel2011_V2.txt +++ b/doc/examples/biomodels/BIOMD0000000936/Ferrel2011_V2.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *ferrel2011___autonomous_biochemical_oscillator_in_cell_cycle_in_Xenopus_laevis_v2() // Compartments and Species: diff --git a/doc/examples/biomodels/Ferrel2011_V3.txt b/doc/examples/biomodels/BIOMD0000000937/Ferrel2011_V3.txt similarity index 99% rename from doc/examples/biomodels/Ferrel2011_V3.txt rename to doc/examples/biomodels/BIOMD0000000937/Ferrel2011_V3.txt index 612f59309..e454b9d24 100644 --- a/doc/examples/biomodels/Ferrel2011_V3.txt +++ b/doc/examples/biomodels/BIOMD0000000937/Ferrel2011_V3.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ferrel2011___Autonomous_biochemical_oscillator_in_regulation_of_CDK1__Plk1__and_APC_in_Xenopus_Laevis_cell_cycle() // Compartments and Species: diff --git a/doc/examples/biomodels/Gerard2013.txt b/doc/examples/biomodels/BIOMD0000000938/Gerard2013.txt similarity index 99% rename from doc/examples/biomodels/Gerard2013.txt rename to doc/examples/biomodels/BIOMD0000000938/Gerard2013.txt index 956724453..80044ac26 100644 --- a/doc/examples/biomodels/Gerard2013.txt +++ b/doc/examples/biomodels/BIOMD0000000938/Gerard2013.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Gerard2013___Model_3___Embryonic_type_eukaryotic_Cell_Cycle_regulation_based_on_negative_feedback_between_Cdk_cyclin_and_APC_and_competitive_inhibition_between_Cdk_cyclin_and_securin_for_polyubiquitylation_1() // Compartments and Species: diff --git a/doc/examples/biomodels/Iwamoto2010.txt b/doc/examples/biomodels/BIOMD0000000939/Iwamoto2010.txt similarity index 99% rename from doc/examples/biomodels/Iwamoto2010.txt rename to doc/examples/biomodels/BIOMD0000000939/Iwamoto2010.txt index 615eab092..5be6e44b3 100644 --- a/doc/examples/biomodels/Iwamoto2010.txt +++ b/doc/examples/biomodels/BIOMD0000000939/Iwamoto2010.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Iwamoto2010___Cell_cycle_reponse_to_DNA_damage() // Compartments and Species: diff --git a/doc/examples/biomodels/Tang2019.txt b/doc/examples/biomodels/BIOMD0000000940/Tang2019.txt similarity index 99% rename from doc/examples/biomodels/Tang2019.txt rename to doc/examples/biomodels/BIOMD0000000940/Tang2019.txt index 2da9d5e08..904b79a32 100644 --- a/doc/examples/biomodels/Tang2019.txt +++ b/doc/examples/biomodels/BIOMD0000000940/Tang2019.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Tang2019___Pharmacology_modelling_of_AURKB_and_ZAK_interaction_in_TNBC() // Compartments and Species: @@ -57,7 +57,7 @@ model *Tang2019___Pharmacology_modelling_of_AURKB_and_ZAK_interaction_in_TNBC() MAP2K4_Prod2: => MAP2K4; Cell*(k_map2k4*ZAK); TGFBR1_Prod: => TGFBR1; Cell*(k_tgfbr1*ZAK); TGFBR1_Degrad: TGFBR1 => ; Cell*kd_tgfbr1*TGFBR1; - BAD_Degrad2: BAD => ; Cell*(kd_bad*BAD*YWHAZ*BAD_Degrad2_const); + BAD_Degrad2: BAD => ; Cell*(kd_bad*BAD*YWHAZ*BAD_Degrad2_const_); PIK3R1_Prod: => PIK3R1; Cell*(k_pik3r1*YWHAZ); CSF1R_Prod: => CSF1R; Cell*(k_csf1r*PIK3R1); TGFBR1_Prod2: => TGFBR1; Cell*(k_tgfbr1*PIK3R1); @@ -68,7 +68,7 @@ model *Tang2019___Pharmacology_modelling_of_AURKB_and_ZAK_interaction_in_TNBC() CSF1R_Degrad: CSF1R => ; Cell*kd_csf1r*CSF1R; ATM_Prod3: => ATM; Cell*(k_atm*AURKB); PRKACA_Prod2: => PRKACA; Cell*(k_prkaca*AURKB); - TP53_Degrad2: TP53 => ; Cell*(kd_tp53*TP53*AURKB*TP53_Degrad2_const); + TP53_Degrad2: TP53 => ; Cell*(kd_tp53*TP53*AURKB*TP53_Degrad2_const_); // Species initializations: PKN1 = 0; @@ -136,8 +136,8 @@ model *Tang2019___Pharmacology_modelling_of_AURKB_and_ZAK_interaction_in_TNBC() kd_ywhaz = 0.072; k_tgfbr1 = 0.5; kd_tgfbr1 = 0.45; - BAD_Degrad2_const = 0.0133; - TP53_Degrad2_const = 0.0067; + BAD_Degrad2_const_ = 0.0133; + TP53_Degrad2_const_ = 0.0067; // Other declarations: const Cell, k_pkn1, kd_pkn1, k_zak, kd_zak, k_map2k3, kd_map2k3, k_mapk14; diff --git a/doc/examples/biomodels/gerard2010.txt b/doc/examples/biomodels/BIOMD0000000941/gerard2010.txt similarity index 99% rename from doc/examples/biomodels/gerard2010.txt rename to doc/examples/biomodels/BIOMD0000000941/gerard2010.txt index c7b091052..a5e7f4dec 100644 --- a/doc/examples/biomodels/gerard2010.txt +++ b/doc/examples/biomodels/BIOMD0000000941/gerard2010.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Gerard2010___Progression_of_mammalian_cell_cycle_by_successive_activation_of_various_cyclin_cdk_complexes() // Compartments and Species: diff --git a/doc/examples/biomodels/Sible2007.txt b/doc/examples/biomodels/BIOMD0000000942/Sible2007.txt similarity index 99% rename from doc/examples/biomodels/Sible2007.txt rename to doc/examples/biomodels/BIOMD0000000942/Sible2007.txt index cb455db1c..7225db044 100644 --- a/doc/examples/biomodels/Sible2007.txt +++ b/doc/examples/biomodels/BIOMD0000000942/Sible2007.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Sible2007___Mitotic_cell_cycle_mecanism_in_Xenopus_Laevis() // Compartments and Species: diff --git a/doc/examples/biomodels/Hat2016.txt b/doc/examples/biomodels/BIOMD0000000943/Hat2016.txt similarity index 99% rename from doc/examples/biomodels/Hat2016.txt rename to doc/examples/biomodels/BIOMD0000000943/Hat2016.txt index ac27cde04..33a56b660 100644 --- a/doc/examples/biomodels/Hat2016.txt +++ b/doc/examples/biomodels/BIOMD0000000943/Hat2016.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hat2016___Reponse_of_p53_System_to_irradiation_in_cell_fate_decision_making() // Compartments and Species: diff --git a/doc/examples/biomodels/Goldbeter2013.txt b/doc/examples/biomodels/BIOMD0000000944/Goldbeter2013.txt similarity index 99% rename from doc/examples/biomodels/Goldbeter2013.txt rename to doc/examples/biomodels/BIOMD0000000944/Goldbeter2013.txt index 0e6714f22..4a6d7dc68 100644 --- a/doc/examples/biomodels/Goldbeter2013.txt +++ b/doc/examples/biomodels/BIOMD0000000944/Goldbeter2013.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Goldbeter2013_Oscillatory_activity_of_cyclin_dependent_kinases_in_the_cell_cycle() // Compartments and Species: diff --git a/doc/examples/biomodels/Evans2004.txt b/doc/examples/biomodels/BIOMD0000000945/Evans2004.txt similarity index 99% rename from doc/examples/biomodels/Evans2004.txt rename to doc/examples/biomodels/BIOMD0000000945/Evans2004.txt index 797ead06c..daf6269dd 100644 --- a/doc/examples/biomodels/Evans2004.txt +++ b/doc/examples/biomodels/BIOMD0000000945/Evans2004.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Evans2004___Cell_based_mathematical_model_of_topotecan() // Compartments and Species: diff --git a/doc/examples/biomodels/Evans2005.txt b/doc/examples/biomodels/BIOMD0000000946/Evans2005.txt similarity index 99% rename from doc/examples/biomodels/Evans2005.txt rename to doc/examples/biomodels/BIOMD0000000946/Evans2005.txt index ee385a22f..8f06ba62a 100644 --- a/doc/examples/biomodels/Evans2005.txt +++ b/doc/examples/biomodels/BIOMD0000000946/Evans2005.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Evans2005___Compartmental_model_for_antineoplastic_drug_topotecan_in_breast_cancer_cells() // Compartments and Species: diff --git a/doc/examples/biomodels/Lee2017_Paracetamol_Metabolism.txt b/doc/examples/biomodels/BIOMD0000000947/Lee2017_Paracetamol_Metabolism.txt similarity index 99% rename from doc/examples/biomodels/Lee2017_Paracetamol_Metabolism.txt rename to doc/examples/biomodels/BIOMD0000000947/Lee2017_Paracetamol_Metabolism.txt index 87cd251f7..15ec6fb5d 100644 --- a/doc/examples/biomodels/Lee2017_Paracetamol_Metabolism.txt +++ b/doc/examples/biomodels/BIOMD0000000947/Lee2017_Paracetamol_Metabolism.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Lee2017___Paracetamol_first_pass_metabolism_PK_model() // Compartments and Species: diff --git a/doc/examples/biomodels/Landberg2009.txt b/doc/examples/biomodels/BIOMD0000000948/Landberg2009.txt similarity index 98% rename from doc/examples/biomodels/Landberg2009.txt rename to doc/examples/biomodels/BIOMD0000000948/Landberg2009.txt index 08b95bf98..6b54c1111 100644 --- a/doc/examples/biomodels/Landberg2009.txt +++ b/doc/examples/biomodels/BIOMD0000000948/Landberg2009.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Landberg2009___Alkylresorcinol_Dose_Response() // Compartments and Species: diff --git a/doc/examples/biomodels/Chitnis2008.txt b/doc/examples/biomodels/BIOMD0000000949/Chitnis2008.txt similarity index 99% rename from doc/examples/biomodels/Chitnis2008.txt rename to doc/examples/biomodels/BIOMD0000000949/Chitnis2008.txt index d012f600a..f56d27629 100644 --- a/doc/examples/biomodels/Chitnis2008.txt +++ b/doc/examples/biomodels/BIOMD0000000949/Chitnis2008.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Chitnis2008___Mathematical_model_of_malaria_transmission() // Compartments and Species: diff --git a/doc/examples/biomodels/Chitnis2012_model_1.txt b/doc/examples/biomodels/BIOMD0000000950/Chitnis2012_model_1.txt similarity index 99% rename from doc/examples/biomodels/Chitnis2012_model_1.txt rename to doc/examples/biomodels/BIOMD0000000950/Chitnis2012_model_1.txt index 926fe3e5b..f35fa29cd 100644 --- a/doc/examples/biomodels/Chitnis2012_model_1.txt +++ b/doc/examples/biomodels/BIOMD0000000950/Chitnis2012_model_1.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Chitnis2012___Model_Rift_Valley_Fever_transmission_between_cattle_and_mosquitoes__Model_1() // Compartments and Species: diff --git a/doc/examples/biomodels/Mitrophanov2015.txt b/doc/examples/biomodels/BIOMD0000000951/Mitrophanov2015.txt similarity index 99% rename from doc/examples/biomodels/Mitrophanov2015.txt rename to doc/examples/biomodels/BIOMD0000000951/Mitrophanov2015.txt index c45ce6017..614da5cde 100644 --- a/doc/examples/biomodels/Mitrophanov2015.txt +++ b/doc/examples/biomodels/BIOMD0000000951/Mitrophanov2015.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Mitrophanov2015___Simulating_extended_Hockin_Blood_Coagulation_Model_under_varied_pH() // Compartments and Species: diff --git a/doc/examples/biomodels/Rodenfels2019_V1.txt b/doc/examples/biomodels/BIOMD0000000952/Rodenfels2019_V1.txt similarity index 99% rename from doc/examples/biomodels/Rodenfels2019_V1.txt rename to doc/examples/biomodels/BIOMD0000000952/Rodenfels2019_V1.txt index 39096cf8e..e0ad58602 100644 --- a/doc/examples/biomodels/Rodenfels2019_V1.txt +++ b/doc/examples/biomodels/BIOMD0000000952/Rodenfels2019_V1.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Rodenfels2019___Heat_Oscillations_Driven_by_the_Embryonic_Cell_Cycle_Reveal_the_Energetic_Costs_of_Signaling() // Compartments and Species: diff --git a/doc/examples/biomodels/queralt2006_final.txt b/doc/examples/biomodels/BIOMD0000000953/queralt2006_final.txt similarity index 99% rename from doc/examples/biomodels/queralt2006_final.txt rename to doc/examples/biomodels/BIOMD0000000953/queralt2006_final.txt index b8923ddbd..46083ff35 100644 --- a/doc/examples/biomodels/queralt2006_final.txt +++ b/doc/examples/biomodels/BIOMD0000000953/queralt2006_final.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Queralt2006___Initiation_of_mitotic_exit_by_downregulation_of_PP2A_in_budding_yeast() // Compartments and Species: diff --git a/doc/examples/biomodels/Pandey2018_wildtype.txt b/doc/examples/biomodels/BIOMD0000000954/Pandey2018_wildtype.txt similarity index 99% rename from doc/examples/biomodels/Pandey2018_wildtype.txt rename to doc/examples/biomodels/BIOMD0000000954/Pandey2018_wildtype.txt index 828ad705e..aa26c3a3d 100644 --- a/doc/examples/biomodels/Pandey2018_wildtype.txt +++ b/doc/examples/biomodels/BIOMD0000000954/Pandey2018_wildtype.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Pandey2018_reversible_transition_between_quiescence_and_proliferation() // Compartments and Species: @@ -177,7 +177,7 @@ model *Pandey2018_reversible_transition_between_quiescence_and_proliferation() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = 1e-3 mole; unit extent = substance; unit substance_per_volume = 1e-3 mole / 1e-3 litre; diff --git a/doc/examples/biomodels/Giordano2020.txt b/doc/examples/biomodels/BIOMD0000000955/Giordano2020.txt similarity index 93% rename from doc/examples/biomodels/Giordano2020.txt rename to doc/examples/biomodels/BIOMD0000000955/Giordano2020.txt index 75aba44b1..6b6e6402b 100644 --- a/doc/examples/biomodels/Giordano2020.txt +++ b/doc/examples/biomodels/BIOMD0000000955/Giordano2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Giordano2020___SIDARTHE_model_of_COVID_19_spread_in_Italy() // Compartments and Species: @@ -22,12 +22,12 @@ model *Giordano2020___SIDARTHE_model_of_COVID_19_spread_in_Italy() Threatened_to_Healed: Threatened => Healed; Italy*sigma*Threatened; // Events: - Day_4: at 0 after time > 4, persistent=false: delta = 0.0057, gamma_ = 0.285, beta = 0.0057, alpha = 0.422; + Day_4: at 0 after time > 4, persistent=false: alpha = 0.422, beta = 0.0057, gamma_ = 0.285, delta = 0.0057; Day_12: at 0 after time > 12, persistent=false: epsilon = 0.143; - Day_22: at 0 after time > 22, persistent=false: eta = 0.034, zeta = 0.034, sigma = 0.017, xi = 0.017, kappa = 0.017, rho = 0.017, lambda = 0.08, nu = 0.015, mu = 0.008, delta = 0.005, gamma_ = 0.2, beta = 0.005, alpha = 0.36; - Day_28: at 0 after time > 28, persistent=false: gamma_ = 0.11, alpha = 0.21; - Day_38: at 0 after time > 38, persistent=false: kappa = 0.02, eta = 0.025, epsilon = 0.2, zeta = 0.025, sigma = 0.01, xi = 0.02, rho = 0.02; - Day_50: at 0 after time > 50, persistent=false: epsilon = 0.2*ModelValue_20 + 0.4*ModelValue_18 + 0.6*ModelValue_19, alpha = 0.209*ModelValue_21 + 0.252*ModelValue_16 + 0.105*ModelValue_17 + 0.42*ModelValue_19; + Day_22: at 0 after time > 22, persistent=false: alpha = 0.36, beta = 0.005, gamma_ = 0.2, delta = 0.005, mu = 0.008, nu = 0.015, lambda = 0.08, rho = 0.017, kappa = 0.017, xi = 0.017, sigma = 0.017, zeta = 0.034, eta = 0.034; + Day_28: at 0 after time > 28, persistent=false: alpha = 0.21, gamma_ = 0.11; + Day_38: at 0 after time > 38, persistent=false: rho = 0.02, xi = 0.02, sigma = 0.01, zeta = 0.025, epsilon = 0.2, eta = 0.025, kappa = 0.02; + Day_50: at 0 after time > 50, persistent=false: alpha = 0.209*ModelValue_21 + 0.252*ModelValue_16 + 0.105*ModelValue_17 + 0.42*ModelValue_19, epsilon = 0.2*ModelValue_20 + 0.4*ModelValue_18 + 0.6*ModelValue_19; // Species initializations: Susceptible = 0.9999963; @@ -114,7 +114,7 @@ model *Giordano2020___SIDARTHE_model_of_COVID_19_spread_in_Italy() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = item; unit unit_0 = 1 / (86400 second * item); unit unit_1 = 1 / 86400 second; diff --git a/doc/examples/biomodels/Bertozzi2020.txt b/doc/examples/biomodels/BIOMD0000000956/Bertozzi2020.txt similarity index 95% rename from doc/examples/biomodels/Bertozzi2020.txt rename to doc/examples/biomodels/BIOMD0000000956/Bertozzi2020.txt index 69086be8f..238c2b71a 100644 --- a/doc/examples/biomodels/Bertozzi2020.txt +++ b/doc/examples/biomodels/BIOMD0000000956/Bertozzi2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bertozzi2020___SIR_model_of_scenarios_of_COVID_19_spread_in_CA() // Compartments and Species: @@ -17,8 +17,8 @@ model *Bertozzi2020___SIR_model_of_scenarios_of_COVID_19_spread_in_CA() Infected_to_Recovered: Infected => Recovered; USA___CA__NY*gamma_*Infected; // Events: - Lockdown_start: at 0 after (ModelValue_14 == 1) && (time > (ModelValue_5*ModelValue_15 + ModelValue_6*ModelValue_17)): Ro_NY = Ro_NY/2, Ro_CA = Ro_CA/2; - Lockdown_end: at 0 after (ModelValue_14 == 1) && (time > (ModelValue_5*ModelValue_16 + ModelValue_6*ModelValue_18)): Ro_NY = ModelValue_8, Ro_CA = ModelValue_1; + Lockdown_start: at 0 after (ModelValue_14 == 1) && (time > (ModelValue_5*ModelValue_15 + ModelValue_6*ModelValue_17)): Ro_CA = Ro_CA/2, Ro_NY = Ro_NY/2; + Lockdown_end: at 0 after (ModelValue_14 == 1) && (time > (ModelValue_5*ModelValue_16 + ModelValue_6*ModelValue_18)): Ro_CA = ModelValue_1, Ro_NY = ModelValue_8; Peak_time_record_start: at 0 after rateOf(Infected) < 1e-12: Peak_Time = time; // Species initializations: @@ -79,7 +79,7 @@ model *Bertozzi2020___SIR_model_of_scenarios_of_COVID_19_spread_in_CA() unit length = metre; unit area = metre^2; unit volume = litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = item; unit extent = substance; unit substance_per_volume = item / litre; diff --git a/doc/examples/biomodels/Roda2020.txt b/doc/examples/biomodels/BIOMD0000000957/Roda2020.txt similarity index 99% rename from doc/examples/biomodels/Roda2020.txt rename to doc/examples/biomodels/BIOMD0000000957/Roda2020.txt index a912679ad..2ddcffce9 100644 --- a/doc/examples/biomodels/Roda2020.txt +++ b/doc/examples/biomodels/BIOMD0000000957/Roda2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Roda2020___SIR_model_of_COVID_19_spread_in_Wuhan() // Compartments and Species: diff --git a/doc/examples/biomodels/Ndairou2020.txt b/doc/examples/biomodels/BIOMD0000000958/Ndairou2020.txt similarity index 99% rename from doc/examples/biomodels/Ndairou2020.txt rename to doc/examples/biomodels/BIOMD0000000958/Ndairou2020.txt index 8f5efd071..688687566 100644 --- a/doc/examples/biomodels/Ndairou2020.txt +++ b/doc/examples/biomodels/BIOMD0000000958/Ndairou2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ndairou2020___early_stage_transmission_of_dynamics_of_COVID_19_in_Wuhan() // Compartments and Species: diff --git a/doc/examples/biomodels/Kok2020.txt b/doc/examples/biomodels/BIOMD0000000959/Kok2020.txt similarity index 99% rename from doc/examples/biomodels/Kok2020.txt rename to doc/examples/biomodels/BIOMD0000000959/Kok2020.txt index 570d6906b..5dbdb2de7 100644 --- a/doc/examples/biomodels/Kok2020.txt +++ b/doc/examples/biomodels/BIOMD0000000959/Kok2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kok2020___IFNalpha_induced_signaling_in_Huh7_5_cells() // Compartments and Species: diff --git a/doc/examples/biomodels/SBML_IFNa_Huh75 (1).txt b/doc/examples/biomodels/BIOMD0000000959/SBML_IFNa_Huh75 (1).txt similarity index 99% rename from doc/examples/biomodels/SBML_IFNa_Huh75 (1).txt rename to doc/examples/biomodels/BIOMD0000000959/SBML_IFNa_Huh75 (1).txt index 90d9d70e3..729b9d099 100644 --- a/doc/examples/biomodels/SBML_IFNa_Huh75 (1).txt +++ b/doc/examples/biomodels/BIOMD0000000959/SBML_IFNa_Huh75 (1).txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *IFNalpha_induced_signaling_in_Huh7_5_cells() // Compartments and Species: diff --git a/doc/examples/biomodels/Paiva2020.txt b/doc/examples/biomodels/BIOMD0000000960/Paiva2020.txt similarity index 97% rename from doc/examples/biomodels/Paiva2020.txt rename to doc/examples/biomodels/BIOMD0000000960/Paiva2020.txt index a8f59ff91..3a5db01fd 100644 --- a/doc/examples/biomodels/Paiva2020.txt +++ b/doc/examples/biomodels/BIOMD0000000960/Paiva2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Paiva2020___SEIAHRD_model_of_transmission_dynamics_of_COVID_19() // Compartments and Species: @@ -42,7 +42,7 @@ model *Paiva2020___SEIAHRD_model_of_transmission_dynamics_of_COVID_19() Cumulative_cases: => Cumulative_Cases; Country*(kappa_rho*Exposed); // Events: - event_: at 0 after time >= ModelValue_26: l_a_1_USA = l_a_2_USA, l_a_1_Spain = l_a_2_Spain, l_a_1_Italy = l_a_2_Italy, l_a_1_Germany = l_a_2_Germany, l_a_1_France = l_a_2_France, l_a_1_China = l_a_2_China, l_1_USA = l_2_USA, l_1_Spain = l_2_Spain, l_1_Italy = l_2_Italy, l_1_Germany = l_2_Germany, l_1_France = l_2_France, l_1_China = l_2_China, beta_1_USA = beta_2_USA, beta_1_Spain = beta_2_Spain, beta_1_Italy = beta_2_Italy, beta_1_Germany = beta_2_Germany, beta_1_France = beta_2_France, beta_1_China = beta_2_China; + event_: at 0 after time >= ModelValue_26: beta_1_China = beta_2_China, beta_1_France = beta_2_France, beta_1_Germany = beta_2_Germany, beta_1_Italy = beta_2_Italy, beta_1_Spain = beta_2_Spain, beta_1_USA = beta_2_USA, l_1_China = l_2_China, l_1_France = l_2_France, l_1_Germany = l_2_Germany, l_1_Italy = l_2_Italy, l_1_Spain = l_2_Spain, l_1_USA = l_2_USA, l_a_1_China = l_a_2_China, l_a_1_France = l_a_2_France, l_a_1_Germany = l_a_2_Germany, l_a_1_Italy = l_a_2_Italy, l_a_1_Spain = l_a_2_Spain, l_a_1_USA = l_a_2_USA; // Species initializations: Susceptible = 0.9*Total_pop; diff --git a/doc/examples/biomodels/McDougal2017.txt b/doc/examples/biomodels/BIOMD0000000961/McDougal2017.txt similarity index 99% rename from doc/examples/biomodels/McDougal2017.txt rename to doc/examples/biomodels/BIOMD0000000961/McDougal2017.txt index c8aaa1511..e6ba7f184 100644 --- a/doc/examples/biomodels/McDougal2017.txt +++ b/doc/examples/biomodels/BIOMD0000000961/McDougal2017.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 // Warnings from automatic translation: // Layout error: unable to add alias #7 for species 's1' to model, because it is not connected to any reactions. Antimony requires that all species and species aliases connect to some reaction. @@ -465,7 +465,7 @@ model *McDougal2017___Metabolism_in_ischemic_cardiomyocytes() re53 is "Glycogen Synthase I-form"; re56 is "Mitochondrial Oxidation of Pyruvate"; - # General layout options + // General layout options model.layout = on model.layout.size = {6000, 4000} model.layout.background = "#FFFFFFFF" @@ -2081,7 +2081,7 @@ model *McDougal2017___Metabolism_in_ischemic_cardiomyocytes() re48.s72.b1 = {0, 0} re48.s72.b2 = {0, 0} re48.s73.b1 = {0, 0} - re48.s73.b2 = {0, 0} + re48.s73.b2 = {0, 0} re48.s74.rxn_end = {2300, 930} re48.s74.b1 = {0, 0} re48.s74.b2 = {0, 0} diff --git a/doc/examples/biomodels/Zhao2020.txt b/doc/examples/biomodels/BIOMD0000000962/Zhao2020.txt similarity index 99% rename from doc/examples/biomodels/Zhao2020.txt rename to doc/examples/biomodels/BIOMD0000000962/Zhao2020.txt index 8d56777b4..7a0691aa6 100644 --- a/doc/examples/biomodels/Zhao2020.txt +++ b/doc/examples/biomodels/BIOMD0000000962/Zhao2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zhao2020___SUQC_model_of_COVID_19_transmission_dynamics_in_Wuhan__Hubei__and_China() // Compartments and Species: diff --git a/doc/examples/biomodels/Weitz2020.txt b/doc/examples/biomodels/BIOMD0000000963/Weitz2020.txt similarity index 96% rename from doc/examples/biomodels/Weitz2020.txt rename to doc/examples/biomodels/BIOMD0000000963/Weitz2020.txt index 7b3d1d579..f2da581e9 100644 --- a/doc/examples/biomodels/Weitz2020.txt +++ b/doc/examples/biomodels/BIOMD0000000963/Weitz2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Weitz2020___SIR_model_of_COVID_19_transmission_with_shielding() // Compartments and Species: @@ -10,7 +10,7 @@ model *Weitz2020___SIR_model_of_COVID_19_transmission_with_shielding() Infected_to_Recovered: Infected => Recovered; Country*Infected_to_Recovered_k1*Infected; // Events: - Simulation_end: at 0 after time == 199: Uninfected = Susceptible, Epidemic_size = Recovered; + Simulation_end: at 0 after time == 199: Epidemic_size = Recovered, Uninfected = Susceptible; // Species initializations: Susceptible = 0.999; diff --git a/doc/examples/biomodels/Mwalili2020.txt b/doc/examples/biomodels/BIOMD0000000964/Mwalili2020.txt similarity index 99% rename from doc/examples/biomodels/Mwalili2020.txt rename to doc/examples/biomodels/BIOMD0000000964/Mwalili2020.txt index 1a79476d2..a2dbb1dfd 100644 --- a/doc/examples/biomodels/Mwalili2020.txt +++ b/doc/examples/biomodels/BIOMD0000000964/Mwalili2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Mwalili2020___SEIR_model_of_COVID_19_transmission_and_environmental_pathogen_prevalence() // Compartments and Species: @@ -82,7 +82,7 @@ model *Mwalili2020___SEIR_model_of_COVID_19_transmission_and_environmental_patho unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = item; unit unit_0 = 1 / item; unit unit_1 = item / 86400 second; diff --git a/doc/examples/biomodels/LeBeau1999_Phosphorylation_CCK.txt b/doc/examples/biomodels/BIOMD0000000965/LeBeau1999_Phosphorylation_CCK.txt similarity index 99% rename from doc/examples/biomodels/LeBeau1999_Phosphorylation_CCK.txt rename to doc/examples/biomodels/BIOMD0000000965/LeBeau1999_Phosphorylation_CCK.txt index 8cedc87e2..3ce74b590 100644 --- a/doc/examples/biomodels/LeBeau1999_Phosphorylation_CCK.txt +++ b/doc/examples/biomodels/BIOMD0000000965/LeBeau1999_Phosphorylation_CCK.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *LeBeau1999___IP3_dependent_intracellular_calcium_oscillations_due_to_agonist_stimulation_from_Cholecytokinin() // Compartments and Species: @@ -97,7 +97,7 @@ model *LeBeau1999___IP3_dependent_intracellular_calcium_oscillations_due_to_agon k_1 is "k-1"; Jinflux_0 is "Jinflux"; - # General layout options + // General layout options model.layout = on model.layout.size = {10, 10} model.layout.background = "#FFFFFFFF" diff --git a/doc/examples/biomodels/Cui2008.txt b/doc/examples/biomodels/BIOMD0000000966/Cui2008.txt similarity index 99% rename from doc/examples/biomodels/Cui2008.txt rename to doc/examples/biomodels/BIOMD0000000966/Cui2008.txt index 9369a0c2a..2e9ce555e 100644 --- a/doc/examples/biomodels/Cui2008.txt +++ b/doc/examples/biomodels/BIOMD0000000966/Cui2008.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 // Warnings from automatic translation: // Layout error in model: unable to draw an arc between the species 'Zn_2' and the reaction 'Formation_of_the_Zn4Zur_complex': 'Zn_2' is not a participant in that reaction. @@ -61,7 +61,7 @@ model *Cui2008___in_vitro_transcriptional_response_of_zinc_homeostasis_system_in unit length = metre; unit area = metre^2; unit volume = litre; - unit time_unit = time_unit; + unit time_unit = 60 second; unit substance = 1e-9 mole; unit unit_0 = litre^2 / ((1e-9 mole)^2 * second); unit unit_1 = 1 / second; @@ -83,7 +83,7 @@ model *Cui2008___in_vitro_transcriptional_response_of_zinc_homeostasis_system_in Formation_of_transcription_initiation_complex is "Formation of transcription initiation complex"; Disassociation_of_transcription_initiation_complex is "Disassociation of transcription initiation complex"; - # General layout options + // General layout options model.layout = on model.layout.size = {135.25, 88.11} model.layout.background = "#FFFFFFFF" diff --git a/doc/examples/biomodels/McLean1991.txt b/doc/examples/biomodels/BIOMD0000000967/McLean1991.txt similarity index 99% rename from doc/examples/biomodels/McLean1991.txt rename to doc/examples/biomodels/BIOMD0000000967/McLean1991.txt index 1d8702e67..aafb2af6e 100644 --- a/doc/examples/biomodels/McLean1991.txt +++ b/doc/examples/biomodels/BIOMD0000000967/McLean1991.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *McLean1991___Behaviour_of_HIV_in_the_presence_of_zidovudine() // Compartments and Species: @@ -50,7 +50,7 @@ model *McLean1991___Behaviour_of_HIV_in_the_presence_of_zidovudine() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = item; unit unit_0 = 1 / dimensionless^-0; unit extent = substance; @@ -70,7 +70,7 @@ model *McLean1991___Behaviour_of_HIV_in_the_presence_of_zidovudine() V_Death is "V Death"; V_Creation is "V Creation"; - # General layout options + // General layout options model.layout = on model.layout.size = {399.09, 492.5} model.layout.background = "#FFFFFFFF" diff --git a/doc/examples/biomodels/Palmer2008.txt b/doc/examples/biomodels/BIOMD0000000968/Palmer2008.txt similarity index 99% rename from doc/examples/biomodels/Palmer2008.txt rename to doc/examples/biomodels/BIOMD0000000968/Palmer2008.txt index f852297fc..32c35558a 100644 --- a/doc/examples/biomodels/Palmer2008.txt +++ b/doc/examples/biomodels/BIOMD0000000968/Palmer2008.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Palmer2008_Negative_Feedback_in_IL_7_mediated_Jak_Stat_signaling() // Compartments and Species: @@ -65,7 +65,7 @@ model *Palmer2008_Negative_Feedback_in_IL_7_mediated_Jak_Stat_signaling() unit length = metre; unit area = metre^2; unit volume = litre; - unit time_unit = time_unit; + unit time_unit = 60 second; unit substance = 1e-9 mole; unit extent = substance; unit substance_per_volume = 1e-9 mole / litre; diff --git a/doc/examples/biomodels/Cuadros2020.txt b/doc/examples/biomodels/BIOMD0000000969/Cuadros2020.txt similarity index 99% rename from doc/examples/biomodels/Cuadros2020.txt rename to doc/examples/biomodels/BIOMD0000000969/Cuadros2020.txt index 0f6825676..c1d37a798 100644 --- a/doc/examples/biomodels/Cuadros2020.txt +++ b/doc/examples/biomodels/BIOMD0000000969/Cuadros2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Cuadros2020___SIHRD_spatiotemporal_model_of_COVID_19_transmission_in_Ohio() // Compartments and Species: @@ -220,7 +220,7 @@ model *Cuadros2020___SIHRD_spatiotemporal_model_of_COVID_19_transmission_in_Ohio unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = item; unit extent = substance; unit substance_per_volume = item / 1e-3 litre; diff --git a/doc/examples/biomodels/Hou2020.txt b/doc/examples/biomodels/BIOMD0000000970/Hou2020.txt similarity index 98% rename from doc/examples/biomodels/Hou2020.txt rename to doc/examples/biomodels/BIOMD0000000970/Hou2020.txt index c7d3a310f..be32a0cff 100644 --- a/doc/examples/biomodels/Hou2020.txt +++ b/doc/examples/biomodels/BIOMD0000000970/Hou2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hou2020___SEIR_model_of_COVID_19_transmission_in_Wuhan() // Compartments and Species: @@ -42,7 +42,7 @@ model *Hou2020___SEIR_model_of_COVID_19_transmission_in_Wuhan() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = item; unit extent = substance; unit substance_per_volume = item / 1e-3 litre; diff --git a/doc/examples/biomodels/BIOMD0000000971/Tang2020.txt b/doc/examples/biomodels/BIOMD0000000971/Tang2020.txt new file mode 100644 index 000000000..d9296b1f7 --- /dev/null +++ b/doc/examples/biomodels/BIOMD0000000971/Tang2020.txt @@ -0,0 +1,173 @@ +// Created by libAntimony v3.2.0 +model *Tang2020___Estimation_of_transmission_risk_of_COVID_19_and_impact_of_public_health_interventions() + + // Compartments and Species: + compartment Wuhan; + species Susceptible in Wuhan, Exposed in Wuhan, Infected in Wuhan, Asymptomatic in Wuhan; + species Susceptible_quarantined in Wuhan, Exposed_quarantined in Wuhan; + species Hospitalised in Wuhan, Recovered in Wuhan; + + // Assignment Rules: + Infected_0 := Infected + Asymptomatic; + + // Reactions: + Susceptible_to_Exposed: Susceptible => Exposed; Wuhan*(beta*c*(1 - q)*Susceptible*(Infected + theta*Asymptomatic)); + Susceptible_to_Susceptible_quarantined: Susceptible => Susceptible_quarantined; Wuhan*(c*q*(1 - beta)*Susceptible*(Infected + theta*Asymptomatic)); + Quarantined_to_Susceptible: Susceptible_quarantined => Susceptible; Wuhan*lambda*Susceptible_quarantined; + Exposed_to_Infected: Exposed => Infected; Wuhan*(sigma*rho*Exposed); + Exposed_to_Asymptomatic: Exposed => Asymptomatic; Wuhan*(sigma*(1 - rho)*Exposed); + Infected_to_Hospitalised: Infected => Hospitalised; Wuhan*delta_I*Infected; + Infected_to_Recovered: Infected => Recovered; Wuhan*gamma_I*Infected; + Asymptomatic_to_Recovered: Asymptomatic => Recovered; Wuhan*gamma_A*Asymptomatic; + Hospitalised_to_Recovered: Hospitalised => Recovered; Wuhan*gamma_H*Hospitalised; + Infected_to_Deceased: Infected => ; Wuhan*alpha*Infected; + Hospitalised_to_Deceased: Hospitalised => ; Wuhan*alpha*Hospitalised; + Susceptible_to_Exposed_quarantined: Susceptible => Exposed_quarantined; Wuhan*(beta*c*q*Susceptible*(Infected + theta*Asymptomatic)); + Exposed_quarantined_to_Hospitalised: Exposed_quarantined => Hospitalised; Wuhan*delta_q*Exposed_quarantined; + + // Events: + Lockdown: at 0 after time > 9, persistent=false: c = c_lockdown, q = q_lockdown; + + // Species initializations: + Susceptible = 11081000; + Susceptible has substance_per_volume; + Exposed = 105.1; + Exposed has substance_per_volume; + Infected = 27.679; + Infected has substance_per_volume; + Asymptomatic = 53.539; + Asymptomatic has substance_per_volume; + Susceptible_quarantined = 739; + Susceptible_quarantined has substance_per_volume; + Exposed_quarantined = 1.1642; + Exposed_quarantined has substance_per_volume; + Hospitalised = 1; + Hospitalised has substance_per_volume; + Recovered = 2; + Recovered has substance_per_volume; + + // Compartment initializations: + Wuhan = 1; + Wuhan has volume; + + // Variable initializations: + c = 14.781; + c_lockdown = 14.781; + q = 1.8887e-07; + q_lockdown = 1.8887e-07; + beta = 2.1011e-08; + sigma = 0.142857; + lambda = 0.0714285; + rho = 0.86834; + delta_I = 0.13266; + delta_q = 0.1259; + gamma_I = 0.33029; + gamma_A = 0.13978; + gamma_H = 0.11624; + alpha = 1.7826e-05; + theta = 1; + + // Other declarations: + var c, q, Infected_0; + const Wuhan, c_lockdown, q_lockdown, beta, sigma, lambda, rho, delta_I; + const delta_q, gamma_I, gamma_A, gamma_H, alpha, theta; + + // Unit definitions: + unit length = metre; + unit area = metre^2; + unit volume = 1e-3 litre; + unit time_unit = 86400 second; + unit substance = item; + unit extent = substance; + unit substance_per_volume = item / 1e-3 litre; + + // Display Names: + time_unit is "time"; + Infected_0 is "Infected"; + + // CV terms: + Wuhan identity "http://identifiers.org/ncit/C25632" + Wuhan isPartOf "http://identifiers.org/ncit/C16428" + Susceptible identity "http://identifiers.org/ido/0000514" + Susceptible isVersionOf "http://identifiers.org/ncit/C171133" + Exposed identity "http://identifiers.org/ido/0000514" + Exposed isVersionOf "http://identifiers.org/ncit/C171133" + Exposed hasProperty "http://identifiers.org/ido/0000597" + Infected identity "http://identifiers.org/ido/0000511" + Infected isVersionOf "http://identifiers.org/ncit/C171133" + Asymptomatic identity "http://identifiers.org/ido/0000569" + Asymptomatic identity "http://identifiers.org/ido/0000511" + Asymptomatic isVersionOf "http://identifiers.org/ncit/C171133" + Susceptible_quarantined identity "http://identifiers.org/ncit/C71902" + Susceptible_quarantined identity "http://identifiers.org/ido/0000514" + Susceptible_quarantined isVersionOf "http://identifiers.org/ncit/C171133" + Exposed_quarantined identity "http://identifiers.org/ncit/C71902" + Exposed_quarantined identity "http://identifiers.org/ido/0000514" + Exposed_quarantined isVersionOf "http://identifiers.org/ncit/C171133" + Exposed_quarantined hasProperty "http://identifiers.org/ido/0000597" + Hospitalised isVersionOf "http://identifiers.org/ido/0000511" + Hospitalised isVersionOf "http://identifiers.org/ncit/C171133" + Hospitalised hasProperty "http://identifiers.org/ncit/C25179" + Recovered hasProperty "http://identifiers.org/ido/0000621" + Susceptible_to_Exposed identity "http://identifiers.org/ido/0000597" + Susceptible_to_Exposed isVersionOf "http://identifiers.org/ncit/C171133" + Susceptible_to_Susceptible_quarantined identity "http://identifiers.org/ncit/C71902" + Susceptible_to_Susceptible_quarantined isVersionOf "http://identifiers.org/ncit/C171133" + Exposed_to_Infected identity "http://identifiers.org/ncit/C171133" + Exposed_to_Asymptomatic identity "http://identifiers.org/ncit/C168121" + Exposed_to_Asymptomatic identity "http://identifiers.org/ncit/C171133" + Infected_to_Hospitalised identity "http://identifiers.org/ncit/C25179" + Infected_to_Hospitalised isVersionOf "http://identifiers.org/ncit/C171133" + Infected_to_Recovered identity "http://identifiers.org/ncit/C25746" + Asymptomatic_to_Recovered identity "http://identifiers.org/ncit/C25746" + Hospitalised_to_Recovered identity "http://identifiers.org/ncit/C25746" + Infected_to_Deceased identity "http://identifiers.org/ncit/C28554" + Infected_to_Deceased isVersionOf "http://identifiers.org/ncit/C171133" + Hospitalised_to_Deceased identity "http://identifiers.org/ncit/C28554" + Hospitalised_to_Deceased isVersionOf "http://identifiers.org/ncit/C171133" + Susceptible_to_Exposed_quarantined identity "http://identifiers.org/ncit/C71902" + Susceptible_to_Exposed_quarantined identity "http://identifiers.org/ido/0000597" + Susceptible_to_Exposed_quarantined isVersionOf "http://identifiers.org/ncit/C171133" + Exposed_quarantined_to_Hospitalised identity "http://identifiers.org/ncit/C25179" + Exposed_quarantined_to_Hospitalised isVersionOf "http://identifiers.org/ncit/C171133" + + model model_source "http://identifiers.org/biomodels.db/MODEL2011020001", + "http://identifiers.org/biomodels.db/BIOMD0000000971" + model identity "http://identifiers.org/doid/DOID:0080600" + model hasTaxon "http://identifiers.org/taxonomy/9606" + model hasTaxon "http://identifiers.org/taxonomy/2697049" + model isDescribedBy "http://identifiers.org/pubmed/32046137" + model hasProperty "http://identifiers.org/mamo/MAMO_0000028" + model created "2020-10-30T01:31:09Z" + model modified "2020-10-30T01:31:09Z" + model creator1.givenName "Kausthubh" + model creator1.familyName "Ramachandran" + model creator1.organization "EMBL-EBI" + model creator1.email "kramachandran@ebi.ac.uk" + + // Notes: + model notes ``` +Since the emergence of the first cases in Wuhan, China, the novel coronavirus (2019-nCoV) +infection has been quickly spreading out to other provinces and neighboring countries. +Estimation of the basic reproduction number by means of mathematical modeling can +be helpful for determining the potential and severity of an outbreak and providing +critical information for identifying the type of disease interventions and intensity. +A deterministic compartmental model was devised based on the clinical progression +of the disease, epidemiological status of the individuals, and intervention measures. +The estimations based on likelihood and model analysis show that the control reproduction +number may be as high as 6.47 (95% CI 5.71–7.23). Sensitivity analyses show that +interventions, such as intensive contact tracing followed by quarantine and isolation, +can effectively reduce the control reproduction number and transmission risk, with +the effect of travel restriction adopted by Wuhan on 2019-nCoV infection in Beijing +being almost equivalent to increasing quarantine by a 100 thousand baseline value. +It is essential to assess how the expensive, resource-intensive measures implemented +by the Chinese authorities can contribute to the prevention and control of the 2019-nCoV +infection, and how long they should be maintained. Under the most restrictive measures, +the outbreak is expected to peak within two weeks (since 23 January 2020) with a +significant low peak value. With travel restriction (no imported exposed individuals +to Beijing), the number of infected individuals in seven days will decrease by 91.14% +in Beijing, compared with the scenario of no travel restriction. +``` +end + +Tang2020___Estimation_of_transmission_risk_of_COVID_19_and_impact_of_public_health_interventions is "Tang2020 - Estimation of transmission risk of COVID-19 and impact of public health interventions" diff --git a/doc/examples/biomodels/Tang2020.txt b/doc/examples/biomodels/BIOMD0000000972/Tang2020.txt similarity index 99% rename from doc/examples/biomodels/Tang2020.txt rename to doc/examples/biomodels/BIOMD0000000972/Tang2020.txt index 71ba13789..f3941def9 100644 --- a/doc/examples/biomodels/Tang2020.txt +++ b/doc/examples/biomodels/BIOMD0000000972/Tang2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Tang2020___Estimation_of_transmission_risk_of_COVID_19_and_impact_of_public_health_interventions___update() // Compartments and Species: @@ -80,7 +80,7 @@ model *Tang2020___Estimation_of_transmission_risk_of_COVID_19_and_impact_of_publ unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = item; unit extent = substance; unit substance_per_volume = item / 1e-3 litre; diff --git a/doc/examples/biomodels/Dasgupta2020.txt b/doc/examples/biomodels/BIOMD0000000973/Dasgupta2020.txt similarity index 98% rename from doc/examples/biomodels/Dasgupta2020.txt rename to doc/examples/biomodels/BIOMD0000000973/Dasgupta2020.txt index 7567a9ccb..fd11fdcbc 100644 --- a/doc/examples/biomodels/Dasgupta2020.txt +++ b/doc/examples/biomodels/BIOMD0000000973/Dasgupta2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Dasgupta2020___Reduced_model_of_receptor_clusturing_and_aggregation() // Compartments and Species: diff --git a/doc/examples/biomodels/Carcione2020.txt b/doc/examples/biomodels/BIOMD0000000974/Carcione2020.txt similarity index 99% rename from doc/examples/biomodels/Carcione2020.txt rename to doc/examples/biomodels/BIOMD0000000974/Carcione2020.txt index 17c06f342..86ad6ad11 100644 --- a/doc/examples/biomodels/Carcione2020.txt +++ b/doc/examples/biomodels/BIOMD0000000974/Carcione2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Carcione2020___Deterministic_SEIR_simulation_of_a_COVID_19_outbreak() // Compartments and Species: @@ -48,7 +48,7 @@ model *Carcione2020___Deterministic_SEIR_simulation_of_a_COVID_19_outbreak() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = item; unit extent = substance; unit substance_per_volume = item / 1e-3 litre; diff --git a/doc/examples/biomodels/Leloup2004_CircadianRhythmsSet4.txt b/doc/examples/biomodels/BIOMD0000000975/Leloup2004_CircadianRhythmsSet4.txt similarity index 99% rename from doc/examples/biomodels/Leloup2004_CircadianRhythmsSet4.txt rename to doc/examples/biomodels/BIOMD0000000975/Leloup2004_CircadianRhythmsSet4.txt index 8e160cf2d..a55249edb 100644 --- a/doc/examples/biomodels/Leloup2004_CircadianRhythmsSet4.txt +++ b/doc/examples/biomodels/BIOMD0000000975/Leloup2004_CircadianRhythmsSet4.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Leloup2004_CircadianRhythms() // Compartments and Species: @@ -338,7 +338,7 @@ model *Leloup2004_CircadianRhythms() Non_specific_degradation_of_BMAL1_P_protein_in_nucleus is "Non-specific degradation of BMAL1-P protein in nucleus"; Non_specific_degradation_of_PER_CRY_BMAL1_CLOCK_complex_in_nucleus is "Non-specific degradation of PER-CRY-BMAL1-CLOCK complex in nucleus"; - # General layout options + // General layout options model.layout = on model.layout.size = {139.59, 87.63} model.layout.background = "#FFFFFFFF" diff --git a/doc/examples/biomodels/Leloup2004_Set1.txt b/doc/examples/biomodels/BIOMD0000000975/Leloup2004_Set1.txt similarity index 99% rename from doc/examples/biomodels/Leloup2004_Set1.txt rename to doc/examples/biomodels/BIOMD0000000975/Leloup2004_Set1.txt index a43387f2c..7da21d596 100644 --- a/doc/examples/biomodels/Leloup2004_Set1.txt +++ b/doc/examples/biomodels/BIOMD0000000975/Leloup2004_Set1.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Leloup2004___Mammalian_Circadian_Rhythm_models_for_23_8_and_24_2_hours_timeperiod() // Compartments and Species: diff --git a/doc/examples/biomodels/Ghanbari2020.txt b/doc/examples/biomodels/BIOMD0000000976/Ghanbari2020.txt similarity index 98% rename from doc/examples/biomodels/Ghanbari2020.txt rename to doc/examples/biomodels/BIOMD0000000976/Ghanbari2020.txt index c0d4583f3..1964e6b8a 100644 --- a/doc/examples/biomodels/Ghanbari2020.txt +++ b/doc/examples/biomodels/BIOMD0000000976/Ghanbari2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ghanbari2020___forecasting_the_second_wave_of_COVID_19_in_Iran() // Compartments and Species: @@ -48,7 +48,7 @@ model *Ghanbari2020___forecasting_the_second_wave_of_COVID_19_in_Iran() unit length = 1 / dimensionless^-0; unit area = 1 / dimensionless^-0; unit volume = 1 / dimensionless^-0; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = item; unit extent = substance; unit substance_per_volume = item / dimensionless^0; diff --git a/doc/examples/biomodels/Sarkar2020.txt b/doc/examples/biomodels/BIOMD0000000977/Sarkar2020.txt similarity index 99% rename from doc/examples/biomodels/Sarkar2020.txt rename to doc/examples/biomodels/BIOMD0000000977/Sarkar2020.txt index 250df39af..415c74f28 100644 --- a/doc/examples/biomodels/Sarkar2020.txt +++ b/doc/examples/biomodels/BIOMD0000000977/Sarkar2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Sarkar2020___SAIR_model_of_COVID_19_transmission_with_quarantine_measures_in_India() // Compartments and Species: @@ -68,7 +68,7 @@ model *Sarkar2020___SAIR_model_of_COVID_19_transmission_with_quarantine_measures unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = item; unit extent = substance; unit substance_per_volume = item / 1e-3 litre; diff --git a/doc/examples/biomodels/Mukandavire2020.txt b/doc/examples/biomodels/BIOMD0000000978/Mukandavire2020.txt similarity index 98% rename from doc/examples/biomodels/Mukandavire2020.txt rename to doc/examples/biomodels/BIOMD0000000978/Mukandavire2020.txt index 128ef82d9..c406f8dbe 100644 --- a/doc/examples/biomodels/Mukandavire2020.txt +++ b/doc/examples/biomodels/BIOMD0000000978/Mukandavire2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Mukandavire2020___SEIR_model_of_early_COVID_19_transmission_in_South_Africa() // Compartments and Species: @@ -47,7 +47,7 @@ model *Mukandavire2020___SEIR_model_of_early_COVID_19_transmission_in_South_Afri unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = item; unit extent = substance; unit substance_per_volume = item / 1e-3 litre; diff --git a/doc/examples/biomodels/BIOMD0000000979/Malkov2020.txt b/doc/examples/biomodels/BIOMD0000000979/Malkov2020.txt new file mode 100644 index 000000000..f3c285069 --- /dev/null +++ b/doc/examples/biomodels/BIOMD0000000979/Malkov2020.txt @@ -0,0 +1,111 @@ +// Created by libAntimony v3.2.0 +model *Malkov2020___SEIRS_model_of_COVID_19_transmission_with_reinfection() + + // Compartments and Species: + compartment USA; + species Susceptible in USA, Total_population in USA, Recovered in USA, Exposed in USA; + species Infected in USA; + + // Assignment Rules: + beta := gamma_*R_fixed; + Fraction_infected := Infected/Total_population; + + // Reactions: + Susceptible_to_Exposed: Susceptible => Exposed; USA*(beta*Susceptible*Infected/Total_population); + Exposed_to_Infected: Exposed => Infected; USA*sigma*Exposed; + Infected_to_Recovered: Infected => Recovered; USA*gamma_*Infected; + Recovered_to_Susceptible__Reinfection: Recovered => Susceptible; USA*omega*Recovered; + + // Species initializations: + Susceptible = Total_population - Recovered - Exposed - Infected; + Susceptible has substance_per_volume; + Total_population = 330052960; + Total_population has substance_per_volume; + Recovered = 0; + Recovered has substance_per_volume; + Exposed = 14439817; + Exposed has substance_per_volume; + Infected = 330052.96; + Infected has substance_per_volume; + + // Compartment initializations: + USA = 1; + USA has volume; + + // Variable initializations: + gamma_ = 0.05556; + R_fixed = 3; + omega = 0.01667; + sigma = 0.19231; + + // Other declarations: + var beta, Fraction_infected; + const USA, gamma_, R_fixed, omega, sigma; + + // Unit definitions: + unit length = 1 / dimensionless^-0; + unit area = 1 / dimensionless^-0; + unit volume = 1 / dimensionless^-0; + unit time_unit = 86400 second; + unit substance = item; + unit extent = substance; + unit substance_per_volume = item / dimensionless^0; + + // Display Names: + time_unit is "time"; + gamma_ is "gamma"; + Recovered_to_Susceptible__Reinfection is "Recovered_to_Susceptible_(Reinfection)"; + + // CV terms: + USA identity "http://identifiers.org/ncit/C17234" + Susceptible identity "http://identifiers.org/ido/0000514" + Recovered identity "http://identifiers.org/ido/0000514" + Recovered hasProperty "http://identifiers.org/ido/0000569" + Exposed identity "http://identifiers.org/ncit/C171133" + Exposed identity "http://identifiers.org/ido/0000514" + Exposed hasProperty "http://identifiers.org/ido/0000597" + Infected identity "http://identifiers.org/ncit/C171133" + Infected identity "http://identifiers.org/ido/0000511" + Susceptible_to_Exposed identity "http://identifiers.org/ido/0000597" + Susceptible_to_Exposed identity "http://identifiers.org/ncit/C171133" + Exposed_to_Infected identity "http://identifiers.org/ncit/C171133" + Infected_to_Recovered identity "http://identifiers.org/ncit/C25746" + Recovered_to_Susceptible__Reinfection identity "http://identifiers.org/ncit/C16710" + Recovered_to_Susceptible__Reinfection identity "http://identifiers.org/ncit/C25559" + + model identity "http://identifiers.org/doid/DOID:0080600" + model hasTaxon "http://identifiers.org/taxonomy/2697049" + model hasTaxon "http://identifiers.org/taxonomy/9606" + model isDescribedBy "http://identifiers.org/pubmed/32982082" + model hasProperty "http://identifiers.org/mamo/MAMO_0000046" + model created "2020-12-04T01:05:32Z" + model modified "2022-10-17T13:05:25Z" + model creator1.givenName "Kausthubh" + model creator1.familyName "Ramachandran" + model creator1.organization "EMBL-EBI" + model creator1.email "kramachandran@ebi.ac.uk" + model creator2.givenName "Matthias" + model creator2.familyName "König" + model creator2.organization "Humboldt-University Berlin" + model creator2.email "koenigmx@hu-berlin.de" + + // Notes: + model notes ``` +Epidemiological models of COVID-19 transmission assume that recovered individuals +have a fully protected immunity. To date, there is no definite answer about whether +people who recover from COVID-19 can be reinfected with the severe acute respiratory +syndrome coronavirus 2 (SARS-CoV-2). In the absence of a clear answer about the risk +of reinfection, it is instructive to consider the possible scenarios. To study the +epidemiological dynamics with the possibility of reinfection, I use a Susceptible-Exposed-Infectious-Resistant-Susceptible +model with the time-varying transmission rate. I consider three different ways of +modeling reinfection. The crucial feature of this study is that I explore both the +difference between the reinfection and no-reinfection scenarios and how the mitigation +measures affect this difference. The principal results are the following. First, +the dynamics of the reinfection and no-reinfection scenarios are indistinguishable +before the infection peak. Second, the mitigation measures delay not only the infection +peak, but also the moment when the difference between the reinfection and no-reinfection +scenarios becomes prominent. These results are robust to various modeling assumptions. +``` +end + +Malkov2020___SEIRS_model_of_COVID_19_transmission_with_reinfection is "Malkov2020 - SEIRS model of COVID-19 transmission with reinfection" diff --git a/doc/examples/biomodels/Malkov2020.txt b/doc/examples/biomodels/BIOMD0000000980/Malkov2020.txt similarity index 98% rename from doc/examples/biomodels/Malkov2020.txt rename to doc/examples/biomodels/BIOMD0000000980/Malkov2020.txt index 998d68e07..45a4a64fe 100644 --- a/doc/examples/biomodels/Malkov2020.txt +++ b/doc/examples/biomodels/BIOMD0000000980/Malkov2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Malkov2020___SEIRS_model_of_COVID_19_transmission_with_reinfection() // Compartments and Species: @@ -53,7 +53,7 @@ model *Malkov2020___SEIRS_model_of_COVID_19_transmission_with_reinfection() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = item; unit extent = substance; unit substance_per_volume = item / 1e-3 litre; diff --git a/doc/examples/biomodels/Wan2020.txt b/doc/examples/biomodels/BIOMD0000000981/Wan2020.txt similarity index 99% rename from doc/examples/biomodels/Wan2020.txt rename to doc/examples/biomodels/BIOMD0000000981/Wan2020.txt index 0aed79cc3..a03e250ca 100644 --- a/doc/examples/biomodels/Wan2020.txt +++ b/doc/examples/biomodels/BIOMD0000000981/Wan2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wan2020___risk_estimation_and_prediction_of_the_transmission_of_COVID_19_in_maninland_China_excluding_Hubei_province() // Compartments and Species: @@ -89,7 +89,7 @@ model *Wan2020___risk_estimation_and_prediction_of_the_transmission_of_COVID_19_ unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = item; unit extent = substance; unit substance_per_volume = item / 1e-3 litre; diff --git a/doc/examples/biomodels/Law2020.txt b/doc/examples/biomodels/BIOMD0000000982/Law2020.txt similarity index 98% rename from doc/examples/biomodels/Law2020.txt rename to doc/examples/biomodels/BIOMD0000000982/Law2020.txt index 48cf4dfd2..35a13ebcc 100644 --- a/doc/examples/biomodels/Law2020.txt +++ b/doc/examples/biomodels/BIOMD0000000982/Law2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Law2020___SIR_model_of_COVID_19_transmission_in_Malyasia_with_time_varying_parameters() // Compartments and Species: @@ -43,7 +43,7 @@ model *Law2020___SIR_model_of_COVID_19_transmission_in_Malyasia_with_time_varyin unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = item; unit extent = substance; unit substance_per_volume = item / 1e-3 litre; diff --git a/doc/examples/biomodels/Zongo2020.txt b/doc/examples/biomodels/BIOMD0000000983/Zongo2020.txt similarity index 98% rename from doc/examples/biomodels/Zongo2020.txt rename to doc/examples/biomodels/BIOMD0000000983/Zongo2020.txt index 627ac137a..c74100228 100644 --- a/doc/examples/biomodels/Zongo2020.txt +++ b/doc/examples/biomodels/BIOMD0000000983/Zongo2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zongo2020___model_of_COVID_19_transmission_dynamics_under_containement_measures_in_France() // Compartments and Species: @@ -24,8 +24,8 @@ model *Zongo2020___model_of_COVID_19_transmission_dynamics_under_containement_me // Events: Phase_1: at 0 after time > tau_1, persistent=false: m_t_phase_1 = 1; - Phase_2: at 0 after time > tau_2, persistent=false: m_t_phase_2 = 1, m_t_phase_1 = 0; - Phase_3: at 0 after time > tau_3, persistent=false: m_t_phase_3 = 1, m_t_phase_2 = 0; + Phase_2: at 0 after time > tau_2, persistent=false: m_t_phase_1 = 0, m_t_phase_2 = 1; + Phase_3: at 0 after time > tau_3, persistent=false: m_t_phase_2 = 0, m_t_phase_3 = 1; End_phase: at 0 after time > tau_f, persistent=false: m_t_phase_3 = 0; // Species initializations: @@ -77,7 +77,7 @@ model *Zongo2020___model_of_COVID_19_transmission_dynamics_under_containement_me unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = item; unit extent = substance; unit substance_per_volume = item / 1e-3 litre; diff --git a/doc/examples/biomodels/Fang2020.txt b/doc/examples/biomodels/BIOMD0000000984/Fang2020.txt similarity index 98% rename from doc/examples/biomodels/Fang2020.txt rename to doc/examples/biomodels/BIOMD0000000984/Fang2020.txt index 9aef59ea7..e2222b841 100644 --- a/doc/examples/biomodels/Fang2020.txt +++ b/doc/examples/biomodels/BIOMD0000000984/Fang2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Fang2020___SEIR_model_of_COVID_19_transmission_considering_government_interventions_in_Wuhan() // Compartments and Species: @@ -44,7 +44,7 @@ model *Fang2020___SEIR_model_of_COVID_19_transmission_considering_government_int unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = item; unit extent = substance; unit substance_per_volume = item / 1e-3 litre; diff --git a/doc/examples/biomodels/Gex-Fabry1984.txt b/doc/examples/biomodels/BIOMD0000000985/Gex-Fabry1984.txt similarity index 99% rename from doc/examples/biomodels/Gex-Fabry1984.txt rename to doc/examples/biomodels/BIOMD0000000985/Gex-Fabry1984.txt index 444471fca..bff25bbca 100644 --- a/doc/examples/biomodels/Gex-Fabry1984.txt +++ b/doc/examples/biomodels/BIOMD0000000985/Gex-Fabry1984.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Gex_Fabry1984___model_of_receptor_mediated_endocytosis_of_EGF_in_BALB_c_3T3_cells() // Compartments and Species: @@ -63,7 +63,7 @@ model *Gex_Fabry1984___model_of_receptor_mediated_endocytosis_of_EGF_in_BALB_c_3 unit length = metre; unit area = metre^2; unit volume = litre; - unit time_unit = time_unit; + unit time_unit = 60 second; unit substance = item; unit extent = substance; unit substance_per_volume = item / litre; diff --git a/doc/examples/biomodels/BIOMD0000000986/Aubry1995.txt b/doc/examples/biomodels/BIOMD0000000986/Aubry1995.txt new file mode 100644 index 000000000..d1c9248a1 --- /dev/null +++ b/doc/examples/biomodels/BIOMD0000000986/Aubry1995.txt @@ -0,0 +1,130 @@ +// Created by libAntimony v3.2.0 +model *Aubry1995___Multi_compartment_model_of_fluid_phase_endocytosis_kinetics_in_Dictyostelium_discoideum() + + // Compartments and Species: + compartment Dictyostelium_discoideum_AX2; + species $FITC_Dextran_single_compartment_model in Dictyostelium_discoideum_AX2; + species $Pyranine_single_compartment_model in Dictyostelium_discoideum_AX2; + species FITC_Dextran_three_compartment_model_compartment_1 in Dictyostelium_discoideum_AX2; + species FITC_Dextran_three_compartment_model_compartment_2 in Dictyostelium_discoideum_AX2; + species FITC_Dextran_three_compartment_model_compartment_3 in Dictyostelium_discoideum_AX2; + species Pyranine_three_compartment_model_compartment_1 in Dictyostelium_discoideum_AX2; + species Pyranine_three_compartment_model_compartment_2 in Dictyostelium_discoideum_AX2; + species Pyranine_three_compartment_model_compartment_3 in Dictyostelium_discoideum_AX2; + + // Assignment Rules: + FITC_Dextran_single_compartment_model := FITC_Dextran_max_uptake_rate*(1 - exp(-lambda_single_compartment_model_FITC_Dextran*time)); + Pyranine_single_compartment_model := Pyranine_addition_trigger*Pyranine_max_uptake_rate*(1 - exp(-lambda_single_compartment_model_Pyranine*(time - 90))); + Total_FITC_Dextran := FITC_Dextran_three_compartment_model_compartment_1 + FITC_Dextran_three_compartment_model_compartment_2 + FITC_Dextran_three_compartment_model_compartment_3; + Total_Pyranine := Pyranine_three_compartment_model_compartment_1 + Pyranine_three_compartment_model_compartment_2 + Pyranine_three_compartment_model_compartment_3; + + // Reactions: + FITC_Dextran_influx_rate_0: => FITC_Dextran_three_compartment_model_compartment_1; Dictyostelium_discoideum_AX2*FITC_Dextran_influx_rate; + FITC_Dextran_transfer_between_endo_lysosomal_compartments_1_and_2: FITC_Dextran_three_compartment_model_compartment_1 => FITC_Dextran_three_compartment_model_compartment_2; Dictyostelium_discoideum_AX2*lambda_compartment_1*FITC_Dextran_three_compartment_model_compartment_1; + FITC_Dextran_transfer_between_endo_lysosomal_compartments_2_and_3: FITC_Dextran_three_compartment_model_compartment_2 => FITC_Dextran_three_compartment_model_compartment_3; Dictyostelium_discoideum_AX2*lambda_compartment_2*FITC_Dextran_three_compartment_model_compartment_2; + FITC_Dextran_efflux_rate: FITC_Dextran_three_compartment_model_compartment_3 => ; Dictyostelium_discoideum_AX2*lambda_compartment_3*FITC_Dextran_three_compartment_model_compartment_3; + Pyranine_influx_rate_0: => Pyranine_three_compartment_model_compartment_1; Dictyostelium_discoideum_AX2*(Pyranine_addition_trigger*Pyranine_influx_rate); + Pyranine_transfer_between_endo_lysosomal_compartments_1_and_2: Pyranine_three_compartment_model_compartment_1 => Pyranine_three_compartment_model_compartment_2; Dictyostelium_discoideum_AX2*lambda_compartment_1*Pyranine_three_compartment_model_compartment_1; + Pyranine_transfer_between_endo_lysosomal_compartments_2_and_3: Pyranine_three_compartment_model_compartment_2 => Pyranine_three_compartment_model_compartment_3; Dictyostelium_discoideum_AX2*lambda_compartment_2*Pyranine_three_compartment_model_compartment_2; + Pyranine_efflux_rate: Pyranine_three_compartment_model_compartment_3 => ; Dictyostelium_discoideum_AX2*lambda_compartment_3*Pyranine_three_compartment_model_compartment_3; + + // Events: + Addition_of_Pyranine: at 0 after time > 90: Pyranine_addition_trigger = 1; + + // Species initializations: + FITC_Dextran_three_compartment_model_compartment_1 = 0; + FITC_Dextran_three_compartment_model_compartment_2 = 0; + FITC_Dextran_three_compartment_model_compartment_3 = 0; + Pyranine_three_compartment_model_compartment_1 = 0; + Pyranine_three_compartment_model_compartment_2 = 0; + Pyranine_three_compartment_model_compartment_3 = 0; + + // Compartment initializations: + Dictyostelium_discoideum_AX2 = 1; + + // Variable initializations: + FITC_Dextran_max_uptake_rate = 585; + lambda_single_compartment_model_FITC_Dextran = 0.016; + Pyranine_addition_trigger = 0; + Pyranine_max_uptake_rate = 578; + lambda_single_compartment_model_Pyranine = 0.01; + FITC_Dextran_influx_rate = 6.7; + lambda_compartment_1 = 0.037; + lambda_compartment_2 = 0.037; + lambda_compartment_3 = 0.035; + Pyranine_influx_rate = 5.3; + + // Other declarations: + var Pyranine_addition_trigger, Total_FITC_Dextran, Total_Pyranine; + const Dictyostelium_discoideum_AX2, FITC_Dextran_max_uptake_rate, lambda_single_compartment_model_FITC_Dextran; + const Pyranine_max_uptake_rate, lambda_single_compartment_model_Pyranine; + const FITC_Dextran_influx_rate, lambda_compartment_1, lambda_compartment_2; + const lambda_compartment_3, Pyranine_influx_rate; + + // Unit definitions: + unit length = metre; + unit area = metre^2; + unit volume = 1e-3 litre; + unit time_unit = 60 second; + unit substance = item; + + // Display Names: + time_unit is "time"; + Dictyostelium_discoideum_AX2 is "Dictyostelium discoideum AX2"; + FITC_Dextran_influx_rate_0 is "FITC_Dextran_influx_rate"; + Pyranine_influx_rate_0 is "Pyranine_influx_rate"; + + // CV terms: + Dictyostelium_discoideum_AX2 hasTaxon "http://identifiers.org/taxonomy/366501" + FITC_Dextran_single_compartment_model hasPart "http://identifiers.org/chebi/CHEBI:52071" + FITC_Dextran_single_compartment_model hasPart "http://identifiers.org/chebi/CHEBI:37926" + Pyranine_single_compartment_model identity "http://identifiers.org/chebi/CHEBI:52083" + FITC_Dextran_three_compartment_model_compartment_1 hasPart "http://identifiers.org/chebi/CHEBI:37926" + FITC_Dextran_three_compartment_model_compartment_1 hasPart "http://identifiers.org/chebi/CHEBI:52071" + FITC_Dextran_three_compartment_model_compartment_2 hasPart "http://identifiers.org/chebi/CHEBI:37926" + FITC_Dextran_three_compartment_model_compartment_2 hasPart "http://identifiers.org/chebi/CHEBI:52071" + FITC_Dextran_three_compartment_model_compartment_3 hasPart "http://identifiers.org/chebi/CHEBI:52071" + FITC_Dextran_three_compartment_model_compartment_3 hasPart "http://identifiers.org/chebi/CHEBI:37926" + Pyranine_three_compartment_model_compartment_1 identity "http://identifiers.org/chebi/CHEBI:52083" + Pyranine_three_compartment_model_compartment_2 identity "http://identifiers.org/chebi/CHEBI:52083" + Pyranine_three_compartment_model_compartment_3 identity "http://identifiers.org/chebi/CHEBI:52083" + FITC_Dextran_influx_rate_0 identity "http://identifiers.org/go/GO:0098657" + FITC_Dextran_transfer_between_endo_lysosomal_compartments_1_and_2 identity "http://identifiers.org/go/GO:0098927" + FITC_Dextran_transfer_between_endo_lysosomal_compartments_2_and_3 identity "http://identifiers.org/go/GO:0098927" + FITC_Dextran_efflux_rate identity "http://identifiers.org/go/GO:0140352" + Pyranine_influx_rate_0 identity "http://identifiers.org/go/GO:0098657" + Pyranine_transfer_between_endo_lysosomal_compartments_1_and_2 identity "http://identifiers.org/go/GO:0098927" + Pyranine_transfer_between_endo_lysosomal_compartments_2_and_3 identity "http://identifiers.org/go/GO:0098927" + Pyranine_efflux_rate identity "http://identifiers.org/go/GO:0140352" + + model publication "http://identifiers.org/doi/10.1007/BF00713556" + model model_source "http://identifiers.org/biomodels.db/MODEL2102090001", + "http://identifiers.org/biomodels.db/BIOMD0000000986" + model identity "http://identifiers.org/go/GO:0006897" + model identity "http://identifiers.org/chebi/CHEBI:37926", + "http://identifiers.org/chebi/CHEBI:52083" + model hasTaxon "http://identifiers.org/taxonomy/366501" + model hasProperty "http://identifiers.org/mamo/MAMO_0000046" + model created "2021-02-08T11:29:50Z" + model modified "2021-02-08T11:29:50Z" + model creator1.givenName "Kausthubh" + model creator1.familyName "Ramachandran" + model creator1.organization "EMBL-EBI" + model creator1.email "kramachandran@ebi.ac.uk" + + // Notes: + model notes ``` +Fluid-phase endoeytosis (pinocytosis) kinetics were studied in Dictyostelium discoideum +amoebae from the axenic strain Ax-2 that exhibits high rates of fluid-phase endoeytosis +when cultured in liquid nutrient media. Fluorescein-labelled dextran (FITC-dextran) +was used as a marker in continuous uptake- and in pulse-chase exocytosis experiments. +In the latter case, efflux of the marker was monitored on cells loaded for short +periods of time and resuspended in marker-free medium. A multicompartmental model +was developed which describes satisfactorily fluid-phase endocytosis kinetics. In +particular, it accounts correctly for the extended latency period before exocytosis +in pulse-chase experiments and it suggests the existence of some sorts of maturation +stages in the pathway. +``` +end + +Aubry1995___Multi_compartment_model_of_fluid_phase_endocytosis_kinetics_in_Dictyostelium_discoideum is "Aubry1995 - Multi-compartment model of fluid-phase endocytosis kinetics in Dictyostelium discoideum" diff --git a/doc/examples/biomodels/Aubry1995.txt b/doc/examples/biomodels/BIOMD0000000987/Aubry1995.txt similarity index 99% rename from doc/examples/biomodels/Aubry1995.txt rename to doc/examples/biomodels/BIOMD0000000987/Aubry1995.txt index 779c52128..e175f005c 100644 --- a/doc/examples/biomodels/Aubry1995.txt +++ b/doc/examples/biomodels/BIOMD0000000987/Aubry1995.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Aubry1995___Nine_compartment_model_of_fluid_phase_endocytosis_kinetics_in_Dictyostelium_discoideum() // Compartments and Species: diff --git a/doc/examples/biomodels/Westerhoff2020.txt b/doc/examples/biomodels/BIOMD0000000988/Westerhoff2020.txt similarity index 99% rename from doc/examples/biomodels/Westerhoff2020.txt rename to doc/examples/biomodels/BIOMD0000000988/Westerhoff2020.txt index ab53e775f..adb508af2 100644 --- a/doc/examples/biomodels/Westerhoff2020.txt +++ b/doc/examples/biomodels/BIOMD0000000988/Westerhoff2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Westerhoff_Nat2020() // Compartments and Species: @@ -130,7 +130,7 @@ model *Westerhoff_Nat2020() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = item; unit unit_0 = 86400 second; unit unit_1 = 1 / dimensionless^-0; diff --git a/doc/examples/biomodels/MODEL1712050001.txt b/doc/examples/biomodels/BIOMD0000000989/MODEL1712050001.txt similarity index 99% rename from doc/examples/biomodels/MODEL1712050001.txt rename to doc/examples/biomodels/BIOMD0000000989/MODEL1712050001.txt index 50fe58fdb..af83e3cdf 100644 --- a/doc/examples/biomodels/MODEL1712050001.txt +++ b/doc/examples/biomodels/BIOMD0000000989/MODEL1712050001.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Strasen2018___TGF__SMAD_Signalling___Dose_dependent_dynamics_upon_TGF__stimulation() // Compartments and Species: diff --git a/doc/examples/biomodels/SMAD2_dose_kinetics.txt b/doc/examples/biomodels/BIOMD0000000989/SMAD2_dose_kinetics.txt similarity index 99% rename from doc/examples/biomodels/SMAD2_dose_kinetics.txt rename to doc/examples/biomodels/BIOMD0000000989/SMAD2_dose_kinetics.txt index d9855868e..47c41a9d2 100644 --- a/doc/examples/biomodels/SMAD2_dose_kinetics.txt +++ b/doc/examples/biomodels/BIOMD0000000989/SMAD2_dose_kinetics.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *NoName() // Compartments and Species: diff --git a/doc/examples/biomodels/Ligand_degradation_kinetics_25pM.txt b/doc/examples/biomodels/BIOMD0000000990/Ligand_degradation_kinetics_25pM.txt similarity index 99% rename from doc/examples/biomodels/Ligand_degradation_kinetics_25pM.txt rename to doc/examples/biomodels/BIOMD0000000990/Ligand_degradation_kinetics_25pM.txt index f9678a229..3d5ec4c27 100644 --- a/doc/examples/biomodels/Ligand_degradation_kinetics_25pM.txt +++ b/doc/examples/biomodels/BIOMD0000000990/Ligand_degradation_kinetics_25pM.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *NoName() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1712050002.txt b/doc/examples/biomodels/BIOMD0000000990/MODEL1712050002.txt similarity index 99% rename from doc/examples/biomodels/MODEL1712050002.txt rename to doc/examples/biomodels/BIOMD0000000990/MODEL1712050002.txt index eb3f2ef61..f42c973ac 100644 --- a/doc/examples/biomodels/MODEL1712050002.txt +++ b/doc/examples/biomodels/BIOMD0000000990/MODEL1712050002.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Strasen2018___TGF__SMAD_Signalling___Degradation_of_25pM_ligand__TGF_() // Compartments and Species: diff --git a/doc/examples/biomodels/Okuonghae2020.txt b/doc/examples/biomodels/BIOMD0000000991/Okuonghae2020.txt similarity index 99% rename from doc/examples/biomodels/Okuonghae2020.txt rename to doc/examples/biomodels/BIOMD0000000991/Okuonghae2020.txt index 74cfd0c53..093bf3988 100644 --- a/doc/examples/biomodels/Okuonghae2020.txt +++ b/doc/examples/biomodels/BIOMD0000000991/Okuonghae2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Okuonghae2020___SEAIR_model_of_COVID_19_transmission_in_Lagos__Nigeria() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1712050003.txt b/doc/examples/biomodels/BIOMD0000000994/MODEL1712050003.txt similarity index 99% rename from doc/examples/biomodels/MODEL1712050003.txt rename to doc/examples/biomodels/BIOMD0000000994/MODEL1712050003.txt index bbb7d0b14..dbd912f24 100644 --- a/doc/examples/biomodels/MODEL1712050003.txt +++ b/doc/examples/biomodels/BIOMD0000000994/MODEL1712050003.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Strasen2018___TGF__SMAD_Signalling___Restimulation_with_5pM_TGF__at_3hr() // Compartments and Species: diff --git a/doc/examples/biomodels/Restimulation_5pM_3HR.txt b/doc/examples/biomodels/BIOMD0000000994/Restimulation_5pM_3HR.txt similarity index 99% rename from doc/examples/biomodels/Restimulation_5pM_3HR.txt rename to doc/examples/biomodels/BIOMD0000000994/Restimulation_5pM_3HR.txt index 80280507b..c5fbdd3a9 100644 --- a/doc/examples/biomodels/Restimulation_5pM_3HR.txt +++ b/doc/examples/biomodels/BIOMD0000000994/Restimulation_5pM_3HR.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Figure4E() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1712050004.txt b/doc/examples/biomodels/BIOMD0000000995/MODEL1712050004.txt similarity index 99% rename from doc/examples/biomodels/MODEL1712050004.txt rename to doc/examples/biomodels/BIOMD0000000995/MODEL1712050004.txt index 709cd76e0..191946bb8 100644 --- a/doc/examples/biomodels/MODEL1712050004.txt +++ b/doc/examples/biomodels/BIOMD0000000995/MODEL1712050004.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Strasen2018___TGF__SMAD_Signalling___Restimulation_with_5pM_TGF__at_8hr() // Compartments and Species: diff --git a/doc/examples/biomodels/Restimulation_5pM_8HR.txt b/doc/examples/biomodels/BIOMD0000000995/Restimulation_5pM_8HR.txt similarity index 99% rename from doc/examples/biomodels/Restimulation_5pM_8HR.txt rename to doc/examples/biomodels/BIOMD0000000995/Restimulation_5pM_8HR.txt index 025bcc412..d85154ecd 100644 --- a/doc/examples/biomodels/Restimulation_5pM_8HR.txt +++ b/doc/examples/biomodels/BIOMD0000000995/Restimulation_5pM_8HR.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Figure_4F() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1712050005.txt b/doc/examples/biomodels/BIOMD0000000996/MODEL1712050005.txt similarity index 99% rename from doc/examples/biomodels/MODEL1712050005.txt rename to doc/examples/biomodels/BIOMD0000000996/MODEL1712050005.txt index 988dc41a3..89fbe7ee4 100644 --- a/doc/examples/biomodels/MODEL1712050005.txt +++ b/doc/examples/biomodels/BIOMD0000000996/MODEL1712050005.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Strasen2018___TGF__SMAD_Signalling___Restimulation_with_100pM_TGF__at_6hr() // Compartments and Species: diff --git a/doc/examples/biomodels/Restimulation_100pM_6HR.txt b/doc/examples/biomodels/BIOMD0000000996/Restimulation_100pM_6HR.txt similarity index 99% rename from doc/examples/biomodels/Restimulation_100pM_6HR.txt rename to doc/examples/biomodels/BIOMD0000000996/Restimulation_100pM_6HR.txt index b855ced0e..d43f3dcfc 100644 --- a/doc/examples/biomodels/Restimulation_100pM_6HR.txt +++ b/doc/examples/biomodels/BIOMD0000000996/Restimulation_100pM_6HR.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *NoName() // Compartments and Species: diff --git a/doc/examples/biomodels/DRB_treatment.txt b/doc/examples/biomodels/BIOMD0000000997/DRB_treatment.txt similarity index 99% rename from doc/examples/biomodels/DRB_treatment.txt rename to doc/examples/biomodels/BIOMD0000000997/DRB_treatment.txt index f231b2331..6fe78698f 100644 --- a/doc/examples/biomodels/DRB_treatment.txt +++ b/doc/examples/biomodels/BIOMD0000000997/DRB_treatment.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *NoName() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1712050006.txt b/doc/examples/biomodels/BIOMD0000000997/MODEL1712050006.txt similarity index 99% rename from doc/examples/biomodels/MODEL1712050006.txt rename to doc/examples/biomodels/BIOMD0000000997/MODEL1712050006.txt index a68ff64d5..ba82fc952 100644 --- a/doc/examples/biomodels/MODEL1712050006.txt +++ b/doc/examples/biomodels/BIOMD0000000997/MODEL1712050006.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Strasen2018___TGF__SMAD_Signalling___DRB_treatment() // Compartments and Species: diff --git a/doc/examples/biomodels/Figure_5A_class1.txt b/doc/examples/biomodels/BIOMD0000000998/Figure_5A_class1.txt similarity index 99% rename from doc/examples/biomodels/Figure_5A_class1.txt rename to doc/examples/biomodels/BIOMD0000000998/Figure_5A_class1.txt index 0c337bacb..ae74e6593 100644 --- a/doc/examples/biomodels/Figure_5A_class1.txt +++ b/doc/examples/biomodels/BIOMD0000000998/Figure_5A_class1.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *C1_Aug_2016() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1712050007.txt b/doc/examples/biomodels/BIOMD0000000998/MODEL1712050007.txt similarity index 99% rename from doc/examples/biomodels/MODEL1712050007.txt rename to doc/examples/biomodels/BIOMD0000000998/MODEL1712050007.txt index 3a46af5c1..0d93814b3 100644 --- a/doc/examples/biomodels/MODEL1712050007.txt +++ b/doc/examples/biomodels/BIOMD0000000998/MODEL1712050007.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Strasen2018___TGF__SMAD_Signalling_Class_1() // Compartments and Species: diff --git a/doc/examples/biomodels/Figure_5A_class2.txt b/doc/examples/biomodels/BIOMD0000000999/Figure_5A_class2.txt similarity index 99% rename from doc/examples/biomodels/Figure_5A_class2.txt rename to doc/examples/biomodels/BIOMD0000000999/Figure_5A_class2.txt index bb16ba23b..c56aee60c 100644 --- a/doc/examples/biomodels/Figure_5A_class2.txt +++ b/doc/examples/biomodels/BIOMD0000000999/Figure_5A_class2.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *C2_Aug_2016() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1712050008.txt b/doc/examples/biomodels/BIOMD0000000999/MODEL1712050008.txt similarity index 99% rename from doc/examples/biomodels/MODEL1712050008.txt rename to doc/examples/biomodels/BIOMD0000000999/MODEL1712050008.txt index e40980bf0..a0c408f83 100644 --- a/doc/examples/biomodels/MODEL1712050008.txt +++ b/doc/examples/biomodels/BIOMD0000000999/MODEL1712050008.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Strasen2018___TGF__SMAD_Signalling_Class_2() // Compartments and Species: diff --git a/doc/examples/biomodels/Figure_5A_class3.txt b/doc/examples/biomodels/BIOMD0000001000/Figure_5A_class3.txt similarity index 99% rename from doc/examples/biomodels/Figure_5A_class3.txt rename to doc/examples/biomodels/BIOMD0000001000/Figure_5A_class3.txt index d027541b3..342a39169 100644 --- a/doc/examples/biomodels/Figure_5A_class3.txt +++ b/doc/examples/biomodels/BIOMD0000001000/Figure_5A_class3.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *C3_Aug_2016() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1712050009.txt b/doc/examples/biomodels/BIOMD0000001000/MODEL1712050009.txt similarity index 99% rename from doc/examples/biomodels/MODEL1712050009.txt rename to doc/examples/biomodels/BIOMD0000001000/MODEL1712050009.txt index bc5a42bd5..c7b6334f7 100644 --- a/doc/examples/biomodels/MODEL1712050009.txt +++ b/doc/examples/biomodels/BIOMD0000001000/MODEL1712050009.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Strasen2018___TGF__SMAD_Signalling_Class_3() // Compartments and Species: diff --git a/doc/examples/biomodels/Figure_5A_class4.txt b/doc/examples/biomodels/BIOMD0000001001/Figure_5A_class4.txt similarity index 99% rename from doc/examples/biomodels/Figure_5A_class4.txt rename to doc/examples/biomodels/BIOMD0000001001/Figure_5A_class4.txt index 8ed8d77c7..35d920e76 100644 --- a/doc/examples/biomodels/Figure_5A_class4.txt +++ b/doc/examples/biomodels/BIOMD0000001001/Figure_5A_class4.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *C4_Aug_2016() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1712050010.txt b/doc/examples/biomodels/BIOMD0000001001/MODEL1712050010.txt similarity index 99% rename from doc/examples/biomodels/MODEL1712050010.txt rename to doc/examples/biomodels/BIOMD0000001001/MODEL1712050010.txt index 0eef31a75..d8387ac7b 100644 --- a/doc/examples/biomodels/MODEL1712050010.txt +++ b/doc/examples/biomodels/BIOMD0000001001/MODEL1712050010.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Strasen2018___TGF__SMAD_Signalling_Class_4() // Compartments and Species: diff --git a/doc/examples/biomodels/Figure_5A_class5.txt b/doc/examples/biomodels/BIOMD0000001002/Figure_5A_class5.txt similarity index 99% rename from doc/examples/biomodels/Figure_5A_class5.txt rename to doc/examples/biomodels/BIOMD0000001002/Figure_5A_class5.txt index 185e48908..657ac33ef 100644 --- a/doc/examples/biomodels/Figure_5A_class5.txt +++ b/doc/examples/biomodels/BIOMD0000001002/Figure_5A_class5.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *C5_Aug_2016() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL1712050011.txt b/doc/examples/biomodels/BIOMD0000001002/MODEL1712050011.txt similarity index 99% rename from doc/examples/biomodels/MODEL1712050011.txt rename to doc/examples/biomodels/BIOMD0000001002/MODEL1712050011.txt index 7b06b7f72..a2173a79c 100644 --- a/doc/examples/biomodels/MODEL1712050011.txt +++ b/doc/examples/biomodels/BIOMD0000001002/MODEL1712050011.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Strasen2018___TGF__SMAD_Signalling_Class_5() // Compartments and Species: diff --git a/doc/examples/biomodels/Figure_5A_class6.txt b/doc/examples/biomodels/BIOMD0000001003/Figure_5A_class6.txt similarity index 99% rename from doc/examples/biomodels/Figure_5A_class6.txt rename to doc/examples/biomodels/BIOMD0000001003/Figure_5A_class6.txt index 840c85d24..b6cb4912e 100644 --- a/doc/examples/biomodels/Figure_5A_class6.txt +++ b/doc/examples/biomodels/BIOMD0000001003/Figure_5A_class6.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *C6_Aug_2016() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL17120500012.txt b/doc/examples/biomodels/BIOMD0000001003/MODEL17120500012.txt similarity index 99% rename from doc/examples/biomodels/MODEL17120500012.txt rename to doc/examples/biomodels/BIOMD0000001003/MODEL17120500012.txt index ff8e7e99f..524aa5efc 100644 --- a/doc/examples/biomodels/MODEL17120500012.txt +++ b/doc/examples/biomodels/BIOMD0000001003/MODEL17120500012.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Strasen2018___TGF__SMAD_Signalling_Class_6() // Compartments and Species: diff --git a/doc/examples/biomodels/12918_2015_223_MOESM2_ESM.txt b/doc/examples/biomodels/BIOMD0000001004/12918_2015_223_MOESM2_ESM.txt similarity index 99% rename from doc/examples/biomodels/12918_2015_223_MOESM2_ESM.txt rename to doc/examples/biomodels/BIOMD0000001004/12918_2015_223_MOESM2_ESM.txt index 50f52104d..3b56a2a3d 100644 --- a/doc/examples/biomodels/12918_2015_223_MOESM2_ESM.txt +++ b/doc/examples/biomodels/BIOMD0000001004/12918_2015_223_MOESM2_ESM.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *th17_core_network() // Compartments and Species: diff --git a/doc/examples/biomodels/Intosalmi2015.txt b/doc/examples/biomodels/BIOMD0000001004/Intosalmi2015.txt similarity index 99% rename from doc/examples/biomodels/Intosalmi2015.txt rename to doc/examples/biomodels/BIOMD0000001004/Intosalmi2015.txt index a7fe86e0c..9f4c383dd 100644 --- a/doc/examples/biomodels/Intosalmi2015.txt +++ b/doc/examples/biomodels/BIOMD0000001004/Intosalmi2015.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Intosalmi2015___Th17_core_network_model() // Compartments and Species: diff --git a/doc/examples/biomodels/Bae2018.txt b/doc/examples/biomodels/BIOMD0000001005/Bae2018.txt similarity index 99% rename from doc/examples/biomodels/Bae2018.txt rename to doc/examples/biomodels/BIOMD0000001005/Bae2018.txt index 8cf656d82..f0e78a8f8 100644 --- a/doc/examples/biomodels/Bae2018.txt +++ b/doc/examples/biomodels/BIOMD0000001005/Bae2018.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bae2017___Mathematical_analysis_of_circadian_disruption_and_metabolic_re_entrainment_of_hepatic_gluconeogenesis() // Compartments and Species: diff --git a/doc/examples/biomodels/Ciliberto2005.txt b/doc/examples/biomodels/BIOMD0000001006/Ciliberto2005.txt similarity index 99% rename from doc/examples/biomodels/Ciliberto2005.txt rename to doc/examples/biomodels/BIOMD0000001006/Ciliberto2005.txt index 70a149606..cff5169ac 100644 --- a/doc/examples/biomodels/Ciliberto2005.txt +++ b/doc/examples/biomodels/BIOMD0000001006/Ciliberto2005.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Ciliberto2005___Steady_states_and_oscillations_in_the_p53_Mdm2_network() // Compartments and Species: diff --git a/doc/examples/biomodels/Zhang2007_M1_highDD.txt b/doc/examples/biomodels/BIOMD0000001007/Zhang2007_M1_highDD.txt similarity index 99% rename from doc/examples/biomodels/Zhang2007_M1_highDD.txt rename to doc/examples/biomodels/BIOMD0000001007/Zhang2007_M1_highDD.txt index ed23fca12..fb29c14db 100644 --- a/doc/examples/biomodels/Zhang2007_M1_highDD.txt +++ b/doc/examples/biomodels/BIOMD0000001007/Zhang2007_M1_highDD.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zhang2007___Mechanism_of_DNA_damage_response__Model1() // Compartments and Species: diff --git a/doc/examples/biomodels/Zhang2007_M1_lowDD.txt b/doc/examples/biomodels/BIOMD0000001007/Zhang2007_M1_lowDD.txt similarity index 99% rename from doc/examples/biomodels/Zhang2007_M1_lowDD.txt rename to doc/examples/biomodels/BIOMD0000001007/Zhang2007_M1_lowDD.txt index 84db97651..c7a7c2b1c 100644 --- a/doc/examples/biomodels/Zhang2007_M1_lowDD.txt +++ b/doc/examples/biomodels/BIOMD0000001007/Zhang2007_M1_lowDD.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zhang2007___Mechanism_of_DNA_damage_response__Model1() // Compartments and Species: diff --git a/doc/examples/biomodels/Scaramellini1997.txt b/doc/examples/biomodels/BIOMD0000001008/Scaramellini1997.txt similarity index 99% rename from doc/examples/biomodels/Scaramellini1997.txt rename to doc/examples/biomodels/BIOMD0000001008/Scaramellini1997.txt index 6e9437635..c5efeae1c 100644 --- a/doc/examples/biomodels/Scaramellini1997.txt +++ b/doc/examples/biomodels/BIOMD0000001008/Scaramellini1997.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Scaramellini1997___Two_receptor_One_transducer__2R1T__model_for_analysis_of_interactions_between_agonists() // Compartments and Species: diff --git a/doc/examples/biomodels/Zhang2007_M2_high_dose.txt b/doc/examples/biomodels/BIOMD0000001009/Zhang2007_M2_high_dose.txt similarity index 99% rename from doc/examples/biomodels/Zhang2007_M2_high_dose.txt rename to doc/examples/biomodels/BIOMD0000001009/Zhang2007_M2_high_dose.txt index c1eb90731..1a1458b4d 100644 --- a/doc/examples/biomodels/Zhang2007_M2_high_dose.txt +++ b/doc/examples/biomodels/BIOMD0000001009/Zhang2007_M2_high_dose.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zhang2007___Mechanism_of_DNA_damage_response__Model2() // Compartments and Species: diff --git a/doc/examples/biomodels/Zhang2007_M2_low_dose.txt b/doc/examples/biomodels/BIOMD0000001009/Zhang2007_M2_low_dose.txt similarity index 99% rename from doc/examples/biomodels/Zhang2007_M2_low_dose.txt rename to doc/examples/biomodels/BIOMD0000001009/Zhang2007_M2_low_dose.txt index cd1033e73..802ef7248 100644 --- a/doc/examples/biomodels/Zhang2007_M2_low_dose.txt +++ b/doc/examples/biomodels/BIOMD0000001009/Zhang2007_M2_low_dose.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zhang2007___Mechanism_of_DNA_damage_response__Model2() // Compartments and Species: diff --git a/doc/examples/biomodels/Zhang2007_M3_high_DD.txt b/doc/examples/biomodels/BIOMD0000001010/Zhang2007_M3_high_DD.txt similarity index 98% rename from doc/examples/biomodels/Zhang2007_M3_high_DD.txt rename to doc/examples/biomodels/BIOMD0000001010/Zhang2007_M3_high_DD.txt index cf7352a32..d8e5c002e 100644 --- a/doc/examples/biomodels/Zhang2007_M3_high_DD.txt +++ b/doc/examples/biomodels/BIOMD0000001010/Zhang2007_M3_high_DD.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zhang2007___Mechanism_of_DNA_damage_response__Model3() // Compartments and Species: @@ -64,7 +64,7 @@ model *Zhang2007___Mechanism_of_DNA_damage_response__Model3() unit length = metre; unit area = metre^2; unit volume = litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = mole; unit extent = substance; unit substance_per_volume = mole / litre; diff --git a/doc/examples/biomodels/Zhang2007_M3_low_DD.txt b/doc/examples/biomodels/BIOMD0000001010/Zhang2007_M3_low_DD.txt similarity index 98% rename from doc/examples/biomodels/Zhang2007_M3_low_DD.txt rename to doc/examples/biomodels/BIOMD0000001010/Zhang2007_M3_low_DD.txt index a67f55e12..958f613f8 100644 --- a/doc/examples/biomodels/Zhang2007_M3_low_DD.txt +++ b/doc/examples/biomodels/BIOMD0000001010/Zhang2007_M3_low_DD.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zhang2007___Mechanism_of_DNA_damage_response__Model3() // Compartments and Species: @@ -64,7 +64,7 @@ model *Zhang2007___Mechanism_of_DNA_damage_response__Model3() unit length = metre; unit area = metre^2; unit volume = litre; - unit time_unit = time_unit; + unit time_unit = second; unit substance = mole; unit extent = substance; unit substance_per_volume = mole / litre; diff --git a/doc/examples/biomodels/Leon-Triana2020 (eqs 4).txt b/doc/examples/biomodels/BIOMD0000001011/Leon-Triana2020 (eqs 4).txt similarity index 99% rename from doc/examples/biomodels/Leon-Triana2020 (eqs 4).txt rename to doc/examples/biomodels/BIOMD0000001011/Leon-Triana2020 (eqs 4).txt index e0a3513c4..528d5b16c 100644 --- a/doc/examples/biomodels/Leon-Triana2020 (eqs 4).txt +++ b/doc/examples/biomodels/BIOMD0000001011/Leon-Triana2020 (eqs 4).txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Leon_Triana2020___CAR_T_cell_therapy_in_B_cell_acute_lymphoblastic_leukaemia() // Compartments and Species: diff --git a/doc/examples/biomodels/Leon-Triana2020 (eqs 3).txt b/doc/examples/biomodels/BIOMD0000001012/Leon-Triana2020 (eqs 3).txt similarity index 99% rename from doc/examples/biomodels/Leon-Triana2020 (eqs 3).txt rename to doc/examples/biomodels/BIOMD0000001012/Leon-Triana2020 (eqs 3).txt index 5a7cfd9a5..8e4758e21 100644 --- a/doc/examples/biomodels/Leon-Triana2020 (eqs 3).txt +++ b/doc/examples/biomodels/BIOMD0000001012/Leon-Triana2020 (eqs 3).txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Leon_Triana2020___CAR_T_cell_therapy_in_B_cell_acute_lymphoblastic_leukaemia_with_contribution_from_immature_B_cells() // Compartments and Species: diff --git a/doc/examples/biomodels/Leon-Triana2021 - eqs 1 and 2.txt b/doc/examples/biomodels/BIOMD0000001013/Leon-Triana2021 - eqs 1 and 2.txt similarity index 99% rename from doc/examples/biomodels/Leon-Triana2021 - eqs 1 and 2.txt rename to doc/examples/biomodels/BIOMD0000001013/Leon-Triana2021 - eqs 1 and 2.txt index 334d41951..18784380b 100644 --- a/doc/examples/biomodels/Leon-Triana2021 - eqs 1 and 2.txt +++ b/doc/examples/biomodels/BIOMD0000001013/Leon-Triana2021 - eqs 1 and 2.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Leon_Triana2021___Competition_between_tumour_cells_and_single_target_CAR_T_cells() // Compartments and Species: diff --git a/doc/examples/biomodels/Leon-Triana2021 (eqs 3-6).txt b/doc/examples/biomodels/BIOMD0000001014/Leon-Triana2021 (eqs 3-6).txt similarity index 99% rename from doc/examples/biomodels/Leon-Triana2021 (eqs 3-6).txt rename to doc/examples/biomodels/BIOMD0000001014/Leon-Triana2021 (eqs 3-6).txt index 2d6caa9f0..4e145bb61 100644 --- a/doc/examples/biomodels/Leon-Triana2021 (eqs 3-6).txt +++ b/doc/examples/biomodels/BIOMD0000001014/Leon-Triana2021 (eqs 3-6).txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Leon_Triana2021___Competition_between_tumour_cells_and_dual_target_CAR_T_cells() // Compartments and Species: diff --git a/doc/examples/biomodels/Jarrah2014.txt b/doc/examples/biomodels/BIOMD0000001015/Jarrah2014.txt similarity index 99% rename from doc/examples/biomodels/Jarrah2014.txt rename to doc/examples/biomodels/BIOMD0000001015/Jarrah2014.txt index 8c8968c0b..73f943771 100644 --- a/doc/examples/biomodels/Jarrah2014.txt +++ b/doc/examples/biomodels/BIOMD0000001015/Jarrah2014.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Jarrah2014___mathematical_model_of_the_immune_response_in_muscle_degeneration_and_subsequent_regeneration_in_Duchenne_muscular_dystrophy_in_mdx_mice() // Compartments and Species: @@ -68,7 +68,7 @@ model *Jarrah2014___mathematical_model_of_the_immune_response_in_muscle_degenera unit length = metre; unit area = metre^2; unit volume = litre; - unit time_unit = time_unit; + unit time_unit = 604800 second; unit substance = mole; unit extent = substance; unit substance_per_volume = mole / litre; diff --git a/doc/examples/biomodels/Bakshi2020 truncated minimal model.txt b/doc/examples/biomodels/BIOMD0000001016/Bakshi2020 truncated minimal model.txt similarity index 99% rename from doc/examples/biomodels/Bakshi2020 truncated minimal model.txt rename to doc/examples/biomodels/BIOMD0000001016/Bakshi2020 truncated minimal model.txt index c322b0db6..c18712ca7 100644 --- a/doc/examples/biomodels/Bakshi2020 truncated minimal model.txt +++ b/doc/examples/biomodels/BIOMD0000001016/Bakshi2020 truncated minimal model.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bakshi2020___Truncated_minimal_model_of_alternative_pathway_of_complement_system() // Compartments and Species: diff --git a/doc/examples/biomodels/Bakshi2020 minimal model.txt b/doc/examples/biomodels/BIOMD0000001017/Bakshi2020 minimal model.txt similarity index 99% rename from doc/examples/biomodels/Bakshi2020 minimal model.txt rename to doc/examples/biomodels/BIOMD0000001017/Bakshi2020 minimal model.txt index d4ae179f3..b96420e51 100644 --- a/doc/examples/biomodels/Bakshi2020 minimal model.txt +++ b/doc/examples/biomodels/BIOMD0000001017/Bakshi2020 minimal model.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bakshi2020___Minimal_model_of_alternative_pathway_of_complement_system() // Compartments and Species: diff --git a/doc/examples/biomodels/Bakshi2020 properdin model.txt b/doc/examples/biomodels/BIOMD0000001018/Bakshi2020 properdin model.txt similarity index 99% rename from doc/examples/biomodels/Bakshi2020 properdin model.txt rename to doc/examples/biomodels/BIOMD0000001018/Bakshi2020 properdin model.txt index 5b58817a5..1354ee478 100644 --- a/doc/examples/biomodels/Bakshi2020 properdin model.txt +++ b/doc/examples/biomodels/BIOMD0000001018/Bakshi2020 properdin model.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bakshi2020___Properdin_model_of_alternative_pathway_of_complement_system() // Compartments and Species: diff --git a/doc/examples/biomodels/Barros2021_HDLM2.txt b/doc/examples/biomodels/BIOMD0000001019/Barros2021_HDLM2.txt similarity index 98% rename from doc/examples/biomodels/Barros2021_HDLM2.txt rename to doc/examples/biomodels/BIOMD0000001019/Barros2021_HDLM2.txt index f684ffd12..18e531304 100644 --- a/doc/examples/biomodels/Barros2021_HDLM2.txt +++ b/doc/examples/biomodels/BIOMD0000001019/Barros2021_HDLM2.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Barros2021___CARTmath__Mathematical_Model_of_CAR_T_Immunotherapy_in_HDLM_2_cell_line() // Compartments and Species: @@ -58,7 +58,7 @@ model *Barros2021___CARTmath__Mathematical_Model_of_CAR_T_Immunotherapy_in_HDLM_ unit length = metre; unit area = metre^2; unit volume = litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = mole; unit unit_0 = 1 / 86400 second; unit unit_1 = 1 / 86400 second; diff --git a/doc/examples/biomodels/Barros2021_RAJI.txt b/doc/examples/biomodels/BIOMD0000001020/Barros2021_RAJI.txt similarity index 98% rename from doc/examples/biomodels/Barros2021_RAJI.txt rename to doc/examples/biomodels/BIOMD0000001020/Barros2021_RAJI.txt index 571b59539..c1b5fd842 100644 --- a/doc/examples/biomodels/Barros2021_RAJI.txt +++ b/doc/examples/biomodels/BIOMD0000001020/Barros2021_RAJI.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Barros2021___CARTmath__Mathematical_Model_of_CAR_T_Immunotherapy_in_Raji_Cell_Line() // Compartments and Species: @@ -65,7 +65,7 @@ model *Barros2021___CARTmath__Mathematical_Model_of_CAR_T_Immunotherapy_in_Raji_ unit length = metre; unit area = metre^2; unit volume = litre; - unit time_unit = time_unit; + unit time_unit = 86400 second; unit substance = mole; unit unit_0 = 1 / 86400 second; unit unit_1 = 1 / 86400 second; diff --git a/doc/examples/biomodels/Lavigne2021 - ODE model.txt b/doc/examples/biomodels/BIOMD0000001021/Lavigne2021 - ODE model.txt similarity index 99% rename from doc/examples/biomodels/Lavigne2021 - ODE model.txt rename to doc/examples/biomodels/BIOMD0000001021/Lavigne2021 - ODE model.txt index 90d694a39..c2cfe1b9f 100644 --- a/doc/examples/biomodels/Lavigne2021 - ODE model.txt +++ b/doc/examples/biomodels/BIOMD0000001021/Lavigne2021 - ODE model.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Lavigne2021___non_spatial_model_of_viral_infection_dynamics_and_interferon_response_of_well_mixed_viral_infection() // Compartments and Species: diff --git a/doc/examples/biomodels/Creemers2021.txt b/doc/examples/biomodels/BIOMD0000001022/Creemers2021.txt similarity index 99% rename from doc/examples/biomodels/Creemers2021.txt rename to doc/examples/biomodels/BIOMD0000001022/Creemers2021.txt index 58ef28f1f..6420eac21 100644 --- a/doc/examples/biomodels/Creemers2021.txt +++ b/doc/examples/biomodels/BIOMD0000001022/Creemers2021.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Creemers2021___Tumor_immune_dynamics_and_implications_on_immunotherapy_responses() // Compartments and Species: diff --git a/doc/examples/biomodels/Alharbi2020.txt b/doc/examples/biomodels/BIOMD0000001023/Alharbi2020.txt similarity index 99% rename from doc/examples/biomodels/Alharbi2020.txt rename to doc/examples/biomodels/BIOMD0000001023/Alharbi2020.txt index 18e75bd38..99fc2a13a 100644 --- a/doc/examples/biomodels/Alharbi2020.txt +++ b/doc/examples/biomodels/BIOMD0000001023/Alharbi2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Alharbi2020___An_ODE_based_model_of_the_dynamics_of_tumor_cell_progression_and_its_effects_on_normal_cell_growth_and_immune_system_functionality() // Compartments and Species: diff --git a/doc/examples/biomodels/Chaudhury2020 Eq 4-5.txt b/doc/examples/biomodels/BIOMD0000001024/Chaudhury2020 Eq 4-5.txt similarity index 99% rename from doc/examples/biomodels/Chaudhury2020 Eq 4-5.txt rename to doc/examples/biomodels/BIOMD0000001024/Chaudhury2020 Eq 4-5.txt index 3a223189b..e142c8212 100644 --- a/doc/examples/biomodels/Chaudhury2020 Eq 4-5.txt +++ b/doc/examples/biomodels/BIOMD0000001024/Chaudhury2020 Eq 4-5.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Chaudhury2020___Lotka_Volterra_mathematical_model_of_CAR_T_cell_and_tumour_kinetics() // Compartments and Species: diff --git a/doc/examples/biomodels/Chaudhury2020 Eq 7-9.txt b/doc/examples/biomodels/BIOMD0000001025/Chaudhury2020 Eq 7-9.txt similarity index 99% rename from doc/examples/biomodels/Chaudhury2020 Eq 7-9.txt rename to doc/examples/biomodels/BIOMD0000001025/Chaudhury2020 Eq 7-9.txt index 05bcd736c..31038f420 100644 --- a/doc/examples/biomodels/Chaudhury2020 Eq 7-9.txt +++ b/doc/examples/biomodels/BIOMD0000001025/Chaudhury2020 Eq 7-9.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Chaudhury2020___EC50_expansion_and_killing_mathematical_model_of_CAR_T_cell_and_tumour_kinetics() // Compartments and Species: diff --git a/doc/examples/biomodels/Independent.txt b/doc/examples/biomodels/BIOMD0000001026/Independent.txt similarity index 99% rename from doc/examples/biomodels/Independent.txt rename to doc/examples/biomodels/BIOMD0000001026/Independent.txt index c84e6bf36..1d3ce7835 100644 --- a/doc/examples/biomodels/Independent.txt +++ b/doc/examples/biomodels/BIOMD0000001026/Independent.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Metformin_partitioning_between_plasma_and_RBC_with_independent_Kin_and_Kout_coefficients() // Compartments and Species: diff --git a/doc/examples/biomodels/Kurlovics2021.txt b/doc/examples/biomodels/BIOMD0000001026/Kurlovics2021.txt similarity index 98% rename from doc/examples/biomodels/Kurlovics2021.txt rename to doc/examples/biomodels/BIOMD0000001026/Kurlovics2021.txt index fa8d8b72e..c6a5e46fc 100644 --- a/doc/examples/biomodels/Kurlovics2021.txt +++ b/doc/examples/biomodels/BIOMD0000001026/Kurlovics2021.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kurlovics2021___Metformin_partitioning_between_plasma_and_RBC_with_independent_Kin_and_Kout_coefficients() // Compartments and Species: @@ -43,7 +43,7 @@ model *Kurlovics2021___Metformin_partitioning_between_plasma_and_RBC_with_indepe unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 3600e2 second; unit extent = substance; unit substance_per_volume = 1e-3 mole / 1e-3 litre; diff --git a/doc/examples/biomodels/Zake2021 - PBPK Metformin Mice PO single dose.txt b/doc/examples/biomodels/BIOMD0000001027/Zake2021 - PBPK Metformin Mice PO single dose.txt similarity index 99% rename from doc/examples/biomodels/Zake2021 - PBPK Metformin Mice PO single dose.txt rename to doc/examples/biomodels/BIOMD0000001027/Zake2021 - PBPK Metformin Mice PO single dose.txt index e0cc4239c..35391c0d7 100644 --- a/doc/examples/biomodels/Zake2021 - PBPK Metformin Mice PO single dose.txt +++ b/doc/examples/biomodels/BIOMD0000001027/Zake2021 - PBPK Metformin Mice PO single dose.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *PBPK_model_of_metformin_in_mice__single_dose_peroral() // Compartments and Species: diff --git a/doc/examples/biomodels/Zake2021_Metformin_Mice_PO.txt b/doc/examples/biomodels/BIOMD0000001027/Zake2021_Metformin_Mice_PO.txt similarity index 97% rename from doc/examples/biomodels/Zake2021_Metformin_Mice_PO.txt rename to doc/examples/biomodels/BIOMD0000001027/Zake2021_Metformin_Mice_PO.txt index 1cbbaf330..888f64500 100644 --- a/doc/examples/biomodels/Zake2021_Metformin_Mice_PO.txt +++ b/doc/examples/biomodels/BIOMD0000001027/Zake2021_Metformin_Mice_PO.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zake2021___PBPK_model_of_metformin_in_mice__single_dose_peroral() // Compartments and Species: @@ -110,45 +110,45 @@ model *Zake2021___PBPK_model_of_metformin_in_mice__single_dose_peroral() // Species initializations: mLiver = 0; - mLiver has substance_per_volume; + mLiver has substance; mKidneyPlasma = 0; - mKidneyPlasma has substance_per_volume; + mKidneyPlasma has substance; mRemainder = 0; - mRemainder has substance_per_volume; + mRemainder has substance; mPlasmaVenous = (1000000*Metformin_Dose_in_Plasma_in_mg/(129.16*PlasmaVenous))*PlasmaVenous; - mPlasmaVenous has substance_per_volume; + mPlasmaVenous has substance; mHeart = 0; - mHeart has substance_per_volume; + mHeart has substance; mMuscle = 0; - mMuscle has substance_per_volume; + mMuscle has substance; mAdipose = 0; - mAdipose has substance_per_volume; + mAdipose has substance; mBrain = 0; - mBrain has substance_per_volume; + mBrain has substance; mFeces = 0; - mFeces has substance_per_volume; + mFeces has substance; mUrine = 0; - mUrine has substance_per_volume; + mUrine has substance; mIntestineLumen = 0; - mIntestineLumen has substance_per_volume; + mIntestineLumen has substance; mPlasmaArterial = 0; - mPlasmaArterial has substance_per_volume; + mPlasmaArterial has substance; mLung = 0; - mLung has substance_per_volume; + mLung has substance; mPortalVein = 0; - mPortalVein has substance_per_volume; + mPortalVein has substance; mStomach = 0; - mStomach has substance_per_volume; + mStomach has substance; mIntestineEnterocytes = 0; - mIntestineEnterocytes has substance_per_volume; + mIntestineEnterocytes has substance; mKidneyTissue = 0; - mKidneyTissue has substance_per_volume; + mKidneyTissue has substance; mIntestineVascular = 0; - mIntestineVascular has substance_per_volume; + mIntestineVascular has substance; mStomachLumen = 0; - mStomachLumen has substance_per_volume; + mStomachLumen has substance; mKidneyTubular = 0; - mKidneyTubular has substance_per_volume; + mKidneyTubular has substance; // Compartment initializations: IntestineLumen = 0.6; @@ -281,10 +281,10 @@ model *Zake2021___PBPK_model_of_metformin_in_mice__single_dose_peroral() unit volume = 1e-3 litre; unit length = metre; unit area = metre^2; - unit time_unit = time_unit; + unit time_unit = 3600e2 second; unit unit_1 = 1e-3 litre; unit extent = substance; - unit substance_per_volume = 1e-9 mole / 1e-3 litre; + unit substance_volume = 1e-9 mole * 1e-3 litre; // Display Names: unit_0 is "mg"; diff --git a/doc/examples/biomodels/Zake2021 - PBPK Metformin Human single PO dose.txt b/doc/examples/biomodels/BIOMD0000001028/Zake2021 - PBPK Metformin Human single PO dose.txt similarity index 99% rename from doc/examples/biomodels/Zake2021 - PBPK Metformin Human single PO dose.txt rename to doc/examples/biomodels/BIOMD0000001028/Zake2021 - PBPK Metformin Human single PO dose.txt index fdc1011b3..20c1b0714 100644 --- a/doc/examples/biomodels/Zake2021 - PBPK Metformin Human single PO dose.txt +++ b/doc/examples/biomodels/BIOMD0000001028/Zake2021 - PBPK Metformin Human single PO dose.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *PBPK_model_of_metformin_in_humans__single_PO_dose() // Compartments and Species: diff --git a/doc/examples/biomodels/Zake2021_Metformin_Human_single_PO_dose.txt b/doc/examples/biomodels/BIOMD0000001028/Zake2021_Metformin_Human_single_PO_dose.txt similarity index 97% rename from doc/examples/biomodels/Zake2021_Metformin_Human_single_PO_dose.txt rename to doc/examples/biomodels/BIOMD0000001028/Zake2021_Metformin_Human_single_PO_dose.txt index 5cfbc0d39..5644cd632 100644 --- a/doc/examples/biomodels/Zake2021_Metformin_Human_single_PO_dose.txt +++ b/doc/examples/biomodels/BIOMD0000001028/Zake2021_Metformin_Human_single_PO_dose.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zake2021___PBPK_model_of_metformin_in_humans__single_PO_dose() // Compartments and Species: @@ -122,47 +122,47 @@ model *Zake2021___PBPK_model_of_metformin_in_humans__single_PO_dose() // Species initializations: mLiver = 0; - mLiver has substance_per_volume; + mLiver has substance; mKidneyPlasma = 0; - mKidneyPlasma has substance_per_volume; + mKidneyPlasma has substance; mRemainder = 0; - mRemainder has substance_per_volume; + mRemainder has substance; mPlasmaVenous = 0; - mPlasmaVenous has substance_per_volume; + mPlasmaVenous has substance; mHeart = 0; - mHeart has substance_per_volume; + mHeart has substance; mMuscle = 0; - mMuscle has substance_per_volume; + mMuscle has substance; mAdipose = 0; - mAdipose has substance_per_volume; + mAdipose has substance; mBrain = 0; - mBrain has substance_per_volume; + mBrain has substance; mFeces = 0; - mFeces has substance_per_volume; + mFeces has substance; mUrineExternal = 0; - mUrineExternal has substance_per_volume; + mUrineExternal has substance; mIntestineLumen = 0; - mIntestineLumen has substance_per_volume; + mIntestineLumen has substance; mPlasmaArterial = 0; - mPlasmaArterial has substance_per_volume; + mPlasmaArterial has substance; mLung = 0; - mLung has substance_per_volume; + mLung has substance; mPortalVein = 0; - mPortalVein has substance_per_volume; + mPortalVein has substance; mStomach = 0; - mStomach has substance_per_volume; + mStomach has substance; mEnterocytes = 0; - mEnterocytes has substance_per_volume; + mEnterocytes has substance; mKidneyTissue = 0; - mKidneyTissue has substance_per_volume; + mKidneyTissue has substance; mIntestineVascular = 0; - mIntestineVascular has substance_per_volume; + mIntestineVascular has substance; mStomachLumen = 0; - mStomachLumen has substance_per_volume; + mStomachLumen has substance; mRBC = 0; - mRBC has substance_per_volume; + mRBC has substance; mKidneyTubular = 0; - mKidneyTubular has substance_per_volume; + mKidneyTubular has substance; // Compartment initializations: IntestineLumen = 500; @@ -295,13 +295,13 @@ model *Zake2021___PBPK_model_of_metformin_in_humans__single_PO_dose() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 3600e2 second; unit substance = 1e-9 mole; unit unit_0 = 1e-3 gram; unit unit_1 = 1e-3 litre; unit unit_2 = 1e-3 litre / 3600e2 second; unit extent = substance; - unit substance_per_volume = 1e-9 mole / 1e-3 litre; + unit substance_volume = 1e-9 mole * 1e-3 litre; // Display Names: time_unit is "time"; diff --git a/doc/examples/biomodels/Zake2021 - PBPK Metformin Human multiple PO dose.txt b/doc/examples/biomodels/BIOMD0000001029/Zake2021 - PBPK Metformin Human multiple PO dose.txt similarity index 99% rename from doc/examples/biomodels/Zake2021 - PBPK Metformin Human multiple PO dose.txt rename to doc/examples/biomodels/BIOMD0000001029/Zake2021 - PBPK Metformin Human multiple PO dose.txt index c92a478d8..d39259fdb 100644 --- a/doc/examples/biomodels/Zake2021 - PBPK Metformin Human multiple PO dose.txt +++ b/doc/examples/biomodels/BIOMD0000001029/Zake2021 - PBPK Metformin Human multiple PO dose.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *PBPK_model_of_metformin_in_humans__eight_PO_administrations_with_12h_interval() // Compartments and Species: diff --git a/doc/examples/biomodels/Zake2021_Metformin_Human_multiple_PO_dose.txt b/doc/examples/biomodels/BIOMD0000001029/Zake2021_Metformin_Human_multiple_PO_dose.txt similarity index 97% rename from doc/examples/biomodels/Zake2021_Metformin_Human_multiple_PO_dose.txt rename to doc/examples/biomodels/BIOMD0000001029/Zake2021_Metformin_Human_multiple_PO_dose.txt index 18857c43d..263726607 100644 --- a/doc/examples/biomodels/Zake2021_Metformin_Human_multiple_PO_dose.txt +++ b/doc/examples/biomodels/BIOMD0000001029/Zake2021_Metformin_Human_multiple_PO_dose.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zake2021___PBPK_model_of_metformin_in_humans__eight_PO_administrations_with_12h_interval() // Compartments and Species: @@ -125,47 +125,47 @@ model *Zake2021___PBPK_model_of_metformin_in_humans__eight_PO_administrations_wi // Species initializations: mLiver = 0; - mLiver has substance_per_volume; + mLiver has substance; mKidneyPlasma = 0; - mKidneyPlasma has substance_per_volume; + mKidneyPlasma has substance; mRemainder = 0; - mRemainder has substance_per_volume; + mRemainder has substance; mPlasmaVenous = 0; - mPlasmaVenous has substance_per_volume; + mPlasmaVenous has substance; mHeart = 0; - mHeart has substance_per_volume; + mHeart has substance; mMuscle = 0; - mMuscle has substance_per_volume; + mMuscle has substance; mAdipose = 0; - mAdipose has substance_per_volume; + mAdipose has substance; mBrain = 0; - mBrain has substance_per_volume; + mBrain has substance; mFeces = 0; - mFeces has substance_per_volume; + mFeces has substance; mUrineExternal = 0; - mUrineExternal has substance_per_volume; + mUrineExternal has substance; mIntestineLumen = 0; - mIntestineLumen has substance_per_volume; + mIntestineLumen has substance; mPlasmaArterial = 0; - mPlasmaArterial has substance_per_volume; + mPlasmaArterial has substance; mLung = 0; - mLung has substance_per_volume; + mLung has substance; mPortalVein = 0; - mPortalVein has substance_per_volume; + mPortalVein has substance; mStomach = 0; - mStomach has substance_per_volume; + mStomach has substance; mEnterocytes = 0; - mEnterocytes has substance_per_volume; + mEnterocytes has substance; mKidneyTissue = 0; - mKidneyTissue has substance_per_volume; + mKidneyTissue has substance; mIntestineVascular = 0; - mIntestineVascular has substance_per_volume; + mIntestineVascular has substance; mStomachLumen = 0; - mStomachLumen has substance_per_volume; + mStomachLumen has substance; mRBC = 0; - mRBC has substance_per_volume; + mRBC has substance; mKidneyTubular = 0; - mKidneyTubular has substance_per_volume; + mKidneyTubular has substance; // Compartment initializations: IntestineLumen = 500; @@ -298,13 +298,13 @@ model *Zake2021___PBPK_model_of_metformin_in_humans__eight_PO_administrations_wi unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 3600e2 second; unit substance = 1e-9 mole; unit unit_0 = 1e-3 gram; unit unit_1 = 1e-3 litre; unit unit_2 = 1e-3 litre / 3600e2 second; unit extent = substance; - unit substance_per_volume = 1e-9 mole / 1e-3 litre; + unit substance_volume = 1e-9 mole * 1e-3 litre; // Display Names: time_unit is "time"; diff --git a/doc/examples/biomodels/Sontag2017.txt b/doc/examples/biomodels/BIOMD0000001030/Sontag2017.txt similarity index 99% rename from doc/examples/biomodels/Sontag2017.txt rename to doc/examples/biomodels/BIOMD0000001030/Sontag2017.txt index 2d51e18aa..211d7dda5 100644 --- a/doc/examples/biomodels/Sontag2017.txt +++ b/doc/examples/biomodels/BIOMD0000001030/Sontag2017.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Sontag2017___Dynamic_model_of_immune_responses_to_antigen_presentation_by_tumor_or_pathogen() // Compartments and Species: diff --git a/doc/examples/biomodels/Al-Tuwairqi2020 - Phase I virotherapy.txt b/doc/examples/biomodels/BIOMD0000001031/Al-Tuwairqi2020 - Phase I virotherapy.txt similarity index 99% rename from doc/examples/biomodels/Al-Tuwairqi2020 - Phase I virotherapy.txt rename to doc/examples/biomodels/BIOMD0000001031/Al-Tuwairqi2020 - Phase I virotherapy.txt index 0363365d4..bcb714411 100644 --- a/doc/examples/biomodels/Al-Tuwairqi2020 - Phase I virotherapy.txt +++ b/doc/examples/biomodels/BIOMD0000001031/Al-Tuwairqi2020 - Phase I virotherapy.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Al_Tuwairqi2020___Dynamics_of_cancer_virotherapy() // Compartments and Species: diff --git a/doc/examples/biomodels/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment.txt b/doc/examples/biomodels/BIOMD0000001032/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment.txt similarity index 98% rename from doc/examples/biomodels/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment.txt rename to doc/examples/biomodels/BIOMD0000001032/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment.txt index 8e8d8acea..bda72add5 100644 --- a/doc/examples/biomodels/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment.txt +++ b/doc/examples/biomodels/BIOMD0000001032/Al-Tuwairqi2020 - Phase II radiovirotherapy treatment.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Al_Tuwairqi2020___Dynamics_of_cancer_radiovirotherapy() // Compartments and Species: @@ -16,7 +16,7 @@ model *Al_Tuwairqi2020___Dynamics_of_cancer_radiovirotherapy() damaged_cell_removal: damaged_cancer_cells => ; Whole_organism*alpha_3*damaged_cancer_cells; // Events: - radiotherapy: at time >= 35: alpha_3 = 0.9, alpha_2 = 0.5, alpha_1 = 0.5; + radiotherapy: at time >= 35: alpha_1 = 0.5, alpha_2 = 0.5, alpha_3 = 0.9; // Species initializations: uninfected_cancer_cells = 0.4; diff --git a/doc/examples/biomodels/Almuallem2020.txt b/doc/examples/biomodels/BIOMD0000001033/Almuallem2020.txt similarity index 99% rename from doc/examples/biomodels/Almuallem2020.txt rename to doc/examples/biomodels/BIOMD0000001033/Almuallem2020.txt index d1044413b..c275cea7f 100644 --- a/doc/examples/biomodels/Almuallem2020.txt +++ b/doc/examples/biomodels/BIOMD0000001033/Almuallem2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Almuallem2020___Virus_macrophage_tumour_interactions_in_oncolytic_viral_therapies() // Compartments and Species: diff --git a/doc/examples/biomodels/Bunimovich-Mendrazitsky2007.txt b/doc/examples/biomodels/BIOMD0000001034/Bunimovich-Mendrazitsky2007.txt similarity index 99% rename from doc/examples/biomodels/Bunimovich-Mendrazitsky2007.txt rename to doc/examples/biomodels/BIOMD0000001034/Bunimovich-Mendrazitsky2007.txt index 2775b85e8..507552b7e 100644 --- a/doc/examples/biomodels/Bunimovich-Mendrazitsky2007.txt +++ b/doc/examples/biomodels/BIOMD0000001034/Bunimovich-Mendrazitsky2007.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Bunimovich_Mendrazitsky2007___Mathematical_model_of_BCG_immunotherapy() // Compartments and Species: diff --git a/doc/examples/biomodels/Al-Tuwairqi2020 - Virotherapy.txt b/doc/examples/biomodels/BIOMD0000001035/Al-Tuwairqi2020 - Virotherapy.txt similarity index 99% rename from doc/examples/biomodels/Al-Tuwairqi2020 - Virotherapy.txt rename to doc/examples/biomodels/BIOMD0000001035/Al-Tuwairqi2020 - Virotherapy.txt index 2664136c9..4a11dd31f 100644 --- a/doc/examples/biomodels/Al-Tuwairqi2020 - Virotherapy.txt +++ b/doc/examples/biomodels/BIOMD0000001035/Al-Tuwairqi2020 - Virotherapy.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Al_Tuwairqi2020___Dynamics_of_cancer_virotherapy_with_immune_response() // Compartments and Species: diff --git a/doc/examples/biomodels/Cappuccio2007.txt b/doc/examples/biomodels/BIOMD0000001036/Cappuccio2007.txt similarity index 99% rename from doc/examples/biomodels/Cappuccio2007.txt rename to doc/examples/biomodels/BIOMD0000001036/Cappuccio2007.txt index 02302615f..4214163db 100644 --- a/doc/examples/biomodels/Cappuccio2007.txt +++ b/doc/examples/biomodels/BIOMD0000001036/Cappuccio2007.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Cappuccio2007___Tumor_immune_system_interactions_and_determination_of_the_optimal_therapeutic_protocol_in_immunotherapy() // Compartments and Species: diff --git a/doc/examples/biomodels/Alharbi2019 TNM.txt b/doc/examples/biomodels/BIOMD0000001037/Alharbi2019 TNM.txt similarity index 99% rename from doc/examples/biomodels/Alharbi2019 TNM.txt rename to doc/examples/biomodels/BIOMD0000001037/Alharbi2019 TNM.txt index 1b74adbee..3369730b7 100644 --- a/doc/examples/biomodels/Alharbi2019 TNM.txt +++ b/doc/examples/biomodels/BIOMD0000001037/Alharbi2019 TNM.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Alharbi2019___Tumor_normal_model__TNM__of_the_development_of_tumor_cells_and_their_impact_on_normal_cell_dynamics() // Compartments and Species: diff --git a/doc/examples/biomodels/Alharbi2019 TNVM.txt b/doc/examples/biomodels/BIOMD0000001038/Alharbi2019 TNVM.txt similarity index 99% rename from doc/examples/biomodels/Alharbi2019 TNVM.txt rename to doc/examples/biomodels/BIOMD0000001038/Alharbi2019 TNVM.txt index 1d3a1ff36..f0ae98dde 100644 --- a/doc/examples/biomodels/Alharbi2019 TNVM.txt +++ b/doc/examples/biomodels/BIOMD0000001038/Alharbi2019 TNVM.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Alharbi2019___Tumor_normal_vitamins_model__TNVM__of_the_effects_of_vitamins_on_delaying_the_growth_of_tumor_cells() // Compartments and Species: diff --git a/doc/examples/biomodels/Zake2021 - PBPK Metformin Mice IV single dose.txt b/doc/examples/biomodels/BIOMD0000001039/Zake2021 - PBPK Metformin Mice IV single dose.txt similarity index 99% rename from doc/examples/biomodels/Zake2021 - PBPK Metformin Mice IV single dose.txt rename to doc/examples/biomodels/BIOMD0000001039/Zake2021 - PBPK Metformin Mice IV single dose.txt index f64268608..bf08bedc5 100644 --- a/doc/examples/biomodels/Zake2021 - PBPK Metformin Mice IV single dose.txt +++ b/doc/examples/biomodels/BIOMD0000001039/Zake2021 - PBPK Metformin Mice IV single dose.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *PBPK_model_of_metformin_in_mice__single_dose_intavenous() // Compartments and Species: diff --git a/doc/examples/biomodels/Zake2021_Metformin_Mice_IV.txt b/doc/examples/biomodels/BIOMD0000001039/Zake2021_Metformin_Mice_IV.txt similarity index 97% rename from doc/examples/biomodels/Zake2021_Metformin_Mice_IV.txt rename to doc/examples/biomodels/BIOMD0000001039/Zake2021_Metformin_Mice_IV.txt index 0afc60bb7..197f3d1e6 100644 --- a/doc/examples/biomodels/Zake2021_Metformin_Mice_IV.txt +++ b/doc/examples/biomodels/BIOMD0000001039/Zake2021_Metformin_Mice_IV.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Zake2021___PBPK_model_of_metformin_in_mice__single_dose_intavenous() // Compartments and Species: @@ -110,45 +110,45 @@ model *Zake2021___PBPK_model_of_metformin_in_mice__single_dose_intavenous() // Species initializations: mLiver = 0; - mLiver has substance_per_volume; + mLiver has substance; mKidneyPlasma = 0; - mKidneyPlasma has substance_per_volume; + mKidneyPlasma has substance; mRemainder = 0; - mRemainder has substance_per_volume; + mRemainder has substance; mPlasmaVenous = (1000000*Metformin_Dose_in_Plasma_in_mg/(129.16*PlasmaVenous))*PlasmaVenous; - mPlasmaVenous has substance_per_volume; + mPlasmaVenous has substance; mHeart = 0; - mHeart has substance_per_volume; + mHeart has substance; mMuscle = 0; - mMuscle has substance_per_volume; + mMuscle has substance; mAdipose = 0; - mAdipose has substance_per_volume; + mAdipose has substance; mBrain = 0; - mBrain has substance_per_volume; + mBrain has substance; mFeces = 0; - mFeces has substance_per_volume; + mFeces has substance; mUrine = 0; - mUrine has substance_per_volume; + mUrine has substance; mIntestineLumen = 0; - mIntestineLumen has substance_per_volume; + mIntestineLumen has substance; mPlasmaArterial = 0; - mPlasmaArterial has substance_per_volume; + mPlasmaArterial has substance; mLung = 0; - mLung has substance_per_volume; + mLung has substance; mPortalVein = 0; - mPortalVein has substance_per_volume; + mPortalVein has substance; mStomach = 0; - mStomach has substance_per_volume; + mStomach has substance; mIntestineEnterocytes = 0; - mIntestineEnterocytes has substance_per_volume; + mIntestineEnterocytes has substance; mKidneyTissue = 0; - mKidneyTissue has substance_per_volume; + mKidneyTissue has substance; mIntestineVascular = 0; - mIntestineVascular has substance_per_volume; + mIntestineVascular has substance; mStomachLumen = 0; - mStomachLumen has substance_per_volume; + mStomachLumen has substance; mKidneyTubular = 0; - mKidneyTubular has substance_per_volume; + mKidneyTubular has substance; // Compartment initializations: IntestineLumen = 0.6; @@ -278,13 +278,13 @@ model *Zake2021___PBPK_model_of_metformin_in_mice__single_dose_intavenous() unit length = metre; unit area = metre^2; unit volume = 1e-3 litre; - unit time_unit = time_unit; + unit time_unit = 3600e2 second; unit substance = 1e-9 mole; unit unit_0 = 1e-3 gram; unit unit_1 = 1e-3 litre; unit unit_2 = 1e-3 litre / 3600e2 second; unit extent = substance; - unit substance_per_volume = 1e-9 mole / 1e-3 litre; + unit substance_volume = 1e-9 mole * 1e-3 litre; // Display Names: time_unit is "time"; diff --git a/doc/examples/biomodels/Kurlovics2021_single.txt b/doc/examples/biomodels/BIOMD0000001040/Kurlovics2021_single.txt similarity index 99% rename from doc/examples/biomodels/Kurlovics2021_single.txt rename to doc/examples/biomodels/BIOMD0000001040/Kurlovics2021_single.txt index 862dc1cf0..df496b929 100644 --- a/doc/examples/biomodels/Kurlovics2021_single.txt +++ b/doc/examples/biomodels/BIOMD0000001040/Kurlovics2021_single.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kurlovics2021___Metformin_partitioning_from_plasma_to_RBC___single_coefficient() // Compartments and Species: diff --git a/doc/examples/biomodels/Single.txt b/doc/examples/biomodels/BIOMD0000001040/Single.txt similarity index 99% rename from doc/examples/biomodels/Single.txt rename to doc/examples/biomodels/BIOMD0000001040/Single.txt index 37329beb8..82267372b 100644 --- a/doc/examples/biomodels/Single.txt +++ b/doc/examples/biomodels/BIOMD0000001040/Single.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Metformin_partitioning_between_plasma_and_RBC_with_a_single_K_diffusion_transport_rate_coefficient() // Compartments and Species: diff --git a/doc/examples/biomodels/Kimmel2021.txt b/doc/examples/biomodels/BIOMD0000001041/Kimmel2021.txt similarity index 99% rename from doc/examples/biomodels/Kimmel2021.txt rename to doc/examples/biomodels/BIOMD0000001041/Kimmel2021.txt index 2d636e898..75f6464e7 100644 --- a/doc/examples/biomodels/Kimmel2021.txt +++ b/doc/examples/biomodels/BIOMD0000001041/Kimmel2021.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kimmel2021___T_cell_competition_and_stochastic_extinction_events_in_CAR_T_cell_therapy() // Compartments and Species: diff --git a/doc/examples/biomodels/Makhlouf2020.txt b/doc/examples/biomodels/BIOMD0000001042/Makhlouf2020.txt similarity index 99% rename from doc/examples/biomodels/Makhlouf2020.txt rename to doc/examples/biomodels/BIOMD0000001042/Makhlouf2020.txt index 95fc68807..d34d1ca77 100644 --- a/doc/examples/biomodels/Makhlouf2020.txt +++ b/doc/examples/biomodels/BIOMD0000001042/Makhlouf2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Makhlouf2020___No_treatment_model_of_the_role_of_CD4_T_cells_in_tumor_immune_interactions() // Compartments and Species: diff --git a/doc/examples/biomodels/Wodarz2001.txt b/doc/examples/biomodels/BIOMD0000001043/Wodarz2001.txt similarity index 99% rename from doc/examples/biomodels/Wodarz2001.txt rename to doc/examples/biomodels/BIOMD0000001043/Wodarz2001.txt index c4b7804a5..cafc4cfe4 100644 --- a/doc/examples/biomodels/Wodarz2001.txt +++ b/doc/examples/biomodels/BIOMD0000001043/Wodarz2001.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Wodarz2001___Viruses_as_antitumor_weapons() // Compartments and Species: diff --git a/doc/examples/biomodels/Csikasz-Nagy2006.txt b/doc/examples/biomodels/BIOMD0000001044/Csikasz-Nagy2006.txt similarity index 99% rename from doc/examples/biomodels/Csikasz-Nagy2006.txt rename to doc/examples/biomodels/BIOMD0000001044/Csikasz-Nagy2006.txt index 83bf4a32c..a689bfa75 100644 --- a/doc/examples/biomodels/Csikasz-Nagy2006.txt +++ b/doc/examples/biomodels/BIOMD0000001044/Csikasz-Nagy2006.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Csikasz_Nagy2006___Mammalian_Cell_Cycle_model() // Compartments and Species: @@ -264,7 +264,7 @@ model *Csikasz_Nagy2006___Mammalian_Cell_Cycle_model() activation_of_Cdh1 is "activation of Cdh1"; inactivation__of_Cdh1 is "inactivation of Cdh1"; - # General layout options + // General layout options model.layout = on model.layout.size = {10, 10} model.layout.background = "#FFFFFFFF" diff --git a/doc/examples/biomodels/MODEL3897771820_url.txt b/doc/examples/biomodels/BIOMD0000001044/MODEL3897771820_url.txt similarity index 96% rename from doc/examples/biomodels/MODEL3897771820_url.txt rename to doc/examples/biomodels/BIOMD0000001044/MODEL3897771820_url.txt index ebf808ae8..6d9c69ec8 100644 --- a/doc/examples/biomodels/MODEL3897771820_url.txt +++ b/doc/examples/biomodels/BIOMD0000001044/MODEL3897771820_url.txt @@ -1,15 +1,14 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MODEL3897771820() // Compartments and Species: compartment cell; - species $APC in cell, APCP in cell, BCKI in cell, $Cdc14 in cell, Cdc20A in cell; - species Cdc20i in cell, $Cdc20T in cell, $Cdc25P in cell, CycB in cell; - species Cdh1 in cell, $Cdh1i in cell, CKI in cell, $CKIT in cell, pBCKI in cell; - species TriA in cell, TriE in cell, CycA in cell, $CycAT in cell, $CycBT in cell; - species pB in cell, $CycD in cell, Mass in cell, CycE in cell, $CycET in cell; - species $preMPF in cell, $TFB in cell, $TFE in cell, $TFI in cell, $TriB in cell; - species $Wee1 in cell; + species $APC in cell, APCP in cell, BCKI in cell, Cdc14 in cell, Cdc20A in cell; + species Cdc20i in cell, Cdc20T in cell, Cdc25P in cell, CycB in cell, Cdh1 in cell; + species $Cdh1i in cell, CKI in cell, CKIT in cell, pBCKI in cell, TriA in cell; + species TriE in cell, CycA in cell, CycAT in cell, CycBT in cell, pB in cell; + species CycD in cell, Mass in cell, CycE in cell, CycET in cell, preMPF in cell; + species TFB in cell, TFE in cell, TFI in cell, TriB in cell, Wee1 in cell; // Assignment Rules: APC := APCT - APCP; diff --git a/doc/examples/biomodels/Smith and moore2004-the SIR Model for Spread of Disease.txt b/doc/examples/biomodels/BIOMD0000001045/Smith and moore2004-the SIR Model for Spread of Disease.txt similarity index 99% rename from doc/examples/biomodels/Smith and moore2004-the SIR Model for Spread of Disease.txt rename to doc/examples/biomodels/BIOMD0000001045/Smith and moore2004-the SIR Model for Spread of Disease.txt index 857eeb62d..26cddfd55 100644 --- a/doc/examples/biomodels/Smith and moore2004-the SIR Model for Spread of Disease.txt +++ b/doc/examples/biomodels/BIOMD0000001045/Smith and moore2004-the SIR Model for Spread of Disease.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Smith_Moore2004___The_SIR_Model_for_Spread_of_Disease() // Compartments and Species: diff --git a/doc/examples/biomodels/MODEL8568434338_url.txt b/doc/examples/biomodels/BIOMD0000001046/MODEL8568434338_url.txt similarity index 99% rename from doc/examples/biomodels/MODEL8568434338_url.txt rename to doc/examples/biomodels/BIOMD0000001046/MODEL8568434338_url.txt index 8e6c71971..c47796d61 100644 --- a/doc/examples/biomodels/MODEL8568434338_url.txt +++ b/doc/examples/biomodels/BIOMD0000001046/MODEL8568434338_url.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *MAP() // Compartments and Species: diff --git a/doc/examples/biomodels/Raman2005_MAP.txt b/doc/examples/biomodels/BIOMD0000001046/Raman2005_MAP.txt similarity index 99% rename from doc/examples/biomodels/Raman2005_MAP.txt rename to doc/examples/biomodels/BIOMD0000001046/Raman2005_MAP.txt index b35aed47b..ebd56a871 100644 --- a/doc/examples/biomodels/Raman2005_MAP.txt +++ b/doc/examples/biomodels/BIOMD0000001046/Raman2005_MAP.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *M_MAP() // Compartments and Species: diff --git a/doc/examples/biomodels/delta_notch.txt b/doc/examples/biomodels/BIOMD0000001047/delta_notch.txt similarity index 99% rename from doc/examples/biomodels/delta_notch.txt rename to doc/examples/biomodels/BIOMD0000001047/delta_notch.txt index 55c7c6c6a..5b1146bd6 100644 --- a/doc/examples/biomodels/delta_notch.txt +++ b/doc/examples/biomodels/BIOMD0000001047/delta_notch.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Collier1996___Delta_Notch_intercellular_signalling_and_lateral_inhibition() // Compartments and Species: diff --git a/doc/examples/biomodels/cancer_therapy.txt b/doc/examples/biomodels/BIOMD0000001048/cancer_therapy.txt similarity index 99% rename from doc/examples/biomodels/cancer_therapy.txt rename to doc/examples/biomodels/BIOMD0000001048/cancer_therapy.txt index b49593747..becfbbb08 100644 --- a/doc/examples/biomodels/cancer_therapy.txt +++ b/doc/examples/biomodels/BIOMD0000001048/cancer_therapy.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Siddhartha2002___Kinetic_modelling_of_cancer_therapies() // Compartments and Species: diff --git a/doc/examples/biomodels/Tumor_cells_immune_system_competition.txt b/doc/examples/biomodels/BIOMD0000001052/Tumor_cells_immune_system_competition.txt similarity index 99% rename from doc/examples/biomodels/Tumor_cells_immune_system_competition.txt rename to doc/examples/biomodels/BIOMD0000001052/Tumor_cells_immune_system_competition.txt index ee05c3f73..22823e954 100644 --- a/doc/examples/biomodels/Tumor_cells_immune_system_competition.txt +++ b/doc/examples/biomodels/BIOMD0000001052/Tumor_cells_immune_system_competition.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Alharbi2020___Tumor_and_immune_system_competition() // Compartments and Species: diff --git a/doc/examples/biomodels/Garde2020.txt b/doc/examples/biomodels/BIOMD0000001053/Garde2020.txt similarity index 99% rename from doc/examples/biomodels/Garde2020.txt rename to doc/examples/biomodels/BIOMD0000001053/Garde2020.txt index ced47164c..01ee161a9 100644 --- a/doc/examples/biomodels/Garde2020.txt +++ b/doc/examples/biomodels/BIOMD0000001053/Garde2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Garde2020___metabolic_oscillations_in_Bacillus_subtilis_biofilms() // Compartments and Species: diff --git a/doc/examples/biomodels/fibrin_polymerization.txt b/doc/examples/biomodels/BIOMD0000001054/fibrin_polymerization.txt similarity index 99% rename from doc/examples/biomodels/fibrin_polymerization.txt rename to doc/examples/biomodels/BIOMD0000001054/fibrin_polymerization.txt index b65e88a3c..8f25ec961 100644 --- a/doc/examples/biomodels/fibrin_polymerization.txt +++ b/doc/examples/biomodels/BIOMD0000001054/fibrin_polymerization.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Pearce2021___Fibrin_Polymerization() // Compartments and Species: diff --git a/doc/examples/biomodels/Enzyme_clustering_in glucose_metabolism.txt b/doc/examples/biomodels/BIOMD0000001055/Enzyme_clustering_in glucose_metabolism.txt similarity index 99% rename from doc/examples/biomodels/Enzyme_clustering_in glucose_metabolism.txt rename to doc/examples/biomodels/BIOMD0000001055/Enzyme_clustering_in glucose_metabolism.txt index 572f096a9..49be6195a 100644 --- a/doc/examples/biomodels/Enzyme_clustering_in glucose_metabolism.txt +++ b/doc/examples/biomodels/BIOMD0000001055/Enzyme_clustering_in glucose_metabolism.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Jeon2018___Enzyme_clustering_in_Glucose_metabolism() // Compartments and Species: diff --git a/doc/examples/biomodels/chulian2021.txt b/doc/examples/biomodels/BIOMD0000001056/chulian2021.txt similarity index 99% rename from doc/examples/biomodels/chulian2021.txt rename to doc/examples/biomodels/BIOMD0000001056/chulian2021.txt index 4ea8f9839..a0b889b9e 100644 --- a/doc/examples/biomodels/chulian2021.txt +++ b/doc/examples/biomodels/BIOMD0000001056/chulian2021.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Chulian2021___feedback_signalling_in_B_lymphopoeisis() // Compartments and Species: diff --git a/doc/examples/biomodels/Nikolov2020.txt b/doc/examples/biomodels/BIOMD0000001057/Nikolov2020.txt similarity index 99% rename from doc/examples/biomodels/Nikolov2020.txt rename to doc/examples/biomodels/BIOMD0000001057/Nikolov2020.txt index cc2894e2d..9366da572 100644 --- a/doc/examples/biomodels/Nikolov2020.txt +++ b/doc/examples/biomodels/BIOMD0000001057/Nikolov2020.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Nikolov2020___p53_miR34_model() // Compartments and Species: diff --git a/doc/examples/biomodels/Novak2022.txt b/doc/examples/biomodels/BIOMD0000001058/Novak2022.txt similarity index 99% rename from doc/examples/biomodels/Novak2022.txt rename to doc/examples/biomodels/BIOMD0000001058/Novak2022.txt index 62242b6ed..75fc440ad 100644 --- a/doc/examples/biomodels/Novak2022.txt +++ b/doc/examples/biomodels/BIOMD0000001058/Novak2022.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Novak2022___Mitotic_kinase_oscillation() // Compartments and Species: diff --git a/doc/examples/biomodels/Stucki2005.txt b/doc/examples/biomodels/BIOMD0000001059/Stucki2005.txt similarity index 98% rename from doc/examples/biomodels/Stucki2005.txt rename to doc/examples/biomodels/BIOMD0000001059/Stucki2005.txt index 5e09497dd..b4e30fc8b 100644 --- a/doc/examples/biomodels/Stucki2005.txt +++ b/doc/examples/biomodels/BIOMD0000001059/Stucki2005.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Stucki2005___caspase_3_metabolism() // Compartments and Species: @@ -32,8 +32,8 @@ model *Stucki2005___caspase_3_metabolism() // Events: Release_of_SMAC: at time == 2000: k7 = 0.025; - cascade__1: at (cascade <= 20) && (c3 >= 4.5): k17 = 0.01, k10_cascade = 0.001, k4 = 0.001; - cascade__2: at cascade > 20: k4 = 0, k17 = 0, k10_cascade = 0; + cascade__1: at (cascade <= 20) && (c3 >= 4.5): k4 = 0.001, k10_cascade = 0.001, k17 = 0.01; + cascade__2: at cascade > 20: k10_cascade = 0, k17 = 0, k4 = 0; // Species initializations: pc3 = 0.1; diff --git a/doc/examples/biomodels/Frank2021.txt b/doc/examples/biomodels/BIOMD0000001060/Frank2021.txt similarity index 99% rename from doc/examples/biomodels/Frank2021.txt rename to doc/examples/biomodels/BIOMD0000001060/Frank2021.txt index 44b79f9a9..77a4c2066 100644 --- a/doc/examples/biomodels/Frank2021.txt +++ b/doc/examples/biomodels/BIOMD0000001060/Frank2021.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Frank2021___Macrophage_polarization() // Compartments and Species: diff --git a/doc/examples/biomodels/Canto-Encalada2022-FBA+of+simultaneous+degradation+of+ammonia+and+pollutants.txt b/doc/examples/biomodels/BIOMD0000001061/Canto-Encalada2022-FBA+of+simultaneous+degradation+of+ammonia+and+pollutants.txt similarity index 99% rename from doc/examples/biomodels/Canto-Encalada2022-FBA+of+simultaneous+degradation+of+ammonia+and+pollutants.txt rename to doc/examples/biomodels/BIOMD0000001061/Canto-Encalada2022-FBA+of+simultaneous+degradation+of+ammonia+and+pollutants.txt index 19cfefa56..ad5e6a907 100644 --- a/doc/examples/biomodels/Canto-Encalada2022-FBA+of+simultaneous+degradation+of+ammonia+and+pollutants.txt +++ b/doc/examples/biomodels/BIOMD0000001061/Canto-Encalada2022-FBA+of+simultaneous+degradation+of+ammonia+and+pollutants.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *ChemoModelGrowth() // Compartments and Species: diff --git a/doc/examples/biomodels/iDK1463.txt b/doc/examples/biomodels/BIOMD0000001062/iDK1463.txt similarity index 99% rename from doc/examples/biomodels/iDK1463.txt rename to doc/examples/biomodels/BIOMD0000001062/iDK1463.txt index 6497d6d71..0f73102a3 100644 --- a/doc/examples/biomodels/iDK1463.txt +++ b/doc/examples/biomodels/BIOMD0000001062/iDK1463.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *iDK1463() // Compartments and Species: @@ -9132,7 +9132,7 @@ model *iDK1463() R_KARA2.geneProductAssociation = G_ECOLIN_RS21680; R_ACCOAC.geneProductAssociation = G_ECOLIN_RS13425 && G_ECOLIN_RS18660 && G_ECOLIN_RS26055 && G_ECOLIN_RS01005; R_NADK.geneProductAssociation = G_ECOLIN_RS14770; - R_GLXCL.geneProductAssociation = G_ECOLIN_RS02955; + R_GLXCL.geneProductAssociation = G_ECOLIN_RS02955; R_ICHORS_copy2.geneProductAssociation = G_ECOLIN_RS13190; R_SUCBZS.geneProductAssociation = G_ECOLIN_RS13170; R_DHBD.geneProductAssociation = G_ECOLIN_RS03270; @@ -24715,7 +24715,7 @@ model *iDK1463() G_ECOLIN_RS13055.sboTerm = 243 R_GPDDA5pp.sboTerm = 176 R_G3PStex.sboTerm = 185 - R_FEOXAMR1.sboTerm = 176 + R_FEOXAMR1.sboTerm = 176 G_ECOLIN_RS25060.sboTerm = 243 R_FEOXAMR2.sboTerm = 176 R_FEOXAMR3.sboTerm = 176 diff --git a/doc/examples/biomodels/yeast-GEM.txt b/doc/examples/biomodels/BIOMD0000001063/yeast-GEM.txt similarity index 99% rename from doc/examples/biomodels/yeast-GEM.txt rename to doc/examples/biomodels/BIOMD0000001063/yeast-GEM.txt index a7f5ed740..40b8a0cef 100644 --- a/doc/examples/biomodels/yeast-GEM.txt +++ b/doc/examples/biomodels/BIOMD0000001063/yeast-GEM.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *M_yeastGEM_v8__46__5__46__0() // Compartments and Species: @@ -15518,7 +15518,7 @@ model *M_yeastGEM_v8__46__5__46__0() s_1110__91__m__93__.charge = 0; s_1111__91__er__93__.charge = 0; s_1112__91__m__93__.charge = 0; - s_1116__91__er__93__.charge = 0; + s_1116__91__er__93__.charge = 0; s_1117__91__g__93__.charge = 0; s_1118__91__m__93__.charge = 0; s_1119__91__er__93__.charge = 0; @@ -29948,7 +29948,7 @@ model *M_yeastGEM_v8__46__5__46__0() s_3406__91__n__93__.sboTerm = 247 s_3407__91__n__93__.sboTerm = 247 s_3408__91__ce__93__.sboTerm = 247 - s_3409__91__ce__93__.sboTerm = 247 + s_3409__91__ce__93__.sboTerm = 247 s_3410__91__ce__93__.sboTerm = 247 s_3411__91__ce__93__.sboTerm = 247 s_3412__91__ce__93__.sboTerm = 247 @@ -35647,7 +35647,7 @@ model *M_yeastGEM_v8__46__5__46__0() r_4341.sboTerm = 655 r_4342.sboTerm = 176 r_4343.sboTerm = 655 - r_4344.sboTerm = 176 + r_4344.sboTerm = 176 r_4345.sboTerm = 176 r_4346.sboTerm = 655 r_4347.sboTerm = 176 diff --git a/doc/examples/biomodels/Kim2011_VvuMBEL943.txt b/doc/examples/biomodels/BIOMD0000001064/Kim2011_VvuMBEL943.txt similarity index 99% rename from doc/examples/biomodels/Kim2011_VvuMBEL943.txt rename to doc/examples/biomodels/BIOMD0000001064/Kim2011_VvuMBEL943.txt index 7684eaf53..92a1abb74 100644 --- a/doc/examples/biomodels/Kim2011_VvuMBEL943.txt +++ b/doc/examples/biomodels/BIOMD0000001064/Kim2011_VvuMBEL943.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Kim2010_VvuMBEL943_V_vulnificus() // Compartments and Species: diff --git a/doc/examples/biomodels/vonDassow2000_1x4.timecourse1.txt b/doc/examples/biomodels/BIOMD0000001065/vonDassow2000_1x4.timecourse1.txt similarity index 99% rename from doc/examples/biomodels/vonDassow2000_1x4.timecourse1.txt rename to doc/examples/biomodels/BIOMD0000001065/vonDassow2000_1x4.timecourse1.txt index ce857e15f..159be8ae8 100644 --- a/doc/examples/biomodels/vonDassow2000_1x4.timecourse1.txt +++ b/doc/examples/biomodels/BIOMD0000001065/vonDassow2000_1x4.timecourse1.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Segment_Polarity_Network_model_on_1x4_grid() // Compartments and Species: @@ -1001,7 +1001,7 @@ model *Segment_Polarity_Network_model_on_1x4_grid() unit length = 1 / dimensionless^-0; unit area = 1 / dimensionless^-0; unit volume = 1 / dimensionless^-0; - unit time_unit = time_unit; + unit time_unit = 1 / dimensionless^-0; unit substance = 1 / dimensionless^-0; unit unit_0 = 1 / dimensionless^-0; unit extent = substance; @@ -1664,7 +1664,7 @@ model *Segment_Polarity_Network_model_on_1x4_grid() R30b_6_0_3 is "R30b_6_0,3"; R31_6_0_3 is "R31_6_0,3"; - # General layout options + // General layout options model.layout = on model.layout.size = {1000, 1000} model.layout.background = "#FFFFFFFF" diff --git a/doc/examples/biomodels/Phillips2013.txt b/doc/examples/biomodels/BIOMD0000001072/Phillips2013.txt similarity index 98% rename from doc/examples/biomodels/Phillips2013.txt rename to doc/examples/biomodels/BIOMD0000001072/Phillips2013.txt index 1c25a1b59..8a7844994 100644 --- a/doc/examples/biomodels/Phillips2013.txt +++ b/doc/examples/biomodels/BIOMD0000001072/Phillips2013.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Phillips2013___physiologically_based_modeling_explaining_Mammalian_rest_activity_patterns() // Compartments and Species: @@ -28,8 +28,8 @@ model *Phillips2013___physiologically_based_modeling_explaining_Mammalian_rest_a X_Y: => Y; individual*(-X*((day/(f*tau_c))^2 + h*B)/kappa); // Events: - asleep: at 0 after (ModelValue_1/(1 + exp(ModelValue_2 - V_m/ModelValue_3))) <= 1: Omega = 0.03, Theta = 1; - awake: at 0 after (ModelValue_1/(1 + exp(ModelValue_2 - V_m/ModelValue_3))) > 1: Omega = 1, Theta = 0; + asleep: at 0 after (ModelValue_1/(1 + exp(ModelValue_2 - V_m/ModelValue_3))) <= 1: Theta = 1, Omega = 0.03; + awake: at 0 after (ModelValue_1/(1 + exp(ModelValue_2 - V_m/ModelValue_3))) > 1: Theta = 0, Omega = 1; day_0: at 0 after time < (12*3600): I = 1; night: at 0 after time >= (12*3600): I = 0; diff --git a/doc/examples/biomodels/Adlung2021 _model_jakstat_pa.txt b/doc/examples/biomodels/BIOMD0000001077/Adlung2021 _model_jakstat_pa.txt similarity index 99% rename from doc/examples/biomodels/Adlung2021 _model_jakstat_pa.txt rename to doc/examples/biomodels/BIOMD0000001077/Adlung2021 _model_jakstat_pa.txt index 002101327..6d90b34d1 100644 --- a/doc/examples/biomodels/Adlung2021 _model_jakstat_pa.txt +++ b/doc/examples/biomodels/BIOMD0000001077/Adlung2021 _model_jakstat_pa.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Adlung2021___Cell_to_cell_variability_in_JAK2_STAT5_pathway() // Compartments and Species: diff --git a/doc/examples/biomodels/model_jakstat_pa.txt b/doc/examples/biomodels/BIOMD0000001077/model_jakstat_pa.txt similarity index 99% rename from doc/examples/biomodels/model_jakstat_pa.txt rename to doc/examples/biomodels/BIOMD0000001077/model_jakstat_pa.txt index db05aef21..920d0bbad 100644 --- a/doc/examples/biomodels/model_jakstat_pa.txt +++ b/doc/examples/biomodels/BIOMD0000001077/model_jakstat_pa.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *model_() // Compartments and Species: diff --git a/doc/examples/biomodels/Hammaren-Geissen2022_PPToP_Model12_withParameterSets.txt b/doc/examples/biomodels/BIOMD0000001078/Hammaren-Geissen2022_PPToP_Model12_withParameterSets.txt similarity index 99% rename from doc/examples/biomodels/Hammaren-Geissen2022_PPToP_Model12_withParameterSets.txt rename to doc/examples/biomodels/BIOMD0000001078/Hammaren-Geissen2022_PPToP_Model12_withParameterSets.txt index 28890beec..8df2e0017 100644 --- a/doc/examples/biomodels/Hammaren-Geissen2022_PPToP_Model12_withParameterSets.txt +++ b/doc/examples/biomodels/BIOMD0000001078/Hammaren-Geissen2022_PPToP_Model12_withParameterSets.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *Hammaren_Geissen2022_PPToP_Model12() // Compartments and Species: diff --git a/doc/examples/biomodels/PPToP_Model12.txt b/doc/examples/biomodels/BIOMD0000001078/PPToP_Model12.txt similarity index 99% rename from doc/examples/biomodels/PPToP_Model12.txt rename to doc/examples/biomodels/BIOMD0000001078/PPToP_Model12.txt index cffb71211..fa04fe9f1 100644 --- a/doc/examples/biomodels/PPToP_Model12.txt +++ b/doc/examples/biomodels/BIOMD0000001078/PPToP_Model12.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *PPToP_Model12() // Compartments and Species: diff --git a/doc/examples/biomodels/DeBoeck2021_cellcycle_bistableapc.txt b/doc/examples/biomodels/BIOMD0000001079/DeBoeck2021_cellcycle_bistableapc.txt similarity index 98% rename from doc/examples/biomodels/DeBoeck2021_cellcycle_bistableapc.txt rename to doc/examples/biomodels/BIOMD0000001079/DeBoeck2021_cellcycle_bistableapc.txt index 93c17cf9f..c0f4e9577 100644 --- a/doc/examples/biomodels/DeBoeck2021_cellcycle_bistableapc.txt +++ b/doc/examples/biomodels/BIOMD0000001079/DeBoeck2021_cellcycle_bistableapc.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *DeBoeck2021___Modular_approach_to_modeling_the_cell_cycle__simple_cell_cycle_model() // Compartments and Species: diff --git a/doc/examples/biomodels/cellcycle_bistableapc.txt b/doc/examples/biomodels/BIOMD0000001079/cellcycle_bistableapc.txt similarity index 97% rename from doc/examples/biomodels/cellcycle_bistableapc.txt rename to doc/examples/biomodels/BIOMD0000001079/cellcycle_bistableapc.txt index df175bedd..d34cf4e42 100644 --- a/doc/examples/biomodels/cellcycle_bistableapc.txt +++ b/doc/examples/biomodels/BIOMD0000001079/cellcycle_bistableapc.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *cellcycle_bistableapc() // Compartments and Species: diff --git a/doc/examples/biomodels/DeBoeck2021_cellcycle_threeswitches.txt b/doc/examples/biomodels/BIOMD0000001080/DeBoeck2021_cellcycle_threeswitches.txt similarity index 99% rename from doc/examples/biomodels/DeBoeck2021_cellcycle_threeswitches.txt rename to doc/examples/biomodels/BIOMD0000001080/DeBoeck2021_cellcycle_threeswitches.txt index 9123751ac..c45b24a79 100644 --- a/doc/examples/biomodels/DeBoeck2021_cellcycle_threeswitches.txt +++ b/doc/examples/biomodels/BIOMD0000001080/DeBoeck2021_cellcycle_threeswitches.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *DeBoeck2021___Modular_approach_to_modeling_the_cell_cycle__5_ODE_model_with_3_bistable_switches() // Compartments and Species: diff --git a/doc/examples/biomodels/cellcycle_threeswitches.txt b/doc/examples/biomodels/BIOMD0000001080/cellcycle_threeswitches.txt similarity index 98% rename from doc/examples/biomodels/cellcycle_threeswitches.txt rename to doc/examples/biomodels/BIOMD0000001080/cellcycle_threeswitches.txt index bf096a0cf..5d475d23a 100644 --- a/doc/examples/biomodels/cellcycle_threeswitches.txt +++ b/doc/examples/biomodels/BIOMD0000001080/cellcycle_threeswitches.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.0 +// Created by libAntimony v3.2.0 model *cellcycle_switches() // Compartments and Species: diff --git a/src/antimony.tab.cpp b/src/antimony.tab.cpp index 2b7ff192e..c9096a39e 100644 --- a/src/antimony.tab.cpp +++ b/src/antimony.tab.cpp @@ -382,22 +382,23 @@ enum yysymbol_kind_t YYSYMBOL_126_11 = 126, /* $@11 */ YYSYMBOL_colonret = 127, /* colonret */ YYSYMBOL_eventmodifications = 128, /* eventmodifications */ - YYSYMBOL_assignmentlist = 129, /* assignmentlist */ - YYSYMBOL_deletion = 130, /* deletion */ - YYSYMBOL_unitdef = 131, /* unitdef */ - YYSYMBOL_constraint = 132, /* constraint */ - YYSYMBOL_objective = 133, /* objective */ - YYSYMBOL_maxormin = 134, /* maxormin */ - YYSYMBOL_stringlist = 135, /* stringlist */ - YYSYMBOL_annotationBlock = 136, /* annotationBlock */ - YYSYMBOL_137_12 = 137, /* $@12 */ - YYSYMBOL_annotations = 138, /* annotations */ - YYSYMBOL_cvterm = 139, /* cvterm */ - YYSYMBOL_toplevel_sbo = 140, /* toplevel_sbo */ - YYSYMBOL_modulename = 141, /* modulename */ - YYSYMBOL_functionname = 142, /* functionname */ - YYSYMBOL_modulecvterm = 143, /* modulecvterm */ - YYSYMBOL_functioncvterm = 144 /* functioncvterm */ + YYSYMBOL_assignmententry = 129, /* assignmententry */ + YYSYMBOL_assignmentlist = 130, /* assignmentlist */ + YYSYMBOL_deletion = 131, /* deletion */ + YYSYMBOL_unitdef = 132, /* unitdef */ + YYSYMBOL_constraint = 133, /* constraint */ + YYSYMBOL_objective = 134, /* objective */ + YYSYMBOL_maxormin = 135, /* maxormin */ + YYSYMBOL_stringlist = 136, /* stringlist */ + YYSYMBOL_annotationBlock = 137, /* annotationBlock */ + YYSYMBOL_138_12 = 138, /* $@12 */ + YYSYMBOL_annotations = 139, /* annotations */ + YYSYMBOL_cvterm = 140, /* cvterm */ + YYSYMBOL_toplevel_sbo = 141, /* toplevel_sbo */ + YYSYMBOL_modulename = 142, /* modulename */ + YYSYMBOL_functionname = 143, /* functionname */ + YYSYMBOL_modulecvterm = 144, /* modulecvterm */ + YYSYMBOL_functioncvterm = 145 /* functioncvterm */ }; typedef enum yysymbol_kind_t yysymbol_kind_t; @@ -725,16 +726,16 @@ union yyalloc /* YYFINAL -- State number of the termination state. */ #define YYFINAL 2 /* YYLAST -- Last index in YYTABLE. */ -#define YYLAST 1267 +#define YYLAST 1343 /* YYNTOKENS -- Number of terminals. */ #define YYNTOKENS 70 /* YYNNTS -- Number of nonterminals. */ -#define YYNNTS 75 +#define YYNNTS 76 /* YYNRULES -- Number of rules. */ -#define YYNRULES 273 +#define YYNRULES 284 /* YYNSTATES -- Number of states. */ -#define YYNSTATES 525 +#define YYNSTATES 545 /* YYMAXUTOK -- Last valid token kind. */ #define YYMAXUTOK 301 @@ -794,28 +795,29 @@ static const yytype_int16 yyrline[] = 213, 216, 217, 218, 228, 229, 230, 233, 234, 242, 249, 250, 261, 264, 265, 266, 267, 270, 271, 272, 273, 274, 277, 278, 281, 282, 283, 284, 287, 294, - 301, 306, 316, 326, 340, 354, 368, 384, 385, 386, - 387, 389, 390, 391, 394, 395, 396, 399, 400, 401, - 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, - 412, 415, 423, 431, 439, 447, 455, 465, 466, 467, - 468, 469, 470, 474, 475, 476, 477, 478, 481, 482, - 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, - 493, 494, 497, 498, 501, 502, 503, 504, 505, 506, - 507, 510, 511, 512, 513, 514, 517, 518, 519, 522, - 523, 524, 525, 526, 527, 528, 529, 530, 533, 534, - 537, 537, 538, 538, 542, 543, 544, 545, 546, 550, - 551, 555, 559, 560, 561, 562, 563, 564, 565, 566, - 567, 570, 571, 572, 573, 574, 575, 576, 577, 578, - 581, 582, 584, 585, 586, 587, 590, 591, 592, 593, - 594, 597, 598, 599, 600, 603, 604, 605, 606, 609, - 610, 611, 612, 616, 617, 618, 619, 620, 623, 624, - 625, 628, 631, 634, 635, 638, 639, 640, 641, 642, - 645, 646, 649, 649, 650, 650, 651, 651, 652, 652, - 655, 656, 659, 660, 667, 668, 669, 670, 671, 674, - 675, 678, 693, 694, 695, 696, 697, 698, 701, 704, - 705, 708, 709, 710, 712, 712, 715, 716, 721, 722, - 723, 726, 737, 747, 757, 771, 785, 799, 815, 817, - 821, 822, 823, 824 + 301, 306, 316, 330, 344, 358, 372, 388, 389, 390, + 391, 393, 394, 395, 398, 399, 400, 403, 404, 405, + 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, + 416, 419, 427, 435, 443, 451, 459, 467, 475, 485, + 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, + 496, 497, 498, 502, 503, 504, 505, 506, 509, 510, + 511, 512, 513, 514, 515, 516, 517, 518, 519, 520, + 521, 522, 525, 526, 529, 530, 531, 532, 533, 534, + 535, 538, 539, 540, 541, 542, 545, 546, 547, 550, + 551, 552, 553, 554, 555, 556, 557, 558, 561, 562, + 565, 565, 566, 566, 570, 571, 572, 573, 574, 578, + 579, 583, 587, 588, 589, 590, 591, 592, 593, 594, + 595, 598, 599, 600, 601, 602, 603, 604, 605, 606, + 609, 610, 612, 613, 614, 615, 618, 619, 620, 621, + 622, 625, 626, 627, 628, 631, 632, 633, 634, 637, + 638, 639, 640, 644, 645, 646, 647, 648, 651, 652, + 653, 656, 659, 662, 663, 666, 667, 668, 669, 670, + 673, 674, 677, 677, 678, 678, 679, 679, 680, 680, + 683, 684, 687, 688, 695, 696, 698, 699, 700, 701, + 704, 705, 708, 723, 724, 725, 726, 727, 728, 731, + 734, 735, 738, 739, 740, 742, 742, 745, 746, 751, + 752, 753, 756, 767, 777, 787, 801, 815, 829, 845, + 847, 851, 852, 853, 854 }; #endif @@ -858,10 +860,10 @@ static const char *const yytname[] = "reactioninit", "dnainit", "geneinit", "operatorinit", "compartmentinit", "varconstinit", "unitinit", "dnadef", "dnastrand", "dnamiddle", "event", "$@8", "$@9", "$@10", "$@11", "colonret", "eventmodifications", - "assignmentlist", "deletion", "unitdef", "constraint", "objective", - "maxormin", "stringlist", "annotationBlock", "$@12", "annotations", - "cvterm", "toplevel_sbo", "modulename", "functionname", "modulecvterm", - "functioncvterm", YY_NULLPTR + "assignmententry", "assignmentlist", "deletion", "unitdef", "constraint", + "objective", "maxormin", "stringlist", "annotationBlock", "$@12", + "annotations", "cvterm", "toplevel_sbo", "modulename", "functionname", + "modulecvterm", "functioncvterm", YY_NULLPTR }; static const char * @@ -871,12 +873,12 @@ yysymbol_name (yysymbol_kind_t yysymbol) } #endif -#define YYPACT_NINF (-423) +#define YYPACT_NINF (-433) #define yypact_value_is_default(Yyn) \ ((Yyn) == YYPACT_NINF) -#define YYTABLE_NINF (-98) +#define YYTABLE_NINF (-100) #define yytable_value_is_error(Yyn) \ 0 @@ -885,59 +887,61 @@ yysymbol_name (yysymbol_kind_t yysymbol) STATE-NUM. */ static const yytype_int16 yypact[] = { - -423, 685, -423, -423, 203, 47, -423, 29, 367, -423, - -423, -423, -423, -423, 357, 480, 20, 279, 47, 47, - 469, -423, 469, 268, 23, 469, 469, -27, -423, -423, - 202, 355, 469, 413, 416, 283, 47, 1214, -423, -423, - -423, -423, -423, 977, 87, 142, -423, -423, 99, 495, - 370, -423, 99, 99, 99, 99, -30, -3, 95, 101, - 107, 114, 190, 205, 224, 99, 99, -423, 47, 99, - 86, 99, 99, -423, -423, 99, -423, -423, -423, -423, - -423, 480, -423, -423, 80, -423, -423, -423, -423, -423, - -423, 80, -423, -423, -423, 748, 171, -423, -423, 53, - -423, 281, -423, -423, -423, 159, 469, 469, 469, 469, - 469, -423, 469, 247, -423, 216, 47, 80, -423, -423, - 257, 271, 295, -423, -423, -423, -423, -423, -423, 349, - 30, 339, -423, 382, 385, 204, -423, -423, -423, 388, - -423, 394, -423, 469, -423, 12, 469, 469, 469, 469, - 469, 469, 469, 366, -423, 294, 185, -423, 47, 80, - 47, -423, 213, -423, 553, 400, -423, 401, 371, 21, - 47, 426, 13, -423, -423, -423, -423, 469, 469, 469, - 469, 469, 469, 469, 469, 469, -423, -423, 244, -423, - 47, -423, -423, -423, 946, -423, -423, 946, 946, 448, - 946, 464, 470, -423, -423, -423, -423, -423, -423, -423, - -423, -423, -423, -423, -423, -423, 417, -423, -423, 80, - -423, -423, -423, 422, -423, -423, 424, 428, 946, 946, - -423, -423, -423, -423, -423, -423, -423, 469, 244, 440, - -423, 125, 99, 451, 140, 489, 125, 99, 449, 465, - 172, 519, 485, 1169, 125, 484, 487, -423, -423, -423, - -423, -423, -423, -423, -423, -423, 469, -423, -423, -423, - 533, 496, 80, 34, 946, -423, -423, 277, 946, 175, - -423, 503, -423, 321, 495, 370, -423, -423, -423, 47, - 426, -423, 14, -423, -423, -423, -423, -423, -423, -423, - -423, -423, -423, -423, 80, 946, 508, 535, -423, -423, - 946, 946, 163, -423, 192, -33, -423, -423, 946, -423, - -423, 946, -423, 562, 215, -423, -423, 47, 561, 340, - 221, -423, -423, -423, 80, 383, 527, 1169, 570, 356, - 222, 47, 480, 531, 310, 608, -423, -423, -423, -423, - -423, 946, -423, 233, 47, 47, -423, 814, -423, 946, - 115, 16, 946, 946, 80, 80, 880, -423, 880, 271, - -423, -423, -423, -423, -423, 576, -423, 27, 946, 946, - 946, -423, -423, 540, 398, 80, 536, -423, -423, -423, - -423, -423, -423, 99, 125, -423, 506, 47, 1004, 538, - -423, -423, 99, 125, 436, 225, -423, -423, -423, 946, - 946, -423, 496, 80, 80, 946, -423, -423, 449, -423, - 17, -423, 47, -423, 880, -423, 496, -33, 946, 542, - -423, 182, -423, -423, 99, 47, 199, -423, -423, 207, - -423, 80, 482, -423, 209, -423, -423, 1169, 946, -33, - 505, 880, -423, 880, 80, -423, 27, -423, -423, 77, - 946, 99, 80, -423, 539, -423, 586, -423, 1169, -423, - 539, -423, 1059, -423, 27, -423, -423, 880, -423, -423, - 946, 522, -423, -423, 99, -423, 80, 242, 260, 544, - 1114, 325, 360, -423, -33, -423, 207, -423, 90, 97, - 129, -423, 36, -423, 580, -423, -423, -423, 27, -423, - 47, -423, 47, -423, 47, 80, -423, 590, -423, 80, - -423, -423, -423, 80, -423 + -433, 764, -433, -433, 209, 255, -433, 160, 491, -433, + -433, -433, -433, -433, 502, 405, 83, 671, 255, 255, + 454, -433, 454, 421, 391, 454, 454, -34, -433, -433, + 221, 383, 454, 534, 544, 368, 255, 1290, -433, -433, + -433, -433, -433, 440, 219, 268, -433, -433, 58, 611, + 35, -433, 58, 58, 58, 58, 52, 107, 117, 130, + 157, 172, 194, 218, 256, 58, 58, -433, 255, 58, + 68, 58, 58, -433, -433, 58, -433, -433, -433, -433, + -433, 46, -433, -433, 287, 71, -433, -433, -433, -433, + -433, -433, 71, -433, -433, -433, 604, 184, -433, -433, + 116, -433, 313, -433, -433, -433, 16, 454, 454, 454, + 454, 454, -433, 454, 13, -433, 48, 255, 71, -433, + -433, 202, 84, 149, -433, -433, -433, -433, -433, -433, + 296, 65, 217, -433, 304, 310, 161, -433, -433, -433, + 329, -433, 343, -433, 454, -433, 44, 454, 454, 454, + 454, 454, 454, 454, 315, -433, 477, 124, -433, 255, + 71, 255, -433, 181, -433, 227, 322, -433, 324, 320, + 39, 425, 255, -433, 287, 21, -433, -433, -433, -433, + 454, 454, 454, 454, 454, 454, 454, 454, 454, -433, + -433, 210, -433, 255, -433, -433, -433, 967, -433, 71, + -433, 71, 967, 967, 359, 967, 379, 385, -433, -433, + -433, -433, -433, -433, -433, -433, -433, -433, -433, -433, + -433, 349, -433, -433, 71, -433, -433, -433, 365, -433, + -433, 367, 369, 967, 967, -433, -433, -433, -433, -433, + -433, -433, 454, 210, 372, -433, 196, 58, 341, 60, + 389, 196, 58, 467, 394, 79, 447, 413, 1245, 196, + 412, 426, -433, -433, -433, -433, -433, -433, -433, -433, + -433, 454, -433, -433, -433, 493, 453, 71, 212, 967, + -433, -433, 298, 967, 330, 82, -433, 463, -433, 515, + 611, 47, -433, -433, -433, 255, 287, 473, 255, 287, + -433, 31, 255, 835, 550, -433, -433, -433, -433, -433, + -433, -433, -433, -433, -433, -433, 71, 967, 461, 503, + -433, -433, 967, 967, 233, -433, 399, 338, -433, -433, + 967, -433, -433, 967, -433, 525, 186, -433, -433, 255, + 533, 387, 121, -433, -433, -433, 71, 300, 492, 1245, + 535, 395, 148, 255, 405, 513, 140, 1025, -433, -433, + -433, -433, -433, 967, -433, 176, 255, 255, -433, 901, + -433, 967, 64, -433, 37, 967, 967, 71, 71, 255, + 71, 71, 71, 835, -433, 255, -433, 835, 84, -433, + -433, -433, -433, -433, 555, -433, 76, 967, 967, 967, + -433, -433, 529, 396, 71, 543, -433, -433, -433, -433, + -433, -433, 58, 196, -433, 561, 255, 1080, 562, -433, + -433, 58, 196, 450, 152, -433, -433, -433, 967, 967, + -433, 453, 71, 71, 967, -433, -433, 467, -433, 62, + 835, -433, 71, -433, 835, 71, -433, 453, 338, 967, + 563, -433, 85, -433, 346, -433, 58, 255, 299, -433, + -433, 12, -433, 71, 536, -433, 316, -433, -433, 1245, + 967, 338, 548, 835, -433, -433, 835, -433, 76, -433, + -433, 123, 76, 254, 967, 58, 71, -433, 565, -433, + 607, -433, 1245, -433, 565, -433, 1135, -433, 76, -433, + -433, 835, -433, 346, 967, 967, 255, -433, -433, -433, + -433, 58, -433, 71, 479, 489, 566, 1190, 507, 532, + -433, 338, 346, 12, -433, -433, 144, -433, 25, -433, + 573, -433, -433, -433, 76, -433, 255, 71, -433, 614, + -433, 71, 346, 71, -433 }; /* YYDEFACT[STATE-NUM] -- Default reduction number in state STATE-NUM. @@ -945,85 +949,87 @@ static const yytype_int16 yypact[] = means the default is an error. */ static const yytype_int16 yydefact[] = { - 2, 0, 1, 14, 0, 0, 138, 0, 37, 108, - 103, 104, 106, 107, 0, 46, 0, 0, 0, 0, - 0, 15, 0, 45, 0, 0, 0, 0, 249, 250, - 0, 0, 0, 0, 0, 0, 0, 0, 137, 136, + 2, 0, 1, 14, 0, 0, 148, 0, 37, 118, + 113, 114, 116, 117, 0, 46, 0, 0, 0, 0, + 0, 15, 0, 45, 0, 0, 0, 0, 260, 261, + 0, 0, 0, 0, 0, 0, 0, 0, 147, 146, 3, 4, 6, 43, 86, 0, 13, 5, 0, 0, - 0, 90, 0, 0, 0, 0, 162, 167, 163, 164, - 165, 166, 168, 169, 170, 0, 0, 213, 219, 0, - 0, 0, 0, 108, 12, 0, 11, 7, 8, 9, - 10, 0, 105, 37, 40, 134, 135, 132, 108, 131, - 133, 98, 108, 254, 108, 222, 0, 46, 45, 43, - 44, 47, 203, 108, 108, 0, 0, 0, 0, 0, - 0, 188, 0, 0, 209, 215, 216, 239, 191, 182, - 0, 0, 0, 27, 30, 29, 195, 180, 16, 0, - 0, 0, 152, 0, 0, 19, 26, 25, 199, 0, - 186, 0, 171, 0, 175, 212, 0, 0, 0, 0, - 0, 0, 0, 0, 208, 0, 37, 220, 0, 99, - 0, 108, 0, 108, 0, 0, 77, 0, 0, 0, - 0, 97, 0, 78, 89, 79, 80, 0, 0, 0, - 0, 0, 0, 0, 0, 0, 83, 81, 217, 82, - 0, 84, 87, 88, 248, 85, 108, 148, 242, 256, - 245, 0, 0, 125, 124, 126, 127, 130, 128, 111, - 108, 112, 109, 113, 121, 108, 0, 108, 129, 110, - 116, 117, 232, 0, 108, 108, 0, 0, 244, 246, - 108, 205, 193, 184, 197, 201, 173, 0, 218, 0, - 251, 0, 0, 0, 0, 0, 0, 0, 154, 23, - 0, 0, 0, 0, 0, 0, 0, 174, 108, 204, - 192, 183, 196, 200, 187, 172, 0, 38, 39, 41, - 0, 258, 42, 0, 241, 147, 144, 141, 140, 0, - 108, 0, 108, 97, 0, 0, 214, 108, 108, 0, - 100, 108, 0, 108, 178, 181, 185, 189, 194, 198, - 202, 206, 210, 221, 240, 243, 0, 0, 119, 120, - 224, 122, 0, 118, 0, 0, 108, 51, 48, 108, - 108, 247, 177, 0, 0, 273, 269, 34, 0, 0, - 0, 270, 268, 157, 155, 0, 0, 0, 0, 0, - 0, 34, 37, 0, 0, 0, 55, 54, 58, 108, - 108, 211, 176, 0, 0, 0, 108, 226, 150, 145, - 0, 0, 139, 146, 101, 102, 52, 108, 52, 0, - 255, 232, 114, 108, 115, 0, 230, 0, 207, 49, - 50, 262, 252, 0, 0, 35, 0, 261, 69, 67, - 70, 68, 263, 0, 0, 159, 0, 34, 0, 0, - 61, 62, 0, 0, 0, 0, 20, 57, 56, 190, - 179, 260, 259, 143, 142, 149, 108, 232, 154, 108, - 0, 108, 0, 93, 52, 95, 257, 0, 123, 0, - 231, 0, 223, 253, 108, 0, 0, 272, 271, 52, - 158, 156, 0, 24, 0, 60, 59, 0, 228, 0, - 0, 52, 108, 52, 53, 92, 0, 108, 108, 0, - 31, 108, 36, 264, 0, 265, 0, 153, 0, 63, - 0, 64, 0, 232, 0, 159, 94, 52, 96, 225, - 233, 234, 28, 33, 32, 74, 71, 0, 0, 0, - 0, 0, 0, 18, 0, 227, 52, 91, 0, 0, - 0, 266, 0, 267, 0, 22, 65, 66, 0, 151, - 0, 237, 0, 235, 0, 72, 75, 0, 161, 160, - 229, 238, 236, 73, 76 + 0, 90, 0, 0, 0, 0, 172, 177, 173, 174, + 175, 176, 178, 179, 180, 0, 0, 223, 229, 0, + 0, 0, 0, 118, 12, 0, 11, 7, 8, 9, + 10, 0, 37, 115, 102, 40, 144, 145, 142, 118, + 141, 143, 100, 118, 265, 118, 232, 0, 46, 45, + 43, 44, 47, 213, 118, 118, 0, 0, 0, 0, + 0, 0, 198, 0, 0, 219, 225, 226, 250, 201, + 192, 0, 0, 0, 27, 30, 29, 205, 190, 16, + 0, 0, 0, 162, 0, 0, 19, 26, 25, 209, + 0, 196, 0, 181, 0, 185, 222, 0, 0, 0, + 0, 0, 0, 0, 0, 218, 0, 37, 230, 0, + 101, 0, 118, 0, 118, 0, 0, 77, 0, 0, + 0, 0, 0, 118, 99, 0, 78, 89, 79, 80, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 83, + 81, 227, 82, 0, 84, 87, 88, 259, 85, 103, + 118, 104, 158, 253, 267, 256, 0, 0, 135, 134, + 136, 137, 140, 138, 121, 118, 122, 119, 123, 131, + 118, 0, 118, 139, 120, 126, 127, 242, 0, 118, + 118, 0, 0, 255, 257, 118, 215, 203, 194, 207, + 211, 183, 0, 228, 0, 262, 0, 0, 0, 0, + 0, 0, 0, 164, 23, 0, 0, 0, 0, 0, + 0, 0, 184, 118, 214, 202, 193, 206, 210, 197, + 182, 0, 38, 39, 41, 0, 269, 42, 0, 252, + 157, 154, 151, 150, 0, 0, 118, 0, 118, 99, + 0, 0, 224, 118, 118, 0, 108, 0, 0, 105, + 118, 0, 0, 52, 0, 118, 188, 191, 195, 199, + 204, 208, 212, 216, 220, 231, 251, 254, 0, 0, + 129, 130, 234, 132, 0, 128, 0, 0, 118, 51, + 48, 118, 118, 258, 187, 0, 0, 284, 280, 34, + 0, 0, 0, 281, 279, 167, 165, 0, 0, 0, + 0, 0, 0, 34, 37, 0, 0, 0, 55, 54, + 58, 118, 118, 221, 186, 0, 0, 0, 118, 236, + 160, 155, 0, 118, 0, 149, 156, 109, 112, 0, + 110, 106, 107, 52, 118, 0, 97, 52, 0, 266, + 242, 124, 118, 125, 0, 240, 244, 217, 49, 50, + 273, 263, 0, 0, 35, 0, 272, 69, 67, 70, + 68, 274, 0, 0, 169, 0, 34, 0, 0, 61, + 62, 0, 0, 0, 0, 20, 57, 56, 200, 189, + 271, 270, 153, 152, 159, 118, 242, 164, 118, 0, + 52, 118, 111, 93, 52, 53, 95, 268, 0, 133, + 0, 241, 0, 246, 233, 264, 118, 0, 0, 283, + 282, 52, 168, 166, 0, 24, 0, 60, 59, 0, + 238, 0, 0, 52, 118, 98, 52, 92, 244, 118, + 118, 244, 244, 0, 31, 118, 36, 275, 0, 276, + 0, 163, 0, 63, 0, 64, 0, 242, 244, 169, + 94, 52, 96, 235, 243, 245, 244, 247, 249, 28, + 33, 32, 74, 71, 0, 0, 0, 0, 0, 0, + 18, 0, 237, 52, 91, 248, 0, 277, 0, 278, + 0, 22, 65, 66, 244, 161, 0, 72, 75, 0, + 171, 170, 239, 73, 76 }; /* YYPGOTO[NTERM-NUM]. */ static const yytype_int16 yypgoto[] = { - -423, -423, -423, -423, -423, -423, -423, -423, -423, -423, - 145, -327, -1, 2, 15, 28, -295, -335, 0, -326, - 137, 139, 6, -423, -45, -39, 328, 395, -423, 4, - 51, -423, -423, -423, -423, -423, 193, 143, -423, -423, - -423, -423, -423, -423, -423, -423, -423, -423, -423, -423, - 453, 606, -423, -423, -423, -423, -423, -419, -362, -422, - -423, 414, -423, -423, 476, -99, -423, -423, -423, -423, - -423, -423, -423, -423, -423 + -433, -433, -433, -433, -433, -433, -433, -433, -433, -433, + 150, -327, -1, 0, 6, 567, -151, -337, 4, -340, + 143, 146, 7, -433, -48, -40, 213, 414, -433, 15, + 142, -433, -433, -433, -433, -433, 201, 147, -433, -433, + -433, -433, -433, -433, -433, -433, -433, -433, -433, -433, + 476, 624, -433, -433, -433, -433, -433, -317, -376, -138, + -432, -433, 416, -433, -433, 482, -83, -433, -433, -433, + -433, -433, -433, -433, -433, -433 }; /* YYDEFGOTO[NTERM-NUM]. */ static const yytype_int16 yydefgoto[] = { - 0, 1, 40, 41, 252, 253, 336, 337, 42, 243, - 459, 384, 99, 100, 101, 102, 423, 345, 346, 392, - 487, 488, 347, 48, 49, 50, 274, 312, 220, 221, - 51, 52, 53, 54, 418, 248, 335, 439, 55, 56, + 0, 1, 40, 41, 257, 258, 348, 349, 42, 248, + 483, 403, 224, 101, 102, 103, 386, 357, 358, 411, + 514, 515, 359, 48, 49, 50, 279, 324, 225, 226, + 51, 52, 53, 54, 437, 253, 347, 461, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, - 67, 68, 69, 222, 371, 417, 473, 377, 315, 432, - 70, 275, 71, 72, 73, 254, 74, 199, 307, 75, - 76, 77, 78, 79, 80 + 67, 68, 69, 227, 390, 436, 497, 482, 327, 453, + 454, 70, 280, 71, 72, 73, 259, 74, 204, 319, + 75, 76, 77, 78, 79, 80 }; /* YYTABLE[YYPACT[STATE-NUM]] -- What to do in state STATE-NUM. If @@ -1031,264 +1037,280 @@ static const yytype_int16 yydefgoto[] = number is the opposite. If YYTABLE_NINF, syntax error. */ static const yytype_int16 yytable[] = { - 43, 46, 398, 44, 84, 172, 91, 47, 456, 427, - 169, 92, 94, 401, 404, 105, 45, 115, 117, 103, - 168, 168, 241, 168, 168, 155, 375, 128, 376, 177, - 474, 246, 5, 5, 479, 145, 170, 83, 83, 5, - 123, 5, 159, 245, 83, 114, 83, 155, 118, 171, - 119, 516, 495, 126, 127, 449, 178, 271, 124, 5, - 138, 140, 142, 144, 83, 154, 155, 188, 85, 86, - 442, 125, 258, 425, 87, 508, 511, 513, 354, 293, - 367, 104, 421, 452, 240, 196, 520, 291, 521, 88, - 522, 6, 430, 155, 219, -44, 158, 89, 90, 166, - 6, 517, 5, 173, 174, 175, 176, 83, 482, 5, - 465, 494, 472, 6, 83, 238, 186, 187, 471, 284, - 189, 191, 192, 193, 292, 285, 195, 5, -44, 455, - 170, -44, 83, 490, 231, 232, 233, 234, 235, 6, - 236, 5, 38, 39, 467, 190, 83, -44, -44, -44, - 160, 38, 39, 328, 179, 510, 476, 272, 478, 273, - 180, 277, 512, 283, 38, 39, 181, 290, 171, 91, - 159, 257, 155, 182, 259, 260, 261, 262, 263, 264, - 265, 419, 497, 161, 324, 338, 162, 5, 223, 304, - 38, 39, 83, 219, 514, 155, 219, 219, 270, 219, - 329, 509, 163, 164, 165, 294, 295, 296, 297, 298, - 299, 300, 301, 302, 463, 129, 388, 251, 81, 130, - 230, 372, 373, 389, 469, 5, 388, 219, 219, 155, - 83, 394, 339, 389, 390, 356, 393, 402, 251, 240, - 361, 403, 458, 157, 390, 360, 131, 334, 411, 183, - 422, 373, 43, 391, 412, 44, 374, 155, 240, 132, - 82, -17, 464, 391, 184, 322, 466, 276, 45, 382, - 426, 303, 470, 219, 239, 240, 240, 219, 91, 240, - 383, 120, 159, 185, 171, 121, 355, 240, 364, 365, - 155, 5, 325, 326, 352, 5, 83, 331, 332, 237, - 83, 500, 106, 97, 219, 348, 501, 97, 107, 219, - 219, 267, 122, 108, 98, 420, 109, 219, 98, 502, - 219, 268, 224, 134, 503, 240, 385, 405, 269, 110, - 111, 112, 113, 5, 155, 143, 43, 95, 83, 44, - 385, 225, 226, 227, 43, 407, 94, 44, 157, 242, - 219, 408, 45, 413, 414, 387, 219, 388, 219, 171, - 45, 219, 219, 133, 389, 219, 244, 219, 134, 5, - 96, 400, 135, 388, 83, 390, 431, 219, 219, 219, - 389, 97, 5, 5, 500, 170, 289, 83, 83, 506, - 136, 390, 98, 247, 391, 441, 385, 43, 407, 249, - 44, 194, 250, 137, 408, 255, 85, 86, 219, 219, - 391, 256, 87, 45, 219, 93, 197, 334, 266, 502, - 198, 454, 200, 219, 507, 5, 139, 219, 5, 141, - 83, 228, 229, 83, 462, 89, 90, 97, 5, 155, - 97, 395, 396, 83, 437, 438, 43, 219, 98, 44, - 219, 98, 219, 445, 446, 431, 434, 435, 82, 219, - 288, 5, 45, 486, 333, 306, 83, 43, 308, 486, - 44, 43, 407, 431, 44, 309, 219, 313, 408, 219, - 219, 5, 316, 45, 319, 461, 83, 45, 320, 43, - 407, 278, 44, 97, 447, 435, 408, 431, 431, 515, - 323, 167, 168, 519, 98, 45, 330, 431, 327, 431, - 483, 431, 461, 523, 10, 11, 12, 13, 5, 85, - 86, 440, -21, 83, 305, 87, 201, 202, 203, 204, - 205, 206, 207, 208, 5, 483, 340, 209, 310, 83, - 468, 435, 341, 311, 349, 311, 211, 350, 89, 90, - 353, 5, 212, 318, 485, 324, 83, 213, 321, 167, - 358, 85, 86, 475, 396, 5, 370, 87, 279, 369, - 83, 280, 10, 11, 12, 13, 214, 381, 386, 215, - 18, 498, 216, 499, 397, 217, 351, 399, 132, 218, - 89, 90, 5, 429, 433, 518, 436, 83, 444, 28, - 29, 281, 457, 489, 504, 524, 484, 491, 357, 492, - 359, 450, 314, 282, 4, 362, 363, 286, 496, 366, - 5, 368, 6, 7, 116, 342, 9, 10, 11, 12, - 13, 14, 15, 16, 17, 18, 19, 20, 317, 406, - 287, 0, 22, 98, 378, 25, 26, 379, 380, 0, - 0, 0, 0, 0, 28, 29, 343, 344, 32, 33, - 34, 35, 0, 36, 37, 0, 0, 0, 0, 0, - 0, 0, 0, 38, 39, 0, 0, 409, 410, 0, - 0, 0, 0, 0, 415, 2, 3, 0, 0, 0, - 0, 4, 0, 0, 0, 424, 0, 5, 0, 6, - 7, 428, 8, 9, 10, 11, 12, 13, 14, 15, - 16, 17, 18, 19, 20, 0, 0, 21, 0, 22, - 23, 24, 25, 26, 0, 0, 0, 27, 0, 0, - 0, 28, 29, 30, 31, 32, 33, 34, 35, 0, - 36, 37, 0, 0, 448, 0, 0, 451, 0, 453, - 38, 39, 201, 202, 203, 204, 205, 206, 207, 208, - 5, 0, 460, 209, 210, 83, 0, 0, 0, 0, - 0, 0, 211, 0, 0, 0, 0, 0, 212, 0, - 477, 0, 0, 213, 0, 480, 481, 85, 86, 460, - 0, 0, 0, 87, 0, 0, 0, 0, 0, 0, - 0, 0, 214, 0, 0, 215, 0, 0, 216, 0, - 0, 217, 0, 0, 0, 218, 89, 90, 201, 202, - 203, 204, 205, 206, 207, 208, 5, 0, 0, 209, - 416, 83, 0, 0, 0, 0, 0, 0, 211, 0, - 0, 0, 0, 0, 212, 0, 0, 0, 0, 213, - 0, 0, 0, 85, 86, 0, 0, 0, 0, 87, - 0, 0, 0, 0, 0, 0, 0, 0, 214, 0, - 0, 215, 0, 0, 216, 0, 0, 217, 0, 0, - 0, 218, 89, 90, 201, 202, 203, 204, 205, 206, - 207, 208, 5, 0, 0, 209, 0, 83, 0, 0, - 0, 0, 0, 0, 211, 0, 0, 0, 0, 0, - 212, 0, 0, 0, 0, 213, 0, 0, 0, 85, - 86, 0, 0, 422, 0, 87, 0, 0, 0, 0, - 0, 0, 0, 0, 214, 0, 0, 215, 0, 0, - 216, 0, 0, 217, 0, 0, 0, 218, 89, 90, - 201, 202, 203, 204, 205, 206, 207, 208, 5, 0, - 0, 209, 0, 83, 0, 0, 0, 0, 0, 0, - 211, 0, 0, 0, 0, 0, 212, 0, 0, 0, - 0, 213, 0, -97, -97, 85, 86, 0, 0, 5, - 155, 87, 0, 0, 156, 0, -97, -97, -97, -97, - 214, 0, 0, 215, 157, 0, 216, 0, 0, 217, - 4, 0, 0, 218, 89, 90, 5, 0, 6, 7, - 158, 342, 9, 10, 11, 12, 13, 14, 15, 16, - 17, 18, 19, 20, 0, 443, 0, 0, 22, 98, - 0, 25, 26, 0, 0, 0, 0, 0, 0, 0, - 28, 29, 343, 344, 32, 33, 34, 35, 0, 36, - 37, 0, 0, 0, 0, 4, 0, 0, 0, 38, - 39, 5, 0, 6, 7, 0, 342, 9, 10, 11, - 12, 13, 14, 15, 16, 17, 18, 19, 20, 0, - 493, 0, 0, 22, 98, 0, 25, 26, 0, 0, - 0, 0, 0, 0, 0, 28, 29, 343, 344, 32, - 33, 34, 35, 0, 36, 37, 0, 0, 0, 0, - 4, 0, 0, 0, 38, 39, 5, 0, 6, 7, - 0, 342, 9, 10, 11, 12, 13, 14, 15, 16, - 17, 18, 19, 20, 0, 505, 0, 0, 22, 98, - 0, 25, 26, 0, 0, 0, 0, 0, 0, 0, - 28, 29, 343, 344, 32, 33, 34, 35, 0, 36, - 37, 0, 0, 0, 0, 4, 0, 0, 0, 38, - 39, 5, 0, 6, 7, 0, 342, 9, 10, 11, - 12, 13, 14, 15, 16, 17, 18, 19, 20, 0, - 0, 0, 0, 22, 98, 0, 25, 26, 0, 0, - 0, 0, 0, 0, 0, 28, 29, 343, 344, 32, - 33, 34, 35, 0, 36, 37, 5, 0, 0, 0, - 0, 83, 0, 0, 38, 39, 0, 146, 97, 0, - 0, 0, 0, 147, 0, 0, 0, 0, 148, 98, - 0, 149, 0, 0, 0, 0, 0, 0, 0, 0, - 0, 0, 0, 0, 150, 151, 152, 153 + 43, 44, 175, 84, 85, 46, 92, 45, 47, 170, + 396, 420, 417, 100, 448, 106, 100, 116, 118, 100, + 129, 100, 93, 95, 100, 100, 423, 304, 169, 156, + 104, 100, 100, 100, 100, 146, 100, 304, 169, 246, + 538, 171, 160, 304, 169, 171, 503, 5, 251, 174, + 172, 5, 82, 171, 172, 385, 82, 156, 5, 5, + 471, 156, 172, 82, 82, 242, 522, 191, 304, 169, + 171, 490, 6, 340, 276, 158, 5, 235, 250, 172, + 199, 82, 6, 201, 156, 86, 87, 305, 5, 464, + 539, 88, 350, 82, 5, 5, 200, 384, 156, 82, + 82, 173, 542, 441, 263, 300, 100, 100, 100, 100, + 100, 180, 100, 373, 90, 91, 243, 290, 489, 245, + 341, 521, 301, 38, 39, 291, 495, 193, 474, 156, + 438, 478, 496, 38, 39, 5, 412, 275, 245, 351, + 82, 451, 368, 100, 105, 480, 100, 100, 100, 100, + 100, 100, 100, 135, 498, 517, 5, 424, 277, 159, + 278, 82, 282, 421, 289, 256, 181, 296, 299, 174, + 84, 92, 5, 160, 256, 245, 182, 82, 245, 100, + 100, 100, 100, 100, 100, 100, 100, 100, 506, 183, + 167, 430, 316, 5, 176, 177, 178, 179, 82, 86, + 87, 228, 245, 247, 534, 88, 245, 189, 190, 536, + 6, 192, 194, 195, 196, 245, 184, 198, -17, 244, + 89, 5, 96, 156, 81, 156, 82, -44, 90, 91, + 245, 185, 443, 284, 130, 281, 446, 315, 131, 5, + 401, 100, 285, 374, 82, 286, 10, 11, 12, 13, + 372, 402, 346, 186, 18, 336, 366, 43, 44, 413, + -44, 38, 39, -44, 45, 132, 83, 5, 6, 422, + 100, 252, 82, 28, 29, 287, 161, 187, 133, -44, + -44, -44, 431, 84, 92, 509, 197, 288, 160, 475, + 174, 391, 392, 477, 377, 378, 380, 381, 382, 5, + 156, 199, 202, 296, 82, 447, 203, 367, 205, 162, + 491, 156, 163, 249, 487, 188, 407, 233, 234, 38, + 39, 254, 500, 408, 439, 502, 297, 255, 164, 165, + 166, 493, 5, 407, 409, 298, 5, 82, 404, 295, + 408, 82, 5, 507, 508, 302, 260, 82, 43, 44, + 524, 409, 404, 410, 229, 45, 43, 44, 414, 415, + 261, 426, 488, 45, 427, 432, 433, 271, 525, 95, + 410, 174, 535, 230, 231, 232, 318, 283, 442, 494, + 5, 83, 294, 320, 445, 82, 303, 83, 337, 338, + 321, 134, 98, 343, 344, 452, 135, 394, 339, 395, + 136, 360, 406, 99, 407, 481, 342, 395, 124, 325, + 419, 408, 407, 317, 463, 404, 43, 44, 137, 408, + 144, 426, 409, 45, 427, 328, 125, 331, 322, 332, + 409, 138, 335, 323, 121, 323, 346, 5, 122, 126, + 302, 410, 82, 330, 86, 87, -99, -99, 333, 410, + 88, -21, 5, 156, 456, 457, 486, 157, 392, -99, + -99, -99, -99, 393, 352, 123, 5, 158, 43, 44, + 353, 82, 361, 90, 91, 45, 363, 452, 98, 5, + 452, 452, 345, 159, 82, 5, 362, 513, 379, 99, + 82, 43, 44, 513, 272, 43, 44, 452, 45, 369, + 426, 371, 45, 427, 273, 452, 375, 376, 469, 457, + 365, 274, 336, 383, 5, 97, 43, 44, 387, 82, + 370, 426, 388, 45, 427, 537, 98, 5, 156, 541, + 86, 87, 82, 452, 389, 543, 88, 99, 526, 94, + 400, 397, 158, 527, 398, 399, 5, 140, 528, 416, + 405, 82, 418, 529, 459, 460, 5, 142, 98, 90, + 91, 82, 5, 467, 468, 295, 526, 82, 98, 99, + 133, 532, 450, 5, 428, 429, 462, 5, 82, 99, + 512, 434, 82, 455, 115, 5, 440, 119, 540, 120, + 82, 528, 127, 128, 492, 457, 533, 444, 485, 139, + 141, 143, 145, 458, 155, 449, 499, 415, 206, 207, + 208, 209, 210, 211, 212, 213, 5, 168, 169, 214, + 215, 82, 466, 479, 516, 510, 530, 485, 216, 544, + 10, 11, 12, 13, 217, 511, 326, 518, 472, 218, + 519, 292, 117, 86, 87, 329, 523, 293, 470, 88, + 0, 473, 0, 510, 476, 0, 0, 0, 219, 0, + 0, 220, 0, 0, 221, 0, 0, 222, 0, 484, + 0, 223, 90, 91, 236, 237, 238, 239, 240, 0, + 241, 0, 0, 5, 0, 0, 0, 501, 82, 0, + 0, 0, 504, 505, 107, 98, 0, 0, 484, 0, + 108, 0, 0, 0, 0, 109, 99, 0, 110, 0, + 0, 262, 0, 0, 264, 265, 266, 267, 268, 269, + 270, 111, 112, 113, 114, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 306, 307, 308, + 309, 310, 311, 312, 313, 314, 0, 0, 0, 0, + 0, 0, 0, 0, 2, 3, 0, 0, 0, 0, + 4, 0, 0, 0, 0, 0, 5, 0, 6, 7, + 0, 8, 9, 10, 11, 12, 13, 14, 15, 16, + 17, 18, 19, 20, 0, 0, 21, 0, 22, 23, + 24, 25, 26, 0, 0, 0, 27, 0, 0, 334, + 28, 29, 30, 31, 32, 33, 34, 35, 0, 36, + 37, 0, 0, 0, 0, 0, 0, 0, 0, 38, + 39, 0, 0, 0, 0, 0, 0, 0, 364, 206, + 207, 208, 209, 210, 211, 212, 213, 5, 0, 0, + 214, 0, 82, 0, 0, 0, 0, 0, 0, 216, + 0, 0, 0, 0, 0, 217, 0, 0, 0, 0, + 218, 0, 0, 0, 86, 87, 0, 0, 385, 0, + 88, 0, 0, 0, 0, 0, 0, 0, 0, 219, + 0, 0, 220, 0, 0, 221, 0, 0, 222, 0, + 0, 0, 223, 90, 91, 206, 207, 208, 209, 210, + 211, 212, 213, 5, 0, 0, 214, 435, 82, 0, + 0, 0, 0, 0, 0, 216, 0, 0, 0, 0, + 0, 217, 0, 0, 0, 0, 218, 0, 0, 0, + 86, 87, 0, 0, 0, 0, 88, 0, 0, 0, + 0, 0, 0, 0, 0, 219, 0, 0, 220, 0, + 0, 221, 0, 0, 222, 0, 0, 0, 223, 90, + 91, 206, 207, 208, 209, 210, 211, 212, 213, 5, + 0, 0, 214, 0, 82, 0, 0, 0, 0, 0, + 0, 216, 0, 0, 0, 0, 0, 217, 0, 0, + 0, 0, 218, 0, 0, 0, 86, 87, 0, 0, + 0, 0, 88, 0, 0, 0, 0, 0, 0, 0, + 0, 219, 0, 0, 220, 0, 0, 221, 0, 0, + 222, 4, 0, 0, 223, 90, 91, 5, 0, 6, + 7, 0, 354, 9, 10, 11, 12, 13, 14, 15, + 16, 17, 18, 19, 20, 0, 425, 0, 0, 22, + 99, 0, 25, 26, 0, 0, 0, 0, 0, 0, + 0, 28, 29, 355, 356, 32, 33, 34, 35, 0, + 36, 37, 0, 0, 0, 0, 4, 0, 0, 0, + 38, 39, 5, 0, 6, 7, 0, 354, 9, 10, + 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, + 0, 465, 0, 0, 22, 99, 0, 25, 26, 0, + 0, 0, 0, 0, 0, 0, 28, 29, 355, 356, + 32, 33, 34, 35, 0, 36, 37, 0, 0, 0, + 0, 4, 0, 0, 0, 38, 39, 5, 0, 6, + 7, 0, 354, 9, 10, 11, 12, 13, 14, 15, + 16, 17, 18, 19, 20, 0, 520, 0, 0, 22, + 99, 0, 25, 26, 0, 0, 0, 0, 0, 0, + 0, 28, 29, 355, 356, 32, 33, 34, 35, 0, + 36, 37, 0, 0, 0, 0, 4, 0, 0, 0, + 38, 39, 5, 0, 6, 7, 0, 354, 9, 10, + 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, + 0, 531, 0, 0, 22, 99, 0, 25, 26, 0, + 0, 0, 0, 0, 0, 0, 28, 29, 355, 356, + 32, 33, 34, 35, 0, 36, 37, 0, 0, 0, + 0, 4, 0, 0, 0, 38, 39, 5, 0, 6, + 7, 0, 354, 9, 10, 11, 12, 13, 14, 15, + 16, 17, 18, 19, 20, 0, 0, 0, 0, 22, + 99, 0, 25, 26, 0, 0, 0, 0, 0, 0, + 0, 28, 29, 355, 356, 32, 33, 34, 35, 0, + 36, 37, 5, 0, 0, 0, 0, 82, 0, 0, + 38, 39, 0, 147, 98, 0, 0, 0, 0, 148, + 0, 0, 0, 0, 149, 99, 0, 150, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 151, 152, 153, 154 }; static const yytype_int16 yycheck[] = { - 1, 1, 337, 1, 5, 50, 7, 1, 427, 371, - 49, 7, 8, 339, 341, 16, 1, 18, 19, 15, - 7, 7, 121, 7, 7, 13, 59, 54, 61, 59, - 449, 130, 12, 12, 456, 36, 15, 17, 17, 12, - 17, 12, 43, 13, 17, 17, 17, 13, 20, 50, - 22, 15, 474, 25, 26, 417, 59, 156, 35, 12, - 32, 33, 34, 35, 17, 37, 13, 68, 39, 40, - 397, 48, 60, 368, 45, 494, 498, 499, 44, 66, - 66, 61, 66, 66, 54, 81, 508, 66, 510, 60, - 512, 14, 65, 13, 95, 8, 43, 68, 69, 48, - 14, 65, 12, 52, 53, 54, 55, 17, 31, 12, - 436, 473, 447, 14, 17, 116, 65, 66, 444, 164, - 69, 70, 71, 72, 169, 164, 75, 12, 41, 424, - 15, 44, 17, 468, 106, 107, 108, 109, 110, 14, - 112, 12, 65, 66, 439, 59, 17, 60, 61, 62, - 8, 65, 66, 13, 59, 65, 451, 158, 453, 160, - 59, 162, 65, 164, 65, 66, 59, 168, 169, 170, - 171, 143, 13, 59, 146, 147, 148, 149, 150, 151, - 152, 66, 477, 41, 59, 13, 44, 12, 17, 190, - 65, 66, 17, 194, 65, 13, 197, 198, 13, 200, - 60, 496, 60, 61, 62, 177, 178, 179, 180, 181, - 182, 183, 184, 185, 15, 13, 17, 13, 15, 17, - 61, 58, 59, 24, 15, 12, 17, 228, 229, 13, - 17, 330, 60, 24, 35, 60, 15, 15, 13, 54, - 285, 340, 60, 27, 35, 284, 44, 248, 15, 59, - 43, 59, 253, 54, 353, 253, 64, 13, 54, 57, - 57, 57, 63, 54, 59, 237, 59, 54, 253, 54, - 369, 27, 63, 274, 17, 54, 54, 278, 279, 54, - 65, 13, 283, 59, 285, 17, 9, 54, 289, 290, - 13, 12, 241, 242, 266, 12, 17, 246, 247, 52, - 17, 59, 23, 24, 305, 254, 64, 24, 29, 310, - 311, 17, 44, 34, 35, 360, 37, 318, 35, 59, - 321, 27, 41, 13, 64, 54, 327, 17, 34, 50, - 51, 52, 53, 12, 13, 52, 337, 9, 17, 337, - 341, 60, 61, 62, 345, 345, 342, 345, 27, 54, - 351, 345, 337, 354, 355, 15, 357, 17, 359, 360, - 345, 362, 363, 8, 24, 366, 17, 368, 13, 12, - 13, 15, 17, 17, 17, 35, 377, 378, 379, 380, - 24, 24, 12, 12, 59, 15, 15, 17, 17, 64, - 35, 35, 35, 54, 54, 396, 397, 398, 398, 17, - 398, 73, 17, 48, 398, 17, 39, 40, 409, 410, - 54, 17, 45, 398, 415, 48, 88, 418, 52, 59, - 92, 422, 94, 424, 64, 12, 13, 428, 12, 13, - 17, 103, 104, 17, 435, 68, 69, 24, 12, 13, - 24, 58, 59, 17, 393, 394, 447, 448, 35, 447, - 451, 35, 453, 402, 403, 456, 58, 59, 57, 460, - 60, 12, 447, 464, 15, 17, 17, 468, 4, 470, - 468, 472, 472, 474, 472, 5, 477, 60, 472, 480, - 481, 12, 60, 468, 60, 434, 17, 472, 60, 490, - 490, 163, 490, 24, 58, 59, 490, 498, 499, 500, - 60, 6, 7, 504, 35, 490, 17, 508, 57, 510, - 459, 512, 461, 514, 19, 20, 21, 22, 12, 39, - 40, 15, 57, 17, 196, 45, 4, 5, 6, 7, - 8, 9, 10, 11, 12, 484, 17, 15, 210, 17, - 58, 59, 57, 215, 60, 217, 24, 60, 68, 69, - 17, 12, 30, 225, 15, 59, 17, 35, 230, 6, - 57, 39, 40, 58, 59, 12, 31, 45, 15, 61, - 17, 18, 19, 20, 21, 22, 54, 15, 17, 57, - 27, 59, 60, 61, 57, 63, 258, 17, 57, 67, - 68, 69, 12, 17, 54, 15, 60, 17, 60, 46, - 47, 48, 60, 17, 60, 15, 461, 470, 280, 470, - 282, 418, 217, 60, 6, 287, 288, 164, 475, 291, - 12, 293, 14, 15, 18, 17, 18, 19, 20, 21, - 22, 23, 24, 25, 26, 27, 28, 29, 224, 31, - 164, -1, 34, 35, 316, 37, 38, 319, 320, -1, - -1, -1, -1, -1, 46, 47, 48, 49, 50, 51, - 52, 53, -1, 55, 56, -1, -1, -1, -1, -1, - -1, -1, -1, 65, 66, -1, -1, 349, 350, -1, - -1, -1, -1, -1, 356, 0, 1, -1, -1, -1, - -1, 6, -1, -1, -1, 367, -1, 12, -1, 14, - 15, 373, 17, 18, 19, 20, 21, 22, 23, 24, - 25, 26, 27, 28, 29, -1, -1, 32, -1, 34, - 35, 36, 37, 38, -1, -1, -1, 42, -1, -1, - -1, 46, 47, 48, 49, 50, 51, 52, 53, -1, - 55, 56, -1, -1, 416, -1, -1, 419, -1, 421, - 65, 66, 4, 5, 6, 7, 8, 9, 10, 11, - 12, -1, 434, 15, 16, 17, -1, -1, -1, -1, - -1, -1, 24, -1, -1, -1, -1, -1, 30, -1, - 452, -1, -1, 35, -1, 457, 458, 39, 40, 461, - -1, -1, -1, 45, -1, -1, -1, -1, -1, -1, - -1, -1, 54, -1, -1, 57, -1, -1, 60, -1, - -1, 63, -1, -1, -1, 67, 68, 69, 4, 5, - 6, 7, 8, 9, 10, 11, 12, -1, -1, 15, - 16, 17, -1, -1, -1, -1, -1, -1, 24, -1, - -1, -1, -1, -1, 30, -1, -1, -1, -1, 35, - -1, -1, -1, 39, 40, -1, -1, -1, -1, 45, - -1, -1, -1, -1, -1, -1, -1, -1, 54, -1, - -1, 57, -1, -1, 60, -1, -1, 63, -1, -1, - -1, 67, 68, 69, 4, 5, 6, 7, 8, 9, - 10, 11, 12, -1, -1, 15, -1, 17, -1, -1, - -1, -1, -1, -1, 24, -1, -1, -1, -1, -1, - 30, -1, -1, -1, -1, 35, -1, -1, -1, 39, - 40, -1, -1, 43, -1, 45, -1, -1, -1, -1, - -1, -1, -1, -1, 54, -1, -1, 57, -1, -1, - 60, -1, -1, 63, -1, -1, -1, 67, 68, 69, - 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, - -1, 15, -1, 17, -1, -1, -1, -1, -1, -1, - 24, -1, -1, -1, -1, -1, 30, -1, -1, -1, - -1, 35, -1, 6, 7, 39, 40, -1, -1, 12, - 13, 45, -1, -1, 17, -1, 19, 20, 21, 22, - 54, -1, -1, 57, 27, -1, 60, -1, -1, 63, - 6, -1, -1, 67, 68, 69, 12, -1, 14, 15, - 43, 17, 18, 19, 20, 21, 22, 23, 24, 25, - 26, 27, 28, 29, -1, 31, -1, -1, 34, 35, - -1, 37, 38, -1, -1, -1, -1, -1, -1, -1, - 46, 47, 48, 49, 50, 51, 52, 53, -1, 55, - 56, -1, -1, -1, -1, 6, -1, -1, -1, 65, - 66, 12, -1, 14, 15, -1, 17, 18, 19, 20, - 21, 22, 23, 24, 25, 26, 27, 28, 29, -1, - 31, -1, -1, 34, 35, -1, 37, 38, -1, -1, - -1, -1, -1, -1, -1, 46, 47, 48, 49, 50, - 51, 52, 53, -1, 55, 56, -1, -1, -1, -1, - 6, -1, -1, -1, 65, 66, 12, -1, 14, 15, + 1, 1, 50, 4, 5, 1, 7, 1, 1, 49, + 327, 351, 349, 14, 390, 16, 17, 18, 19, 20, + 54, 22, 7, 8, 25, 26, 353, 6, 7, 13, + 15, 32, 33, 34, 35, 36, 37, 6, 7, 122, + 15, 6, 43, 6, 7, 6, 478, 12, 131, 50, + 15, 12, 17, 6, 15, 43, 17, 13, 12, 12, + 436, 13, 15, 17, 17, 52, 498, 68, 6, 7, + 6, 59, 14, 13, 157, 27, 12, 61, 13, 15, + 81, 17, 14, 84, 13, 39, 40, 66, 12, 416, + 65, 45, 13, 17, 12, 12, 81, 66, 13, 17, + 17, 66, 534, 66, 60, 66, 107, 108, 109, 110, + 111, 59, 113, 66, 68, 69, 117, 165, 458, 54, + 60, 497, 170, 65, 66, 165, 466, 59, 66, 13, + 66, 448, 469, 65, 66, 12, 15, 13, 54, 60, + 17, 65, 60, 144, 61, 60, 147, 148, 149, 150, + 151, 152, 153, 13, 471, 492, 12, 17, 159, 43, + 161, 17, 163, 15, 165, 13, 59, 168, 169, 170, + 171, 172, 12, 174, 13, 54, 59, 17, 54, 180, + 181, 182, 183, 184, 185, 186, 187, 188, 65, 59, + 48, 15, 193, 12, 52, 53, 54, 55, 17, 39, + 40, 17, 54, 54, 521, 45, 54, 65, 66, 65, + 14, 69, 70, 71, 72, 54, 59, 75, 57, 17, + 60, 12, 9, 13, 15, 13, 17, 8, 68, 69, + 54, 59, 383, 6, 13, 54, 387, 27, 17, 12, + 54, 242, 15, 291, 17, 18, 19, 20, 21, 22, + 290, 65, 253, 59, 27, 59, 44, 258, 258, 342, + 41, 65, 66, 44, 258, 44, 57, 12, 14, 352, + 271, 54, 17, 46, 47, 48, 8, 59, 57, 60, + 61, 62, 365, 284, 285, 31, 73, 60, 289, 440, + 291, 58, 59, 444, 295, 296, 297, 298, 299, 12, + 13, 302, 89, 304, 17, 388, 93, 9, 95, 41, + 461, 13, 44, 17, 15, 59, 17, 104, 105, 65, + 66, 17, 473, 24, 372, 476, 6, 17, 60, 61, + 62, 15, 12, 17, 35, 15, 12, 17, 339, 15, + 24, 17, 12, 481, 482, 15, 17, 17, 349, 349, + 501, 35, 353, 54, 41, 349, 357, 357, 58, 59, + 17, 357, 63, 357, 357, 366, 367, 52, 506, 354, + 54, 372, 523, 60, 61, 62, 17, 164, 379, 63, + 12, 57, 60, 4, 385, 17, 173, 57, 246, 247, + 5, 8, 24, 251, 252, 396, 13, 59, 57, 61, + 17, 259, 15, 35, 17, 59, 17, 61, 17, 60, + 15, 24, 17, 200, 415, 416, 417, 417, 35, 24, + 52, 417, 35, 417, 417, 60, 35, 60, 215, 60, + 35, 48, 60, 220, 13, 222, 437, 12, 17, 48, + 15, 54, 17, 230, 39, 40, 6, 7, 235, 54, + 45, 57, 12, 13, 58, 59, 457, 17, 59, 19, + 20, 21, 22, 64, 17, 44, 12, 27, 469, 469, + 57, 17, 60, 68, 69, 469, 263, 478, 24, 12, + 481, 482, 15, 43, 17, 12, 60, 488, 15, 35, + 17, 492, 492, 494, 17, 496, 496, 498, 492, 286, + 496, 288, 496, 496, 27, 506, 293, 294, 58, 59, + 17, 34, 59, 300, 12, 13, 517, 517, 305, 17, + 57, 517, 61, 517, 517, 526, 24, 12, 13, 530, + 39, 40, 17, 534, 31, 536, 45, 35, 59, 48, + 15, 328, 27, 64, 331, 332, 12, 13, 59, 57, + 17, 17, 17, 64, 412, 413, 12, 13, 24, 68, + 69, 17, 12, 421, 422, 15, 59, 17, 24, 35, + 57, 64, 17, 12, 361, 362, 15, 12, 17, 35, + 15, 368, 17, 54, 17, 12, 373, 20, 15, 22, + 17, 59, 25, 26, 58, 59, 64, 384, 456, 32, + 33, 34, 35, 60, 37, 392, 58, 59, 4, 5, + 6, 7, 8, 9, 10, 11, 12, 6, 7, 15, + 16, 17, 60, 60, 17, 483, 60, 485, 24, 15, + 19, 20, 21, 22, 30, 485, 222, 494, 437, 35, + 494, 165, 18, 39, 40, 229, 499, 165, 435, 45, + -1, 438, -1, 511, 441, -1, -1, -1, 54, -1, + -1, 57, -1, -1, 60, -1, -1, 63, -1, 456, + -1, 67, 68, 69, 107, 108, 109, 110, 111, -1, + 113, -1, -1, 12, -1, -1, -1, 474, 17, -1, + -1, -1, 479, 480, 23, 24, -1, -1, 485, -1, + 29, -1, -1, -1, -1, 34, 35, -1, 37, -1, + -1, 144, -1, -1, 147, 148, 149, 150, 151, 152, + 153, 50, 51, 52, 53, -1, -1, -1, -1, -1, + -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, + -1, -1, -1, -1, -1, -1, -1, 180, 181, 182, + 183, 184, 185, 186, 187, 188, -1, -1, -1, -1, + -1, -1, -1, -1, 0, 1, -1, -1, -1, -1, + 6, -1, -1, -1, -1, -1, 12, -1, 14, 15, -1, 17, 18, 19, 20, 21, 22, 23, 24, 25, - 26, 27, 28, 29, -1, 31, -1, -1, 34, 35, - -1, 37, 38, -1, -1, -1, -1, -1, -1, -1, + 26, 27, 28, 29, -1, -1, 32, -1, 34, 35, + 36, 37, 38, -1, -1, -1, 42, -1, -1, 242, 46, 47, 48, 49, 50, 51, 52, 53, -1, 55, - 56, -1, -1, -1, -1, 6, -1, -1, -1, 65, - 66, 12, -1, 14, 15, -1, 17, 18, 19, 20, - 21, 22, 23, 24, 25, 26, 27, 28, 29, -1, - -1, -1, -1, 34, 35, -1, 37, 38, -1, -1, - -1, -1, -1, -1, -1, 46, 47, 48, 49, 50, - 51, 52, 53, -1, 55, 56, 12, -1, -1, -1, - -1, 17, -1, -1, 65, 66, -1, 23, 24, -1, - -1, -1, -1, 29, -1, -1, -1, -1, 34, 35, - -1, 37, -1, -1, -1, -1, -1, -1, -1, -1, - -1, -1, -1, -1, 50, 51, 52, 53 + 56, -1, -1, -1, -1, -1, -1, -1, -1, 65, + 66, -1, -1, -1, -1, -1, -1, -1, 271, 4, + 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, + 15, -1, 17, -1, -1, -1, -1, -1, -1, 24, + -1, -1, -1, -1, -1, 30, -1, -1, -1, -1, + 35, -1, -1, -1, 39, 40, -1, -1, 43, -1, + 45, -1, -1, -1, -1, -1, -1, -1, -1, 54, + -1, -1, 57, -1, -1, 60, -1, -1, 63, -1, + -1, -1, 67, 68, 69, 4, 5, 6, 7, 8, + 9, 10, 11, 12, -1, -1, 15, 16, 17, -1, + -1, -1, -1, -1, -1, 24, -1, -1, -1, -1, + -1, 30, -1, -1, -1, -1, 35, -1, -1, -1, + 39, 40, -1, -1, -1, -1, 45, -1, -1, -1, + -1, -1, -1, -1, -1, 54, -1, -1, 57, -1, + -1, 60, -1, -1, 63, -1, -1, -1, 67, 68, + 69, 4, 5, 6, 7, 8, 9, 10, 11, 12, + -1, -1, 15, -1, 17, -1, -1, -1, -1, -1, + -1, 24, -1, -1, -1, -1, -1, 30, -1, -1, + -1, -1, 35, -1, -1, -1, 39, 40, -1, -1, + -1, -1, 45, -1, -1, -1, -1, -1, -1, -1, + -1, 54, -1, -1, 57, -1, -1, 60, -1, -1, + 63, 6, -1, -1, 67, 68, 69, 12, -1, 14, + 15, -1, 17, 18, 19, 20, 21, 22, 23, 24, + 25, 26, 27, 28, 29, -1, 31, -1, -1, 34, + 35, -1, 37, 38, -1, -1, -1, -1, -1, -1, + -1, 46, 47, 48, 49, 50, 51, 52, 53, -1, + 55, 56, -1, -1, -1, -1, 6, -1, -1, -1, + 65, 66, 12, -1, 14, 15, -1, 17, 18, 19, + 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, + -1, 31, -1, -1, 34, 35, -1, 37, 38, -1, + -1, -1, -1, -1, -1, -1, 46, 47, 48, 49, + 50, 51, 52, 53, -1, 55, 56, -1, -1, -1, + -1, 6, -1, -1, -1, 65, 66, 12, -1, 14, + 15, -1, 17, 18, 19, 20, 21, 22, 23, 24, + 25, 26, 27, 28, 29, -1, 31, -1, -1, 34, + 35, -1, 37, 38, -1, -1, -1, -1, -1, -1, + -1, 46, 47, 48, 49, 50, 51, 52, 53, -1, + 55, 56, -1, -1, -1, -1, 6, -1, -1, -1, + 65, 66, 12, -1, 14, 15, -1, 17, 18, 19, + 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, + -1, 31, -1, -1, 34, 35, -1, 37, 38, -1, + -1, -1, -1, -1, -1, -1, 46, 47, 48, 49, + 50, 51, 52, 53, -1, 55, 56, -1, -1, -1, + -1, 6, -1, -1, -1, 65, 66, 12, -1, 14, + 15, -1, 17, 18, 19, 20, 21, 22, 23, 24, + 25, 26, 27, 28, 29, -1, -1, -1, -1, 34, + 35, -1, 37, 38, -1, -1, -1, -1, -1, -1, + -1, 46, 47, 48, 49, 50, 51, 52, 53, -1, + 55, 56, 12, -1, -1, -1, -1, 17, -1, -1, + 65, 66, -1, 23, 24, -1, -1, -1, -1, 29, + -1, -1, -1, -1, 34, 35, -1, 37, -1, -1, + -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, + 50, 51, 52, 53 }; /* YYSTOS[STATE-NUM] -- The symbol kind of the accessing symbol of @@ -1302,52 +1324,54 @@ static const yytype_uint8 yystos[] = 72, 73, 78, 82, 83, 84, 88, 92, 93, 94, 95, 100, 101, 102, 103, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, - 130, 132, 133, 134, 136, 139, 140, 141, 142, 143, - 144, 15, 57, 17, 82, 39, 40, 45, 60, 68, - 69, 82, 99, 48, 99, 96, 13, 24, 35, 82, - 83, 84, 85, 99, 61, 82, 23, 29, 34, 37, - 50, 51, 52, 53, 85, 82, 121, 82, 85, 85, - 13, 17, 44, 17, 35, 48, 85, 85, 54, 13, - 17, 44, 57, 8, 13, 17, 35, 48, 85, 13, - 85, 13, 85, 52, 85, 82, 23, 29, 34, 37, - 50, 51, 52, 53, 85, 13, 17, 27, 43, 82, - 8, 41, 44, 60, 61, 62, 100, 6, 7, 95, - 15, 82, 94, 100, 100, 100, 100, 59, 59, 59, - 59, 59, 59, 59, 59, 59, 100, 100, 82, 100, - 59, 100, 100, 100, 96, 100, 99, 96, 96, 137, - 96, 4, 5, 6, 7, 8, 9, 10, 11, 15, - 16, 24, 30, 35, 54, 57, 60, 63, 67, 82, - 98, 99, 123, 17, 41, 60, 61, 62, 96, 96, - 61, 85, 85, 85, 85, 85, 85, 52, 82, 17, - 54, 135, 54, 79, 17, 13, 135, 54, 105, 17, - 17, 13, 74, 75, 135, 17, 17, 85, 60, 85, - 85, 85, 85, 85, 85, 85, 52, 17, 27, 34, - 13, 135, 82, 82, 96, 131, 54, 82, 96, 15, - 18, 48, 60, 82, 94, 95, 120, 134, 60, 15, - 82, 66, 94, 66, 85, 85, 85, 85, 85, 85, - 85, 85, 85, 27, 82, 96, 17, 138, 4, 5, - 96, 96, 97, 60, 97, 128, 60, 131, 96, 60, - 60, 96, 85, 60, 59, 100, 100, 57, 13, 60, - 17, 100, 100, 15, 82, 106, 76, 77, 13, 60, - 17, 57, 17, 48, 49, 87, 88, 92, 100, 60, - 60, 96, 85, 17, 44, 9, 60, 96, 57, 96, - 95, 94, 96, 96, 82, 82, 96, 66, 96, 61, - 31, 124, 58, 59, 64, 59, 61, 127, 96, 96, - 96, 15, 54, 65, 81, 82, 17, 15, 17, 24, - 35, 54, 89, 15, 135, 58, 59, 57, 87, 17, - 15, 89, 15, 135, 81, 17, 31, 88, 92, 96, - 96, 15, 135, 82, 82, 96, 16, 125, 104, 66, - 94, 66, 43, 86, 96, 86, 135, 128, 96, 17, - 65, 82, 129, 54, 58, 59, 60, 100, 100, 107, - 15, 82, 81, 31, 60, 100, 100, 58, 96, 128, - 106, 96, 66, 96, 82, 86, 127, 60, 60, 80, - 96, 100, 82, 15, 63, 89, 59, 86, 58, 15, - 63, 89, 87, 126, 127, 58, 86, 96, 86, 129, - 96, 96, 31, 100, 80, 15, 82, 90, 91, 17, - 87, 90, 91, 31, 128, 129, 107, 86, 59, 61, - 59, 64, 59, 64, 60, 31, 64, 64, 127, 86, - 65, 129, 65, 129, 65, 82, 15, 65, 15, 82, - 129, 129, 129, 82, 15 + 131, 133, 134, 135, 137, 140, 141, 142, 143, 144, + 145, 15, 17, 57, 82, 82, 39, 40, 45, 60, + 68, 69, 82, 99, 48, 99, 96, 13, 24, 35, + 82, 83, 84, 85, 99, 61, 82, 23, 29, 34, + 37, 50, 51, 52, 53, 85, 82, 121, 82, 85, + 85, 13, 17, 44, 17, 35, 48, 85, 85, 54, + 13, 17, 44, 57, 8, 13, 17, 35, 48, 85, + 13, 85, 13, 85, 52, 85, 82, 23, 29, 34, + 37, 50, 51, 52, 53, 85, 13, 17, 27, 43, + 82, 8, 41, 44, 60, 61, 62, 100, 6, 7, + 95, 6, 15, 66, 82, 94, 100, 100, 100, 100, + 59, 59, 59, 59, 59, 59, 59, 59, 59, 100, + 100, 82, 100, 59, 100, 100, 100, 96, 100, 82, + 99, 82, 96, 96, 138, 96, 4, 5, 6, 7, + 8, 9, 10, 11, 15, 16, 24, 30, 35, 54, + 57, 60, 63, 67, 82, 98, 99, 123, 17, 41, + 60, 61, 62, 96, 96, 61, 85, 85, 85, 85, + 85, 85, 52, 82, 17, 54, 136, 54, 79, 17, + 13, 136, 54, 105, 17, 17, 13, 74, 75, 136, + 17, 17, 85, 60, 85, 85, 85, 85, 85, 85, + 85, 52, 17, 27, 34, 13, 136, 82, 82, 96, + 132, 54, 82, 96, 6, 15, 18, 48, 60, 82, + 94, 95, 120, 135, 60, 15, 82, 6, 15, 82, + 66, 94, 15, 96, 6, 66, 85, 85, 85, 85, + 85, 85, 85, 85, 85, 27, 82, 96, 17, 139, + 4, 5, 96, 96, 97, 60, 97, 128, 60, 132, + 96, 60, 60, 96, 85, 60, 59, 100, 100, 57, + 13, 60, 17, 100, 100, 15, 82, 106, 76, 77, + 13, 60, 17, 57, 17, 48, 49, 87, 88, 92, + 100, 60, 60, 96, 85, 17, 44, 9, 60, 96, + 57, 96, 95, 66, 94, 96, 96, 82, 82, 15, + 82, 82, 82, 96, 66, 43, 86, 96, 61, 31, + 124, 58, 59, 64, 59, 61, 127, 96, 96, 96, + 15, 54, 65, 81, 82, 17, 15, 17, 24, 35, + 54, 89, 15, 136, 58, 59, 57, 87, 17, 15, + 89, 15, 136, 81, 17, 31, 88, 92, 96, 96, + 15, 136, 82, 82, 96, 16, 125, 104, 66, 94, + 96, 66, 82, 86, 96, 82, 86, 136, 128, 96, + 17, 65, 82, 129, 130, 54, 58, 59, 60, 100, + 100, 107, 15, 82, 81, 31, 60, 100, 100, 58, + 96, 128, 106, 96, 66, 86, 96, 86, 127, 60, + 60, 59, 127, 80, 96, 100, 82, 15, 63, 89, + 59, 86, 58, 15, 63, 89, 87, 126, 127, 58, + 86, 96, 86, 130, 96, 96, 65, 129, 129, 31, + 100, 80, 15, 82, 90, 91, 17, 87, 90, 91, + 31, 128, 130, 107, 86, 129, 59, 64, 59, 64, + 60, 31, 64, 64, 127, 86, 65, 82, 15, 65, + 15, 82, 130, 82, 15 }; /* YYR1[RULE-NUM] -- Symbol kind of the left-hand side of rule RULE-NUM. */ @@ -1362,7 +1386,8 @@ static const yytype_uint8 yyr1[] = 88, 88, 88, 88, 88, 88, 88, 89, 89, 89, 89, 90, 90, 90, 91, 91, 91, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, - 92, 93, 93, 93, 93, 93, 93, 94, 94, 94, + 92, 93, 93, 93, 93, 93, 93, 93, 93, 94, + 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 95, 95, 95, 95, 95, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 97, 97, 98, 98, 98, 98, 98, 98, @@ -1376,11 +1401,11 @@ static const yytype_uint8 yyr1[] = 115, 115, 115, 116, 116, 116, 116, 116, 117, 117, 117, 118, 118, 119, 119, 120, 120, 120, 120, 120, 121, 121, 123, 122, 124, 122, 125, 122, 126, 122, - 127, 127, 128, 128, 129, 129, 129, 129, 129, 130, - 130, 131, 132, 132, 132, 132, 132, 132, 133, 134, - 134, 135, 135, 135, 137, 136, 138, 138, 139, 139, - 139, 140, 140, 140, 140, 140, 140, 140, 141, 142, - 143, 143, 143, 144 + 127, 127, 128, 128, 129, 129, 130, 130, 130, 130, + 131, 131, 132, 133, 133, 133, 133, 133, 133, 134, + 135, 135, 136, 136, 136, 138, 137, 139, 139, 140, + 140, 140, 141, 141, 141, 141, 141, 141, 141, 142, + 143, 144, 144, 144, 145 }; /* YYR2[RULE-NUM] -- Number of symbols on the right-hand side of rule RULE-NUM. */ @@ -1395,8 +1420,9 @@ static const yytype_int8 yyr2[] = 6, 5, 5, 7, 7, 9, 9, 1, 1, 1, 1, 1, 3, 4, 1, 3, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, - 1, 8, 6, 5, 7, 5, 7, 1, 2, 2, - 3, 4, 4, 1, 1, 2, 1, 1, 0, 2, + 1, 8, 6, 5, 7, 5, 7, 4, 6, 1, + 2, 2, 2, 3, 3, 3, 4, 4, 3, 4, + 4, 5, 4, 1, 1, 2, 1, 1, 0, 2, 2, 2, 2, 2, 4, 4, 2, 2, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, @@ -1409,11 +1435,11 @@ static const yytype_int8 yyr2[] = 3, 3, 3, 2, 3, 3, 3, 5, 2, 2, 3, 4, 2, 1, 3, 2, 2, 2, 3, 1, 2, 3, 0, 6, 0, 8, 0, 8, 0, 10, - 1, 2, 0, 5, 3, 5, 6, 5, 6, 2, - 3, 1, 3, 4, 3, 3, 3, 4, 2, 1, - 1, 1, 3, 4, 0, 5, 0, 3, 3, 5, - 5, 5, 5, 5, 7, 7, 9, 9, 4, 4, - 4, 6, 6, 4 + 1, 2, 0, 5, 0, 3, 1, 3, 4, 3, + 2, 3, 1, 3, 4, 3, 3, 3, 4, 2, + 1, 1, 1, 3, 4, 0, 5, 0, 3, 3, + 5, 5, 5, 5, 5, 7, 7, 9, 9, 4, + 4, 4, 6, 6, 4 }; @@ -2149,91 +2175,91 @@ yyparse (void) case 3: /* input: input import */ #line 165 "antimony.ypp" {} -#line 2153 "antimony.tab.cpp" +#line 2179 "antimony.tab.cpp" break; case 4: /* input: input module */ #line 166 "antimony.ypp" { /*cout << endl << $2->ToString() << endl << endl;*/ } -#line 2159 "antimony.tab.cpp" +#line 2185 "antimony.tab.cpp" break; case 5: /* input: input modulepart */ #line 167 "antimony.ypp" {} -#line 2165 "antimony.tab.cpp" +#line 2191 "antimony.tab.cpp" break; case 6: /* input: input function */ #line 168 "antimony.ypp" {} -#line 2171 "antimony.tab.cpp" +#line 2197 "antimony.tab.cpp" break; case 7: /* input: input modulename */ #line 169 "antimony.ypp" {} -#line 2177 "antimony.tab.cpp" +#line 2203 "antimony.tab.cpp" break; case 8: /* input: input functionname */ #line 170 "antimony.ypp" {} -#line 2183 "antimony.tab.cpp" +#line 2209 "antimony.tab.cpp" break; case 9: /* input: input modulecvterm */ #line 171 "antimony.ypp" {} -#line 2189 "antimony.tab.cpp" +#line 2215 "antimony.tab.cpp" break; case 10: /* input: input functioncvterm */ #line 172 "antimony.ypp" {} -#line 2195 "antimony.tab.cpp" +#line 2221 "antimony.tab.cpp" break; case 11: /* input: input toplevel_sbo */ #line 173 "antimony.ypp" {} -#line 2201 "antimony.tab.cpp" +#line 2227 "antimony.tab.cpp" break; case 12: /* input: input annotationBlock */ #line 174 "antimony.ypp" {} -#line 2207 "antimony.tab.cpp" +#line 2233 "antimony.tab.cpp" break; case 13: /* input: input moduleannotation */ #line 175 "antimony.ypp" {} -#line 2213 "antimony.tab.cpp" +#line 2239 "antimony.tab.cpp" break; case 14: /* input: input error */ #line 176 "antimony.ypp" {YYABORT;} -#line 2219 "antimony.tab.cpp" +#line 2245 "antimony.tab.cpp" break; case 15: /* input: input "an error" */ #line 177 "antimony.ypp" {YYABORT;} -#line 2225 "antimony.tab.cpp" +#line 2251 "antimony.tab.cpp" break; case 16: /* import: "'import'" "text string" */ #line 180 "antimony.ypp" { if (g_registry.OpenFile(*((yyvsp[0].word)))==0) YYABORT;} -#line 2231 "antimony.tab.cpp" +#line 2257 "antimony.tab.cpp" break; case 17: /* $@1: %empty */ #line 183 "antimony.ypp" {g_registry.NewCurrentModule((yyvsp[0].word), NULL, false);} -#line 2237 "antimony.tab.cpp" +#line 2263 "antimony.tab.cpp" break; case 18: /* module: "'model' or 'module'" "element name" $@1 '(' variableexportlist ')' modulebody "'end'" */ @@ -2243,13 +2269,13 @@ yyparse (void) if ((yyval.module)->Finalize()) YYABORT; g_registry.RevertToPreviousModule(); } -#line 2247 "antimony.tab.cpp" +#line 2273 "antimony.tab.cpp" break; case 19: /* $@2: %empty */ #line 189 "antimony.ypp" {g_registry.NewCurrentModule((yyvsp[0].word), NULL, false);} -#line 2253 "antimony.tab.cpp" +#line 2279 "antimony.tab.cpp" break; case 20: /* module: "'model' or 'module'" "element name" $@2 modulebody "'end'" */ @@ -2259,13 +2285,13 @@ yyparse (void) if ((yyval.module)->Finalize()) YYABORT; g_registry.RevertToPreviousModule(); } -#line 2263 "antimony.tab.cpp" +#line 2289 "antimony.tab.cpp" break; case 21: /* $@3: %empty */ #line 195 "antimony.ypp" {g_registry.NewCurrentModule((yyvsp[0].word), NULL, true);} -#line 2269 "antimony.tab.cpp" +#line 2295 "antimony.tab.cpp" break; case 22: /* module: "'model' or 'module'" '*' "element name" $@3 '(' variableexportlist ')' modulebody "'end'" */ @@ -2275,13 +2301,13 @@ yyparse (void) if ((yyval.module)->Finalize()) YYABORT; g_registry.RevertToPreviousModule(); } -#line 2279 "antimony.tab.cpp" +#line 2305 "antimony.tab.cpp" break; case 23: /* $@4: %empty */ #line 201 "antimony.ypp" {g_registry.NewCurrentModule((yyvsp[0].word), NULL, true);} -#line 2285 "antimony.tab.cpp" +#line 2311 "antimony.tab.cpp" break; case 24: /* module: "'model' or 'module'" '*' "element name" $@4 modulebody "'end'" */ @@ -2291,85 +2317,85 @@ yyparse (void) if ((yyval.module)->Finalize()) YYABORT; g_registry.RevertToPreviousModule(); } -#line 2295 "antimony.tab.cpp" +#line 2321 "antimony.tab.cpp" break; case 25: /* module: "'model' or 'module'" "name of an existing module" */ #line 207 "antimony.ypp" {g_registry.SetError("module '" + *((yyvsp[0].word)) + "' already defined."); YYABORT;} -#line 2301 "antimony.tab.cpp" +#line 2327 "antimony.tab.cpp" break; case 26: /* module: "'model' or 'module'" "name of an existing function" */ #line 208 "antimony.ypp" {g_registry.SetError("Cannot define '" + *((yyvsp[0].word)) + "' as a module because it is already a defined function."); YYABORT;} -#line 2307 "antimony.tab.cpp" +#line 2333 "antimony.tab.cpp" break; case 27: /* $@5: %empty */ #line 211 "antimony.ypp" {g_registry.NewUserFunction((yyvsp[0].word));} -#line 2313 "antimony.tab.cpp" +#line 2339 "antimony.tab.cpp" break; case 28: /* function: "'function'" "element name" $@5 '(' variableexportlist ')' spacedformula "'end'" */ #line 211 "antimony.ypp" {if (g_registry.SetUserFunction((yyvsp[-1].formula))) YYABORT;} -#line 2319 "antimony.tab.cpp" +#line 2345 "antimony.tab.cpp" break; case 29: /* function: "'function'" "name of an existing module" */ #line 212 "antimony.ypp" {g_registry.SetError("Cannot use '" + *((yyvsp[0].word)) +"' as a function name because it is already the name of a module."); YYABORT;} -#line 2325 "antimony.tab.cpp" +#line 2351 "antimony.tab.cpp" break; case 30: /* function: "'function'" "name of an existing function" */ #line 213 "antimony.ypp" {g_registry.SetError("Cannot define '" + *((yyvsp[0].word)) + "' as a new function because it is already a defined function."); YYABORT;} -#line 2331 "antimony.tab.cpp" +#line 2357 "antimony.tab.cpp" break; case 31: /* spacedformula: formula */ #line 216 "antimony.ypp" {(yyval.formula) = (yyvsp[0].formula);} -#line 2337 "antimony.tab.cpp" +#line 2363 "antimony.tab.cpp" break; case 32: /* spacedformula: lineend spacedformula */ #line 217 "antimony.ypp" {(yyval.formula) = (yyvsp[0].formula);} -#line 2343 "antimony.tab.cpp" +#line 2369 "antimony.tab.cpp" break; case 33: /* spacedformula: spacedformula lineend */ #line 218 "antimony.ypp" {(yyval.formula) = (yyvsp[-1].formula);} -#line 2349 "antimony.tab.cpp" +#line 2375 "antimony.tab.cpp" break; case 34: /* variableexportlist: %empty */ #line 228 "antimony.ypp" {} -#line 2355 "antimony.tab.cpp" +#line 2381 "antimony.tab.cpp" break; case 35: /* variableexportlist: variable */ #line 229 "antimony.ypp" {if (g_registry.AddVariableToCurrentExportList((yyvsp[0].variable))) YYABORT; } -#line 2361 "antimony.tab.cpp" +#line 2387 "antimony.tab.cpp" break; case 36: /* variableexportlist: variableexportlist ',' variable */ #line 230 "antimony.ypp" { if (g_registry.AddVariableToCurrentExportList((yyvsp[0].variable))) YYABORT; } -#line 2367 "antimony.tab.cpp" +#line 2393 "antimony.tab.cpp" break; case 37: /* variable: "element name" */ #line 233 "antimony.ypp" {(yyval.variable) = g_registry.AddVariableToCurrent((yyvsp[0].word)); } -#line 2373 "antimony.tab.cpp" +#line 2399 "antimony.tab.cpp" break; case 38: /* variable: variable '.' "element name" */ @@ -2382,7 +2408,7 @@ yyparse (void) YYABORT; } } -#line 2386 "antimony.tab.cpp" +#line 2412 "antimony.tab.cpp" break; case 39: /* variable: variable '.' "--" */ @@ -2394,13 +2420,13 @@ yyparse (void) YYABORT; } } -#line 2398 "antimony.tab.cpp" +#line 2424 "antimony.tab.cpp" break; case 40: /* variable: '$' variable */ #line 249 "antimony.ypp" {(yyval.variable) = (yyvsp[0].variable); if ((yyval.variable)->SetIsConst(true)) YYABORT;} -#line 2404 "antimony.tab.cpp" +#line 2430 "antimony.tab.cpp" break; case 41: /* variable: variable '.' "'formula'" */ @@ -2414,103 +2440,103 @@ yyparse (void) YYABORT; } } -#line 2418 "antimony.tab.cpp" +#line 2444 "antimony.tab.cpp" break; case 42: /* variablein: variable "'in'" variable */ #line 261 "antimony.ypp" {if ((yyvsp[-2].variable)->SetCompartment((yyvsp[0].variable))) YYABORT; (yyval.variable) = (yyvsp[-2].variable);} -#line 2424 "antimony.tab.cpp" +#line 2450 "antimony.tab.cpp" break; case 43: /* varmaybein: variable */ #line 264 "antimony.ypp" {(yyval.variable) = (yyvsp[0].variable);} -#line 2430 "antimony.tab.cpp" +#line 2456 "antimony.tab.cpp" break; case 44: /* varmaybein: variablein */ #line 265 "antimony.ypp" {(yyval.variable) = (yyvsp[0].variable);} -#line 2436 "antimony.tab.cpp" +#line 2462 "antimony.tab.cpp" break; case 45: /* varmaybein: "name of an existing function" */ #line 266 "antimony.ypp" {(yyval.variable) = NULL; g_registry.SetError("'" + *(yyvsp[0].word) + "' is a reserved word in Antimony (the name of a built-in function) and cannot be used as the name of a variable or other named element."); YYABORT;} -#line 2442 "antimony.tab.cpp" +#line 2468 "antimony.tab.cpp" break; case 46: /* varmaybein: "name of a pre-defined constant" */ #line 267 "antimony.ypp" {(yyval.variable) = NULL; g_registry.SetError("'" + *(yyvsp[0].word) + "' is a reserved word in Antimony (the name of a built-in constant) and cannot be used as the name of a variable or other named element."); YYABORT;} -#line 2448 "antimony.tab.cpp" +#line 2474 "antimony.tab.cpp" break; case 47: /* varmaybeis: varmaybein */ #line 270 "antimony.ypp" {(yyval.variable) = (yyvsp[0].variable);} -#line 2454 "antimony.tab.cpp" +#line 2480 "antimony.tab.cpp" break; case 48: /* varmaybeis: varmaybein '=' formula */ #line 271 "antimony.ypp" {(yyval.variable) = (yyvsp[-2].variable); if ((yyvsp[-2].variable)->SetFormula((yyvsp[0].formula))) YYABORT; } -#line 2460 "antimony.tab.cpp" +#line 2486 "antimony.tab.cpp" break; case 49: /* varmaybeis: varmaybein ':' '=' formula */ #line 272 "antimony.ypp" {(yyval.variable) = (yyvsp[-3].variable); if ((yyvsp[-3].variable)->SetAssignmentRule((yyvsp[0].formula))) YYABORT; } -#line 2466 "antimony.tab.cpp" +#line 2492 "antimony.tab.cpp" break; case 50: /* varmaybeis: varmaybein '\'' '=' formula */ #line 273 "antimony.ypp" {(yyval.variable) = (yyvsp[-3].variable); if ((yyvsp[-3].variable)->SetRateRule((yyvsp[0].formula))) YYABORT; } -#line 2472 "antimony.tab.cpp" +#line 2498 "antimony.tab.cpp" break; case 51: /* varmaybeis: varmaybein "'has'" unitdef */ #line 274 "antimony.ypp" {(yyval.variable) = (yyvsp[-2].variable); if ((yyvsp[-2].variable)->SetUnit((yyvsp[0].variable))) YYABORT; } -#line 2478 "antimony.tab.cpp" +#line 2504 "antimony.tab.cpp" break; case 52: /* maybein: %empty */ #line 277 "antimony.ypp" {(yyval.variable) = NULL;} -#line 2484 "antimony.tab.cpp" +#line 2510 "antimony.tab.cpp" break; case 53: /* maybein: "'in'" variable */ #line 278 "antimony.ypp" {(yyval.variable) = (yyvsp[0].variable);} -#line 2490 "antimony.tab.cpp" +#line 2516 "antimony.tab.cpp" break; case 54: /* modulebody: modulepart */ #line 281 "antimony.ypp" {} -#line 2496 "antimony.tab.cpp" +#line 2522 "antimony.tab.cpp" break; case 55: /* modulebody: moduleannotation */ #line 282 "antimony.ypp" {} -#line 2502 "antimony.tab.cpp" +#line 2528 "antimony.tab.cpp" break; case 56: /* modulebody: modulebody modulepart */ #line 283 "antimony.ypp" {} -#line 2508 "antimony.tab.cpp" +#line 2534 "antimony.tab.cpp" break; case 57: /* modulebody: modulebody moduleannotation */ #line 284 "antimony.ypp" {} -#line 2514 "antimony.tab.cpp" +#line 2540 "antimony.tab.cpp" break; case 58: /* moduleannotation: "'model' or 'module'" "element name" stringlist lineend */ @@ -2521,7 +2547,7 @@ yyparse (void) delete (yyvsp[-1].stringlist); if (cverr) YYABORT; } -#line 2525 "antimony.tab.cpp" +#line 2551 "antimony.tab.cpp" break; case 59: /* moduleannotation: "'model' or 'module'" "element name" '.' "element name" stringlist lineend */ @@ -2532,7 +2558,7 @@ yyparse (void) delete (yyvsp[-1].stringlist); if (cverr) YYABORT; } -#line 2536 "antimony.tab.cpp" +#line 2562 "antimony.tab.cpp" break; case 60: /* moduleannotation: "'model' or 'module'" "element name" '.' "element name" "number" lineend */ @@ -2541,7 +2567,7 @@ yyparse (void) string modname = g_registry.CurrentModuleName(); if (g_registry.ProcessGlobalCreatorTerm(&modname, (yyvsp[-4].word), (yyvsp[-2].word), (yyvsp[-1].num))) YYABORT; } -#line 2545 "antimony.tab.cpp" +#line 2571 "antimony.tab.cpp" break; case 61: /* moduleannotation: "'model' or 'module'" '.' "element name" '=' "number" */ @@ -2555,7 +2581,7 @@ yyparse (void) YYABORT; } } -#line 2559 "antimony.tab.cpp" +#line 2585 "antimony.tab.cpp" break; case 62: /* moduleannotation: "'model' or 'module'" '.' "element name" '=' stringConstant */ @@ -2564,16 +2590,20 @@ yyparse (void) if (module && (yyvsp[-2].word) && CaselessStrCmp(true, *((yyvsp[-2].word)), "layout")) { if (module->SetLayout((yyvsp[0].word))) YYABORT; } + else if (module && (yyvsp[-2].word) && CaselessStrCmp(true, *((yyvsp[-2].word)), "conversionFactor")) { + Variable* cfvar = g_registry.CurrentModule()->AddOrFindVariable((yyvsp[0].word)); + if (module->SetConversionFactor(cfvar)) YYABORT; + } else { - g_registry.SetError("Invalid syntax 'model." + *((yyvsp[-2].word)) + "'. The only thing that can be set on the model to a string is 'layout'."); + g_registry.SetError("Invalid syntax 'model." + *((yyvsp[-2].word)) + "'. The only thing that can be set on the model to a string is 'layout', and the only thing that can be set on the model to a variable is 'conversionFactor'."); YYABORT; } } -#line 2573 "antimony.tab.cpp" +#line 2603 "antimony.tab.cpp" break; case 63: /* moduleannotation: "'model' or 'module'" '.' "element name" '.' "element name" '=' "number" */ -#line 327 "antimony.ypp" +#line 331 "antimony.ypp" { Module* module = g_registry.CurrentModule(); if (module && (yyvsp[-4].word) && CaselessStrCmp(true, *((yyvsp[-4].word)), "autolayout")) { if (module->SetAutoLayout((yyvsp[-2].word), (yyvsp[0].num))) YYABORT; @@ -2587,11 +2617,11 @@ yyparse (void) } module->SetLayout("on"); } -#line 2591 "antimony.tab.cpp" +#line 2621 "antimony.tab.cpp" break; case 64: /* moduleannotation: "'model' or 'module'" '.' "element name" '.' "element name" '=' stringConstant */ -#line 341 "antimony.ypp" +#line 345 "antimony.ypp" { Module* module = g_registry.CurrentModule(); if (module && (yyvsp[-4].word) && CaselessStrCmp(true, *((yyvsp[-4].word)), "autolayout")) { if (module->SetAutoLayout((yyvsp[-2].word), (yyvsp[0].word))) YYABORT; @@ -2605,11 +2635,11 @@ yyparse (void) } module->SetLayout("on"); } -#line 2609 "antimony.tab.cpp" +#line 2639 "antimony.tab.cpp" break; case 65: /* moduleannotation: "'model' or 'module'" '.' "element name" '.' "element name" '=' '{' variablelist '}' */ -#line 355 "antimony.ypp" +#line 359 "antimony.ypp" { Module* module = g_registry.CurrentModule(); if (module && (yyvsp[-6].word) && CaselessStrCmp(true, *((yyvsp[-6].word)), "autolayout")) { if (module->SetAutoLayout((yyvsp[-4].word), (yyvsp[-1].variablelist))) YYABORT; @@ -2623,11 +2653,11 @@ yyparse (void) } module->SetLayout("on"); } -#line 2627 "antimony.tab.cpp" +#line 2657 "antimony.tab.cpp" break; case 66: /* moduleannotation: "'model' or 'module'" '.' "element name" '.' "element name" '=' '{' numlist '}' */ -#line 369 "antimony.ypp" +#line 373 "antimony.ypp" { Module* module = g_registry.CurrentModule(); if (module && (yyvsp[-6].word) && CaselessStrCmp(true, *((yyvsp[-6].word)), "autolayout")) { if (module->SetAutoLayout((yyvsp[-4].word), (yyvsp[-1].numlist))) YYABORT; @@ -2641,155 +2671,155 @@ yyparse (void) } module->SetLayout("on"); } -#line 2645 "antimony.tab.cpp" +#line 2675 "antimony.tab.cpp" break; case 67: /* stringConstant: "name of a pre-defined constant" */ -#line 384 "antimony.ypp" +#line 388 "antimony.ypp" {(yyval.word) = (yyvsp[0].word);} -#line 2651 "antimony.tab.cpp" +#line 2681 "antimony.tab.cpp" break; case 68: /* stringConstant: "text string" */ -#line 385 "antimony.ypp" +#line 389 "antimony.ypp" {(yyval.word) = (yyvsp[0].word);} -#line 2657 "antimony.tab.cpp" +#line 2687 "antimony.tab.cpp" break; case 69: /* stringConstant: "element name" */ -#line 386 "antimony.ypp" +#line 390 "antimony.ypp" {(yyval.word) = (yyvsp[0].word);} -#line 2663 "antimony.tab.cpp" +#line 2693 "antimony.tab.cpp" break; case 70: /* stringConstant: "name of an existing function" */ -#line 387 "antimony.ypp" +#line 391 "antimony.ypp" {(yyval.word) = (yyvsp[0].word);} -#line 2669 "antimony.tab.cpp" +#line 2699 "antimony.tab.cpp" break; case 71: /* variablelist: variable */ -#line 389 "antimony.ypp" +#line 393 "antimony.ypp" { (yyval.variablelist) = new std::vector(); (yyval.variablelist)->push_back((yyvsp[0].variable));} -#line 2675 "antimony.tab.cpp" +#line 2705 "antimony.tab.cpp" break; case 72: /* variablelist: variablelist ',' variable */ -#line 390 "antimony.ypp" +#line 394 "antimony.ypp" { (yyval.variablelist) = (yyvsp[-2].variablelist); (yyval.variablelist)->push_back((yyvsp[0].variable)); } -#line 2681 "antimony.tab.cpp" +#line 2711 "antimony.tab.cpp" break; case 73: /* variablelist: variablelist ',' '\n' variable */ -#line 391 "antimony.ypp" +#line 395 "antimony.ypp" { (yyval.variablelist) = (yyvsp[-3].variablelist); (yyval.variablelist)->push_back((yyvsp[0].variable)); } -#line 2687 "antimony.tab.cpp" +#line 2717 "antimony.tab.cpp" break; case 74: /* numlist: "number" */ -#line 394 "antimony.ypp" +#line 398 "antimony.ypp" { (yyval.numlist) = new std::vector(); (yyval.numlist)->push_back((yyvsp[0].num)); } -#line 2693 "antimony.tab.cpp" +#line 2723 "antimony.tab.cpp" break; case 75: /* numlist: numlist ',' "number" */ -#line 395 "antimony.ypp" +#line 399 "antimony.ypp" { (yyval.numlist) = (yyvsp[-2].numlist); (yyval.numlist)->push_back((yyvsp[0].num)); } -#line 2699 "antimony.tab.cpp" +#line 2729 "antimony.tab.cpp" break; case 76: /* numlist: numlist ',' '\n' "number" */ -#line 396 "antimony.ypp" +#line 400 "antimony.ypp" { (yyval.numlist) = (yyvsp[-3].numlist); (yyval.numlist)->push_back((yyvsp[0].num)); } -#line 2705 "antimony.tab.cpp" +#line 2735 "antimony.tab.cpp" break; case 77: /* modulepart: reaction lineend */ -#line 399 "antimony.ypp" +#line 403 "antimony.ypp" {} -#line 2711 "antimony.tab.cpp" +#line 2741 "antimony.tab.cpp" break; case 78: /* modulepart: assignment lineend */ -#line 400 "antimony.ypp" +#line 404 "antimony.ypp" {} -#line 2717 "antimony.tab.cpp" +#line 2747 "antimony.tab.cpp" break; case 79: /* modulepart: submodule lineend */ -#line 401 "antimony.ypp" +#line 405 "antimony.ypp" {} -#line 2723 "antimony.tab.cpp" +#line 2753 "antimony.tab.cpp" break; case 80: /* modulepart: varinitialize lineend */ -#line 402 "antimony.ypp" +#line 406 "antimony.ypp" {} -#line 2729 "antimony.tab.cpp" +#line 2759 "antimony.tab.cpp" break; case 81: /* modulepart: dnadef lineend */ -#line 403 "antimony.ypp" +#line 407 "antimony.ypp" {} -#line 2735 "antimony.tab.cpp" +#line 2765 "antimony.tab.cpp" break; case 82: /* modulepart: event lineend */ -#line 404 "antimony.ypp" +#line 408 "antimony.ypp" {} -#line 2741 "antimony.tab.cpp" +#line 2771 "antimony.tab.cpp" break; case 83: /* modulepart: unitinit lineend */ -#line 405 "antimony.ypp" +#line 409 "antimony.ypp" {} -#line 2747 "antimony.tab.cpp" +#line 2777 "antimony.tab.cpp" break; case 84: /* modulepart: deletion lineend */ -#line 406 "antimony.ypp" +#line 410 "antimony.ypp" {} -#line 2753 "antimony.tab.cpp" +#line 2783 "antimony.tab.cpp" break; case 85: /* modulepart: cvterm lineend */ -#line 407 "antimony.ypp" +#line 411 "antimony.ypp" {} -#line 2759 "antimony.tab.cpp" +#line 2789 "antimony.tab.cpp" break; case 86: /* modulepart: variablein */ -#line 408 "antimony.ypp" +#line 412 "antimony.ypp" {} -#line 2765 "antimony.tab.cpp" +#line 2795 "antimony.tab.cpp" break; case 87: /* modulepart: constraint lineend */ -#line 409 "antimony.ypp" +#line 413 "antimony.ypp" {} -#line 2771 "antimony.tab.cpp" +#line 2801 "antimony.tab.cpp" break; case 88: /* modulepart: objective lineend */ -#line 410 "antimony.ypp" +#line 414 "antimony.ypp" {} -#line 2777 "antimony.tab.cpp" +#line 2807 "antimony.tab.cpp" break; case 89: /* modulepart: algrule lineend */ -#line 411 "antimony.ypp" +#line 415 "antimony.ypp" {} -#line 2783 "antimony.tab.cpp" +#line 2813 "antimony.tab.cpp" break; case 90: /* modulepart: lineend */ -#line 412 "antimony.ypp" +#line 416 "antimony.ypp" {} -#line 2789 "antimony.tab.cpp" +#line 2819 "antimony.tab.cpp" break; case 91: /* reaction: varmaybein ':' reactantList reactionDivider reactantList ';' formula maybein */ -#line 416 "antimony.ypp" +#line 420 "antimony.ypp" { Variable* var = g_registry.AddNewReactionToCurrent((yyvsp[-4].reactionDivider), (yyvsp[-1].formula), (yyvsp[-7].variable), 0); if (var == NULL) YYABORT; @@ -2797,11 +2827,11 @@ yyparse (void) if ((yyvsp[-7].variable)->SetCompartment((yyvsp[0].variable))) YYABORT; } } -#line 2801 "antimony.tab.cpp" +#line 2831 "antimony.tab.cpp" break; case 92: /* reaction: reactantList reactionDivider reactantList ';' formula maybein */ -#line 424 "antimony.ypp" +#line 428 "antimony.ypp" { Variable* var = g_registry.AddNewReactionToCurrent((yyvsp[-4].reactionDivider), (yyvsp[-1].formula), 0); if (var == NULL) YYABORT; @@ -2809,11 +2839,11 @@ yyparse (void) if (var->SetCompartment((yyvsp[0].variable))) YYABORT; } } -#line 2813 "antimony.tab.cpp" +#line 2843 "antimony.tab.cpp" break; case 93: /* reaction: reactantList reactionDivider ';' formula maybein */ -#line 432 "antimony.ypp" +#line 436 "antimony.ypp" { Variable* var = g_registry.AddNewReactionToCurrent((yyvsp[-3].reactionDivider), (yyvsp[-1].formula), 1); if (var == NULL) YYABORT; @@ -2821,11 +2851,11 @@ yyparse (void) if (var->SetCompartment((yyvsp[0].variable))) YYABORT; } } -#line 2825 "antimony.tab.cpp" +#line 2855 "antimony.tab.cpp" break; case 94: /* reaction: varmaybein ':' reactantList reactionDivider ';' formula maybein */ -#line 440 "antimony.ypp" +#line 444 "antimony.ypp" { Variable* var = g_registry.AddNewReactionToCurrent((yyvsp[-3].reactionDivider), (yyvsp[-1].formula), (yyvsp[-6].variable), 1); if (var == NULL) YYABORT; @@ -2833,11 +2863,11 @@ yyparse (void) if ((yyvsp[-6].variable)->SetCompartment((yyvsp[0].variable))) YYABORT; } } -#line 2837 "antimony.tab.cpp" +#line 2867 "antimony.tab.cpp" break; case 95: /* reaction: reactionDivider reactantList ';' formula maybein */ -#line 448 "antimony.ypp" +#line 452 "antimony.ypp" { Variable* var = g_registry.AddNewReactionToCurrent((yyvsp[-4].reactionDivider), (yyvsp[-1].formula), 2); if (var == NULL) YYABORT; @@ -2845,11 +2875,11 @@ yyparse (void) if (var->SetCompartment((yyvsp[0].variable))) YYABORT; } } -#line 2849 "antimony.tab.cpp" +#line 2879 "antimony.tab.cpp" break; case 96: /* reaction: varmaybein ':' reactionDivider reactantList ';' formula maybein */ -#line 456 "antimony.ypp" +#line 460 "antimony.ypp" { Variable* var = g_registry.AddNewReactionToCurrent((yyvsp[-4].reactionDivider), (yyvsp[-1].formula), (yyvsp[-6].variable), 2); if (var == NULL) YYABORT; @@ -2857,885 +2887,963 @@ yyparse (void) if ((yyvsp[-6].variable)->SetCompartment((yyvsp[0].variable))) YYABORT; } } -#line 2861 "antimony.tab.cpp" - break; - - case 97: /* reactantList: variable */ -#line 465 "antimony.ypp" - {(yyval.reactantList) = g_registry.NewBlankReactantList(); if((yyval.reactantList)->AddReactant((yyvsp[0].variable))) YYABORT; } -#line 2867 "antimony.tab.cpp" - break; - - case 98: /* reactantList: "number" variable */ -#line 466 "antimony.ypp" - {(yyval.reactantList) = g_registry.NewBlankReactantList(); if((yyval.reactantList)->AddReactant((yyvsp[0].variable), (yyvsp[-1].num))) YYABORT; } -#line 2873 "antimony.tab.cpp" - break; - - case 99: /* reactantList: variable variable */ -#line 467 "antimony.ypp" - {(yyval.reactantList) = g_registry.NewBlankReactantList(); if((yyval.reactantList)->AddReactant((yyvsp[0].variable), (yyvsp[-1].variable))) YYABORT; } -#line 2879 "antimony.tab.cpp" - break; - - case 100: /* reactantList: reactantList '+' variable */ -#line 468 "antimony.ypp" - {(yyval.reactantList) = (yyvsp[-2].reactantList); if((yyvsp[-2].reactantList)->AddReactant((yyvsp[0].variable))) YYABORT; } -#line 2885 "antimony.tab.cpp" - break; - - case 101: /* reactantList: reactantList '+' "number" variable */ -#line 469 "antimony.ypp" - {(yyval.reactantList) = (yyvsp[-3].reactantList); if((yyvsp[-3].reactantList)->AddReactant((yyvsp[0].variable), (yyvsp[-1].num))) YYABORT; } #line 2891 "antimony.tab.cpp" break; - case 102: /* reactantList: reactantList '+' variable variable */ -#line 470 "antimony.ypp" - {(yyval.reactantList) = (yyvsp[-3].reactantList); if((yyvsp[-3].reactantList)->AddReactant((yyvsp[0].variable), (yyvsp[-1].variable))) YYABORT; } -#line 2897 "antimony.tab.cpp" - break; - - case 103: /* reactionDivider: "->" */ -#line 474 "antimony.ypp" - {(yyval.reactionDivider) = rdBecomes;} + case 97: /* reaction: reactionDivider ';' formula maybein */ +#line 468 "antimony.ypp" + { + Variable* var = g_registry.AddNewReactionToCurrent((yyvsp[-3].reactionDivider), (yyvsp[-1].formula), 3); + if (var == NULL) YYABORT; + if ((yyvsp[0].variable) != NULL) { + if (var->SetCompartment((yyvsp[0].variable))) YYABORT; + } + } #line 2903 "antimony.tab.cpp" break; - case 104: /* reactionDivider: "-|" */ -#line 475 "antimony.ypp" - {(yyval.reactionDivider) = rdInhibits;} -#line 2909 "antimony.tab.cpp" - break; - - case 105: /* reactionDivider: '-' '(' */ + case 98: /* reaction: varmaybein ':' reactionDivider ';' formula maybein */ #line 476 "antimony.ypp" - {(yyval.reactionDivider) = rdInfluences;} + { + Variable* var = g_registry.AddNewReactionToCurrent((yyvsp[-3].reactionDivider), (yyvsp[-1].formula), (yyvsp[-5].variable), 3); + if (var == NULL) YYABORT; + if ((yyvsp[0].variable) != NULL) { + if ((yyvsp[-5].variable)->SetCompartment((yyvsp[0].variable))) YYABORT; + } + } #line 2915 "antimony.tab.cpp" break; - case 106: /* reactionDivider: "-o" */ -#line 477 "antimony.ypp" - {(yyval.reactionDivider) = rdActivates;} + case 99: /* reactantList: variable */ +#line 485 "antimony.ypp" + {(yyval.reactantList) = g_registry.NewBlankReactantList(); if((yyval.reactantList)->AddReactant((yyvsp[0].variable))) YYABORT; } #line 2921 "antimony.tab.cpp" break; - case 107: /* reactionDivider: "=>" */ -#line 478 "antimony.ypp" - {(yyval.reactionDivider) = rdBecomesIrreversibly;} + case 100: /* reactantList: "number" variable */ +#line 486 "antimony.ypp" + {(yyval.reactantList) = g_registry.NewBlankReactantList(); if((yyval.reactantList)->AddReactant((yyvsp[0].variable), (yyvsp[-1].num))) YYABORT; } #line 2927 "antimony.tab.cpp" break; - case 108: /* formula: %empty */ -#line 481 "antimony.ypp" - {(yyval.formula) = g_registry.NewBlankFormula(); } + case 101: /* reactantList: variable variable */ +#line 487 "antimony.ypp" + {(yyval.reactantList) = g_registry.NewBlankReactantList(); if((yyval.reactantList)->AddReactant((yyvsp[0].variable), (yyvsp[-1].variable))) YYABORT; } #line 2933 "antimony.tab.cpp" break; - case 109: /* formula: formula "..." */ -#line 482 "antimony.ypp" - {(yyval.formula) = (yyvsp[-1].formula); (yyvsp[-1].formula)->AddEllipses();} + case 102: /* reactantList: '-' variable */ +#line 488 "antimony.ypp" + {(yyval.reactantList) = g_registry.NewBlankReactantList(); if((yyval.reactantList)->AddReactant((yyvsp[0].variable), -1)) YYABORT; } #line 2939 "antimony.tab.cpp" break; - case 110: /* formula: formula variable */ -#line 483 "antimony.ypp" - {(yyval.formula) = (yyvsp[-1].formula); if((yyvsp[-1].formula)->AddVariable((yyvsp[0].variable))) YYABORT; } + case 103: /* reactantList: '-' "number" variable */ +#line 489 "antimony.ypp" + {(yyval.reactantList) = g_registry.NewBlankReactantList(); if((yyval.reactantList)->AddReactant((yyvsp[0].variable), -(yyvsp[-1].num))) YYABORT; } #line 2945 "antimony.tab.cpp" break; - case 111: /* formula: formula "number" */ -#line 484 "antimony.ypp" - {(yyval.formula) = (yyvsp[-1].formula); (yyvsp[-1].formula)->AddNum((yyvsp[0].num)); } + case 104: /* reactantList: '-' variable variable */ +#line 490 "antimony.ypp" + {g_registry.SetError("Cannot set the variable stoichiometry '" + (yyvsp[-1].variable)->GetNameDelimitedBy(".") + "' to be negative. Either flip the sign of its value, give it a new name and value, or change the side of the reaction it's on."); YYABORT; } #line 2951 "antimony.tab.cpp" break; - case 112: /* formula: formula "name of a pre-defined constant" */ -#line 485 "antimony.ypp" - {(yyval.formula) = (yyvsp[-1].formula); (yyvsp[-1].formula)->AddText((yyvsp[0].word)); } + case 105: /* reactantList: reactantList '+' variable */ +#line 491 "antimony.ypp" + {(yyval.reactantList) = (yyvsp[-2].reactantList); if((yyvsp[-2].reactantList)->AddReactant((yyvsp[0].variable))) YYABORT; } #line 2957 "antimony.tab.cpp" break; - case 113: /* formula: formula "name of an existing function" */ -#line 486 "antimony.ypp" - {(yyval.formula) = (yyvsp[-1].formula); (yyvsp[-1].formula)->AddText((yyvsp[0].word)); } + case 106: /* reactantList: reactantList '+' "number" variable */ +#line 492 "antimony.ypp" + {(yyval.reactantList) = (yyvsp[-3].reactantList); if((yyvsp[-3].reactantList)->AddReactant((yyvsp[0].variable), (yyvsp[-1].num))) YYABORT; } #line 2963 "antimony.tab.cpp" break; - case 114: /* formula: formula '(' commaformula ')' */ -#line 487 "antimony.ypp" - {(yyval.formula) = (yyvsp[-3].formula); (yyvsp[-1].formula)->AddParentheses(); (yyval.formula)->AddFormula((yyvsp[-1].formula)); } + case 107: /* reactantList: reactantList '+' variable variable */ +#line 493 "antimony.ypp" + {(yyval.reactantList) = (yyvsp[-3].reactantList); if((yyvsp[-3].reactantList)->AddReactant((yyvsp[0].variable), (yyvsp[-1].variable))) YYABORT; } #line 2969 "antimony.tab.cpp" break; - case 115: /* formula: formula '{' commaformula '}' */ -#line 488 "antimony.ypp" - {(yyval.formula) = (yyvsp[-3].formula); (yyvsp[-1].formula)->AddCurlyBrackets(); (yyval.formula)->AddFormula((yyvsp[-1].formula)); } + case 108: /* reactantList: reactantList '-' variable */ +#line 494 "antimony.ypp" + {(yyval.reactantList) = (yyvsp[-2].reactantList); if((yyvsp[-2].reactantList)->AddReactant((yyvsp[0].variable), -1)) YYABORT; } #line 2975 "antimony.tab.cpp" break; - case 116: /* formula: formula mathThing */ -#line 489 "antimony.ypp" - {(yyval.formula) = (yyvsp[-1].formula); (yyvsp[-1].formula)->AddMathThing((yyvsp[0].character)); } + case 109: /* reactantList: reactantList '-' "number" variable */ +#line 495 "antimony.ypp" + {(yyval.reactantList) = (yyvsp[-3].reactantList); if((yyvsp[-3].reactantList)->AddReactant((yyvsp[0].variable), -(yyvsp[-1].num))) YYABORT; } #line 2981 "antimony.tab.cpp" break; - case 117: /* formula: formula inequality */ -#line 490 "antimony.ypp" - {(yyval.formula) = (yyvsp[-1].formula); (yyvsp[-1].formula)->AddInequality((yyvsp[0].inequality)); } + case 110: /* reactantList: reactantList '+' '-' variable */ +#line 496 "antimony.ypp" + {(yyval.reactantList) = (yyvsp[-3].reactantList); if((yyvsp[-3].reactantList)->AddReactant((yyvsp[0].variable), -1)) YYABORT; } #line 2987 "antimony.tab.cpp" break; - case 118: /* formula: formula '=' '=' */ -#line 491 "antimony.ypp" - {(yyval.formula) = (yyvsp[-2].formula); (yyvsp[-2].formula)->AddMathThing('='); (yyvsp[-2].formula)->AddMathThing('='); } + case 111: /* reactantList: reactantList '+' '-' "number" variable */ +#line 497 "antimony.ypp" + {(yyval.reactantList) = (yyvsp[-4].reactantList); if((yyvsp[-4].reactantList)->AddReactant((yyvsp[0].variable), -(yyvsp[-1].num))) YYABORT; } #line 2993 "antimony.tab.cpp" break; - case 119: /* formula: formula '&' '&' */ -#line 492 "antimony.ypp" - {(yyval.formula) = (yyvsp[-2].formula); (yyvsp[-2].formula)->AddMathThing('&'); (yyvsp[-2].formula)->AddMathThing('&'); } + case 112: /* reactantList: reactantList '-' variable variable */ +#line 498 "antimony.ypp" + {g_registry.SetError("Cannot set the variable stoichiometry '" + (yyvsp[-1].variable)->GetNameDelimitedBy(".") + "' to be negative. Either flip the sign of its value, give it a new name and value, or change the side of the reaction it's on."); YYABORT; } #line 2999 "antimony.tab.cpp" break; - case 120: /* formula: formula '|' '|' */ -#line 493 "antimony.ypp" - {(yyval.formula) = (yyvsp[-2].formula); (yyvsp[-2].formula)->AddMathThing('|'); (yyvsp[-2].formula)->AddMathThing('|'); } + case 113: /* reactionDivider: "->" */ +#line 502 "antimony.ypp" + {(yyval.reactionDivider) = rdBecomes;} #line 3005 "antimony.tab.cpp" break; - case 121: /* formula: formula "text string" */ -#line 494 "antimony.ypp" - {(yyval.formula) = (yyvsp[-1].formula); (yyvsp[-1].formula)->AddText((yyvsp[0].word), true); } + case 114: /* reactionDivider: "-|" */ +#line 503 "antimony.ypp" + {(yyval.reactionDivider) = rdInhibits;} #line 3011 "antimony.tab.cpp" break; - case 122: /* commaformula: formula */ -#line 497 "antimony.ypp" - {(yyval.formula) = (yyvsp[0].formula);} + case 115: /* reactionDivider: '-' '(' */ +#line 504 "antimony.ypp" + {(yyval.reactionDivider) = rdInfluences;} #line 3017 "antimony.tab.cpp" break; - case 123: /* commaformula: commaformula ',' formula */ -#line 498 "antimony.ypp" - {(yyval.formula) = (yyvsp[-2].formula); (yyval.formula)->AddMathThing(','); (yyval.formula)->AddFormula((yyvsp[0].formula)); } + case 116: /* reactionDivider: "-o" */ +#line 505 "antimony.ypp" + {(yyval.reactionDivider) = rdActivates;} #line 3023 "antimony.tab.cpp" break; - case 124: /* mathThing: '+' */ -#line 501 "antimony.ypp" - {(yyval.character) = '+';} + case 117: /* reactionDivider: "=>" */ +#line 506 "antimony.ypp" + {(yyval.reactionDivider) = rdBecomesIrreversibly;} #line 3029 "antimony.tab.cpp" break; - case 125: /* mathThing: '-' */ -#line 502 "antimony.ypp" - {(yyval.character) = '-';} + case 118: /* formula: %empty */ +#line 509 "antimony.ypp" + {(yyval.formula) = g_registry.NewBlankFormula(); } #line 3035 "antimony.tab.cpp" break; - case 126: /* mathThing: '*' */ -#line 503 "antimony.ypp" - {(yyval.character) = '*';} + case 119: /* formula: formula "..." */ +#line 510 "antimony.ypp" + {(yyval.formula) = (yyvsp[-1].formula); (yyvsp[-1].formula)->AddEllipses();} #line 3041 "antimony.tab.cpp" break; - case 127: /* mathThing: '/' */ -#line 504 "antimony.ypp" - {(yyval.character) = '/';} + case 120: /* formula: formula variable */ +#line 511 "antimony.ypp" + {(yyval.formula) = (yyvsp[-1].formula); if((yyvsp[-1].formula)->AddVariable((yyvsp[0].variable))) YYABORT; } #line 3047 "antimony.tab.cpp" break; - case 128: /* mathThing: '^' */ -#line 505 "antimony.ypp" - {(yyval.character) = '^';} + case 121: /* formula: formula "number" */ +#line 512 "antimony.ypp" + {(yyval.formula) = (yyvsp[-1].formula); (yyvsp[-1].formula)->AddNum((yyvsp[0].num)); } #line 3053 "antimony.tab.cpp" break; - case 129: /* mathThing: '!' */ -#line 506 "antimony.ypp" - {(yyval.character) = '!';} + case 122: /* formula: formula "name of a pre-defined constant" */ +#line 513 "antimony.ypp" + {(yyval.formula) = (yyvsp[-1].formula); (yyvsp[-1].formula)->AddText((yyvsp[0].word)); } #line 3059 "antimony.tab.cpp" break; - case 130: /* mathThing: '%' */ -#line 507 "antimony.ypp" - {(yyval.character) = '%';} + case 123: /* formula: formula "name of an existing function" */ +#line 514 "antimony.ypp" + {(yyval.formula) = (yyvsp[-1].formula); (yyvsp[-1].formula)->AddText((yyvsp[0].word)); } #line 3065 "antimony.tab.cpp" break; - case 131: /* inequality: '<' */ -#line 510 "antimony.ypp" - {(yyval.inequality) = constLT;} + case 124: /* formula: formula '(' commaformula ')' */ +#line 515 "antimony.ypp" + {(yyval.formula) = (yyvsp[-3].formula); (yyvsp[-1].formula)->AddParentheses(); (yyval.formula)->AddFormula((yyvsp[-1].formula)); } #line 3071 "antimony.tab.cpp" break; - case 132: /* inequality: "<=" */ -#line 511 "antimony.ypp" - {(yyval.inequality) = constLEQ;} + case 125: /* formula: formula '{' commaformula '}' */ +#line 516 "antimony.ypp" + {(yyval.formula) = (yyvsp[-3].formula); (yyvsp[-1].formula)->AddCurlyBrackets(); (yyval.formula)->AddFormula((yyvsp[-1].formula)); } #line 3077 "antimony.tab.cpp" break; - case 133: /* inequality: '>' */ -#line 512 "antimony.ypp" - {(yyval.inequality) = constGT;} + case 126: /* formula: formula mathThing */ +#line 517 "antimony.ypp" + {(yyval.formula) = (yyvsp[-1].formula); (yyvsp[-1].formula)->AddMathThing((yyvsp[0].character)); } #line 3083 "antimony.tab.cpp" break; - case 134: /* inequality: ">=" */ -#line 513 "antimony.ypp" - {(yyval.inequality) = constGEQ;} + case 127: /* formula: formula inequality */ +#line 518 "antimony.ypp" + {(yyval.formula) = (yyvsp[-1].formula); (yyvsp[-1].formula)->AddInequality((yyvsp[0].inequality)); } #line 3089 "antimony.tab.cpp" break; - case 135: /* inequality: "!=" */ -#line 514 "antimony.ypp" - {(yyval.inequality) = constNEQ;} + case 128: /* formula: formula '=' '=' */ +#line 519 "antimony.ypp" + {(yyval.formula) = (yyvsp[-2].formula); (yyvsp[-2].formula)->AddMathThing('='); (yyvsp[-2].formula)->AddMathThing('='); } #line 3095 "antimony.tab.cpp" break; - case 136: /* lineend: ';' */ -#line 517 "antimony.ypp" - {} + case 129: /* formula: formula '&' '&' */ +#line 520 "antimony.ypp" + {(yyval.formula) = (yyvsp[-2].formula); (yyvsp[-2].formula)->AddMathThing('&'); (yyvsp[-2].formula)->AddMathThing('&'); } #line 3101 "antimony.tab.cpp" break; - case 137: /* lineend: '\n' */ -#line 518 "antimony.ypp" - {} + case 130: /* formula: formula '|' '|' */ +#line 521 "antimony.ypp" + {(yyval.formula) = (yyvsp[-2].formula); (yyvsp[-2].formula)->AddMathThing('|'); (yyvsp[-2].formula)->AddMathThing('|'); } #line 3107 "antimony.tab.cpp" break; - case 138: /* lineend: "end of line" */ -#line 519 "antimony.ypp" - {} + case 131: /* formula: formula "text string" */ +#line 522 "antimony.ypp" + {(yyval.formula) = (yyvsp[-1].formula); (yyvsp[-1].formula)->AddText((yyvsp[0].word), true); } #line 3113 "antimony.tab.cpp" break; - case 139: /* assignment: varmaybein ':' maxormin formula */ -#line 522 "antimony.ypp" - {if (g_registry.CurrentModule()->AddObjective((yyvsp[-3].variable), (yyvsp[0].formula), (yyvsp[-1].maxormin))) YYABORT;} + case 132: /* commaformula: formula */ +#line 525 "antimony.ypp" + {(yyval.formula) = (yyvsp[0].formula);} #line 3119 "antimony.tab.cpp" break; - case 140: /* assignment: varmaybein '=' formula */ -#line 523 "antimony.ypp" - {if ((yyvsp[-2].variable)->SetFormula((yyvsp[0].formula))) YYABORT; } + case 133: /* commaformula: commaformula ',' formula */ +#line 526 "antimony.ypp" + {(yyval.formula) = (yyvsp[-2].formula); (yyval.formula)->AddMathThing(','); (yyval.formula)->AddFormula((yyvsp[0].formula)); } #line 3125 "antimony.tab.cpp" break; - case 141: /* assignment: varmaybein "'is'" variable */ -#line 524 "antimony.ypp" - {if ((yyvsp[-2].variable)->Synchronize((yyvsp[0].variable), NULL)) YYABORT;} -#line 3131 "antimony.tab.cpp" + case 134: /* mathThing: '+' */ +#line 529 "antimony.ypp" + {(yyval.character) = '+';} +#line 3131 "antimony.tab.cpp" break; - case 142: /* assignment: varmaybein "'is'" variable '/' variable */ -#line 525 "antimony.ypp" - {if ((yyvsp[-4].variable)->Synchronize((yyvsp[-2].variable), (yyvsp[0].variable))) YYABORT;} + case 135: /* mathThing: '-' */ +#line 530 "antimony.ypp" + {(yyval.character) = '-';} #line 3137 "antimony.tab.cpp" break; - case 143: /* assignment: varmaybein '*' variable "'is'" variable */ -#line 526 "antimony.ypp" - {if ((yyvsp[-4].variable)->Synchronize((yyvsp[0].variable), (yyvsp[-2].variable))) YYABORT;} + case 136: /* mathThing: '*' */ +#line 531 "antimony.ypp" + {(yyval.character) = '*';} #line 3143 "antimony.tab.cpp" break; - case 144: /* assignment: varmaybein "'is'" "text string" */ -#line 527 "antimony.ypp" - {if ((yyvsp[-2].variable)->SetDisplayName(*((yyvsp[0].word)))) YYABORT;} + case 137: /* mathThing: '/' */ +#line 532 "antimony.ypp" + {(yyval.character) = '/';} #line 3149 "antimony.tab.cpp" break; - case 145: /* assignment: varmaybein ':' '=' formula */ -#line 528 "antimony.ypp" - {if ((yyvsp[-3].variable)->SetAssignmentRule((yyvsp[0].formula))) YYABORT;} + case 138: /* mathThing: '^' */ +#line 533 "antimony.ypp" + {(yyval.character) = '^';} #line 3155 "antimony.tab.cpp" break; - case 146: /* assignment: varmaybein '\'' '=' formula */ -#line 529 "antimony.ypp" - {if ((yyvsp[-3].variable)->SetRateRule((yyvsp[0].formula))) YYABORT;} + case 139: /* mathThing: '!' */ +#line 534 "antimony.ypp" + {(yyval.character) = '!';} #line 3161 "antimony.tab.cpp" break; - case 147: /* assignment: varmaybein "'has'" unitdef */ -#line 530 "antimony.ypp" - {if ((yyvsp[-2].variable)->SetUnit((yyvsp[0].variable))) YYABORT; } + case 140: /* mathThing: '%' */ +#line 535 "antimony.ypp" + {(yyval.character) = '%';} #line 3167 "antimony.tab.cpp" break; - case 148: /* algrule: "number" '=' formula */ -#line 533 "antimony.ypp" - {if (g_registry.AddNewAlgebraicRuleToCurrent((yyvsp[-2].num), (yyvsp[0].formula))) YYABORT; } + case 141: /* inequality: '<' */ +#line 538 "antimony.ypp" + {(yyval.inequality) = constLT;} #line 3173 "antimony.tab.cpp" break; - case 149: /* algrule: varmaybein ':' "number" '=' formula */ -#line 534 "antimony.ypp" - {if ((yyvsp[-4].variable)->SetAlgebraicRule((yyvsp[-2].num), (yyvsp[0].formula)) ) YYABORT;} + case 142: /* inequality: "<=" */ +#line 539 "antimony.ypp" + {(yyval.inequality) = constLEQ;} #line 3179 "antimony.tab.cpp" break; - case 150: /* $@6: %empty */ -#line 537 "antimony.ypp" - {if ((yyvsp[-3].variable)->SetModule((yyvsp[-1].word))) YYABORT;} + case 143: /* inequality: '>' */ +#line 540 "antimony.ypp" + {(yyval.inequality) = constGT;} #line 3185 "antimony.tab.cpp" break; - case 151: /* submodule: varmaybein ':' "name of an existing module" '(' $@6 variableimportlist ')' submodifications maybein */ -#line 537 "antimony.ypp" - {if ((yyvsp[0].variable) != NULL) {if ((yyvsp[-8].variable)->SetCompartment((yyvsp[0].variable))) YYABORT;}} + case 144: /* inequality: ">=" */ +#line 541 "antimony.ypp" + {(yyval.inequality) = constGEQ;} #line 3191 "antimony.tab.cpp" break; - case 152: /* $@7: %empty */ -#line 538 "antimony.ypp" - {if(g_registry.CurrentModule()->SetModule((yyvsp[-1].word))) YYABORT;} + case 145: /* inequality: "!=" */ +#line 542 "antimony.ypp" + {(yyval.inequality) = constNEQ;} #line 3197 "antimony.tab.cpp" break; - case 153: /* submodule: "name of an existing module" '(' $@7 variableimportlist ')' submodifications maybein */ -#line 538 "antimony.ypp" - {if ((yyvsp[0].variable) != NULL) {if (g_registry.GetCurrentSubmodel()->SetCompartment((yyvsp[0].variable))) YYABORT;}} + case 146: /* lineend: ';' */ +#line 545 "antimony.ypp" + {} #line 3203 "antimony.tab.cpp" break; - case 154: /* variableimportlist: %empty */ -#line 542 "antimony.ypp" - {} + case 147: /* lineend: '\n' */ +#line 546 "antimony.ypp" + {} #line 3209 "antimony.tab.cpp" break; - case 155: /* variableimportlist: variable */ -#line 543 "antimony.ypp" - {if (g_registry.AddVariableToCurrentImportList((yyvsp[0].variable))) YYABORT; } + case 148: /* lineend: "end of line" */ +#line 547 "antimony.ypp" + {} #line 3215 "antimony.tab.cpp" break; - case 156: /* variableimportlist: variableimportlist ',' variable */ -#line 544 "antimony.ypp" - { if (g_registry.AddVariableToCurrentImportList((yyvsp[0].variable))) YYABORT; } + case 149: /* assignment: varmaybein ':' maxormin formula */ +#line 550 "antimony.ypp" + {if (g_registry.CurrentModule()->AddObjective((yyvsp[-3].variable), (yyvsp[0].formula), (yyvsp[-1].maxormin))) YYABORT;} #line 3221 "antimony.tab.cpp" break; - case 157: /* variableimportlist: "number" */ -#line 545 "antimony.ypp" - {if (g_registry.AddNumberToCurrentImportList((yyvsp[0].num))) YYABORT; } + case 150: /* assignment: varmaybein '=' formula */ +#line 551 "antimony.ypp" + {if ((yyvsp[-2].variable)->SetFormula((yyvsp[0].formula))) YYABORT; } #line 3227 "antimony.tab.cpp" break; - case 158: /* variableimportlist: variableimportlist ',' "number" */ -#line 546 "antimony.ypp" - { if (g_registry.AddNumberToCurrentImportList((yyvsp[0].num))) YYABORT; } + case 151: /* assignment: varmaybein "'is'" variable */ +#line 552 "antimony.ypp" + {if ((yyvsp[-2].variable)->Synchronize((yyvsp[0].variable), NULL)) YYABORT;} #line 3233 "antimony.tab.cpp" break; - case 159: /* submodifications: %empty */ -#line 550 "antimony.ypp" - {} + case 152: /* assignment: varmaybein "'is'" variable '/' variable */ +#line 553 "antimony.ypp" + {if ((yyvsp[-4].variable)->Synchronize((yyvsp[-2].variable), (yyvsp[0].variable))) YYABORT;} #line 3239 "antimony.tab.cpp" break; - case 160: /* submodifications: submodifications ',' "element name" '=' variable */ -#line 551 "antimony.ypp" + case 153: /* assignment: varmaybein '*' variable "'is'" variable */ +#line 554 "antimony.ypp" + {if ((yyvsp[-4].variable)->Synchronize((yyvsp[0].variable), (yyvsp[-2].variable))) YYABORT;} +#line 3245 "antimony.tab.cpp" + break; + + case 154: /* assignment: varmaybein "'is'" "text string" */ +#line 555 "antimony.ypp" + {if ((yyvsp[-2].variable)->SetDisplayName(*((yyvsp[0].word)))) YYABORT;} +#line 3251 "antimony.tab.cpp" + break; + + case 155: /* assignment: varmaybein ':' '=' formula */ +#line 556 "antimony.ypp" + {if ((yyvsp[-3].variable)->SetAssignmentRule((yyvsp[0].formula))) YYABORT;} +#line 3257 "antimony.tab.cpp" + break; + + case 156: /* assignment: varmaybein '\'' '=' formula */ +#line 557 "antimony.ypp" + {if ((yyvsp[-3].variable)->SetRateRule((yyvsp[0].formula))) YYABORT;} +#line 3263 "antimony.tab.cpp" + break; + + case 157: /* assignment: varmaybein "'has'" unitdef */ +#line 558 "antimony.ypp" + {if ((yyvsp[-2].variable)->SetUnit((yyvsp[0].variable))) YYABORT; } +#line 3269 "antimony.tab.cpp" + break; + + case 158: /* algrule: "number" '=' formula */ +#line 561 "antimony.ypp" + {if (g_registry.AddNewAlgebraicRuleToCurrent((yyvsp[-2].num), (yyvsp[0].formula))) YYABORT; } +#line 3275 "antimony.tab.cpp" + break; + + case 159: /* algrule: varmaybein ':' "number" '=' formula */ +#line 562 "antimony.ypp" + {if ((yyvsp[-4].variable)->SetAlgebraicRule((yyvsp[-2].num), (yyvsp[0].formula)) ) YYABORT;} +#line 3281 "antimony.tab.cpp" + break; + + case 160: /* $@6: %empty */ +#line 565 "antimony.ypp" + {if ((yyvsp[-3].variable)->SetModule((yyvsp[-1].word))) YYABORT;} +#line 3287 "antimony.tab.cpp" + break; + + case 161: /* submodule: varmaybein ':' "name of an existing module" '(' $@6 variableimportlist ')' submodifications maybein */ +#line 565 "antimony.ypp" + {if ((yyvsp[0].variable) != NULL) {if ((yyvsp[-8].variable)->SetCompartment((yyvsp[0].variable))) YYABORT;}} +#line 3293 "antimony.tab.cpp" + break; + + case 162: /* $@7: %empty */ +#line 566 "antimony.ypp" + {if(g_registry.CurrentModule()->SetModule((yyvsp[-1].word))) YYABORT;} +#line 3299 "antimony.tab.cpp" + break; + + case 163: /* submodule: "name of an existing module" '(' $@7 variableimportlist ')' submodifications maybein */ +#line 566 "antimony.ypp" + {if ((yyvsp[0].variable) != NULL) {if (g_registry.GetCurrentSubmodel()->SetCompartment((yyvsp[0].variable))) YYABORT;}} +#line 3305 "antimony.tab.cpp" + break; + + case 164: /* variableimportlist: %empty */ +#line 570 "antimony.ypp" + {} +#line 3311 "antimony.tab.cpp" + break; + + case 165: /* variableimportlist: variable */ +#line 571 "antimony.ypp" + {if (g_registry.AddVariableToCurrentImportList((yyvsp[0].variable))) YYABORT; } +#line 3317 "antimony.tab.cpp" + break; + + case 166: /* variableimportlist: variableimportlist ',' variable */ +#line 572 "antimony.ypp" + { if (g_registry.AddVariableToCurrentImportList((yyvsp[0].variable))) YYABORT; } +#line 3323 "antimony.tab.cpp" + break; + + case 167: /* variableimportlist: "number" */ +#line 573 "antimony.ypp" + {if (g_registry.AddNumberToCurrentImportList((yyvsp[0].num))) YYABORT; } +#line 3329 "antimony.tab.cpp" + break; + + case 168: /* variableimportlist: variableimportlist ',' "number" */ +#line 574 "antimony.ypp" + { if (g_registry.AddNumberToCurrentImportList((yyvsp[0].num))) YYABORT; } +#line 3335 "antimony.tab.cpp" + break; + + case 169: /* submodifications: %empty */ +#line 578 "antimony.ypp" + {} +#line 3341 "antimony.tab.cpp" + break; + + case 170: /* submodifications: submodifications ',' "element name" '=' variable */ +#line 579 "antimony.ypp" {if (CaselessStrCmp(false, *(yyvsp[-2].word), "extentconv")) {g_registry.GetCurrentSubmodel()->SetExtentConversionFactor((yyvsp[0].variable));} else if (CaselessStrCmp(false, *(yyvsp[-2].word), "timeconv")) {if (g_registry.GetCurrentSubmodel()->SetTimeConversionFactor((yyvsp[0].variable))) YYABORT;} else { g_registry.SetError("Illegal term '" + *(yyvsp[-2].word) + "' in submodel declaration. You may use the terms 'extentconv' and 'timeconv' to set the extent and time conversion factors for this submodel, respectively."); YYABORT;}} -#line 3247 "antimony.tab.cpp" +#line 3349 "antimony.tab.cpp" break; - case 161: /* submodifications: submodifications ',' "element name" '=' "number" */ -#line 555 "antimony.ypp" + case 171: /* submodifications: submodifications ',' "element name" '=' "number" */ +#line 583 "antimony.ypp" {if (CaselessStrCmp(false, *(yyvsp[-2].word), "extentconv")) {g_registry.GetCurrentSubmodel()->SetExtentConversionFactor((yyvsp[0].num));} else if (CaselessStrCmp(false, *(yyvsp[-2].word), "timeconv")) {if (g_registry.GetCurrentSubmodel()->SetTimeConversionFactor((yyvsp[0].num))) YYABORT;} else { g_registry.SetError("Illegal term '" + *(yyvsp[-2].word) + "' in submodel declaration. You may use the terms 'extentconv' and 'timeconv' to set the extent and time conversion factors for this submodel, respectively."); YYABORT;}} -#line 3255 "antimony.tab.cpp" +#line 3357 "antimony.tab.cpp" break; - case 162: /* varinitialize: specinit */ -#line 559 "antimony.ypp" + case 172: /* varinitialize: specinit */ +#line 587 "antimony.ypp" { } -#line 3261 "antimony.tab.cpp" +#line 3363 "antimony.tab.cpp" break; - case 163: /* varinitialize: formulainit */ -#line 560 "antimony.ypp" + case 173: /* varinitialize: formulainit */ +#line 588 "antimony.ypp" { } -#line 3267 "antimony.tab.cpp" +#line 3369 "antimony.tab.cpp" break; - case 164: /* varinitialize: reactioninit */ -#line 561 "antimony.ypp" + case 174: /* varinitialize: reactioninit */ +#line 589 "antimony.ypp" { } -#line 3273 "antimony.tab.cpp" +#line 3375 "antimony.tab.cpp" break; - case 165: /* varinitialize: dnainit */ -#line 562 "antimony.ypp" + case 175: /* varinitialize: dnainit */ +#line 590 "antimony.ypp" { } -#line 3279 "antimony.tab.cpp" +#line 3381 "antimony.tab.cpp" break; - case 166: /* varinitialize: geneinit */ -#line 563 "antimony.ypp" + case 176: /* varinitialize: geneinit */ +#line 591 "antimony.ypp" { } -#line 3285 "antimony.tab.cpp" +#line 3387 "antimony.tab.cpp" break; - case 167: /* varinitialize: geneProductInit */ -#line 564 "antimony.ypp" + case 177: /* varinitialize: geneProductInit */ +#line 592 "antimony.ypp" { } -#line 3291 "antimony.tab.cpp" +#line 3393 "antimony.tab.cpp" break; - case 168: /* varinitialize: operatorinit */ -#line 565 "antimony.ypp" + case 178: /* varinitialize: operatorinit */ +#line 593 "antimony.ypp" { } -#line 3297 "antimony.tab.cpp" +#line 3399 "antimony.tab.cpp" break; - case 169: /* varinitialize: compartmentinit */ -#line 566 "antimony.ypp" + case 179: /* varinitialize: compartmentinit */ +#line 594 "antimony.ypp" { } -#line 3303 "antimony.tab.cpp" +#line 3405 "antimony.tab.cpp" break; - case 170: /* varinitialize: varconstinit */ -#line 567 "antimony.ypp" + case 180: /* varinitialize: varconstinit */ +#line 595 "antimony.ypp" { } -#line 3309 "antimony.tab.cpp" +#line 3411 "antimony.tab.cpp" break; - case 171: /* specinit: "'species'" varmaybeis */ -#line 570 "antimony.ypp" + case 181: /* specinit: "'species'" varmaybeis */ +#line 598 "antimony.ypp" {g_registry.SetConstness(constDEFAULT); g_registry.SetSubstOnly(false); (yyvsp[0].variable)->SetRegSpecVals(); if ((yyvsp[0].variable)->SetType(varSpeciesUndef)) YYABORT; } -#line 3315 "antimony.tab.cpp" +#line 3417 "antimony.tab.cpp" break; - case 172: /* specinit: "'var'" "'species'" varmaybeis */ -#line 571 "antimony.ypp" + case 182: /* specinit: "'var'" "'species'" varmaybeis */ +#line 599 "antimony.ypp" {g_registry.SetConstness(constVAR); g_registry.SetSubstOnly(false); (yyvsp[0].variable)->SetRegSpecVals(); if ((yyvsp[0].variable)->SetType(varSpeciesUndef)) YYABORT; } -#line 3321 "antimony.tab.cpp" +#line 3423 "antimony.tab.cpp" break; - case 173: /* specinit: "'const'" "'species'" varmaybeis */ -#line 572 "antimony.ypp" + case 183: /* specinit: "'const'" "'species'" varmaybeis */ +#line 600 "antimony.ypp" {g_registry.SetConstness(constCONST); g_registry.SetSubstOnly(false); (yyvsp[0].variable)->SetRegSpecVals(); if ((yyvsp[0].variable)->SetType(varSpeciesUndef)) YYABORT; } -#line 3327 "antimony.tab.cpp" +#line 3429 "antimony.tab.cpp" break; - case 174: /* specinit: "'substanceOnly'" "'species'" varmaybeis */ -#line 573 "antimony.ypp" + case 184: /* specinit: "'substanceOnly'" "'species'" varmaybeis */ +#line 601 "antimony.ypp" {g_registry.SetConstness(constDEFAULT); g_registry.SetSubstOnly(true); (yyvsp[0].variable)->SetRegSpecVals(); if ((yyvsp[0].variable)->SetType(varSpeciesUndef)) YYABORT; } -#line 3333 "antimony.tab.cpp" +#line 3435 "antimony.tab.cpp" break; - case 175: /* specinit: "'substanceOnly'" varmaybeis */ -#line 574 "antimony.ypp" + case 185: /* specinit: "'substanceOnly'" varmaybeis */ +#line 602 "antimony.ypp" {g_registry.SetConstness(constDEFAULT); g_registry.SetSubstOnly(true); (yyvsp[0].variable)->SetRegSpecVals(); if ((yyvsp[0].variable)->SetType(varSpeciesUndef)) YYABORT; } -#line 3339 "antimony.tab.cpp" +#line 3441 "antimony.tab.cpp" break; - case 176: /* specinit: "'var'" "'substanceOnly'" "'species'" varmaybeis */ -#line 575 "antimony.ypp" + case 186: /* specinit: "'var'" "'substanceOnly'" "'species'" varmaybeis */ +#line 603 "antimony.ypp" {g_registry.SetConstness(constVAR); g_registry.SetSubstOnly(true); (yyvsp[0].variable)->SetRegSpecVals(); if ((yyvsp[0].variable)->SetType(varSpeciesUndef)) YYABORT; } -#line 3345 "antimony.tab.cpp" +#line 3447 "antimony.tab.cpp" break; - case 177: /* specinit: "'const'" "'substanceOnly'" "'species'" varmaybeis */ -#line 576 "antimony.ypp" + case 187: /* specinit: "'const'" "'substanceOnly'" "'species'" varmaybeis */ +#line 604 "antimony.ypp" {g_registry.SetConstness(constCONST); g_registry.SetSubstOnly(true); (yyvsp[0].variable)->SetRegSpecVals(); if ((yyvsp[0].variable)->SetType(varSpeciesUndef)) YYABORT; } -#line 3351 "antimony.tab.cpp" +#line 3453 "antimony.tab.cpp" break; - case 178: /* specinit: specinit ',' varmaybeis */ -#line 577 "antimony.ypp" + case 188: /* specinit: specinit ',' varmaybeis */ +#line 605 "antimony.ypp" {(yyvsp[0].variable)->SetRegSpecVals(); if ((yyvsp[0].variable)->SetType(varSpeciesUndef)) YYABORT; } -#line 3357 "antimony.tab.cpp" +#line 3459 "antimony.tab.cpp" break; - case 179: /* specinit: "'species'" '.' "element name" '=' formula */ -#line 578 "antimony.ypp" + case 189: /* specinit: "'species'" '.' "element name" '=' formula */ +#line 606 "antimony.ypp" {if (g_registry.CurrentModule()->AddSpeciesLayoutInfo((yyvsp[-2].word), (yyvsp[0].formula))) YYABORT;} -#line 3363 "antimony.tab.cpp" +#line 3465 "antimony.tab.cpp" break; - case 180: /* geneProductInit: "'geneProduct'" varmaybeis */ -#line 581 "antimony.ypp" + case 190: /* geneProductInit: "'geneProduct'" varmaybeis */ +#line 609 "antimony.ypp" {if ((yyvsp[0].variable)->SetType(varGeneProduct)) YYABORT; } -#line 3369 "antimony.tab.cpp" +#line 3471 "antimony.tab.cpp" break; - case 181: /* geneProductInit: geneProductInit ',' varmaybeis */ -#line 582 "antimony.ypp" + case 191: /* geneProductInit: geneProductInit ',' varmaybeis */ +#line 610 "antimony.ypp" {if ((yyvsp[0].variable)->SetType(varGeneProduct)) YYABORT;} -#line 3375 "antimony.tab.cpp" +#line 3477 "antimony.tab.cpp" break; - case 182: /* formulainit: "'formula'" varmaybeis */ -#line 584 "antimony.ypp" + case 192: /* formulainit: "'formula'" varmaybeis */ +#line 612 "antimony.ypp" {g_registry.SetConstness(constDEFAULT); (yyvsp[0].variable)->SetRegConst(); if ((yyvsp[0].variable)->SetType(varFormulaUndef)) YYABORT; } -#line 3381 "antimony.tab.cpp" +#line 3483 "antimony.tab.cpp" break; - case 183: /* formulainit: "'var'" "'formula'" varmaybeis */ -#line 585 "antimony.ypp" + case 193: /* formulainit: "'var'" "'formula'" varmaybeis */ +#line 613 "antimony.ypp" {g_registry.SetConstness(constVAR); (yyvsp[0].variable)->SetRegConst(); if ((yyvsp[0].variable)->SetType(varFormulaUndef)) YYABORT; } -#line 3387 "antimony.tab.cpp" +#line 3489 "antimony.tab.cpp" break; - case 184: /* formulainit: "'const'" "'formula'" varmaybeis */ -#line 586 "antimony.ypp" + case 194: /* formulainit: "'const'" "'formula'" varmaybeis */ +#line 614 "antimony.ypp" {g_registry.SetConstness(constCONST); (yyvsp[0].variable)->SetRegConst(); if ((yyvsp[0].variable)->SetType(varFormulaUndef)) YYABORT; } -#line 3393 "antimony.tab.cpp" +#line 3495 "antimony.tab.cpp" break; - case 185: /* formulainit: formulainit ',' varmaybeis */ -#line 587 "antimony.ypp" + case 195: /* formulainit: formulainit ',' varmaybeis */ +#line 615 "antimony.ypp" {(yyvsp[0].variable)->SetRegConst(); if ((yyvsp[0].variable)->SetType(varFormulaUndef)) YYABORT; } -#line 3399 "antimony.tab.cpp" +#line 3501 "antimony.tab.cpp" break; - case 186: /* reactioninit: "'reaction'" varmaybeis */ -#line 590 "antimony.ypp" + case 196: /* reactioninit: "'reaction'" varmaybeis */ +#line 618 "antimony.ypp" {g_registry.SetConstness(constDEFAULT); (yyvsp[0].variable)->SetRegConst(); if ((yyvsp[0].variable)->SetType(varReactionUndef)) YYABORT; } -#line 3405 "antimony.tab.cpp" +#line 3507 "antimony.tab.cpp" break; - case 187: /* reactioninit: "'var'" "'reaction'" varmaybeis */ -#line 591 "antimony.ypp" + case 197: /* reactioninit: "'var'" "'reaction'" varmaybeis */ +#line 619 "antimony.ypp" {g_registry.SetConstness(constVAR); (yyvsp[0].variable)->SetRegConst(); if ((yyvsp[0].variable)->SetType(varReactionUndef)) YYABORT; } -#line 3411 "antimony.tab.cpp" +#line 3513 "antimony.tab.cpp" break; - case 188: /* reactioninit: "'const'" "'reaction'" */ -#line 592 "antimony.ypp" + case 198: /* reactioninit: "'const'" "'reaction'" */ +#line 620 "antimony.ypp" {g_registry.SetError("Reactions may not be set 'const'."); YYABORT; } -#line 3417 "antimony.tab.cpp" +#line 3519 "antimony.tab.cpp" break; - case 189: /* reactioninit: reactioninit ',' varmaybeis */ -#line 593 "antimony.ypp" + case 199: /* reactioninit: reactioninit ',' varmaybeis */ +#line 621 "antimony.ypp" {(yyvsp[0].variable)->SetRegConst(); if ((yyvsp[0].variable)->SetType(varReactionUndef)) YYABORT; } -#line 3423 "antimony.tab.cpp" +#line 3525 "antimony.tab.cpp" break; - case 190: /* reactioninit: "'reaction'" '.' "element name" '=' formula */ -#line 594 "antimony.ypp" + case 200: /* reactioninit: "'reaction'" '.' "element name" '=' formula */ +#line 622 "antimony.ypp" {if (g_registry.CurrentModule()->AddReactionLayoutInfo((yyvsp[-2].word), (yyvsp[0].formula))) YYABORT;} -#line 3429 "antimony.tab.cpp" +#line 3531 "antimony.tab.cpp" break; - case 191: /* dnainit: "'DNA'" varmaybeis */ -#line 597 "antimony.ypp" + case 201: /* dnainit: "'DNA'" varmaybeis */ +#line 625 "antimony.ypp" {g_registry.SetConstness(constDEFAULT); (yyvsp[0].variable)->SetRegConst(); if ((yyvsp[0].variable)->SetType(varDNA)) YYABORT; } -#line 3435 "antimony.tab.cpp" +#line 3537 "antimony.tab.cpp" break; - case 192: /* dnainit: "'var'" "'DNA'" varmaybeis */ -#line 598 "antimony.ypp" + case 202: /* dnainit: "'var'" "'DNA'" varmaybeis */ +#line 626 "antimony.ypp" {g_registry.SetConstness(constVAR); (yyvsp[0].variable)->SetRegConst(); if ((yyvsp[0].variable)->SetType(varDNA)) YYABORT; } -#line 3441 "antimony.tab.cpp" +#line 3543 "antimony.tab.cpp" break; - case 193: /* dnainit: "'const'" "'DNA'" varmaybeis */ -#line 599 "antimony.ypp" + case 203: /* dnainit: "'const'" "'DNA'" varmaybeis */ +#line 627 "antimony.ypp" {g_registry.SetConstness(constCONST); (yyvsp[0].variable)->SetRegConst(); if ((yyvsp[0].variable)->SetType(varDNA)) YYABORT; } -#line 3447 "antimony.tab.cpp" +#line 3549 "antimony.tab.cpp" break; - case 194: /* dnainit: dnainit ',' varmaybeis */ -#line 600 "antimony.ypp" + case 204: /* dnainit: dnainit ',' varmaybeis */ +#line 628 "antimony.ypp" {(yyvsp[0].variable)->SetRegConst(); if ((yyvsp[0].variable)->SetType(varDNA)) YYABORT; } -#line 3453 "antimony.tab.cpp" +#line 3555 "antimony.tab.cpp" break; - case 195: /* geneinit: "'gene'" varmaybeis */ -#line 603 "antimony.ypp" + case 205: /* geneinit: "'gene'" varmaybeis */ +#line 631 "antimony.ypp" {g_registry.SetConstness(constDEFAULT); (yyvsp[0].variable)->SetRegConst(); if ((yyvsp[0].variable)->SetType(varReactionGene)) YYABORT; } -#line 3459 "antimony.tab.cpp" +#line 3561 "antimony.tab.cpp" break; - case 196: /* geneinit: "'var'" "'gene'" varmaybeis */ -#line 604 "antimony.ypp" + case 206: /* geneinit: "'var'" "'gene'" varmaybeis */ +#line 632 "antimony.ypp" {g_registry.SetConstness(constVAR); (yyvsp[0].variable)->SetRegConst(); if ((yyvsp[0].variable)->SetType(varReactionGene)) YYABORT; } -#line 3465 "antimony.tab.cpp" +#line 3567 "antimony.tab.cpp" break; - case 197: /* geneinit: "'const'" "'gene'" varmaybeis */ -#line 605 "antimony.ypp" + case 207: /* geneinit: "'const'" "'gene'" varmaybeis */ +#line 633 "antimony.ypp" {g_registry.SetError("Genes may not be set 'const'."); YYABORT; } -#line 3471 "antimony.tab.cpp" +#line 3573 "antimony.tab.cpp" break; - case 198: /* geneinit: geneinit ',' varmaybeis */ -#line 606 "antimony.ypp" + case 208: /* geneinit: geneinit ',' varmaybeis */ +#line 634 "antimony.ypp" {(yyvsp[0].variable)->SetRegConst(); if ((yyvsp[0].variable)->SetType(varReactionGene)) YYABORT; } -#line 3477 "antimony.tab.cpp" +#line 3579 "antimony.tab.cpp" break; - case 199: /* operatorinit: "'operator'" varmaybeis */ -#line 609 "antimony.ypp" + case 209: /* operatorinit: "'operator'" varmaybeis */ +#line 637 "antimony.ypp" {g_registry.SetConstness(constDEFAULT); (yyvsp[0].variable)->SetRegConst(); if ((yyvsp[0].variable)->SetType(varFormulaOperator)) YYABORT; } -#line 3483 "antimony.tab.cpp" +#line 3585 "antimony.tab.cpp" break; - case 200: /* operatorinit: "'var'" "'operator'" varmaybeis */ -#line 610 "antimony.ypp" + case 210: /* operatorinit: "'var'" "'operator'" varmaybeis */ +#line 638 "antimony.ypp" {g_registry.SetConstness(constVAR); (yyvsp[0].variable)->SetRegConst(); if ((yyvsp[0].variable)->SetType(varFormulaOperator)) YYABORT; } -#line 3489 "antimony.tab.cpp" +#line 3591 "antimony.tab.cpp" break; - case 201: /* operatorinit: "'const'" "'operator'" varmaybeis */ -#line 611 "antimony.ypp" + case 211: /* operatorinit: "'const'" "'operator'" varmaybeis */ +#line 639 "antimony.ypp" {g_registry.SetConstness(constCONST); (yyvsp[0].variable)->SetRegConst(); if ((yyvsp[0].variable)->SetType(varFormulaOperator)) YYABORT; } -#line 3495 "antimony.tab.cpp" +#line 3597 "antimony.tab.cpp" break; - case 202: /* operatorinit: operatorinit ',' varmaybeis */ -#line 612 "antimony.ypp" + case 212: /* operatorinit: operatorinit ',' varmaybeis */ +#line 640 "antimony.ypp" {(yyvsp[0].variable)->SetRegConst(); if ((yyvsp[0].variable)->SetType(varFormulaOperator)) YYABORT; } -#line 3501 "antimony.tab.cpp" +#line 3603 "antimony.tab.cpp" break; - case 203: /* compartmentinit: "'compartment'" varmaybeis */ -#line 616 "antimony.ypp" + case 213: /* compartmentinit: "'compartment'" varmaybeis */ +#line 644 "antimony.ypp" {g_registry.SetConstness(constDEFAULT); (yyvsp[0].variable)->SetRegConst(); if ((yyvsp[0].variable)->SetType(varCompartment)) YYABORT; } -#line 3507 "antimony.tab.cpp" +#line 3609 "antimony.tab.cpp" break; - case 204: /* compartmentinit: "'var'" "'compartment'" varmaybeis */ -#line 617 "antimony.ypp" + case 214: /* compartmentinit: "'var'" "'compartment'" varmaybeis */ +#line 645 "antimony.ypp" {g_registry.SetConstness(constVAR); (yyvsp[0].variable)->SetRegConst(); if ((yyvsp[0].variable)->SetType(varCompartment)) YYABORT; } -#line 3513 "antimony.tab.cpp" +#line 3615 "antimony.tab.cpp" break; - case 205: /* compartmentinit: "'const'" "'compartment'" varmaybeis */ -#line 618 "antimony.ypp" + case 215: /* compartmentinit: "'const'" "'compartment'" varmaybeis */ +#line 646 "antimony.ypp" {g_registry.SetConstness(constCONST); (yyvsp[0].variable)->SetRegConst(); if ((yyvsp[0].variable)->SetType(varCompartment)) YYABORT; } -#line 3519 "antimony.tab.cpp" +#line 3621 "antimony.tab.cpp" break; - case 206: /* compartmentinit: compartmentinit ',' varmaybeis */ -#line 619 "antimony.ypp" + case 216: /* compartmentinit: compartmentinit ',' varmaybeis */ +#line 647 "antimony.ypp" {(yyvsp[0].variable)->SetRegConst(); if ((yyvsp[0].variable)->SetType(varCompartment)) YYABORT; } -#line 3525 "antimony.tab.cpp" +#line 3627 "antimony.tab.cpp" break; - case 207: /* compartmentinit: "'compartment'" '.' "element name" '=' formula */ -#line 620 "antimony.ypp" + case 217: /* compartmentinit: "'compartment'" '.' "element name" '=' formula */ +#line 648 "antimony.ypp" {if (g_registry.CurrentModule()->AddCompartmentLayoutInfo((yyvsp[-2].word), (yyvsp[0].formula))) YYABORT;} -#line 3531 "antimony.tab.cpp" +#line 3633 "antimony.tab.cpp" break; - case 208: /* varconstinit: "'var'" varmaybeis */ -#line 623 "antimony.ypp" + case 218: /* varconstinit: "'var'" varmaybeis */ +#line 651 "antimony.ypp" {g_registry.SetConstness(constVAR); (yyvsp[0].variable)->SetRegConst();} -#line 3537 "antimony.tab.cpp" +#line 3639 "antimony.tab.cpp" break; - case 209: /* varconstinit: "'const'" varmaybeis */ -#line 624 "antimony.ypp" + case 219: /* varconstinit: "'const'" varmaybeis */ +#line 652 "antimony.ypp" {g_registry.SetConstness(constCONST); (yyvsp[0].variable)->SetRegConst();} -#line 3543 "antimony.tab.cpp" +#line 3645 "antimony.tab.cpp" break; - case 210: /* varconstinit: varconstinit ',' varmaybeis */ -#line 625 "antimony.ypp" + case 220: /* varconstinit: varconstinit ',' varmaybeis */ +#line 653 "antimony.ypp" {(yyvsp[0].variable)->SetRegConst();} -#line 3549 "antimony.tab.cpp" +#line 3651 "antimony.tab.cpp" break; - case 211: /* unitinit: "'unit'" variable '=' formula */ -#line 628 "antimony.ypp" + case 221: /* unitinit: "'unit'" variable '=' formula */ +#line 656 "antimony.ypp" {if ((yyvsp[-2].variable)->SetType(varUnitDefinition)) YYABORT; if ((yyvsp[0].formula)->MakeAllVariablesUnits()) YYABORT; if ((yyvsp[-2].variable)->GetUnitDef()->SetFromFormula((yyvsp[0].formula))) YYABORT;} -#line 3557 "antimony.tab.cpp" +#line 3659 "antimony.tab.cpp" break; - case 212: /* unitinit: "'unit'" variable */ -#line 631 "antimony.ypp" + case 222: /* unitinit: "'unit'" variable */ +#line 659 "antimony.ypp" {if ((yyvsp[0].variable)->SetType(varUnitDefinition)) YYABORT;} -#line 3563 "antimony.tab.cpp" +#line 3665 "antimony.tab.cpp" break; - case 213: /* dnadef: dnastrand */ -#line 634 "antimony.ypp" + case 223: /* dnadef: dnastrand */ +#line 662 "antimony.ypp" {if (g_registry.SaveWorkingStrand()) YYABORT;} -#line 3569 "antimony.tab.cpp" +#line 3671 "antimony.tab.cpp" break; - case 214: /* dnadef: varmaybein ':' dnastrand */ -#line 635 "antimony.ypp" + case 224: /* dnadef: varmaybein ':' dnastrand */ +#line 663 "antimony.ypp" {if (g_registry.SetStrandAs((yyvsp[-2].variable))) YYABORT;} -#line 3575 "antimony.tab.cpp" +#line 3677 "antimony.tab.cpp" break; - case 215: /* dnastrand: "--" variable */ -#line 638 "antimony.ypp" + case 225: /* dnastrand: "--" variable */ +#line 666 "antimony.ypp" {if (g_registry.SetNewUpstreamOpen((yyvsp[0].variable))) YYABORT;} -#line 3581 "antimony.tab.cpp" +#line 3683 "antimony.tab.cpp" break; - case 216: /* dnastrand: "--" dnamiddle */ -#line 639 "antimony.ypp" + case 226: /* dnastrand: "--" dnamiddle */ +#line 667 "antimony.ypp" {g_registry.SetOpenUpstream(); } -#line 3587 "antimony.tab.cpp" +#line 3689 "antimony.tab.cpp" break; - case 217: /* dnastrand: dnamiddle variable */ -#line 640 "antimony.ypp" + case 227: /* dnastrand: dnamiddle variable */ +#line 668 "antimony.ypp" {if (g_registry.SetDownstreamEnd((yyvsp[0].variable))) YYABORT;} -#line 3593 "antimony.tab.cpp" +#line 3695 "antimony.tab.cpp" break; - case 218: /* dnastrand: "--" dnamiddle variable */ -#line 641 "antimony.ypp" + case 228: /* dnastrand: "--" dnamiddle variable */ +#line 669 "antimony.ypp" {g_registry.SetOpenUpstream(); if(g_registry.SetDownstreamEnd((yyvsp[0].variable))) YYABORT;} -#line 3599 "antimony.tab.cpp" +#line 3701 "antimony.tab.cpp" break; - case 219: /* dnastrand: dnamiddle */ -#line 642 "antimony.ypp" + case 229: /* dnastrand: dnamiddle */ +#line 670 "antimony.ypp" { } -#line 3605 "antimony.tab.cpp" +#line 3707 "antimony.tab.cpp" break; - case 220: /* dnamiddle: variable "--" */ -#line 645 "antimony.ypp" + case 230: /* dnamiddle: variable "--" */ +#line 673 "antimony.ypp" {if (g_registry.SetNewDownstreamOpen((yyvsp[-1].variable))) YYABORT;} -#line 3611 "antimony.tab.cpp" +#line 3713 "antimony.tab.cpp" break; - case 221: /* dnamiddle: dnamiddle variable "--" */ -#line 646 "antimony.ypp" + case 231: /* dnamiddle: dnamiddle variable "--" */ +#line 674 "antimony.ypp" {if (g_registry.SetDownstreamOpen((yyvsp[-1].variable))) YYABORT;} -#line 3617 "antimony.tab.cpp" +#line 3719 "antimony.tab.cpp" break; - case 222: /* $@8: %empty */ -#line 649 "antimony.ypp" + case 232: /* $@8: %empty */ +#line 677 "antimony.ypp" {if (g_registry.SetNewCurrentEvent((yyvsp[0].formula))) YYABORT;} -#line 3623 "antimony.tab.cpp" +#line 3725 "antimony.tab.cpp" break; - case 223: /* event: "'at'" formula $@8 eventmodifications colonret assignmentlist */ -#line 649 "antimony.ypp" + case 233: /* event: "'at'" formula $@8 eventmodifications colonret assignmentlist */ +#line 677 "antimony.ypp" {} -#line 3629 "antimony.tab.cpp" +#line 3731 "antimony.tab.cpp" break; - case 224: /* $@9: %empty */ -#line 650 "antimony.ypp" + case 234: /* $@9: %empty */ +#line 678 "antimony.ypp" {if (g_registry.SetNewCurrentEvent((yyvsp[-2].formula), (yyvsp[0].formula))) YYABORT;} -#line 3635 "antimony.tab.cpp" +#line 3737 "antimony.tab.cpp" break; - case 225: /* event: "'at'" formula "'after'" formula $@9 eventmodifications colonret assignmentlist */ -#line 650 "antimony.ypp" + case 235: /* event: "'at'" formula "'after'" formula $@9 eventmodifications colonret assignmentlist */ +#line 678 "antimony.ypp" {} -#line 3641 "antimony.tab.cpp" +#line 3743 "antimony.tab.cpp" break; - case 226: /* $@10: %empty */ -#line 651 "antimony.ypp" + case 236: /* $@10: %empty */ +#line 679 "antimony.ypp" {if (g_registry.SetNewCurrentEvent((yyvsp[0].formula), (yyvsp[-3].variable))) YYABORT;} -#line 3647 "antimony.tab.cpp" +#line 3749 "antimony.tab.cpp" break; - case 227: /* event: varmaybein ':' "'at'" formula $@10 eventmodifications colonret assignmentlist */ -#line 651 "antimony.ypp" + case 237: /* event: varmaybein ':' "'at'" formula $@10 eventmodifications colonret assignmentlist */ +#line 679 "antimony.ypp" {} -#line 3653 "antimony.tab.cpp" +#line 3755 "antimony.tab.cpp" break; - case 228: /* $@11: %empty */ -#line 652 "antimony.ypp" + case 238: /* $@11: %empty */ +#line 680 "antimony.ypp" {if (g_registry.SetNewCurrentEvent((yyvsp[-2].formula), (yyvsp[0].formula), (yyvsp[-5].variable))) YYABORT;} -#line 3659 "antimony.tab.cpp" +#line 3761 "antimony.tab.cpp" break; - case 229: /* event: varmaybein ':' "'at'" formula "'after'" formula $@11 eventmodifications colonret assignmentlist */ -#line 652 "antimony.ypp" + case 239: /* event: varmaybein ':' "'at'" formula "'after'" formula $@11 eventmodifications colonret assignmentlist */ +#line 680 "antimony.ypp" {} -#line 3665 "antimony.tab.cpp" +#line 3767 "antimony.tab.cpp" break; - case 230: /* colonret: ':' */ -#line 655 "antimony.ypp" + case 240: /* colonret: ':' */ +#line 683 "antimony.ypp" {} -#line 3671 "antimony.tab.cpp" +#line 3773 "antimony.tab.cpp" break; - case 231: /* colonret: colonret '\n' */ -#line 656 "antimony.ypp" + case 241: /* colonret: colonret '\n' */ +#line 684 "antimony.ypp" {} -#line 3677 "antimony.tab.cpp" +#line 3779 "antimony.tab.cpp" break; - case 232: /* eventmodifications: %empty */ -#line 659 "antimony.ypp" + case 242: /* eventmodifications: %empty */ +#line 687 "antimony.ypp" {} -#line 3683 "antimony.tab.cpp" +#line 3785 "antimony.tab.cpp" break; - case 233: /* eventmodifications: eventmodifications ',' "element name" '=' formula */ -#line 660 "antimony.ypp" + case 243: /* eventmodifications: eventmodifications ',' "element name" '=' formula */ +#line 688 "antimony.ypp" {if (CaselessStrCmp(false, *(yyvsp[-2].word), "priority")) {g_registry.GetCurrentEvent()->SetPriority(*(yyvsp[0].formula));} else if (CaselessStrCmp(false, *(yyvsp[-2].word), "t0")) {if (g_registry.GetCurrentEvent()->SetInitialValue(*(yyvsp[0].formula))) YYABORT;} else if (CaselessStrCmp(false, *(yyvsp[-2].word), "fromTrigger")) {if (g_registry.GetCurrentEvent()->SetUseValuesFromTriggerTime(*(yyvsp[0].formula))) YYABORT;} else if (CaselessStrCmp(false, *(yyvsp[-2].word), "persistent")) {if (g_registry.GetCurrentEvent()->SetPersistent(*(yyvsp[0].formula))) YYABORT;} else { g_registry.SetError("Illegal term '" + *(yyvsp[-2].word) + "' in event defintion. You may use the terms 'priority', 't0', 'fromTrigger', and 'persistent' here to set those properties of an event."); YYABORT;}} -#line 3693 "antimony.tab.cpp" +#line 3795 "antimony.tab.cpp" break; - case 234: /* assignmentlist: variable '=' formula */ -#line 667 "antimony.ypp" - {if (g_registry.GetCurrentEvent()->AddResult((yyvsp[-2].variable), (yyvsp[0].formula))) YYABORT;} -#line 3699 "antimony.tab.cpp" + case 244: /* assignmententry: %empty */ +#line 695 "antimony.ypp" + {} +#line 3801 "antimony.tab.cpp" break; - case 235: /* assignmentlist: variable '=' formula ':' assignmentlist */ -#line 668 "antimony.ypp" - {if (g_registry.GetCurrentEvent()->AddResult((yyvsp[-4].variable), (yyvsp[-2].formula))) YYABORT;} -#line 3705 "antimony.tab.cpp" + case 245: /* assignmententry: variable '=' formula */ +#line 696 "antimony.ypp" + {if (g_registry.GetCurrentEvent()->AddResult((yyvsp[-2].variable), (yyvsp[0].formula))) YYABORT;} +#line 3807 "antimony.tab.cpp" break; - case 236: /* assignmentlist: variable '=' formula ':' '\n' assignmentlist */ -#line 669 "antimony.ypp" - {if (g_registry.GetCurrentEvent()->AddResult((yyvsp[-5].variable), (yyvsp[-3].formula))) YYABORT;} -#line 3711 "antimony.tab.cpp" + case 246: /* assignmentlist: assignmententry */ +#line 698 "antimony.ypp" + {} +#line 3813 "antimony.tab.cpp" break; - case 237: /* assignmentlist: variable '=' formula ',' assignmentlist */ -#line 670 "antimony.ypp" - {if (g_registry.GetCurrentEvent()->AddResult((yyvsp[-4].variable), (yyvsp[-2].formula))) YYABORT;} -#line 3717 "antimony.tab.cpp" + case 247: /* assignmentlist: assignmentlist ',' assignmententry */ +#line 699 "antimony.ypp" + {} +#line 3819 "antimony.tab.cpp" break; - case 238: /* assignmentlist: variable '=' formula ',' '\n' assignmentlist */ -#line 671 "antimony.ypp" - {if (g_registry.GetCurrentEvent()->AddResult((yyvsp[-5].variable), (yyvsp[-3].formula))) YYABORT;} -#line 3723 "antimony.tab.cpp" + case 248: /* assignmentlist: assignmentlist ',' '\n' assignmententry */ +#line 700 "antimony.ypp" + {} +#line 3825 "antimony.tab.cpp" break; - case 239: /* deletion: "'delete'" variable */ -#line 674 "antimony.ypp" + case 249: /* assignmentlist: assignmentlist colonret assignmententry */ +#line 701 "antimony.ypp" + {} +#line 3831 "antimony.tab.cpp" + break; + + case 250: /* deletion: "'delete'" variable */ +#line 704 "antimony.ypp" {if (g_registry.CurrentModule()->AddDeletion((yyvsp[0].variable))) YYABORT;} -#line 3729 "antimony.tab.cpp" +#line 3837 "antimony.tab.cpp" break; - case 240: /* deletion: deletion ',' variable */ -#line 675 "antimony.ypp" + case 251: /* deletion: deletion ',' variable */ +#line 705 "antimony.ypp" {if (g_registry.CurrentModule()->AddDeletion((yyvsp[0].variable))) YYABORT;} -#line 3735 "antimony.tab.cpp" +#line 3843 "antimony.tab.cpp" break; - case 241: /* unitdef: formula */ -#line 678 "antimony.ypp" + case 252: /* unitdef: formula */ +#line 708 "antimony.ypp" { if ((yyvsp[0].formula)->MakeAllVariablesUnits()) YYABORT; if ((yyvsp[0].formula)->IsSingleVariable()) { @@ -3749,125 +3857,125 @@ yyparse (void) (yyval.variable) = g_registry.CurrentModule()->AddOrFindUnitDef(ud); } } -#line 3753 "antimony.tab.cpp" +#line 3861 "antimony.tab.cpp" break; - case 242: /* constraint: "number" inequality formula */ -#line 693 "antimony.ypp" + case 253: /* constraint: "number" inequality formula */ +#line 723 "antimony.ypp" {if (g_registry.CurrentModule()->AddConstraint((yyvsp[-2].num), (yyvsp[0].formula), (yyvsp[-1].inequality))) YYABORT;} -#line 3759 "antimony.tab.cpp" +#line 3867 "antimony.tab.cpp" break; - case 243: /* constraint: '-' "number" inequality formula */ -#line 694 "antimony.ypp" + case 254: /* constraint: '-' "number" inequality formula */ +#line 724 "antimony.ypp" {if (g_registry.CurrentModule()->AddConstraint(-(yyvsp[-2].num), (yyvsp[0].formula), (yyvsp[-1].inequality))) YYABORT;} -#line 3765 "antimony.tab.cpp" +#line 3873 "antimony.tab.cpp" break; - case 244: /* constraint: "name of a pre-defined constant" inequality formula */ -#line 695 "antimony.ypp" + case 255: /* constraint: "name of a pre-defined constant" inequality formula */ +#line 725 "antimony.ypp" {if (g_registry.CurrentModule()->AddConstraint((yyvsp[-2].word), (yyvsp[0].formula), (yyvsp[-1].inequality))) YYABORT;} -#line 3771 "antimony.tab.cpp" +#line 3879 "antimony.tab.cpp" break; - case 245: /* constraint: "element name" inequality formula */ -#line 696 "antimony.ypp" + case 256: /* constraint: "element name" inequality formula */ +#line 726 "antimony.ypp" {if (g_registry.CurrentModule()->AddConstraint((yyvsp[-2].word), (yyvsp[0].formula), (yyvsp[-1].inequality))) YYABORT;} -#line 3777 "antimony.tab.cpp" +#line 3885 "antimony.tab.cpp" break; - case 246: /* constraint: "'constraint'" ':' formula */ -#line 697 "antimony.ypp" + case 257: /* constraint: "'constraint'" ':' formula */ +#line 727 "antimony.ypp" {if (g_registry.CurrentModule()->AddConstraint((yyvsp[0].formula))) YYABORT;} -#line 3783 "antimony.tab.cpp" +#line 3891 "antimony.tab.cpp" break; - case 247: /* constraint: "'constraint'" variable ':' formula */ -#line 698 "antimony.ypp" + case 258: /* constraint: "'constraint'" variable ':' formula */ +#line 728 "antimony.ypp" {if (g_registry.CurrentModule()->AddConstraint((yyvsp[-2].variable), (yyvsp[0].formula))) YYABORT;} -#line 3789 "antimony.tab.cpp" +#line 3897 "antimony.tab.cpp" break; - case 248: /* objective: maxormin formula */ -#line 701 "antimony.ypp" + case 259: /* objective: maxormin formula */ +#line 731 "antimony.ypp" {if (g_registry.CurrentModule()->AddObjective((yyvsp[0].formula), (yyvsp[-1].maxormin))) YYABORT;} -#line 3795 "antimony.tab.cpp" +#line 3903 "antimony.tab.cpp" break; - case 249: /* maxormin: "'maximize'" */ -#line 704 "antimony.ypp" + case 260: /* maxormin: "'maximize'" */ +#line 734 "antimony.ypp" {(yyval.maxormin) = true;} -#line 3801 "antimony.tab.cpp" +#line 3909 "antimony.tab.cpp" break; - case 250: /* maxormin: "'minimize'" */ -#line 705 "antimony.ypp" + case 261: /* maxormin: "'minimize'" */ +#line 735 "antimony.ypp" {(yyval.maxormin) = false;} -#line 3807 "antimony.tab.cpp" +#line 3915 "antimony.tab.cpp" break; - case 251: /* stringlist: "text string" */ -#line 708 "antimony.ypp" + case 262: /* stringlist: "text string" */ +#line 738 "antimony.ypp" { (yyval.stringlist) = new std::vector(); (yyval.stringlist)->push_back(*((yyvsp[0].word))); } -#line 3813 "antimony.tab.cpp" +#line 3921 "antimony.tab.cpp" break; - case 252: /* stringlist: stringlist ',' "text string" */ -#line 709 "antimony.ypp" + case 263: /* stringlist: stringlist ',' "text string" */ +#line 739 "antimony.ypp" { (yyval.stringlist) = (yyvsp[-2].stringlist); (yyval.stringlist)->push_back(*(yyvsp[0].word)); } -#line 3819 "antimony.tab.cpp" +#line 3927 "antimony.tab.cpp" break; - case 253: /* stringlist: stringlist ',' '\n' "text string" */ -#line 710 "antimony.ypp" + case 264: /* stringlist: stringlist ',' '\n' "text string" */ +#line 740 "antimony.ypp" { (yyval.stringlist) = (yyvsp[-3].stringlist); (yyval.stringlist)->push_back(*(yyvsp[0].word)); } -#line 3825 "antimony.tab.cpp" +#line 3933 "antimony.tab.cpp" break; - case 254: /* $@12: %empty */ -#line 712 "antimony.ypp" + case 265: /* $@12: %empty */ +#line 742 "antimony.ypp" {if (g_registry.SetCurrentModuleIf((yyvsp[0].word), (yyvsp[-1].word))) YYABORT;} -#line 3831 "antimony.tab.cpp" +#line 3939 "antimony.tab.cpp" break; - case 255: /* annotationBlock: "element name" "name of an existing module" $@12 annotations "'end'" */ -#line 712 "antimony.ypp" + case 266: /* annotationBlock: "element name" "name of an existing module" $@12 annotations "'end'" */ +#line 742 "antimony.ypp" {g_registry.RevertToPreviousModule();} -#line 3837 "antimony.tab.cpp" +#line 3945 "antimony.tab.cpp" break; - case 256: /* annotations: %empty */ -#line 715 "antimony.ypp" + case 267: /* annotations: %empty */ +#line 745 "antimony.ypp" {} -#line 3843 "antimony.tab.cpp" +#line 3951 "antimony.tab.cpp" break; - case 257: /* annotations: "element name" ':' stringlist */ -#line 716 "antimony.ypp" + case 268: /* annotations: "element name" ':' stringlist */ +#line 746 "antimony.ypp" {string modname = g_registry.CurrentModuleName(); g_registry.ProcessGlobalCVTerm(&modname, (yyvsp[-2].word), *(yyvsp[0].stringlist)); delete (yyvsp[0].stringlist);} -#line 3849 "antimony.tab.cpp" +#line 3957 "antimony.tab.cpp" break; - case 258: /* cvterm: variable "element name" stringlist */ -#line 721 "antimony.ypp" + case 269: /* cvterm: variable "element name" stringlist */ +#line 751 "antimony.ypp" {bool cverr = g_registry.CurrentModule()->ProcessCVTerm((yyvsp[-2].variable),(yyvsp[-1].word),*(yyvsp[0].stringlist)); delete (yyvsp[0].stringlist); if (cverr) YYABORT;} -#line 3855 "antimony.tab.cpp" +#line 3963 "antimony.tab.cpp" break; - case 259: /* cvterm: variable "element name" '.' "element name" stringlist */ -#line 722 "antimony.ypp" + case 270: /* cvterm: variable "element name" '.' "element name" stringlist */ +#line 752 "antimony.ypp" {bool cverr = g_registry.ProcessCreatorTerm((yyvsp[-4].variable), (yyvsp[-3].word), (yyvsp[-1].word), *(yyvsp[0].stringlist)); delete (yyvsp[0].stringlist); if (cverr) YYABORT;} -#line 3861 "antimony.tab.cpp" +#line 3969 "antimony.tab.cpp" break; - case 260: /* cvterm: variable "element name" '.' "element name" "number" */ -#line 723 "antimony.ypp" + case 271: /* cvterm: variable "element name" '.' "element name" "number" */ +#line 753 "antimony.ypp" {if (g_registry.ProcessCreatorTerm((yyvsp[-4].variable), (yyvsp[-3].word), (yyvsp[-1].word), (yyvsp[0].num))) YYABORT;} -#line 3867 "antimony.tab.cpp" +#line 3975 "antimony.tab.cpp" break; - case 261: /* toplevel_sbo: "name of an existing module" '.' "element name" '=' "number" */ -#line 727 "antimony.ypp" + case 272: /* toplevel_sbo: "name of an existing module" '.' "element name" '=' "number" */ +#line 757 "antimony.ypp" { Module* module = g_registry.GetModule(*(yyvsp[-4].word)); if (module && (yyvsp[-2].word) && CaselessStrCmp(true, *((yyvsp[-2].word)), "sboTerm")) { module->SetSBOTerm(lround((yyvsp[0].num))); @@ -3877,11 +3985,11 @@ yyparse (void) YYABORT; } } -#line 3881 "antimony.tab.cpp" +#line 3989 "antimony.tab.cpp" break; - case 262: /* toplevel_sbo: "name of an existing function" '.' "element name" '=' "number" */ -#line 738 "antimony.ypp" + case 273: /* toplevel_sbo: "name of an existing function" '.' "element name" '=' "number" */ +#line 768 "antimony.ypp" { Module* function = g_registry.GetModule(*(yyvsp[-4].word)); if (function && (yyvsp[-2].word) && CaselessStrCmp(true, *((yyvsp[-2].word)), "sboTerm")) { function->SetSBOTerm(lround((yyvsp[0].num))); @@ -3891,11 +3999,11 @@ yyparse (void) YYABORT; } } -#line 3895 "antimony.tab.cpp" +#line 4003 "antimony.tab.cpp" break; - case 263: /* toplevel_sbo: "name of an existing module" '.' "element name" '=' stringConstant */ -#line 748 "antimony.ypp" + case 274: /* toplevel_sbo: "name of an existing module" '.' "element name" '=' stringConstant */ +#line 778 "antimony.ypp" { Module* function = g_registry.GetModule(*(yyvsp[-4].word)); if (function && (yyvsp[-2].word) && CaselessStrCmp(true, *((yyvsp[-2].word)), "autolayout")) { if (function->SetLayout((yyvsp[0].word))) YYABORT; @@ -3905,11 +4013,11 @@ yyparse (void) YYABORT; } } -#line 3909 "antimony.tab.cpp" +#line 4017 "antimony.tab.cpp" break; - case 264: /* toplevel_sbo: "name of an existing module" '.' "element name" '.' "element name" '=' "number" */ -#line 758 "antimony.ypp" + case 275: /* toplevel_sbo: "name of an existing module" '.' "element name" '.' "element name" '=' "number" */ +#line 788 "antimony.ypp" { Module* module = g_registry.CurrentModule(); if (module && (yyvsp[-4].word) && CaselessStrCmp(true, *((yyvsp[-4].word)), "autolayout")) { if (module->SetAutoLayout((yyvsp[-2].word), (yyvsp[0].num))) YYABORT; @@ -3923,11 +4031,11 @@ yyparse (void) } module->SetLayout("on"); } -#line 3927 "antimony.tab.cpp" +#line 4035 "antimony.tab.cpp" break; - case 265: /* toplevel_sbo: "name of an existing module" '.' "element name" '.' "element name" '=' stringConstant */ -#line 772 "antimony.ypp" + case 276: /* toplevel_sbo: "name of an existing module" '.' "element name" '.' "element name" '=' stringConstant */ +#line 802 "antimony.ypp" { Module* module = g_registry.CurrentModule(); if (module && (yyvsp[-4].word) && CaselessStrCmp(true, *((yyvsp[-4].word)), "autolayout")) { if (module->SetAutoLayout((yyvsp[-2].word), (yyvsp[0].word))) YYABORT; @@ -3941,11 +4049,11 @@ yyparse (void) } module->SetLayout("on"); } -#line 3945 "antimony.tab.cpp" +#line 4053 "antimony.tab.cpp" break; - case 266: /* toplevel_sbo: "name of an existing module" '.' "element name" '.' "element name" '=' '{' variablelist '}' */ -#line 786 "antimony.ypp" + case 277: /* toplevel_sbo: "name of an existing module" '.' "element name" '.' "element name" '=' '{' variablelist '}' */ +#line 816 "antimony.ypp" { Module* module = g_registry.CurrentModule(); if (module && (yyvsp[-6].word) && CaselessStrCmp(true, *((yyvsp[-6].word)), "autolayout")) { if (module->SetAutoLayout((yyvsp[-4].word), (yyvsp[-1].variablelist))) YYABORT; @@ -3959,11 +4067,11 @@ yyparse (void) } module->SetLayout("on"); } -#line 3963 "antimony.tab.cpp" +#line 4071 "antimony.tab.cpp" break; - case 267: /* toplevel_sbo: "name of an existing module" '.' "element name" '.' "element name" '=' '{' numlist '}' */ -#line 800 "antimony.ypp" + case 278: /* toplevel_sbo: "name of an existing module" '.' "element name" '.' "element name" '=' '{' numlist '}' */ +#line 830 "antimony.ypp" { Module* module = g_registry.CurrentModule(); if (module && (yyvsp[-6].word) && CaselessStrCmp(true, *((yyvsp[-6].word)), "autolayout")) { if (module->SetAutoLayout((yyvsp[-4].word), (yyvsp[-1].numlist))) YYABORT; @@ -3977,47 +4085,47 @@ yyparse (void) } module->SetLayout("on"); } -#line 3981 "antimony.tab.cpp" +#line 4089 "antimony.tab.cpp" break; - case 268: /* modulename: "name of an existing module" "'is'" "text string" lineend */ -#line 816 "antimony.ypp" + case 279: /* modulename: "name of an existing module" "'is'" "text string" lineend */ +#line 846 "antimony.ypp" { g_registry.GetModule(*(yyvsp[-3].word))->SetDisplayName(*(yyvsp[-1].word)); } -#line 3987 "antimony.tab.cpp" +#line 4095 "antimony.tab.cpp" break; - case 269: /* functionname: "name of an existing function" "'is'" "text string" lineend */ -#line 818 "antimony.ypp" + case 280: /* functionname: "name of an existing function" "'is'" "text string" lineend */ +#line 848 "antimony.ypp" { g_registry.GetModule(*(yyvsp[-3].word))->SetDisplayName(*(yyvsp[-1].word)); } -#line 3993 "antimony.tab.cpp" +#line 4101 "antimony.tab.cpp" break; - case 270: /* modulecvterm: "name of an existing module" "element name" stringlist lineend */ -#line 821 "antimony.ypp" + case 281: /* modulecvterm: "name of an existing module" "element name" stringlist lineend */ +#line 851 "antimony.ypp" {bool cverr = g_registry.ProcessGlobalCVTerm((yyvsp[-3].word),(yyvsp[-2].word),*(yyvsp[-1].stringlist)); delete (yyvsp[-1].stringlist); if (cverr) YYABORT;} -#line 3999 "antimony.tab.cpp" +#line 4107 "antimony.tab.cpp" break; - case 271: /* modulecvterm: "name of an existing module" "element name" '.' "element name" stringlist lineend */ -#line 822 "antimony.ypp" + case 282: /* modulecvterm: "name of an existing module" "element name" '.' "element name" stringlist lineend */ +#line 852 "antimony.ypp" {bool cverr = g_registry.ProcessGlobalCreatorTerm((yyvsp[-5].word), (yyvsp[-4].word), (yyvsp[-2].word), *(yyvsp[-1].stringlist)); delete (yyvsp[-1].stringlist); if (cverr) YYABORT;} -#line 4005 "antimony.tab.cpp" +#line 4113 "antimony.tab.cpp" break; - case 272: /* modulecvterm: "name of an existing module" "element name" '.' "element name" "number" lineend */ -#line 823 "antimony.ypp" + case 283: /* modulecvterm: "name of an existing module" "element name" '.' "element name" "number" lineend */ +#line 853 "antimony.ypp" {if (g_registry.ProcessGlobalCreatorTerm((yyvsp[-5].word), (yyvsp[-4].word), (yyvsp[-2].word), (yyvsp[-1].num))) YYABORT;} -#line 4011 "antimony.tab.cpp" +#line 4119 "antimony.tab.cpp" break; - case 273: /* functioncvterm: "name of an existing function" "element name" stringlist lineend */ -#line 824 "antimony.ypp" + case 284: /* functioncvterm: "name of an existing function" "element name" stringlist lineend */ +#line 854 "antimony.ypp" {bool cverr = g_registry.ProcessGlobalCVTerm((yyvsp[-3].word),(yyvsp[-2].word),*(yyvsp[-1].stringlist)); delete (yyvsp[-1].stringlist); if (cverr) YYABORT;} -#line 4017 "antimony.tab.cpp" +#line 4125 "antimony.tab.cpp" break; -#line 4021 "antimony.tab.cpp" +#line 4129 "antimony.tab.cpp" default: break; } @@ -4241,7 +4349,7 @@ yyparse (void) return yyresult; } -#line 826 "antimony.ypp" +#line 856 "antimony.ypp" diff --git a/src/antimony.ypp b/src/antimony.ypp index e05bed234..8056471fd 100644 --- a/src/antimony.ypp +++ b/src/antimony.ypp @@ -318,8 +318,12 @@ moduleannotation: MODULE ANTWORD stringlist lineend if (module && $3 && CaselessStrCmp(true, *($3), "layout")) { if (module->SetLayout($5)) YYABORT; } + else if (module && $3 && CaselessStrCmp(true, *($3), "conversionFactor")) { + Variable* cfvar = g_registry.CurrentModule()->AddOrFindVariable($5); + if (module->SetConversionFactor(cfvar)) YYABORT; + } else { - g_registry.SetError("Invalid syntax 'model." + *($3) + "'. The only thing that can be set on the model to a string is 'layout'."); + g_registry.SetError("Invalid syntax 'model." + *($3) + "'. The only thing that can be set on the model to a string is 'layout', and the only thing that can be set on the model to a variable is 'conversionFactor'."); YYABORT; } } @@ -460,14 +464,38 @@ reaction: varmaybein ':' reactantList reactionDivider reactantList ';' for if ($1->SetCompartment($7)) YYABORT; } } + | reactionDivider ';' formula maybein + { + Variable* var = g_registry.AddNewReactionToCurrent($1, $3, 3); + if (var == NULL) YYABORT; + if ($4 != NULL) { + if (var->SetCompartment($4)) YYABORT; + } + } + | varmaybein ':' reactionDivider ';' formula maybein + { + Variable* var = g_registry.AddNewReactionToCurrent($3, $5, $1, 3); + if (var == NULL) YYABORT; + if ($6 != NULL) { + if ($1->SetCompartment($6)) YYABORT; + } + } ; reactantList: variable {$$ = g_registry.NewBlankReactantList(); if($$->AddReactant($1)) YYABORT; } | NUM variable {$$ = g_registry.NewBlankReactantList(); if($$->AddReactant($2, $1)) YYABORT; } | variable variable {$$ = g_registry.NewBlankReactantList(); if($$->AddReactant($2, $1)) YYABORT; } + | '-' variable {$$ = g_registry.NewBlankReactantList(); if($$->AddReactant($2, -1)) YYABORT; } + | '-' NUM variable {$$ = g_registry.NewBlankReactantList(); if($$->AddReactant($3, -$2)) YYABORT; } + | '-' variable variable {g_registry.SetError("Cannot set the variable stoichiometry '" + $2->GetNameDelimitedBy(".") + "' to be negative. Either flip the sign of its value, give it a new name and value, or change the side of the reaction it's on."); YYABORT; } | reactantList '+' variable {$$ = $1; if($1->AddReactant($3)) YYABORT; } | reactantList '+' NUM variable {$$ = $1; if($1->AddReactant($4, $3)) YYABORT; } | reactantList '+' variable variable {$$ = $1; if($1->AddReactant($4, $3)) YYABORT; } + | reactantList '-' variable {$$ = $1; if($1->AddReactant($3, -1)) YYABORT; } + | reactantList '-' NUM variable {$$ = $1; if($1->AddReactant($4, -$3)) YYABORT; } + | reactantList '+' '-' variable {$$ = $1; if($1->AddReactant($4, -1)) YYABORT; } + | reactantList '+' '-' NUM variable {$$ = $1; if($1->AddReactant($5, -$4)) YYABORT; } + | reactantList '-' variable variable {g_registry.SetError("Cannot set the variable stoichiometry '" + $3->GetNameDelimitedBy(".") + "' to be negative. Either flip the sign of its value, give it a new name and value, or change the side of the reaction it's on."); YYABORT; } ; reactionDivider: @@ -664,11 +692,13 @@ eventmodifications: /* empty */ {} else { g_registry.SetError("Illegal term '" + *$3 + "' in event defintion. You may use the terms 'priority', 't0', 'fromTrigger', and 'persistent' here to set those properties of an event."); YYABORT;}} ; -assignmentlist: variable '=' formula {if (g_registry.GetCurrentEvent()->AddResult($1, $3)) YYABORT;} - | variable '=' formula ':' assignmentlist {if (g_registry.GetCurrentEvent()->AddResult($1, $3)) YYABORT;} - | variable '=' formula ':' '\n' assignmentlist {if (g_registry.GetCurrentEvent()->AddResult($1, $3)) YYABORT;} - | variable '=' formula ',' assignmentlist {if (g_registry.GetCurrentEvent()->AddResult($1, $3)) YYABORT;} - | variable '=' formula ',' '\n' assignmentlist {if (g_registry.GetCurrentEvent()->AddResult($1, $3)) YYABORT;} +assignmententry: /* empty */ {} + | variable '=' formula {if (g_registry.GetCurrentEvent()->AddResult($1, $3)) YYABORT;} + +assignmentlist: assignmententry {} + | assignmentlist ',' assignmententry {} + | assignmentlist ',' '\n' assignmententry {} + | assignmentlist colonret assignmententry {} ; deletion: DELETEWORD variable {if (g_registry.CurrentModule()->AddDeletion($2)) YYABORT;} diff --git a/src/antimony_api.cpp b/src/antimony_api.cpp index 68c543f09..4b9901749 100644 --- a/src/antimony_api.cpp +++ b/src/antimony_api.cpp @@ -640,7 +640,14 @@ LIB_EXTERN char* getNthModuleName(unsigned long n) LIB_EXTERN char* getMainModuleName() { const Module* mainmod = g_registry.GetMainModule(); - if (mainmod==NULL) return NULL; + if (mainmod==NULL) { + string error = "There is no main module."; + if (g_registry.GetNumModules() == 0) { + error += " In fact, there are no modules at all. Try running loadModule(filename)."; + } + g_registry.SetError(error); + return NULL; + } char* retval = getCharStar(mainmod->GetModuleName().c_str()); return retval; } @@ -806,6 +813,103 @@ LIB_EXTERN char* getNthReplacementSymbolNameBetween(const char* moduleName, cons return getCharStar(replacement.second.c_str()); } +LIB_EXTERN unsigned long getNumUserFunctions() +{ + return static_cast(g_registry.GetNumUserFunctions()); +} + +void reportUserFunctionIndexProblem(unsigned long n, unsigned long actualsize) +{ + string error = "There is no user-defined function with index " + SizeTToString(n) + "."; + if (actualsize == 0) { + error += " In fact, there are no user-defined functions at all."; + } + else if (actualsize == 1) { + error += " There is a single user-defined function with index 0."; + } + else { + error += " Valid index values are 0 through " + SizeTToString(actualsize-1) + "."; + } + g_registry.SetError(error); +} + +LIB_EXTERN char* getNthUserFunctionName(unsigned long n) +{ + const UserFunction* func = g_registry.GetNthUserFunction(n); + if (func == NULL) { + reportUserFunctionIndexProblem(n, static_cast(g_registry.GetNumUserFunctions())); + return NULL; + } + return getCharStar(func->GetModuleName().c_str()); +} + +LIB_EXTERN unsigned long getNumUserFunctionArguments(unsigned long n) +{ + const UserFunction* func = g_registry.GetNthUserFunction(n); + if (func == NULL) { + reportUserFunctionIndexProblem(n, static_cast(g_registry.GetNumUserFunctions())); + return 0; + } + return static_cast(func->GetNumExportVariables()); +} + +LIB_EXTERN char** getNthUserFunctionArguments(unsigned long n) +{ + const UserFunction* func = g_registry.GetNthUserFunction(n); + if (func == NULL) { + reportUserFunctionIndexProblem(n, static_cast(g_registry.GetNumUserFunctions())); + return NULL; + } + unsigned long numargs = static_cast(func->GetNumExportVariables()); + char** args = getCharStarStar(numargs); + if (args == NULL) return NULL; + for (unsigned long arg=0; argGetNthExportVariable(arg)[0].c_str()); + if (args[arg] == NULL) return NULL; + } + return args; +} + +void reportUserFunctionArgumentIndexProblem(unsigned long arg, unsigned long actualsize, unsigned long func) +{ + string error = "There is no argument with index " + SizeTToString(arg) + " in user-defined function " + SizeTToString(func) + "."; + if (actualsize == 0) { + error += " In fact, that function has no arguments at all."; + } + else if (actualsize == 1) { + error += " There is a single argument with index 0."; + } + else { + error += " Valid index values are 0 through " + SizeTToString(actualsize - 1) + "."; + } + g_registry.SetError(error); +} + +LIB_EXTERN char* getNthUserFunctionMthArgument(unsigned long n, unsigned long m) +{ + const UserFunction* userfunc = g_registry.GetNthUserFunction(n); + if (userfunc == NULL) { + reportUserFunctionIndexProblem(n, static_cast(g_registry.GetNumUserFunctions())); + return NULL; + } + unsigned long numargs = static_cast(userfunc->GetNumExportVariables()); + if (m >= numargs) { + reportUserFunctionArgumentIndexProblem(m, numargs, n); + return NULL; + } + return getCharStar(userfunc->GetNthExportVariable(m)[0].c_str()); +} + +LIB_EXTERN char* getNthUserFunctionBody(unsigned long n) +{ + const UserFunction* func = g_registry.GetNthUserFunction(n); + if (func == NULL) { + reportUserFunctionIndexProblem(n, static_cast(g_registry.GetNumUserFunctions())); + return NULL; + } + return getCharStar(func->GetFormula().ToDelimitedStringWithEllipses(g_registry.GetCC()).c_str()); +} + LIB_EXTERN unsigned long getNumModules() { return static_cast(g_registry.GetNumModules()); @@ -1024,7 +1128,7 @@ unsigned long getNumReactOrProdForRxnOrInt(const char* moduleName, unsigned long reportReactionIndexProblem(n, getNumSymbolsOfType(moduleName, rtype), moduleName, reaction); } const Variable* rxn = mod->GetNthVariableOfType(rtype, n, false); - if (rxn->GetReaction() == NULL) { + if (rxn == NULL || rxn->GetReaction() == NULL) { return 0; } if (reactant) { @@ -1090,6 +1194,15 @@ char* getNthRxnorIntMthReactantOrProductName(const char* moduleName, unsigned lo char** getNthRxnOrIntReactantOrProductNames(const char* moduleName, unsigned long n, bool reaction, bool reactant) { if (!checkModule(moduleName)) return NULL; + return_type rtype = allReactions; + if (!reaction) { + rtype = allInteractions; + } + unsigned long numlines = getNumSymbolsOfType(moduleName, rtype); + if (n >= numlines) { + reportReactionIndexProblem(n, numlines, moduleName, reaction); + return NULL; + } unsigned long vnum = getNumReactOrProdForRxnOrInt(moduleName, n, reaction, reactant); char** names = getCharStarStar(vnum); if (names == NULL) return NULL; @@ -1210,6 +1323,38 @@ double getNthRxnOrIntMthReactantOrProductStoichiometries(const char* moduleName, return stoichiometries[m]; } +char* getNthRxnOrIntMthReactantOrProductStoichiometryString(const char* moduleName, unsigned long n, unsigned long m, bool reaction, bool reactant) +{ + if (!checkModule(moduleName)) return NULL; + return_type rtype = allReactions; + if (!reaction) { + rtype = allInteractions; + } + unsigned long numlines = getNumSymbolsOfType(moduleName, rtype); + if (n >= numlines) { + reportReactionIndexProblem(n, numlines, moduleName, reaction); + return NULL; + } + const Module* mod = g_registry.GetModule(moduleName); + const Variable* rxn = mod->GetNthVariableOfType(rtype, n, false); + if (rxn->GetReaction() == NULL) { + return NULL; + } + const ReactantList* rlist = reactant ? rxn->GetReaction()->GetLeft() : rxn->GetReaction()->GetRight(); + unsigned long rsize = static_cast(rlist->Size()); + if (m >= rsize) { + reportReactionSubIndexProblem(m, rsize, n, moduleName, reaction, reactant); + return NULL; + } + const Variable* stoichvar = rlist->GetNthStoichiometryVar(m); + if (stoichvar != NULL) { + return getCharStar(stoichvar->GetNameDelimitedBy(g_registry.GetCC()).c_str()); + } + stringstream stoich; + stoich << rlist->GetStoichiometryFor(m); + return getCharStar(stoich.str().c_str()); +} + double* getNthRxnOrIntReactantOrProductStoichiometries(const char* moduleName, unsigned long n, bool reaction, bool reactant) { if (!checkModule(moduleName)) return NULL; @@ -1279,6 +1424,16 @@ LIB_EXTERN double getNthReactionMthProductStoichiometries(const char* moduleName return getNthRxnOrIntMthReactantOrProductStoichiometries(moduleName, rxn, reactant, true, false); } +LIB_EXTERN char* getNthReactionMthReactantStoichiometryString(const char* moduleName, unsigned long rxn, unsigned long reactant) +{ + return getNthRxnOrIntMthReactantOrProductStoichiometryString(moduleName, rxn, reactant, true, true); +} + +LIB_EXTERN char* getNthReactionMthProductStoichiometryString(const char* moduleName, unsigned long rxn, unsigned long product) +{ + return getNthRxnOrIntMthReactantOrProductStoichiometryString(moduleName, rxn, product, true, false); +} + LIB_EXTERN double** getProductStoichiometries(const char* moduleName) { return getReactantOrProductStoichiometriesForRxnOrInt(moduleName, true, false); @@ -1402,7 +1557,11 @@ LIB_EXTERN unsigned long getNumAssignmentsForEvent(const char* moduleName, unsig { if (!checkModule(moduleName)) return 0; const Variable* var = g_registry.GetModule(moduleName)->GetNthVariableOfType(allEvents, eventno, false); - if (var==NULL) return 0; + if (var==NULL) { + unsigned long numvars = static_cast(g_registry.GetModule(moduleName)->GetNumVariablesOfType(allEvents, false)); + reportVariableTypeIndexProblem(eventno, allEvents, numvars, moduleName); + return 0; + } return static_cast(var->GetEvent()->GetNumAssignments()); } @@ -1410,7 +1569,11 @@ LIB_EXTERN char* getTriggerForEvent(const char* moduleName, unsigned long eventn { if (!checkModule(moduleName)) return NULL; const Variable* var = g_registry.GetModule(moduleName)->GetNthVariableOfType(allEvents, eventno, false); - if (var==NULL) return NULL; + if (var==NULL) { + unsigned long numvars = static_cast(g_registry.GetModule(moduleName)->GetNumVariablesOfType(allEvents, false)); + reportVariableTypeIndexProblem(eventno, allEvents, numvars, moduleName); + return NULL; + } string trig = var->GetEvent()->GetTrigger()->ToDelimitedStringWithEllipses(g_registry.GetCC()); return getCharStar(trig.c_str()); } @@ -1419,7 +1582,11 @@ LIB_EXTERN char* getDelayForEvent(const char* moduleName, unsigned long eventno) { if (!checkModule(moduleName)) return NULL; const Variable* var = g_registry.GetModule(moduleName)->GetNthVariableOfType(allEvents, eventno, false); - if (var==NULL) return NULL; + if (var==NULL) { + unsigned long numvars = static_cast(g_registry.GetModule(moduleName)->GetNumVariablesOfType(allEvents, false)); + reportVariableTypeIndexProblem(eventno, allEvents, numvars, moduleName); + return NULL; + } string trig = var->GetEvent()->GetDelay()->ToDelimitedStringWithEllipses(g_registry.GetCC()); return getCharStar(trig.c_str()); } @@ -1428,7 +1595,11 @@ LIB_EXTERN bool getEventHasDelay(const char* moduleName, unsigned long eventno) { if (!checkModule(moduleName)) return false; const Variable* var = g_registry.GetModule(moduleName)->GetNthVariableOfType(allEvents, eventno, false); - if (var==NULL) return false; + if (var==NULL) { + unsigned long numvars = static_cast(g_registry.GetModule(moduleName)->GetNumVariablesOfType(allEvents, false)); + reportVariableTypeIndexProblem(eventno, allEvents, numvars, moduleName); + return false; + } return (!var->GetEvent()->GetDelay()->IsEmpty()); } @@ -1436,7 +1607,11 @@ LIB_EXTERN char* getPriorityForEvent(const char* moduleName, unsigned long eve { if (!checkModule(moduleName)) return NULL; const Variable* var = g_registry.GetModule(moduleName)->GetNthVariableOfType(allEvents, eventno, false); - if (var==NULL) return NULL; + if (var==NULL) { + unsigned long numvars = static_cast(g_registry.GetModule(moduleName)->GetNumVariablesOfType(allEvents, false)); + reportVariableTypeIndexProblem(eventno, allEvents, numvars, moduleName); + return NULL; + } string trig = var->GetEvent()->GetPriority()->ToDelimitedStringWithEllipses(g_registry.GetCC()); return getCharStar(trig.c_str()); } @@ -1445,7 +1620,11 @@ LIB_EXTERN bool getEventHasPriority(const char* moduleName, unsigned long eve { if (!checkModule(moduleName)) return false; const Variable* var = g_registry.GetModule(moduleName)->GetNthVariableOfType(allEvents, eventno, false); - if (var==NULL) return false; + if (var==NULL) { + unsigned long numvars = static_cast(g_registry.GetModule(moduleName)->GetNumVariablesOfType(allEvents, false)); + reportVariableTypeIndexProblem(eventno, allEvents, numvars, moduleName); + return false; + } return (!var->GetEvent()->GetPriority()->IsEmpty()); } @@ -1453,7 +1632,11 @@ LIB_EXTERN bool getPersistenceForEvent(const char* moduleName, unsigned long e { if (!checkModule(moduleName)) return false; const Variable* var = g_registry.GetModule(moduleName)->GetNthVariableOfType(allEvents, eventno, false); - if (var==NULL) return false; + if (var==NULL) { + unsigned long numvars = static_cast(g_registry.GetModule(moduleName)->GetNumVariablesOfType(allEvents, false)); + reportVariableTypeIndexProblem(eventno, allEvents, numvars, moduleName); + return false; + } return var->GetEvent()->GetPersistent(); } @@ -1461,7 +1644,11 @@ LIB_EXTERN bool getT0ForEvent(const char* moduleName, unsigned long eventno) { if (!checkModule(moduleName)) return false; const Variable* var = g_registry.GetModule(moduleName)->GetNthVariableOfType(allEvents, eventno, false); - if (var==NULL) return false; + if (var==NULL) { + unsigned long numvars = static_cast(g_registry.GetModule(moduleName)->GetNumVariablesOfType(allEvents, false)); + reportVariableTypeIndexProblem(eventno, allEvents, numvars, moduleName); + return false; + } return var->GetEvent()->GetInitialValue(); } @@ -1469,7 +1656,11 @@ LIB_EXTERN bool getFromTriggerForEvent(const char* moduleName, unsigned long e { if (!checkModule(moduleName)) return false; const Variable* var = g_registry.GetModule(moduleName)->GetNthVariableOfType(allEvents, eventno, false); - if (var==NULL) return false; + if (var==NULL) { + unsigned long numvars = static_cast(g_registry.GetModule(moduleName)->GetNumVariablesOfType(allEvents, false)); + reportVariableTypeIndexProblem(eventno, allEvents, numvars, moduleName); + return false; + } return var->GetEvent()->GetUseValuesFromTriggerTime(); } @@ -1477,7 +1668,11 @@ LIB_EXTERN char* getNthAssignmentVariableForEvent(const char* moduleName, unsign { if (!checkModule(moduleName)) return NULL; const Variable* var = g_registry.GetModule(moduleName)->GetNthVariableOfType(allEvents, eventno, false); - if (var==NULL) return NULL; + if (var==NULL) { + unsigned long numvars = static_cast(g_registry.GetModule(moduleName)->GetNumVariablesOfType(allEvents, false)); + reportVariableTypeIndexProblem(eventno, allEvents, numvars, moduleName); + return NULL; + } string asnt = var->GetEvent()->GetNthAssignmentVariableName(n, g_registry.GetCC()); if (asnt=="") return NULL; return getCharStar(asnt.c_str()); @@ -1487,7 +1682,11 @@ LIB_EXTERN char* getNthAssignmentEquationForEvent(const char* moduleName, unsign { if (!checkModule(moduleName)) return NULL; const Variable* var = g_registry.GetModule(moduleName)->GetNthVariableOfType(allEvents, eventno, false); - if (var==NULL) return NULL; + if (var==NULL) { + unsigned long numvars = static_cast(g_registry.GetModule(moduleName)->GetNumVariablesOfType(allEvents, false)); + reportVariableTypeIndexProblem(eventno, allEvents, numvars, moduleName); + return NULL; + } string formula = var->GetEvent()->GetNthAssignmentFormulaString(n, g_registry.GetCC(), false); if (formula=="") return NULL; return getCharStar(formula.c_str()); @@ -1586,6 +1785,27 @@ LIB_EXTERN char** getNthDNAStrand(const char* moduleName, unsigned long n) LIB_EXTERN bool getIsNthDNAStrandOpen(const char* moduleName, unsigned long n, bool upstream) { + if (!checkModule(moduleName)) return false; + unsigned long actualsize = getNumDNAStrands(moduleName); + if (actualsize <= n) { + string error = "There is no DNA strand with index " + SizeTToString(n); + error += " in module "; + error += moduleName; + error += "."; + if (actualsize == 0) { + error += " In fact, there are no DNA strands at all in that module."; + } + else if (actualsize == 1) { + error += " There is a single DNA strand with index 0."; + } + else if (actualsize > 1) { + error += " Valid DNA strand index values are 0 through "; + error += SizeTToString(actualsize-1); + error += "."; + } + g_registry.SetError(error); + return false; + } const DNAStrand* strand = g_registry.GetModule(moduleName)->GetNthVariableOfType(expandedStrands, n, false)->GetDNAStrand(); if (upstream) { return strand->GetUpstreamOpen(); @@ -1690,6 +1910,27 @@ LIB_EXTERN char** getNthModularDNAStrand(const char* moduleName, unsigned long n LIB_EXTERN bool getIsNthModularDNAStrandOpen(const char* moduleName, unsigned long n, bool upstream) { + if (!checkModule(moduleName)) return false; + unsigned long actualsize = getNumModularDNAStrands(moduleName); + if (actualsize <= n) { + string error = "There is no Modular DNA strand with index " + SizeTToString(n); + error += " in module "; + error += moduleName; + error += "."; + if (actualsize == 0) { + error += " In fact, there are no Modular DNA strands at all in that module."; + } + else if (actualsize == 1) { + error += " There is a single Modular DNA strand with index 0."; + } + else if (actualsize > 1) { + error += " Valid Modular DNA strand index values are 0 through "; + error += SizeTToString(actualsize-1); + error += "."; + } + g_registry.SetError(error); + return false; + } const DNAStrand* strand = g_registry.GetModule(moduleName)->GetNthVariableOfType(modularStrands, n, false)->GetDNAStrand(); if (upstream) { return strand->GetUpstreamOpen(); @@ -1705,6 +1946,10 @@ LIB_EXTERN return_type getTypeOfSymbol(const char* moduleName, const char* symbo if (!checkModule(moduleName)) return allUnknown; const Variable* var = g_registry.GetModule(moduleName)->GetVariableFromSymbol(symbolName); if (var == NULL) { + string error = "No such variable: '"; + error += symbolName; + error += "'."; + g_registry.SetError(error); return allUnknown; } var_type vtype = var->GetType(); @@ -1734,6 +1979,8 @@ LIB_EXTERN return_type getTypeOfSymbol(const char* moduleName, const char* symbo case varSpeciesCharge: case varSpeciesChemicalFormula: return allSpeciesFbcInfo; + case varSpeciesConversionFactor: + return allSpeciesConversionFactors; case varUndefined: case varSboTermWrapper: case varUncertWrapper: @@ -1772,7 +2019,7 @@ LIB_EXTERN formula_type getTypeOfEquationForSymbol(const char* moduleName, const const Variable* var = g_registry.GetModule(moduleName)->GetVariableFromSymbol(symbolName); if (var == NULL) { string error = "No such variable: '"; - error += *symbolName; + error += symbolName; error += "'."; g_registry.SetError(error); return formulaINITIAL; @@ -1784,7 +2031,13 @@ LIB_EXTERN char* getCompartmentForSymbol(const char* moduleName, const char* sym { if (!checkModule(moduleName)) return NULL; const Variable* var = g_registry.GetModule(moduleName)->GetVariableFromSymbol(symbolName); - if (var == NULL) return NULL; + if (var == NULL) { + string error = "No such variable: '"; + error += symbolName; + error += "'."; + g_registry.SetError(error); + return NULL; + } const Variable* varcomp = var->GetCompartment(); string retval; if (varcomp == NULL) { @@ -1796,6 +2049,34 @@ LIB_EXTERN char* getCompartmentForSymbol(const char* moduleName, const char* sym return getCharStar(retval.c_str()); } +LIB_EXTERN bool getSymbolSubstanceOnly(const char* moduleName, const char* symbolName) +{ + if (!checkModule(moduleName)) return false; + const Variable* var = g_registry.GetModule(moduleName)->GetVariableFromSymbol(symbolName); + if (var == NULL) { + string error = "No such variable: '"; + error += symbolName; + error += "'."; + g_registry.SetError(error); + return false; + } + return var->GetSubstOnly(); +} + +LIB_EXTERN bool getSymbolHasValue(const char* moduleName, const char* symbolName) +{ + if (!checkModule(moduleName)) return false; + const Variable* var = g_registry.GetModule(moduleName)->GetVariableFromSymbol(symbolName); + if (var == NULL) { + string error = "No such variable: '"; + error += symbolName; + error += "'."; + g_registry.SetError(error); + return false; + } + return !var->GetFormula()->IsEmpty(); +} + LIB_EXTERN int writeAntimonyFile(const char* filename, const char* moduleName) { string oldlocale = setlocale(LC_ALL, NULL); diff --git a/src/antimony_api.h.in b/src/antimony_api.h.in index e76e239ee..d79fbc62f 100644 --- a/src/antimony_api.h.in +++ b/src/antimony_api.h.in @@ -485,6 +485,43 @@ LIB_EXTERN char* getNthReplacementSymbolNameBetween(const char* moduleName, cons +/** + * @name User-defined Functions + */ +/** \{ */ + +/** + * Returns the number of user-defined functions ('function f(...) ... end' blocks) in the current active set of modules. Unlike most other queries in this API, this is not scoped to a single module, since Antimony function definitions are not scoped to any one module. + */ +LIB_EXTERN unsigned long getNumUserFunctions(); + +/** + * Returns the name of the Nth user-defined function. If no such function exists, NULL is returned and an error is set. + */ +LIB_EXTERN char* getNthUserFunctionName(unsigned long n); + +/** + * Returns the number of arguments of the Nth user-defined function. If no such function exists, 0 is returned and an error is set. + */ +LIB_EXTERN unsigned long getNumUserFunctionArguments(unsigned long n); + +/** + * Returns the names of the arguments of the Nth user-defined function, in the order in which they appear in the function's declaration. If no such function exists, NULL is returned and an error is set. + */ +LIB_EXTERN char** getNthUserFunctionArguments(unsigned long n); + +/** + * Returns the name of the Mth argument of the Nth user-defined function. If no such function or argument exists, NULL is returned and an error is set. + */ +LIB_EXTERN char* getNthUserFunctionMthArgument(unsigned long n, unsigned long m); + +/** + * Returns the body of the Nth user-defined function, as a formula making use of the function's arguments. If no such function exists, NULL is returned and an error is set. + */ +LIB_EXTERN char* getNthUserFunctionBody(unsigned long n); + +/** \} */ + /** * @name Symbols and symbol information */ @@ -503,6 +540,8 @@ LIB_EXTERN char** getSymbolNamesOfType(const char* moduleName, return_type rtype /** * Returns the 'display names' of the symbols of the given return type. (In SBML, these are the 'name's.) + * + * NOTE: Two return types repurpose this field for something other than a display name: for allConstraints, this returns the constraint's message text, if any; for the chemical-formula entries in allSpeciesFbcInfo, this returns the chemical formula itself (getSymbolEquationsOfType returns an empty string for those entries--see below). */ LIB_EXTERN char** getSymbolDisplayNamesOfType(const char* moduleName, return_type rtype); @@ -517,6 +556,12 @@ LIB_EXTERN char** getSymbolDisplayNamesOfType(const char* moduleName, return_typ * - Events: The trigger condition * - Interactions: Nothing * - Modules: Nothing + * - Constraints: The right-hand side of the constraint only, as a value or formula. The comparison operator (>, <, ==, etc.) and left-hand side are not included and cannot currently be retrieved through this API. + * - Unit definitions: Nothing. A unit's composition (its kind, exponent, multiplier, and scale) is not retrievable through this API; convert to SBML and use libSBML if you need it. + * - Gene products: The associated species, if any. + * - Gene product associations: The AND/OR gene product association, as a formula string. There is no structured (tree) accessor for this; you must parse the string yourself if you need the boolean structure. + * - Species charge (part of allSpeciesFbcInfo): The charge value. + * - Species chemical formula (part of allSpeciesFbcInfo): Nothing--see getSymbolDisplayNamesOfType instead. * * For elements that could have either initial assignments or assignment rules, use getTypeOfEquationForSymbol, or just use getSymbolInitialAssignmentsOfType and getSymbolAssignmentRulesOfType explicitly. */ @@ -548,6 +593,8 @@ LIB_EXTERN char** getSymbolInitialAssignmentsOfType(const char* moduleName, retu * - Events: Nothing * - Interactions: Nothing * - Modules: Nothing + * + * @warning Because reactions and genes are included, querying with rtype=allSymbols will return every reaction's kinetic law in this array, not just symbols that actually have assignment rules. If you want to know whether a model uses assignment rules, query the six symbol classes that can actually carry one (species, formulas, and compartments, each in their const and var forms) instead of allSymbols. */ LIB_EXTERN char** getSymbolAssignmentRulesOfType(const char* moduleName, return_type rtype); @@ -618,6 +665,16 @@ LIB_EXTERN formula_type getTypeOfEquationForSymbol(const char* moduleName, const * Returns the name of the compartment the given symbol is a member of. In antimony, all symbols may have compartments, not just species. If a symbol has no set compartment, and is not a member of a symbol with a set compartment, this will return "default_compartment" */ LIB_EXTERN char* getCompartmentForSymbol(const char* moduleName, const char* symbolName); + +/** + * Returns 'true' if the given symbol was declared 'substanceOnly' (i.e. its value is defined in amounts rather than concentrations), 'false' otherwise, including if no such symbol or module is found (in which case an error is also set). + */ +LIB_EXTERN bool getSymbolSubstanceOnly(const char* moduleName, const char* symbolName); + +/** + * Returns 'false' if the given symbol was declared with no value at all (as can happen with an SBML parameter with no 'value' attribute, or a compartment with no 'size'), and 'true' otherwise, including for symbols whose value is zero. This lets you distinguish "no value was given" from "the value is zero" when a symbol's equation (as returned by the functions above) is empty. Also returns 'false' if no such symbol or module is found, in which case an error is also set. + */ +LIB_EXTERN bool getSymbolHasValue(const char* moduleName, const char* symbolName); /** \} */ /** @@ -630,6 +687,16 @@ LIB_EXTERN char* getCompartmentForSymbol(const char* moduleName, const char* s */ LIB_EXTERN unsigned long getNumReactions(const char* moduleName); +/** + * Returns the names of the reactions (including genes) in the module. Is the same as 'getSymbolNamesOfType(moduleName, allReactions)', but is provided for convenience. + */ +LIB_EXTERN char** getReactionNames(const char* moduleName); + +/** + * Returns the name of the Nth reaction (including genes) in the module. Is the same as 'getNthSymbolNameOfType(moduleName, allReactions, n)', but is provided for convenience. If no such reaction exists, NULL is returned and an error is set. + */ +LIB_EXTERN char* getNthReactionName(const char* moduleName, unsigned long n); + /** * Returns the number of reactants (species on the left side of the reaction) for the given reaction. If no such reaction is present, '0' is returned and an error is set. Sadly, if there are no reactants, '0' is also returned, though no error is set. So you'll have to keep track of this one on your own, most likely. */ @@ -700,6 +767,16 @@ LIB_EXTERN double getNthReactionMthReactantStoichiometries(const char* moduleNam */ LIB_EXTERN double getNthReactionMthProductStoichiometries(const char* moduleName, unsigned long rxn, unsigned long product); +/** + * Returns the stoichiometry for the Mth reactant of the Nth reaction in the module, as it was written, as a string. If the stoichiometry was written as a plain number, that number is returned as text. If it was written as a symbol (as in 'reaction1: S1 + n S2 => S3; n = 2*p1;'), the symbol's name is returned, and its value can then be looked up like any other symbol's. This is provided because getNthReactionMthReactantStoichiometries returns 'NaN' in the latter case, with no way to recover what was actually written. If no such reactant or reaction exists, an error is set and NULL is returned. + */ +LIB_EXTERN char* getNthReactionMthReactantStoichiometryString(const char* moduleName, unsigned long rxn, unsigned long reactant); + +/** + * Returns the stoichiometry for the Mth product of the Nth reaction in the module, as it was written, as a string. See getNthReactionMthReactantStoichiometryString for details. If no such product or reaction exists, an error is set and NULL is returned. + */ +LIB_EXTERN char* getNthReactionMthProductStoichiometryString(const char* moduleName, unsigned long rxn, unsigned long product); + /** \} */ /** diff --git a/src/bindings/CMakeLists.txt b/src/bindings/CMakeLists.txt index 65706c459..5e6f2276d 100644 --- a/src/bindings/CMakeLists.txt +++ b/src/bindings/CMakeLists.txt @@ -15,15 +15,6 @@ mark_as_advanced(ANTIMONY_REMOVE_WRAPPERS) # and build selected language bindings # -# antimony_api.h has a couple includes, which are easy enough to follow, and -# means we don't have to explicitly include them all the time otherwise. -SET(SWIG_EXTRA_ARGS ${SWIG_EXTRA_ARGS} "-includeall") - -if(NOT WITH_CELLML) - SET(SWIG_EXTRA_ARGS ${SWIG_EXTRA_ARGS} "-DNCELLML") -endif() - - if(WITH_CSHARP) add_subdirectory(csharp) endif() diff --git a/src/bindings/python/createAntimonyLib.py b/src/bindings/python/createAntimonyLib.py index 586a8c9bc..21d5ddd6a 100644 --- a/src/bindings/python/createAntimonyLib.py +++ b/src/bindings/python/createAntimonyLib.py @@ -311,7 +311,11 @@ def getPointerDetanglerFor(funcid): return("getNumReactions(moduleName)", "getNthReactionRate(moduleName, n)") if funcid=="getEventNames": return("getNumEvents(moduleName)", "getNthEventName(moduleName, n)") - + if funcid=="getReactionNames": + return("getNumReactions(moduleName)", "getNthReactionName(moduleName, n)") + if funcid=="getNthUserFunctionArguments": + return("getNumUserFunctionArguments(func)", "getNthUserFunctionMthArgument(func, n)") + print("Unhandled function", funcid) return ("", "") diff --git a/src/bindings/python/sbml_test_suite/conftest.py b/src/bindings/python/sbml_test_suite/conftest.py new file mode 100644 index 000000000..d091fe990 --- /dev/null +++ b/src/bindings/python/sbml_test_suite/conftest.py @@ -0,0 +1,14 @@ +import os + +import pytest + + +def pytest_addoption(parser): + parser.addoption( + "--sbml-test-suite-dir", + action="store", + default=os.environ.get("SBML_TEST_SUITE_DIR"), + help="Path to the SBML Test Suite 'semantic' cases directory (the one " + "containing numbered subdirectories like 00001/, 00002/, ...). " + "May also be set via the SBML_TEST_SUITE_DIR environment variable.", + ) diff --git a/src/bindings/python/sbml_test_suite/requirements.txt b/src/bindings/python/sbml_test_suite/requirements.txt new file mode 100644 index 000000000..8c05da09e --- /dev/null +++ b/src/bindings/python/sbml_test_suite/requirements.txt @@ -0,0 +1,3 @@ +tellurium +pytest +numpy diff --git a/src/bindings/python/sbml_test_suite/test_roundtrip.py b/src/bindings/python/sbml_test_suite/test_roundtrip.py new file mode 100644 index 000000000..c89bb0b0b --- /dev/null +++ b/src/bindings/python/sbml_test_suite/test_roundtrip.py @@ -0,0 +1,416 @@ +""" +Round-trips each SBML Test Suite semantic case through libAntimony +(SBML -> Antimony -> SBML) and checks that a roadrunner simulation of the +round-tripped model still matches a simulation of the original model. + +For each test case, the earliest and latest available SBML level/version +files are used, since the Antimony import/export code paths can differ by +level and version. + +Run with e.g.: + pytest --sbml-test-suite-dir=/path/to/sbml-test-suite/cases/semantic +""" + +import os +import re +import tempfile +import warnings + +import antimony +import numpy as np +import pytest +import tellurium as te + +# The simulations that feed the comparison are run at a tighter tolerance +# than the one used for the pass/fail comparison itself, so that numerical +# integration error doesn't masquerade as a round-trip discrepancy (or hide +# one). +SIMULATION_TOLERANCE_FACTOR = 0.01 + +SBML_FILENAME_RE = re.compile(r"^(\d{5})-sbml-l(\d+)v(\d+)\.xml$") +CASE_DIRNAME_RE = re.compile(r"^\d{5}$") +MISSING_SYMBOL_RE = re.compile(r"No sbml element exists for symbol '([^']+)'") + +# Known, expected roadrunner limitations. Match by category (via these +# patterns) rather than exact error text, since the round trip can reformat +# the offending formula, rename a reaction, etc. +# +# fast_reactions is also known to trip *asymmetrically* -- see the `elif` +# branch below for why: original fails, round-tripped succeeds. +KNOWN_LIMITATION_PATTERNS = { + "algebraic_rules": re.compile(r"unable to support algebraic rules", re.IGNORECASE), + "fast_reactions": re.compile(r"unable to support 'fast' reactions", re.IGNORECASE), + "delay_differential_equations": re.compile(r"delay differential equations", re.IGNORECASE), +} + + +def _known_limitation(exc): + """Returns the name of the known roadrunner limitation `exc` matches, or + None if it doesn't match any of them.""" + if exc is None: + return None + text = str(exc) + for name, pattern in KNOWN_LIMITATION_PATTERNS.items(): + if pattern.search(text): + return name + return None + + +def discover_cases(root): + """Find every SBML Test Suite case under `root`, and for each one return + the earliest and latest available SBML level/version file (deduplicated + if there's only one).""" + cases = [] + for entry in sorted(os.listdir(root)): + case_dir = os.path.join(root, entry) + if not CASE_DIRNAME_RE.match(entry) or not os.path.isdir(case_dir): + continue + + settings_path = os.path.join(case_dir, f"{entry}-settings.txt") + if not os.path.isfile(settings_path): + continue + + sbml_files = [] + for fname in os.listdir(case_dir): + match = SBML_FILENAME_RE.match(fname) + if match: + level, version = int(match.group(2)), int(match.group(3)) + sbml_files.append((level, version, os.path.join(case_dir, fname))) + if not sbml_files: + continue + sbml_files.sort(key=lambda t: (t[0], t[1])) + + earliest_path = sbml_files[0][2] + latest_path = sbml_files[-1][2] + + cases.append((entry, "earliest", earliest_path, settings_path)) + if latest_path != earliest_path: + cases.append((entry, "latest", latest_path, settings_path)) + + return cases + + +def parse_settings(path): + raw = {} + with open(path) as f: + for line in f: + key, sep, value = line.strip().partition(":") + if sep: + raw[key.strip()] = value.strip() + + def csv_list(key): + return [v.strip() for v in raw.get(key, "").split(",") if v.strip()] + + # start/duration/steps are blank for non-time-course cases (e.g. FBC + # steady-state/objective-value cases), which this test doesn't cover -- + # left as None here so the caller can skip those cases explicitly instead + # of blowing up trying to float(""). + def optional_float(key): + value = raw.get(key, "") + return float(value) if value else None + + return { + "start": optional_float("start"), + "duration": optional_float("duration"), + "steps": int(raw["steps"]) if raw.get("steps") else None, + "variables": csv_list("variables"), + "absolute": float(raw["absolute"]), + "relative": float(raw["relative"]), + "amount": set(csv_list("amount")), + "concentration": set(csv_list("concentration")), + } + + +def build_selections(settings): + selections = ["time"] + for var in settings["variables"]: + if var in settings["concentration"]: + selections.append(f"[{var}]") + else: + selections.append(var) + return selections + + +def build_roundtrip_selections(selections): + """Antimony renames a model variable literally named 'time' to 'time_' + on export, to avoid colliding with its own reserved 'time' keyword. But + bare 'time' is *also* always a legitimate roadrunner selection (the + simulation clock), which resolves successfully whether or not the model + defines its own 'time' symbol -- so a shadowed 'time' variable doesn't + raise an error to trigger the general rename-retry logic in + simulate_model, it just silently returns the clock instead of the real + value. Special-cased here rather than relying on that retry, since it's + a silent-wrong-answer bug, not a missing-symbol one. + + selections[0] is always the clock column we add ourselves in + build_selections, not a model symbol, so it's left untouched.""" + def rename(selection): + if selection == "time": + return "time_" + if selection == "[time]": + return "[time_]" + return selection + + return selections[:1] + [rename(sel) for sel in selections[1:]] + + +def _load_model(model_source): + """Loads model_source via te.loads(). Roadrunner only flattens comp SBML + models when loading from a file -- loading the same SBML passed directly + as a string skips flattening entirely (a roadrunner bug, currently being + fixed upstream). Until that lands, write anything that isn't already a + file to a temp file first, so the original and round-tripped models both + get flattened the same way.""" + if os.path.isfile(model_source): + return te.loads(model_source) + fd, temp_path = tempfile.mkstemp(suffix=".xml") + try: + with os.fdopen(fd, "w") as f: + f.write(model_source) + return te.loads(temp_path) + finally: + os.remove(temp_path) + + +def _rename_candidates(missing): + """Given an SBML symbol name that roadrunner couldn't find, returns + candidate names it might have been renamed to during Antimony's round + trip, in order of likelihood: + - missing + '_': Antimony appends '_' to identifiers that collide with + reserved words (e.g. INF -> INF_). + - the bare suffix after the last '__': a compliant comp flattener + prefixes a submodel-local element with its submodel id (e.g. + sub1__p1) only when needed to avoid a collision. Antimony doesn't + have local (reaction/submodel)-scoped parameters, so when a + submodel-local parameter shadows a global one, round-tripping can + merge them into a single top-level variable -- no collision, no + prefix. + - every '__' collapsed to a single '_': settings.txt uses a double + underscore as the submodel/element separator (e.g. sub1__t1), but + Antimony's own promoted name for the same element uses a single + underscore (sub1_t1). + """ + candidates = [missing + "_"] + if "__" in missing: + candidates.append(missing.rsplit("__", 1)[-1]) + candidates.append(missing.replace("__", "_")) + return candidates + + +def _bare_name(selection): + """Strips the "[...]" concentration wrapper from a selection, if any.""" + if selection.startswith("[") and selection.endswith("]"): + return selection[1:-1] + return selection + + +def simulate_model(model_source, settings, selections): + """Returns (result, renames), where renames is a list of (original, + replacement) pairs used to resolve any selection roadrunner couldn't + find under its settings.txt name -- see _rename_candidates. Renaming + means the round trip structurally changed something (not just relabeled + it 1:1), so callers shouldn't treat a non-empty renames list as an + apples-to-apples comparison. + + More than one selection can need renaming at once (e.g. several + reserved-word collisions in the same model), and roadrunner only reports + one missing symbol per attempt, so this retries selection-by-selection: + each failure identifies which selection is still broken from its + *current* value, and advances that selection's own candidate list + (always generated from its original settings.txt name, not the last + guess) rather than giving up as soon as any one candidate doesn't fully + resolve the model.""" + rr = _load_model(model_source) + rr.integrator.setValue("absolute_tolerance", settings["absolute"] * SIMULATION_TOLERANCE_FACTOR) + rr.integrator.setValue("relative_tolerance", settings["relative"] * SIMULATION_TOLERANCE_FACTOR) + n_points = settings["steps"] + 1 + + def run(sels): + result = rr.simulate(settings["start"], settings["start"] + settings["duration"], n_points, selections=sels) + return np.asarray(result) + + current = list(selections) + renamed_to = {} # original bare name -> candidate currently in use + tried = {} # index into current -> number of candidates already tried + + max_attempts = 2 * len(current) + 1 + for _ in range(max_attempts): + try: + renames = [(name, candidate) for name, candidate in renamed_to.items()] + return run(current), renames + except RuntimeError as exc: + match = MISSING_SYMBOL_RE.search(str(exc)) + if not match: + raise + bad = match.group(1) + idx = next((i for i, sel in enumerate(current) if _bare_name(sel) == bad), None) + if idx is None: + raise + original_bare = _bare_name(selections[idx]) + candidates = _rename_candidates(original_bare) + already_tried = tried.get(idx, 0) + if already_tried >= len(candidates): + raise + candidate = candidates[already_tried] + tried[idx] = already_tried + 1 + current[idx] = f"[{candidate}]" if selections[idx].startswith("[") else candidate + renamed_to[original_bare] = candidate + + raise RuntimeError(f"Gave up resolving renamed selections after {max_attempts} attempts") + + +def _try_simulate(model_source, settings, selections): + """Runs simulate_model, catching any roadrunner runtime error. Returns + (result, renames, None) on success, or (None, [], exception) if + roadrunner couldn't simulate the model.""" + try: + result, renames = simulate_model(model_source, settings, selections) + return result, renames, None + except Exception as exc: + return None, [], exc + + +def pytest_generate_tests(metafunc): + if "sbml_case" not in metafunc.fixturenames: + return + root = metafunc.config.getoption("--sbml-test-suite-dir") + if not root or not os.path.isdir(root): + metafunc.parametrize("sbml_case", []) + return + cases = discover_cases(root) + ids = [f"{case_id}-{which}" for case_id, which, _, _ in cases] + metafunc.parametrize("sbml_case", cases, ids=ids) + + +def test_roundtrip(sbml_case): + case_id, which, sbml_path, settings_path = sbml_case + settings = parse_settings(settings_path) + if settings["start"] is None or settings["duration"] is None or settings["steps"] is None: + pytest.skip(f"{case_id} ({which}): no time course defined in settings.txt (steady-state/FBC case)") + selections = build_selections(settings) + roundtrip_selections = build_roundtrip_selections(selections) + + antimony.clearPreviousLoads() + + # Some models use constructs roadrunner can't simulate at all (e.g. + # algebraic rules). That's a roadrunner limitation, not a round-trip + # problem, so it's fine as long as the *same kind* of error happens both + # before and after the round trip. The one exception is variable + # stoichiometry: a stoichiometryMath can be simulatable in its original + # form but not after being canonicalized by Antimony's round trip, so + # it's OK for the original to succeed while only the round-tripped model + # fails, but only for that specific error. + original_result, original_renames, original_error = _try_simulate(sbml_path, settings, selections) + + load_index = antimony.loadSBMLFile(sbml_path) + assert load_index >= 0, f"Failed to load {sbml_path} into libAntimony: {antimony.getLastError()}" + + antimony_text = antimony.getAntimonyString() + assert antimony_text, f"Failed to convert {sbml_path} to Antimony: {antimony.getLastError()}" + + load_index = antimony.loadAntimonyString(antimony_text) + assert load_index >= 0, f"Failed to reload converted Antimony for {sbml_path}: {antimony.getLastError()}" + + roundtripped_sbml = antimony.getCompSBMLString() + assert roundtripped_sbml, f"Failed to export round-tripped SBML for {sbml_path}: {antimony.getLastError()}" + + roundtrip_result, roundtrip_renames, roundtrip_error = _try_simulate(roundtripped_sbml, settings, roundtrip_selections) + + # A selection only resolving after being renamed (see _rename_candidates) + # doesn't make the comparison invalid: roadrunner always simulates the + # *flattened* model, and the flattened models should be structurally + # identical between original and round-tripped. + rename_note = ( + f" (used renamed selections -- original: {original_renames or 'none'}, " + f"round-tripped: {roundtrip_renames or 'none'})" + if original_renames or roundtrip_renames else "" + ) + + if original_error is not None or roundtrip_error is not None: + original_limitation = _known_limitation(original_error) + roundtrip_limitation = _known_limitation(roundtrip_error) + + # Every error, known or not, gets embedded directly in the skip/failure + # message below rather than raised via warnings.warn() -- pytest's + # --junitxml output doesn't capture warnings, only the skip/failure + # text itself, so that's the only place this is guaranteed to show up. + error_detail = f"Original error: {original_error!r}. Round-tripped error: {roundtrip_error!r}." + + if ( + original_error is not None + and roundtrip_error is not None + and original_limitation is not None + and original_limitation == roundtrip_limitation + ): + outcome = "roadrunner raised the same kind of error simulating both the original and the round-tripped model" + limitation = original_limitation + elif ( + original_error is not None + and roundtrip_error is not None + and str(original_error) == str(roundtrip_error) + ): + # Not a category in KNOWN_LIMITATION_PATTERNS yet, but the error + # text is byte-identical on both sides, so it's the same kind of + # error by definition -- not a round-trip bug. Flagged via + # warnings.warn() (in addition to the skip message below) since + # these are exactly the ones worth turning into a real + # KNOWN_LIMITATION_PATTERNS entry once someone's looked at them. + outcome = "roadrunner raised a byte-identical, but not yet categorized, error simulating both the original and the round-tripped model" + limitation = "uncategorized" + warnings.warn( + f"{case_id} ({which}, {os.path.basename(sbml_path)}): uncategorized error, identical on both " + f"sides -- consider adding a KNOWN_LIMITATION_PATTERNS entry: {original_error!r}" + ) + elif original_limitation == "fast_reactions": + # Antimony doesn't preserve SBML's 'fast' reaction attribute -- + # deliberately: 'fast' is deprecated in current SBML, vanishingly + # few models use it, and it's not worth supporting. Once + # roadrunner rejects the original for using 'fast', the + # round-tripped side is unconstrained: it can succeed (fast=true + # silently dropped) or fail for its own unrelated reason (e.g. + # the same model also has a delay differential equation) -- + # either way it's not a round-trip bug caused by dropping 'fast'. + outcome = "roadrunner couldn't simulate the original model due to 'fast' (round-tripped outcome doesn't matter)" + limitation = original_limitation + else: + # Anything else -- a one-sided failure that isn't the known + # fast_reactions asymmetric exception above, or a symmetric + # failure where the two errors aren't the same *kind* of known + # limitation -- is a real problem, not a known limitation. + def _label(err, limitation): + if err is None: + return "no error" + return limitation if limitation is not None else "unrecognized error" + + raise AssertionError( + f"{case_id} ({which}, {os.path.basename(sbml_path)}): true failure -- roadrunner's errors " + f"don't match each other (original: {_label(original_error, original_limitation)}; " + f"round-tripped: {_label(roundtrip_error, roundtrip_limitation)}). {error_detail}" + ) from (original_error if original_error is not None else roundtrip_error) + + pytest.skip( + f"{case_id} ({which}, {os.path.basename(sbml_path)}): {outcome} -- {limitation}. {error_detail}" + ) + + assert original_result.shape == roundtrip_result.shape, ( + f"{case_id} ({which}): result shapes differ{rename_note}: " + f"{original_result.shape} vs {roundtrip_result.shape}" + ) + + mismatches = [] + for col in range(1, len(selections)): + original = original_result[:, col] + roundtrip = roundtrip_result[:, col] + if not np.allclose(original, roundtrip, rtol=settings["relative"], atol=settings["absolute"], equal_nan=True): + diff = np.abs(original - roundtrip) + worst = int(np.argmax(diff)) + mismatches.append( + f" {selections[col]}: max |diff|={diff[worst]:.6g} at t={original_result[worst, 0]:.6g} " + f"(original={original[worst]:.6g}, roundtrip={roundtrip[worst]:.6g})" + ) + + assert not mismatches, ( + f"{case_id} ({which}, {os.path.basename(sbml_path)}): round-tripped SBML diverged beyond " + f"tolerance (absolute={settings['absolute']}, relative={settings['relative']}){rename_note}:\n" + + "\n".join(mismatches) + ) diff --git a/src/enums.h b/src/enums.h index 60cb5209f..b3c9a306d 100644 --- a/src/enums.h +++ b/src/enums.h @@ -38,6 +38,7 @@ enum rd_type {rdBecomes = 0, rdActivates, rdInhibits, rdInfluences, rdBecomesIrr * - varGeneProductAssociation: A gene product association (as defined in the FBC package) * - varSpeciesCharge: The charge of a species (defined in the FBC package) * - varSpeciesChemicalFormula: The chemical formula of a species (defined in the FBC package) + * - varSpeciesConversionFactor: A species' conversion factor, a reference to an existing parameter * - varKineticLawWrapper: The kineticLaw sub-object of a reaction, addressed as 'reaction.kineticLaw' (used to set its sboTerm, annotations, etc. separately from the reaction itself) */ @@ -66,11 +67,12 @@ enum var_type {varSpeciesUndef = 0, varGeneProductAssociation, varSpeciesCharge, varSpeciesChemicalFormula, + varSpeciesConversionFactor, varKineticLawWrapper, }; /** * return_types are used in the API when requesting information about different symbols. Each return_type refers to a different group of symbols, and are overlapping--i.e. a single symbol can be included in 'allGenes' and 'allReactions'. - * - allSymbols: Every symbol of every type in Antimony + * - allSymbols: Every symbol of every type in Antimony. * - allSpecies: All species, both const (border) and variable. * - allFormulas: All formulas (values defined by an equation), both const and variable. * - allDNA: All symbols defined to be DNA (operators and genes, but not strands). @@ -94,8 +96,13 @@ enum var_type {varSpeciesUndef = 0, * - modularStrands: All defined DNA strands, with some being subparts of the others. * - allUnits: All unit definitions. * - allDeleted: All submodel elements that have been deleted from the containing model. + * - allConstraints: All constraints. * - allStoichiometries: All reaction stoichiometries (aka 'species references') in the model. * - allAlgebraicRules: All algebraic rules in the model. + * - allGeneProducts: All gene products (as defined in the FBC package). + * - allGeneProductAssociations: All gene product associations (as defined in the FBC package). + * - allSpeciesFbcInfo: A species' charge and/or chemical formula (as defined in the FBC package). + * - allSpeciesConversionFactors: A species' conversion factor. */ enum return_type {allSymbols = 0, allSpecies, @@ -127,6 +134,7 @@ enum return_type {allSymbols = 0, allGeneProducts, allGeneProductAssociations, allSpeciesFbcInfo, + allSpeciesConversionFactors, }; /** diff --git a/src/event.cpp b/src/event.cpp index d154dd2cb..6908c24cc 100644 --- a/src/event.cpp +++ b/src/event.cpp @@ -67,11 +67,6 @@ bool AntimonyEvent::SetPriority(const Formula& priority) g_registry.SetError("The priority \"" + priority.ToDelimitedStringWithEllipses(".") + "\" seems to be incorrect, and cannot be parsed into an Abstract Syntax Tree (AST)."); return true; } - else if (ASTpriority->isBoolean()) { - g_registry.SetError("The priority \"" + priority.ToDelimitedStringWithEllipses(".") + "\" is boolean, and it is therefore illegal to use it as the priority for an event. Perhaps this was meant as the trigger? If the line is being misparsed, try adding parentheses."); - delete ASTpriority; - return true; - } delete ASTpriority; } m_priority = priority; @@ -110,8 +105,8 @@ bool AntimonyEvent::SetInitialValue(const Formula& form) bool AntimonyEvent::AddResult(Variable* var, Formula* form) { - m_varresults.insert(m_varresults.begin(), var->GetName()); - m_formresults.insert(m_formresults.begin(), *form); + m_varresults.push_back(var->GetName()); + m_formresults.push_back(*form); var->SetType(varFormulaUndef); if (!IsSpecies(var->GetType())) { var->SetIsConst(false);//It might be a straight value, but the event changes it. @@ -234,10 +229,9 @@ bool AntimonyEvent::ClearReferencesTo(Variable* deletedvar, setGetNameDelimitedBy(cc); } +Variable* AntimonyEvent::GetNthAssignmentVariable(size_t n) const +{ + if (n >= m_varresults.size()) { + return NULL; + } + return g_registry.GetModule(m_module)->GetVariable(m_varresults[n]); +} + string AntimonyEvent::GetNthAssignmentFormulaString(size_t n, string cc, bool SBML) const { if (n >= m_formresults.size()) { diff --git a/src/event.h b/src/event.h index 8d9ff4fff..d110bcc2f 100644 --- a/src/event.h +++ b/src/event.h @@ -59,6 +59,7 @@ class AntimonyEvent size_t GetNumAssignments() const {return m_varresults.size();}; std::string GetNthAssignmentVariableName(size_t n, std::string cc) const; + Variable* GetNthAssignmentVariable(size_t n) const; std::string GetNthAssignmentFormulaString(size_t n, std::string cc, bool SBML) const; const Formula* GetAssignmentFormula(size_t n) const; std::string ToStringDelimitedBy(std::string cc) const; diff --git a/src/formula.cpp b/src/formula.cpp index 26cd23435..2371a6cb5 100644 --- a/src/formula.cpp +++ b/src/formula.cpp @@ -434,21 +434,6 @@ bool Formula::GetIsConst() const return true; } -//bool - -bool Formula::CheckIncludes(string modname, const ReactantList* rlist) const -{ - string cc = g_registry.GetCC(); - vector > varlist = rlist->GetVariableList(); - for (size_t var=0; varGetVariable(varlist[var])->GetNameDelimitedBy(cc) + "' (either directly or indirectly), but it does not."); - return true; - } - } - return false; -} - bool Formula::ContainsVar(string modname, vector vname) const { Module* module = g_registry.GetModule(modname); diff --git a/src/formula.h b/src/formula.h index a1d36d3a6..998842095 100644 --- a/src/formula.h +++ b/src/formula.h @@ -58,7 +58,6 @@ class Formula : public Annotated bool IsOneComponent() const; bool isValidGeneProductAssociation() const; bool GetIsConst() const; - bool CheckIncludes(std::string modname, const ReactantList* rlist) const; bool ContainsVar(std::string modname, std::vector vname) const; bool ContainsVar(const Variable* outervar) const; bool ContainsDeletedVar() const; diff --git a/src/module-cellml.cpp b/src/module-cellml.cpp index 621bdcfc3..d7cc0b202 100644 --- a/src/module-cellml.cpp +++ b/src/module-cellml.cpp @@ -571,6 +571,7 @@ void Module::CreateCellMLComponent(Module* topmod) case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: //Need to figure out what to do with these. assert(false); break; diff --git a/src/module-sbml.cpp b/src/module-sbml.cpp index e8f9b99bd..db09408f4 100644 --- a/src/module-sbml.cpp +++ b/src/module-sbml.cpp @@ -298,6 +298,7 @@ void Module::FindOrCreateLocalVersionOf(const Variable* var, libsbml::Model* sbm case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: assert(false); //Unhandled type break; } @@ -726,7 +727,7 @@ void Module::TranslateRulesAndAssignmentsTo(const SBase* obj, Variable* var) } parent = parent->getParentSBMLObject(); } - if (localparent) { + if (localparent && ia->isSetMath()) { Formula formula; string formulastring(parseASTNodeToString(ia->getMath())); setFormulaWithString(formulastring, &formula, this); @@ -790,7 +791,7 @@ void Module::TranslateRulesAndAssignmentsTo(const SBase* obj, Variable* var) } parent = parent->getParentSBMLObject(); } - if (localparent) { + if (localparent && rule->isSetMath()) { var->SetWithRule(rule); } } @@ -832,8 +833,23 @@ void Module::LoadSBML(Model* sbml) SetDisplayName(sbml->getName()); PopulateCVTerms((SBase*)sbml); ReadAnnotationFrom(sbml); + if (sbml->isSetConversionFactor()) { + string cfid = sbml->getConversionFactor(); + Variable* cftarget = AddOrFindVariable(&cfid); + SetConversionFactor(cftarget); + } //Load submodels const CompModelPlugin* mplugin = static_cast(sbml->getPlugin("comp")); + //Events whose Priority/Delay/EventAssignment/Trigger was directly + //deleted, as opposed to becoming empty because a variable it + //referenced was itself fully deleted. Collected across all submodels; + //decided on and, if needed, promoted at the very end of this function, + //once every element of this module (including anything joined via + //comp:replacedElement) has been read. + set touchedEvents; + //Reactions whose species reference(s) or kinetic law were directly + //deleted, for the same reason. + set touchedReactions; if (mplugin != NULL) { for (unsigned int sm = 0; sm < mplugin->getNumSubmodels(); sm++) { const Submodel* submodel = mplugin->getSubmodel(sm); @@ -934,6 +950,10 @@ void Module::LoadSBML(Model* sbml) targetname.push_back(event->getId()); deletedvar = GetVariable(targetname); assert(deletedvar != NULL); + if (deletedvar->GetType() == varDeleted) { + //The whole event was already deleted separately; nothing more to do here. + break; + } switch (target->getTypeCode()) { case SBML_PRIORITY: var->AddDeletion(targetname, delEventPriority); @@ -956,6 +976,14 @@ void Module::LoadSBML(Model* sbml) //We added variables from the strings in the event, but they are superfluous; take them back out. m_variables.pop_back(); } + //We don't yet know whether this event still needs to be promoted: + //if the only reason it now differs from its submodel's original + //is that some other deletion (processed earlier or later in this + //same list) fully deletes a variable it referenced, the existing + //'delete A.X;' mechanism already covers it and no promotion is + //needed. That can only be determined once all of this submodel's + //deletions have been processed, below. + touchedEvents.insert(deletedvar); break; case SBML_CONSTRAINT: g_registry.AddWarning("Unable to process deletion " + delname + "from submodel " + submodname + " in model " + GetModuleName() + ", because Constraints do not have IDs in SBML."); @@ -994,6 +1022,9 @@ void Module::LoadSBML(Model* sbml) break; } deletedvar->GetReaction()->ClearReferencesTo(origparam, &(var->m_deletions)); + //As with events, we don't yet know whether this reaction still + //needs to be promoted; see the check after this loop, below. + touchedReactions.insert(deletedvar); break; case SBML_KINETIC_LAW: assert(reaction != NULL); @@ -1004,8 +1035,13 @@ void Module::LoadSBML(Model* sbml) paramname.push_back(reaction->getId()); deletedvar = GetVariable(paramname); assert(deletedvar != NULL); + if (deletedvar->GetType() == varDeleted) { + //Don't need to delete a child of a deleted thing + break; + } deletedvar->GetReaction()->GetFormula()->Clear(); var->AddDeletion(paramname, delKineticLaw); + touchedReactions.insert(deletedvar); break; case SBML_MODIFIER_SPECIES_REFERENCE: assert(reaction != NULL); @@ -1328,6 +1364,16 @@ void Module::LoadSBML(Model* sbml) spec_form->SetDisplayName(fsp->getChemicalFormula()); } } + if (species->isSetConversionFactor()) { + string cfid = species->getConversionFactor(); + Variable* cftarget = AddOrFindVariable(&cfid); + string cfvarid = sbmlname + "-cf"; + Variable* spec_cf = AddOrFindVariable(&cfvarid); + spec_cf->SetType(varSpeciesConversionFactor); + formula.Clear(); + formula.AddVariable(cftarget); + spec_cf->SetFormula(&formula); + } } //Events: @@ -1348,6 +1394,10 @@ void Module::LoadSBML(Model* sbml) vector constraints; for (unsigned int c = 0; c < sbml->getNumConstraints(); c++) { const Constraint* constraint = sbml->getConstraint(c); + if (!constraint->isSetMath()) { + //No math means the constraint doesn't actually constrain anything; skip. + continue; + } sbmlname = getNameFromSBMLObject(constraint, "_con"); Variable* var = AddOrFindVariable(&sbmlname); var->ReadAnnotationFrom(constraint); @@ -1356,16 +1406,14 @@ void Module::LoadSBML(Model* sbml) msg = StripMsgXML(msg); var->SetDisplayName(msg); } - if (constraint->isSetMath()) { - AntimonyConstraint acon(var); - const ASTNode* astn = constraint->getMath(); - if (!m_usedDistributions && UsesDistrib(astn)) { - m_usedDistributions = true; - } - acon.SetWithASTNode(astn); - var->SetConstraint(&acon); - constraints.push_back(acon); + AntimonyConstraint acon(var); + const ASTNode* astn = constraint->getMath(); + if (!m_usedDistributions && UsesDistrib(astn)) { + m_usedDistributions = true; } + acon.SetWithASTNode(astn); + var->SetConstraint(&acon); + constraints.push_back(acon); } //Parameters @@ -1442,6 +1490,7 @@ void Module::LoadSBML(Model* sbml) string reactantId = specref->getId(); if (reactantId.empty()) { reactantId = reactionName + "_" + specref->getSpecies() + "_stoichiometry"; + reactantId = getNameFromSBMLObject(specref, reactantId); } stoichvar = AddOrFindVariable(&reactantId); assert(!stoichvar->SetType(varStoichiometry)); //Since the SBML file is valid. @@ -1453,19 +1502,61 @@ void Module::LoadSBML(Model* sbml) stoichvar->SetAssignmentRule(&formula); } else if (specref->isSetIdAttribute()) { - stoichvar = AddOrFindVariable(&(specref->getIdAttribute())); - bool setret = stoichvar->SetType(varStoichiometry); //Since the SBML file is valid. - assert(!setret); - if (specref->isSetStoichiometry() && !stoichvar->HasFormula()) { - Formula formula; - formula.AddNum(specref->getStoichiometry()); - stoichvar->SetFormula(&formula); + string stoichid = specref->getIdAttribute(); + //Restrictive check: only collapse this speciesReference back to a + //shared Antimony symbol (rather than giving it its own named + //stoichiometry) if it exactly matches what our writer generates + //for a reused stoichiometry: SBO:0000481 ("stoichiometric + //coefficient"), an id of the form "__stoich[N]", + //and an assignment rule that's nothing but a bare reference to + //another stoichiometry. + Variable* collapseTarget = NULL; + if (specref->getSBOTerm() == 481) { + string expectedPrefix = reactionName + "_" + specref->getSpecies() + "_stoich"; + if (stoichid.rfind(expectedPrefix, 0) == 0) { + string suffix = stoichid.substr(expectedPrefix.size()); + bool nameMatches = suffix.empty() || + suffix.find_first_not_of("0123456789") == string::npos; + if (nameMatches) { + const Rule* aliasrule = sbml->getRule(stoichid); + if (aliasrule != NULL && aliasrule->isAssignment() && aliasrule->isSetMath() && + aliasrule->getMath()->getType() == AST_NAME) { + string targetname = aliasrule->getMath()->getName(); + Variable* target = AddOrFindVariable(&targetname); + if (target->GetType() == varStoichiometry) { + collapseTarget = target; + } + } + } + } + } + if (collapseTarget != NULL) { + stoichvar = collapseTarget; + } + else { + stoichvar = AddOrFindVariable(&stoichid); + bool setret = stoichvar->SetType(varStoichiometry); //Since the SBML file is valid. + assert(!setret); + if (specref->isSetStoichiometry() && !stoichvar->HasFormula()) { + Formula formula; + formula.AddNum(specref->getStoichiometry()); + if (specref->getLevel() == 1 && specref->getDenominator() != 1) { + formula.AddMathThing('/'); + formula.AddNum(specref->getDenominator()); + } + stoichvar->SetFormula(&formula); + } + TranslateRulesAndAssignmentsTo(specref, stoichvar); } - TranslateRulesAndAssignmentsTo(specref, stoichvar); } else { if (specref->isSetStoichiometry()) { - stoichiometry = specref->getStoichiometry(); + if (specref->getLevel() == 1 && specref->getDenominator() != 1) { + stoichiometry = specref->getStoichiometry()/specref->getDenominator(); + } + else { + stoichiometry = specref->getStoichiometry(); + } } } sbmlname = specref->getSpecies(); @@ -1806,6 +1897,99 @@ void Module::LoadSBML(Model* sbml) */ } + //Now that every element of this module has been read (including + //anything joined to a submodel via comp:replacedElement), decide which + //touched events actually need to be promoted to new top-level elements: + //if an event only differs from what the submodel would produce on its + //own because some variable it referenced was itself separately, fully + //deleted, the existing 'delete A.X;' mechanism (and + //AntimonyEvent::Matches's handling of it) already covers it, and + //promoting it too would be redundant. + for (set::iterator te = touchedEvents.begin(); te != touchedEvents.end(); te++) { + Variable* eventvar = *te; + bool needspromotion = true; + if (eventvar->IsPointer()) { + //Already promoted/aliased via some other mechanism (e.g. a + //comp:replacedElement); nothing more to do. + needspromotion = false; + } + else { + vector submodname(1, eventvar->GetName()[0]); + Variable* submodvar = GetVariable(submodname); + Module* origmod = submodvar == NULL ? NULL : g_registry.GetModule(submodvar->GetModule()->GetModuleName()); + if (origmod != NULL) { + vector origevname(1, eventvar->GetName().back()); + Variable* origeventvar = origmod->GetVariable(origevname); + if (origeventvar != NULL) { + Variable copied(*origeventvar); + copied.ClearSameName(); + copied.SetNewTopName(GetModuleName(), submodname[0]); + if (copied.GetEvent()->Matches(eventvar->GetEvent())) { + needspromotion = false; + } + } + } + } + if (needspromotion) { + Variable* promotedvar = PromoteToTopLevel(eventvar); + AntimonyEvent* promotedevent = promotedvar->GetEvent(); + PromoteReferencedVariables(promotedevent->GetTrigger()); + PromoteReferencedVariables(promotedevent->GetDelay()); + PromoteReferencedVariables(promotedevent->GetPriority()); + for (size_t n=0; nGetNumAssignments(); n++) { + PromoteToTopLevel(promotedevent->GetNthAssignmentVariable(n)); + PromoteReferencedVariables(promotedevent->GetAssignmentFormula(n)); + } + } + } + //Same idea, for reactions: only promote if the difference isn't + //already fully explained by a separately, fully-deleted variable. + for (set::iterator tr = touchedReactions.begin(); tr != touchedReactions.end(); tr++) { + Variable* rxnvar = *tr; + bool needspromotion = true; + if (rxnvar->IsPointer()) { + //Already promoted/aliased via some other mechanism (e.g. a + //comp:replacedElement); nothing more to do. + needspromotion = false; + } + else { + vector submodname(1, rxnvar->GetName()[0]); + Variable* submodvar = GetVariable(submodname); + Module* origmod = submodvar == NULL ? NULL : g_registry.GetModule(submodvar->GetModule()->GetModuleName()); + if (origmod != NULL) { + vector origrxnname(1, rxnvar->GetName().back()); + Variable* origrxnvar = origmod->GetVariable(origrxnname); + if (origrxnvar != NULL) { + Variable copied(*origrxnvar); + copied.ClearSameName(); + copied.SetNewTopName(GetModuleName(), submodname[0]); + if (copied.GetReaction()->Matches(rxnvar->GetReaction())) { + needspromotion = false; + } + } + } + } + if (needspromotion) { + Variable* promotedvar = PromoteToTopLevel(rxnvar); + AntimonyReaction* promotedrxn = promotedvar->GetReaction(); + PromoteReferencedVariables(promotedrxn->GetFormula()); + const ReactantList* sides[2] = {promotedrxn->GetLeft(), promotedrxn->GetRight()}; + for (int side = 0; side < 2; side++) { + const ReactantList* rl = sides[side]; + for (size_t n = 0; n < rl->Size(); n++) { + const Variable* reactant = rl->GetNthReactant(n); + if (reactant != NULL) { + PromoteToTopLevel(GetVariable(reactant->GetName())); + } + const Variable* stoich = rl->GetNthStoichiometryVar(n); + if (stoich != NULL) { + PromoteToTopLevel(GetVariable(stoich->GetName())); + } + } + } + } + } + //Finally, fix the fact that 'time' used to be OK in functions (l2v1), but is no longer (l2v2). g_registry.FixTimeInFunctions(); LoadLayout(sbml); @@ -2387,6 +2571,9 @@ void Module::CreateSBMLModel(bool comp) //Reactions size_t numrxns = GetNumVariablesOfType(allReactions, comp); + //Tracks which named stoichiometry variables have already claimed their + //own name as an SBML id in this document; reused ones get an alias id. + set usedNamedStoichIds; for (size_t rxn=0; rxn < numrxns; rxn++) { const Variable* rxnvar = GetNthVariableOfType(allReactions, rxn, comp); const AntimonyReaction* reaction = rxnvar->GetReaction(); @@ -2451,7 +2638,9 @@ void Module::CreateSBMLModel(bool comp) sr->setConstant(true); sr->setStoichiometry(nthstoich); } - else { + else if (usedNamedStoichIds.insert(namedstoich).second) { + //First time this stoichiometry variable's name is being used + //as an SBML id in this document: keep it as-is. sr->setIdAttribute(namedstoich->GetNameDelimitedBy(cc)); if (namedstoich->GetFormulaType() != formulaINITIAL) { sr->setConstant(false); @@ -2464,6 +2653,35 @@ void Module::CreateSBMLModel(bool comp) } SetAssignmentFor(sbmlmod, namedstoich, syncmap, comp, referencedVars); } + else { + //This stoichiometry variable's name has already been claimed + //by an earlier SpeciesReference in this document (Antimony + //allows the same symbol to be reused as a stoichiometry more + //than once, but SBML ids must be unique). Give this one its + //own id, driven by an assignment rule back to the original, + //and mark it as an alias with SBO:0000481 ("stoichiometric + //coefficient") plus a "__stoich[N]" name, + //so that a restrictive SBML importer can recognize and + //collapse it back to the shared symbol. + string aliasbase = rxnvar->GetNameDelimitedBy("_") + "_" + nthr->GetNameDelimitedBy("_") + "_stoich"; + string aliasname = aliasbase; + int aliassuffix = 1; + while (sbmlmod->getElementBySId(aliasname) != NULL) { + aliassuffix++; + stringstream aliasnum; + aliasnum << aliassuffix; + aliasname = aliasbase + aliasnum.str(); + } + Variable aliasvar(aliasname, this); + aliasvar.SetType(varStoichiometry); + Formula aliasformula; + aliasformula.AddVariable(namedstoich); + aliasvar.SetAssignmentRule(&aliasformula); + sr->setIdAttribute(aliasname); + sr->setSBOTerm(481); + sr->setConstant(false); + SetAssignmentFor(sbmlmod, &aliasvar, syncmap, comp, referencedVars); + } } } //Find 'modifiers' and add them. @@ -2520,8 +2738,7 @@ void Module::CreateSBMLModel(bool comp) sbmlevent->getTrigger()->setPersistent(event->GetPersistent()); long numasnts = static_cast(event->GetNumAssignments()); - for (long asnt=numasnts-1; asnt>=0; asnt--) { - //events are stored in reverse order. Don't ask... + for (long asnt=0; asntcreateEventAssignment(); sbmlasnt->setVariable(event->GetNthAssignmentVariableName(asnt, cc)); ASTNode* ASTasnt = parseStringToASTNode(event->GetNthAssignmentFormulaString(asnt, cc, true)); @@ -2655,6 +2872,7 @@ void Module::CreateSBMLModel(bool comp) for (size_t ar = 0; ar < numcharges; ar++) { const Variable* spec_fbc = GetNthVariableOfType(allSpeciesFbcInfo, ar, comp); if (spec_fbc->GetType() == varSpeciesCharge) { + if (spec_fbc->GetFormula()->IsEmpty()) continue; string specname = spec_fbc->GetNameDelimitedBy(cc); specname.replace(specname.find("-charge"), 7, ""); @@ -2669,6 +2887,7 @@ void Module::CreateSBMLModel(bool comp) } else { assert(spec_fbc->GetType() == varSpeciesChemicalFormula); + if (spec_fbc->GetDisplayName().empty()) continue; string specname = spec_fbc->GetNameDelimitedBy(cc); specname.replace(specname.find("-formula"), 8, ""); Species* spec = sbmlmod->getSpecies(specname); @@ -2683,6 +2902,24 @@ void Module::CreateSBMLModel(bool comp) } + //Species conversion factors: + size_t numcfs = GetNumVariablesOfType(allSpeciesConversionFactors, comp); + for (size_t ar = 0; ar < numcfs; ar++) { + const Variable* spec_cf = GetNthVariableOfType(allSpeciesConversionFactors, ar, comp); + if (spec_cf->GetFormula()->IsEmpty()) continue; + string specname = spec_cf->GetNameDelimitedBy(cc); + specname.replace(specname.find("-cf"), 3, ""); + Species* spec = sbmlmod->getSpecies(specname); + if (spec == NULL) { + g_registry.SetError("Couldn't find the species associated with the species conversion factor '" + spec_cf->GetNameDelimitedBy(cc) + "'."); + assert(false); //Shouldn't get this? + } + vector cfvars = spec_cf->GetFormula()->GetVariables(); + assert(cfvars.size() == 1); + spec->setConversionFactor(cfvars[0]->GetNameDelimitedBy(cc)); + } + + //Unknown variables (turn into parameters) size_t numunknown = GetNumVariablesOfType(allUnknown, comp); for (size_t form=0; form < numunknown; form++) { @@ -2728,6 +2965,12 @@ void Module::CreateSBMLModel(bool comp) objective->GetFormula()->AddFluxObjective(sbmlmod, m_maximize, objective); } + //The model's conversion factor (if present) + if (m_modelConversionFactor.size() > 0) { + Variable* cf = GetVariable(m_modelConversionFactor)->GetSameVariable(); + sbmlmod->setConversionFactor(cf->GetNameDelimitedBy(cc)); + } + //Ports if (comp) { set portnames; @@ -3110,7 +3353,8 @@ bool Module::SynchronizeAssignments(Model* sbmlmod, const Variable* var, const v for (size_t v=0; v::const_iterator syncmapiter = syncmap.find(synchronized[v]); if (syncmapiter == syncmap.end()) { - assert(false); + //We have no cached original to compare against (this can happen with + //deeply-nested submodel deletions); nothing to clean up for this one. continue; } const Variable* orig = &syncmapiter->second; @@ -3179,17 +3423,11 @@ bool Module::SynchronizeRates(Model* sbmlmod, const Variable* var, const vector< for (size_t v=0; v::const_iterator syncmapiter = syncmap.find(synchronized[v]); if (syncmapiter == syncmap.end()) { - assert(false); + //We have no cached original to compare against (this can happen with + //deeply-nested submodel deletions); nothing to clean up for this one. continue; } const Variable* orig = &syncmapiter->second; - if (ret && notblank && var->GetFormulaType() == orig->GetFormulaType() && - orig->GetRateRule()->Matches(currentform)) { - ret = false; //We can leave the original definition there. - continue; - } - if (orig->GetRateRule()->IsEmpty()) continue; //There won't be any rr's in the original. - //Otherwise, delete any rate rules in the submodel. vector syncname = synchronized[v]->GetName(); vector submodname = syncname; submodname.pop_back(); @@ -3198,6 +3436,27 @@ bool Module::SynchronizeRates(Model* sbmlmod, const Variable* var, const vector< assert(false); continue; } + //Any submodel rules were converted by the time conversion factor, + // if present. Check to see if that's the only change that was made. + Variable* tcf = submod->GetTimeConversionFactor(); + bool matches = false; + if (ret && notblank && var->GetFormulaType() == orig->GetFormulaType()) { + if (tcf == NULL) { + matches = orig->GetRateRule()->Matches(currentform); + } + else { + Formula convertedOrig(*(orig->GetRateRule())); + convertedOrig.AddInvTimeConversionFactor(tcf); + convertedOrig.ConvertTime(tcf); + matches = convertedOrig.Matches(currentform); + } + } + if (matches) { + ret = false; //We can leave the original definition there. + continue; + } + if (orig->GetRateRule()->IsEmpty()) continue; //There won't be any rr's in the original. + //Otherwise, delete any rate rules in the submodel. if (submod->HasDeletion(syncname, delRateRule)) continue; Model* md = sbmlmod; for (size_t sm=0; smGetNameDelimitedBy("_"); diff --git a/src/module.cpp b/src/module.cpp index 5433b0efc..9db706624 100644 --- a/src/module.cpp +++ b/src/module.cpp @@ -440,6 +440,57 @@ void Module::AddSynchronizedPair(const Variable* oldvar, const Variable* newvar, } } +//Promote a variable local to a submodule (e.g. 'sub1.E0') to a new top-level +//variable (e.g. 'sub1_E0'), synchronizing the two so that 'subvar' becomes an +//alias of the new variable ('sub1.E0 is sub1_E0;'). If 'subvar' is already +//promoted (or is already top-level), it's returned unchanged. +Variable* Module::PromoteToTopLevel(Variable* subvar) +{ + if (subvar == NULL) { + return NULL; + } + if (subvar->IsPointer()) { + return subvar->GetSameVariable(); + } + vector name = subvar->GetName(); + if (name.size() <= 1) { + return subvar; + } + string newname = name[0]; + for (size_t n=1; n candidate(1, newname); + Variable* newvar = GetVariable(candidate); + if (newvar == NULL) { + newvar = AddOrFindVariable(&newname); + } + else { + newvar = AddNewNumberedVariable(newname); + } + if (subvar->Synchronize(newvar, NULL)) { + //An error occurred (already set in the registry); leave things as they were. + return subvar; + } + return subvar->GetSameVariable(); +} + +//Promote every submodule-local variable referenced by 'formula' that isn't +//already promoted. See PromoteToTopLevel. +void Module::PromoteReferencedVariables(const Formula* formula) +{ + if (formula == NULL) { + return; + } + vector vars = formula->GetVariables(); + for (size_t v=0; vIsPointer() && var->GetName().size() > 1 && var->GetType() != varDeleted) { + PromoteToTopLevel(var); + } + } +} + void Module::AddTimeToUserFunction(string function) { for (size_t var=0; var 0) { + g_registry.SetError("Unable to set a new conversion factor for the model, since '" + ToStringFromVecDelimitedBy(m_modelConversionFactor, ".") + "' is already set as this model's conversion factor."); + return true; + } + if (var->SetType(varFormulaUndef)) { + g_registry.SetError("Cannot set the model's conversion factor to be '" + var->GetNameDelimitedBy(".") + "', because it cannot be used as a parameter."); + return true; + } + m_modelConversionFactor = var->GetName(); + return false; +} + +const Variable* Module::GetConversionFactor() const +{ + if (m_modelConversionFactor.size() == 0) return NULL; + return GetVariable(m_modelConversionFactor); +} + void Module::ClearReferencesTo(Variable* deletedvar, set, deletion_type> >* ret) { set, deletion_type> > temp; @@ -660,9 +731,16 @@ void Module::ClearReferencesTo(Variable* deletedvar, set, de if (deletedvar->GetIsEquivalentTo(GetVariable(m_returnvalue))) { m_returnvalue.clear(); } + if (deletedvar->GetIsEquivalentTo(GetConversionFactor())) { + m_modelConversionFactor.clear(); + } for (size_t sync=0; syncGetSameVariable() == deletedvar) { + if (convvar != NULL && convvar->GetSameVariable() == deletedvar) { m_conversionFactors[sync].clear(); } } @@ -866,6 +944,7 @@ void Module::AddDefaultInitialValues() case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: break; } } @@ -1239,18 +1318,6 @@ bool Module::Finalize() if (m_variables[var]->GetType() == varCompartment){ if (m_variables[var]->AnyCompartmentLoops()) return true; } - else if (m_variables[var]->GetType() == varInteraction) { - vector > rxns = m_variables[var]->GetReaction()->GetRight()->GetVariableList(); - for (size_t rxn=0; rxnGetFormula(); - if (!form->IsEmpty() && - form->CheckIncludes(m_variables[var]->GetNamespace(), m_variables[var]->GetReaction()->GetLeft())) { - g_registry.AddErrorPrefix("According to the interaction '" + m_variables[var]->GetNameDelimitedBy(cc) + "', the formula for '" + rightvar->GetNameDelimitedBy(cc) + "' ('" + form->ToDelimitedStringWithEllipses(cc) + "') "); - return true; - } - } - } } //Phase 2: Check for undefined functions @@ -1267,6 +1334,26 @@ bool Module::Finalize() } } } + //Phase 2.5: Check that conversion factors reference constant variables. + for (size_t var=0; varGetType() == varSpeciesConversionFactor) { + vector cfvars = m_variables[var]->GetFormula()->GetVariables(); + if (cfvars.size() == 1 && !cfvars[0]->GetIsConst()) { + string specname = m_variables[var]->GetNameDelimitedBy(cc); + specname.replace(specname.find("-cf"), 3, ""); + g_registry.SetError("Unable to set the conversion factor for species '" + specname + "' to '" + cfvars[0]->GetNameDelimitedBy(cc) + "', because conversion factors must be constant."); + return true; + } + } + } + if (m_modelConversionFactor.size() > 0) { + Variable* cf = GetVariable(m_modelConversionFactor); + if (cf && !cf->GetIsConst()) { + g_registry.SetError("Unable to set the model's conversion factor to '" + cf->GetNameDelimitedBy(cc) + "', because conversion factors must be constant."); + return true; + } + } + //Now check if the functions themselves use distributions for (size_t uf = 0; uf < g_registry.GetNumUserFunctions(); uf++) { if (g_registry.GetNthUserFunction(uf)->UsesDistrib()) { @@ -1316,6 +1403,7 @@ bool Module::Finalize() case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: g_registry.SetError("Unable to add layout or render information to " + m_variables[var]->GetNameDelimitedBy(".") + ": only species, reactions, and compartments can be visualized, and this element is of type '" + VarTypeToString(m_variables[var]->GetType()) + "'."); return true; } @@ -1663,7 +1751,6 @@ const Variable* Module::GetNthConstVariableOfType(return_type rtype, size_t n, b { const vector& result = GetVariablesOfTypeCached(rtype, comp); if (n >= result.size()) { - assert(false); return NULL; } return result[n]; @@ -1742,6 +1829,8 @@ bool Module::AreEquivalent(return_type rtype, var_type vtype) const return (vtype == varGeneProductAssociation); case allSpeciesFbcInfo: return (vtype == varSpeciesCharge || vtype == varSpeciesChemicalFormula); + case allSpeciesConversionFactors: + return (vtype == varSpeciesConversionFactor); } //This is just to to get compiler warnings if we switch vtype later, so // we remember to change the rest of this function: @@ -1772,6 +1861,7 @@ bool Module::AreEquivalent(return_type rtype, var_type vtype) const case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: break; } assert(false); //uncaught return type @@ -1813,6 +1903,7 @@ bool Module::AreEquivalent(return_type rtype, bool isconst) const case allGeneProducts: case allGeneProductAssociations: case allSpeciesFbcInfo: + case allSpeciesConversionFactors: return true; } assert(false); //uncaught return_type @@ -1839,7 +1930,8 @@ string Module::OutputOnly(vector types, string name, string indent, st formula_type ftype = var->GetFormulaType(); if (form != NULL && !form->IsEllipsesOnly() && (ftype == formulaINITIAL || ftype == formulaRATE)) { if (OrigFormulaIsAlready(var, origmap, form)) continue; - if ((type == varGeneProduct || type == varGeneProductAssociation) + if ((type == varGeneProduct || type == varGeneProductAssociation + || type == varSpeciesCharge || type == varSpeciesConversionFactor) && var->GetFormula()->IsEmpty()) { continue; } @@ -1857,6 +1949,9 @@ string Module::OutputOnly(vector types, string name, string indent, st else if (type == varSpeciesCharge) { name.replace(name.find("-charge"), 7, ".charge"); } + else if (type == varSpeciesConversionFactor) { + name.replace(name.find("-cf"), 3, ".conversionFactor"); + } retval += indent + name + " = " + form->ToDelimitedStringWithEllipses(cc) + ";\n"; } Variable* unit = var->GetUnitVariable(); @@ -2190,6 +2285,17 @@ string Module::GetAntimony(set& usedmods, bool funcsincluded, boo } } + //The model's conversion factor, if any + if (m_modelConversionFactor.size() > 0) { + const Variable* cf = GetVariable(m_modelConversionFactor); + if (cf) { + retval += "\n" + indent + "model.conversionFactor = " + ToStringFromVecDelimitedBy(cf->GetName(), ".") + ";\n"; + } + else { + assert(false); //A nonexistent variable? + } + } + //Then events: firstone = true; for (size_t vnum=0; vnum& usedmods, bool funcsincluded, boo types.push_back(varSpeciesCharge); retval += OutputOnly(types, "Species charges", indent, cc, origmap); + //The species conversion factors: + types.clear(); + types.push_back(varSpeciesConversionFactor); + retval += OutputOnly(types, "Species conversion factors", indent, cc, origmap); + //The associated species of gene products: types.clear(); types.push_back(varGeneProduct); @@ -2353,6 +2464,7 @@ string Module::GetAntimony(set& usedmods, bool funcsincluded, boo case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: break; } } @@ -2688,6 +2800,11 @@ void Module::FixNames() void Module::FillInOrigmap(map& origmap) const { map::iterator origmapiter; + //Variables synchronized with more than one, unrelated submodule element + //have no single submodule default to compare against; once we find such + //a conflict we exclude the variable from origmap for good, so its + //top-level value always gets printed explicitly rather than guessed at. + set conflicted; for (size_t var=0; varGetType() == varModule) { @@ -2696,6 +2813,13 @@ void Module::FillInOrigmap(map& origmap) const //cout << "Module " << mname[0] << endl; const Module* submod = m_variables[var]->GetModule(); const Module* origmod = g_registry.GetModule(submod->GetModuleName()); + //If this submodel has a time conversion factor, all rules were + // rescaled on import. We'll need to compare every rule within it was + //automatically rescaled when the submodel was set up (see + //Module::ConvertTime/ConvertExtent). Reproduce those same + //transformations here. + Variable* tcf = m_variables[var]->GetTimeConversionFactor(); + Variable* xcf = m_variables[var]->GetExtentConversionFactor(); for (size_t uniq=0; uniqm_uniquevars.size(); uniq++) { const Variable* origmodvar = origmod->m_uniquevars[uniq]; //cout << "Original: " << origmodvar->GetNameDelimitedBy(".") << ": " << FormulaTypeToString(origmodvar->GetFormulaType()); @@ -2705,6 +2829,20 @@ void Module::FillInOrigmap(map& origmap) const Variable copied(*(origmod->m_uniquevars[uniq])); copied.ClearSameName(); copied.SetNewTopName(m_modulename, mname[0]); + if (tcf != NULL) { + copied.GetRateRule()->AddInvTimeConversionFactor(tcf); + copied.GetRateRule()->ConvertTime(tcf); + } + var_type ctype = copied.GetType(); + if (IsReaction(ctype) || ctype == varInteraction) { + if (tcf != NULL) { + copied.GetReaction()->GetFormula()->AddInvTimeConversionFactor(tcf); + copied.GetReaction()->GetFormula()->ConvertTime(tcf); + } + if (xcf != NULL) { + copied.GetReaction()->GetFormula()->AddConversionFactor(xcf); + } + } const Variable* origvar = GetVariable(copied.GetName()); if (origvar == NULL) { assert(false); @@ -2712,8 +2850,27 @@ void Module::FillInOrigmap(map& origmap) const } origvar = origvar->GetSameVariable(); assert(find(m_uniquevars.begin(), m_uniquevars.end(), origvar) != m_uniquevars.end()); + if (conflicted.find(origvar) != conflicted.end()) continue; origmapiter = origmap.find(origvar); if (origmapiter == origmap.end()) { + //If this variable was synchronized with a conversion factor, the value + //it started with isn't directly comparable to the outer model's value + //anymore; apply the conversion factor here so later comparisons (and + //thus decisions about whether the outer value is redundant) are fair. + for (size_t sync=0; syncGetName()) || + (m_synchronized[sync].second == copied.GetName() && m_synchronized[sync].first == origvar->GetName())) { + const Variable* conversionFactor = GetVariable(m_conversionFactors[sync]); + if (conversionFactor != NULL) { + copied.GetFormula()->AddConversionFactor(conversionFactor); + copied.GetRateRule()->AddConversionFactor(conversionFactor); + if (IsReaction(ctype) || ctype == varInteraction) { + copied.GetReaction()->GetFormula()->AddConversionFactor(conversionFactor); + } + } + break; + } + } origmap.insert(make_pair(origvar, copied)); } else { @@ -2743,14 +2900,11 @@ void Module::FillInOrigmap(map& origmap) const } } if (!synched) { - //Sync them randomly LS DEBUG - //assert(false); - origmapiter->second.Synchronize(&copied, NULL); - //copied.Synchronize(&origmapiter->second); - if (!copied.IsPointer()) { - //The synchronization worked backwards from what we tried. - origmapiter->second = copied; - } + //These two submodules aren't related to each other, so we have + //no principled way to pick one's default over the other's; + //don't guess, just require the top-level value to be printed. + origmap.erase(origmapiter); + conflicted.insert(origvar); } //cout << "Final: " << origmapiter->second.ToString() << endl; } @@ -2946,18 +3100,19 @@ void Module::FillInSyncmap(map& syncmap) const { for (size_t s=0; s 1) { var = GetVariable(m_synchronized[s].first); - AddVarToSyncMap(var, syncmap); + AddVarToSyncMap(var, conversionFactor, syncmap); } if (m_synchronized[s].second.size() > 1) { var = GetVariable(m_synchronized[s].second); - AddVarToSyncMap(var, syncmap); + AddVarToSyncMap(var, conversionFactor, syncmap); } } } -void Module::AddVarToSyncMap(const Variable* var, map& syncmap) const +void Module::AddVarToSyncMap(const Variable* var, const Variable* conversionFactor, map& syncmap) const { vector origname = var->GetName(); if (origname.size() <=1) { @@ -2974,6 +3129,18 @@ void Module::AddVarToSyncMap(const Variable* var, mapAddConversionFactor(conversionFactor); + copied.GetRateRule()->AddConversionFactor(conversionFactor); + if (IsReaction(ctype) || ctype == varInteraction) { + copied.GetReaction()->GetFormula()->AddConversionFactor(conversionFactor); + } + } syncmap.insert(make_pair(var, copied)); } @@ -3009,6 +3176,7 @@ void Module::Convert(Variable* conv, Variable* cf, string modulename) case varGeneProduct: case varGeneProductAssociation: case varSpeciesCharge: + case varSpeciesConversionFactor: form = subvar->GetFormula(); origform = *origsubvar->GetFormula(); for (size_t vn=m_variablename.size() - origsubvar->GetName().size() + 1; vn > 0; vn--) { @@ -3093,6 +3261,7 @@ void Module::ConvertTime(Variable* tcf) case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: break; } } @@ -3135,6 +3304,7 @@ void Module::ConvertExtent(Variable* xcf) case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: break; } } @@ -3181,6 +3351,7 @@ void Module::UndoTimeExtentConversions(Variable* tcf, Variable* xcf) case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: break; } } diff --git a/src/module.h b/src/module.h index 171ad4740..712cb38a7 100644 --- a/src/module.h +++ b/src/module.h @@ -76,6 +76,7 @@ class Module : public Annotated bool m_usedDistributions; std::vector m_objective; bool m_maximize; + std::vector m_modelConversionFactor; size_t m_currentexportvar; bool m_ismain; @@ -139,6 +140,8 @@ class Module : public Annotated bool SetModule(const std::string* modname); void SetComponentCompartments(Variable* compartment); void AddSynchronizedPair(const Variable* oldvar, const Variable* newvar, const Variable* conversionFactor); + Variable* PromoteToTopLevel(Variable* subvar); + void PromoteReferencedVariables(const Formula* formula); void AddTimeToUserFunction(std::string function); void CreateLocalVariablesForSubmodelInterfaceIfNeeded(); void SetIsMain(bool ismain) {m_ismain=ismain;}; @@ -154,6 +157,8 @@ class Module : public Annotated bool AddObjective(Formula* formula, bool maximize); bool AddObjective(Variable* var, Formula* formula, bool maximize); bool AddObjective(const Variable* var, bool maximize); + bool SetConversionFactor(Variable* var); + const Variable* GetConversionFactor() const; bool DeleteFromSynchronized(Variable* deletedvar); void ClearReferencesTo(Variable* deletedvar, std::set, deletion_type> >* ret); Variable* AddOrFindUnitDef(const UnitDef& unitdef); @@ -247,7 +252,7 @@ class Module : public Annotated void FindOrCreateLocalVersionOf(const Variable* var, libsbml::Model* sbmlmod); std::vector GetSynchronizedVariablesFor(const Variable* var); void FillInSyncmap(std::map& syncmap) const; - void AddVarToSyncMap(const Variable* var, std::map& syncmap) const; + void AddVarToSyncMap(const Variable* var, const Variable* conversionFactor, std::map& syncmap) const; void setUsedDistrib(bool useddistrib); diff --git a/src/reactantlist.cpp b/src/reactantlist.cpp index deb6bc968..5727807fd 100644 --- a/src/reactantlist.cpp +++ b/src/reactantlist.cpp @@ -307,10 +307,16 @@ bool ReactantList::Matches(const ReactantList* newrl) const bool ReactantList::HasReactantFor(const Variable* species) const { - vector specid = species->GetName(); + if (m_module.empty()) { + //There are no reactants in this list, so it can't have one for 'species'. + return false; + } + const Variable* target = species->GetSameVariable(); + Module* module = g_registry.GetModule(m_module); + assert(module != NULL); for (size_t component = 0; component < m_components.size(); component++) { - //Check stoichiometry value - if (get<2>(m_components[component]) == specid) { + const Variable* reactant = module->GetVariable(get<2>(m_components[component])); + if (reactant != NULL && reactant->GetSameVariable() == target) { return true; } } diff --git a/src/registry.cpp b/src/registry.cpp index 244de9e19..d7c51ecc6 100644 --- a/src/registry.cpp +++ b/src/registry.cpp @@ -1010,6 +1010,10 @@ Variable* Registry::AddNewReactionToCurrent(rd_type divider, Formula* formula, i { retval = CurrentModule()->AddNewReaction(blank, divider, m_currentReactantLists[0], formula); } + else if (type == 3) + { + retval = CurrentModule()->AddNewReaction(blank, divider, blank, formula); + } m_currentReactantLists.clear(); return retval; } @@ -1030,9 +1034,13 @@ Variable* Registry::AddNewReactionToCurrent(rd_type divider, Formula* formula, V { retval = CurrentModule()->AddNewReaction( blank, divider, m_currentReactantLists[0], formula, var); } + else if (type == 3) + { + retval = CurrentModule()->AddNewReaction(blank, divider, blank, formula, var); + } else { - assert(false); //Should only be three options. + assert(false); //Should only be four options. } m_currentReactantLists.clear(); return retval; diff --git a/src/rehashantimony.cpp b/src/rehashantimony.cpp index cc841f8c7..e852798bc 100644 --- a/src/rehashantimony.cpp +++ b/src/rehashantimony.cpp @@ -52,7 +52,9 @@ int main(int argc, char** argv) } //cout << "Dirname = " << dirname << endl; string command = "mkdir -p rehash/" + dirname; - system(command.c_str()); + if (system(command.c_str()) != 0) { + cout << "Problem creating directory rehash/" << dirname << endl; + } size_t modnum = nummods-1; string antimonyname = "rehash/" + dirname + "/" + filename; //antimonyname += ".txt"; diff --git a/src/test/CMakeLists.txt b/src/test/CMakeLists.txt index a7b5466e4..a1170d21e 100644 --- a/src/test/CMakeLists.txt +++ b/src/test/CMakeLists.txt @@ -82,11 +82,19 @@ function(add_test_executable TEST_TARGET) # Still set "srcdir" for ctest-driven runs too, so CI/distcheck-style # invocations that want to point at a different checkout can override it. - gtest_discover_tests( - ${TEST_TARGET} - DISCOVERY_TIMEOUT 500 - DISCOVERY_MODE PRE_TEST - PROPERTIES + # + # Uses gtest_add_tests (source parsing) rather than gtest_discover_tests + # (executes the binary at build/ctest time), since the latter is + # intermittently unreliable: it can fail with a ParseTestList.cmake JSON + # error if the freshly-built binary doesn't run cleanly on its first + # invocation. + gtest_add_tests( + TARGET ${TEST_TARGET} + SOURCES ${ARGN} + WORKING_DIRECTORY $ + TEST_LIST ${TEST_TARGET}_GTESTS + ) + set_tests_properties(${${TEST_TARGET}_GTESTS} PROPERTIES TIMEOUT 500 ENVIRONMENT "srcdir=${CMAKE_CURRENT_SOURCE_DIR}" ) diff --git a/src/test/TestAntimonyAPI.cpp b/src/test/TestAntimonyAPI.cpp index 3df4c1d49..2773dae93 100644 --- a/src/test/TestAntimonyAPI.cpp +++ b/src/test/TestAntimonyAPI.cpp @@ -5,7 +5,13 @@ * ---------------------------------------------------------------------- -->*/ #include "antimony_api.h" +#include "registry.h" +#include +#include +#include +#include #include +#include #include #include "gtest/gtest.h" @@ -413,7 +419,7 @@ TEST(AntimonyAPI, test_moduleNames) freeAll(); } - + TEST(AntimonyAPI, test_moduleInterfaceNames) { int ret = loadString("model foo(a, b, c)\na=3\nend"); @@ -601,6 +607,22 @@ TEST(AntimonyAPI, test_event_modifications) EXPECT_TRUE(getFromTriggerForEvent("__main", 0) == true); EXPECT_TRUE(getFromTriggerForEvent("__main", 1) == false); + //Error cases, out-of-range event index: + EXPECT_TRUE(getDelayForEvent("__main", 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getEventHasDelay("__main", 5) == false); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getPriorityForEvent("__main", 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getEventHasPriority("__main", 5) == false); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getPersistenceForEvent("__main", 5) == false); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getT0ForEvent("__main", 5) == false); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getFromTriggerForEvent("__main", 5) == false); + EXPECT_STRNE(getLastError(), ""); + freeAll(); } @@ -665,6 +687,732 @@ TEST(AntimonyAPI, test_rxns) freeAll(); } - - +TEST(AntimonyAPI, test_substanceOnly) +{ + int ret = loadString("substanceOnly species S1;\nspecies S2;\n"); + EXPECT_TRUE(ret != -1); + + EXPECT_TRUE(getSymbolSubstanceOnly("__main", "S1") == true); + EXPECT_TRUE(getSymbolSubstanceOnly("__main", "S2") == false); + + EXPECT_TRUE(getSymbolSubstanceOnly("__main", "nosuchsymbol") == false); + EXPECT_STRNE(getLastError(), ""); + + EXPECT_TRUE(getSymbolSubstanceOnly("nosuchmodule", "S1") == false); + EXPECT_STRNE(getLastError(), ""); + + freeAll(); +} + +TEST(AntimonyAPI, test_hasValue) +{ + int ret = loadString("x = ;\ny = 5\n"); + EXPECT_TRUE(ret != -1); + + EXPECT_TRUE(getSymbolHasValue("__main", "x") == false); + EXPECT_TRUE(getSymbolHasValue("__main", "y") == true); + + EXPECT_TRUE(getSymbolHasValue("__main", "nosuchsymbol") == false); + EXPECT_STRNE(getLastError(), ""); + + freeAll(); +} + +TEST(AntimonyAPI, test_stoichiometryStrings) +{ + int ret = loadString( + "J0: sr1 a->;\n" + "sr1 = 2\n" + "J1: 2 c -> 3 d;\n" + "J2: e -> f;\n" + ); + EXPECT_TRUE(ret != -1); + + //A named (symbolic) stoichiometry returns the symbol's name, and the plain-double getter returns NaN for it. + EXPECT_STREQ(getNthReactionMthReactantStoichiometryString("__main", 0, 0), "sr1"); + EXPECT_TRUE(std::isnan(getNthReactionMthReactantStoichiometries("__main", 0, 0))); + + //Plain numeric stoichiometries are returned as text. + EXPECT_STREQ(getNthReactionMthReactantStoichiometryString("__main", 1, 0), "2"); + EXPECT_STREQ(getNthReactionMthProductStoichiometryString("__main", 1, 0), "3"); + + //The default stoichiometry (no coefficient written) is 1. + EXPECT_STREQ(getNthReactionMthReactantStoichiometryString("__main", 2, 0), "1"); + EXPECT_STREQ(getNthReactionMthProductStoichiometryString("__main", 2, 0), "1"); + + //Error cases: + EXPECT_TRUE(getNthReactionMthReactantStoichiometryString("__main", 5, 0) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthReactionMthReactantStoichiometryString("__main", 1, 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthReactionMthProductStoichiometryString("__main", 5, 0) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthReactionMthProductStoichiometryString("__main", 1, 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + + freeAll(); +} + +TEST(AntimonyAPI, test_userFunctions) +{ + int ret = loadString( + "function f(x, y)\n" + " x+y*2;\n" + "end\n" + "a := f(b, c)\n" + ); + EXPECT_TRUE(ret != -1); + + EXPECT_TRUE(getNumUserFunctions() == 1); + EXPECT_STREQ(getNthUserFunctionName(0), "f"); + + EXPECT_TRUE(getNumUserFunctionArguments(0) == 2); + char** args = getNthUserFunctionArguments(0); + EXPECT_STREQ(args[0], "x"); + EXPECT_STREQ(args[1], "y"); + + EXPECT_STREQ(getNthUserFunctionBody(0), "x + y*2"); + + //Error cases: + EXPECT_TRUE(getNthUserFunctionName(5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNumUserFunctionArguments(5) == 0); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthUserFunctionArguments(5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthUserFunctionBody(5) == NULL); + EXPECT_STRNE(getLastError(), ""); + + freeAll(); + clearPreviousLoads(); +} + +TEST(AntimonyAPI, test_nthSymbolOfTypeGetters) +{ + int ret = loadString( + "a = 3\n" + "b := a+2\n" + "rr = 0\n" + "rr' = 1\n" + "species S1 in C1;\n" + "S1 is \"the first species\"\n" + "C1 = 1.5\n" + ); + EXPECT_TRUE(ret != -1); + + //allFormulas, in declaration order: a (initial only), b (assignment rule), rr (rate rule). + EXPECT_STREQ(getNthSymbolEquationOfType("__main", allFormulas, 0), "3"); + EXPECT_STREQ(getNthSymbolInitialAssignmentOfType("__main", allFormulas, 0), "3"); + EXPECT_STREQ(getNthSymbolAssignmentRuleOfType("__main", allFormulas, 0), ""); + EXPECT_STREQ(getNthSymbolRateRuleOfType("__main", allFormulas, 0), ""); + + EXPECT_STREQ(getNthSymbolEquationOfType("__main", allFormulas, 1), "a+2"); + EXPECT_STREQ(getNthSymbolInitialAssignmentOfType("__main", allFormulas, 1), ""); + EXPECT_STREQ(getNthSymbolAssignmentRuleOfType("__main", allFormulas, 1), "a+2"); + EXPECT_STREQ(getNthSymbolRateRuleOfType("__main", allFormulas, 1), ""); + + EXPECT_STREQ(getNthSymbolEquationOfType("__main", allFormulas, 2), "0"); + EXPECT_STREQ(getNthSymbolInitialAssignmentOfType("__main", allFormulas, 2), "0"); + EXPECT_STREQ(getNthSymbolAssignmentRuleOfType("__main", allFormulas, 2), ""); + EXPECT_STREQ(getNthSymbolRateRuleOfType("__main", allFormulas, 2), "1"); + + //The bulk 'OfType' versions should agree with the singular versions above. + char** assignmentRules = getSymbolAssignmentRulesOfType("__main", allFormulas); + EXPECT_STREQ(assignmentRules[0], ""); + EXPECT_STREQ(assignmentRules[1], "a+2"); + EXPECT_STREQ(assignmentRules[2], ""); + + char** initialAssignments = getSymbolInitialAssignmentsOfType("__main", allFormulas); + EXPECT_STREQ(initialAssignments[0], "3"); + EXPECT_STREQ(initialAssignments[1], ""); + EXPECT_STREQ(initialAssignments[2], "0"); + + //Species/compartment-specific getters. + EXPECT_STREQ(getNthSymbolDisplayNameOfType("__main", allSpecies, 0), "the first species"); + EXPECT_STREQ(getNthSymbolCompartmentOfType("__main", allSpecies, 0), "C1"); + EXPECT_STREQ(getCompartmentForSymbol("__main", "S1"), "C1"); + EXPECT_STREQ(getCompartmentForSymbol("__main", "a"), "default_compartment"); + + //Error cases: + EXPECT_TRUE(getNthSymbolEquationOfType("__main", allFormulas, 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthSymbolInitialAssignmentOfType("__main", allFormulas, 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthSymbolAssignmentRuleOfType("__main", allFormulas, 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthSymbolRateRuleOfType("__main", allFormulas, 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthSymbolCompartmentOfType("__main", allFormulas, 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthSymbolDisplayNameOfType("__main", allFormulas, 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getCompartmentForSymbol("__main", "nosuchsymbol") == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getCompartmentForSymbol("nosuchmodule", "a") == NULL); + EXPECT_STRNE(getLastError(), ""); + + freeAll(); +} + +//Documents (and locks in) the caveat added to getSymbolAssignmentRulesOfType's +//documentation: querying with rtype=allSymbols returns a reaction's kinetic law +//in the 'assignment rule' slot, not just symbols that actually have one. +TEST(AntimonyAPI, test_symbolAssignmentRulesOfTypeAllSymbolsIncludesKineticLaw) +{ + int ret = loadString("J0: S1 -> S2; k1*S1\n"); + EXPECT_TRUE(ret != -1); + + char** names = getSymbolNamesOfType("__main", allSymbols); + char** assignmentRules = getSymbolAssignmentRulesOfType("__main", allSymbols); + unsigned long numsymbols = getNumSymbolsOfType("__main", allSymbols); + + bool foundIt = false; + for (unsigned long n=0; n S2; k1*S1\n" + " J1: S2 -> ; k2*S2*S3\n" + " E0: at(time>2): a = 0\n" + " S2 in C1\n" + " C1 = 1.5\n" + " DNA1: P--Q--R\n" + " DNA2: DNA1--S\n" + " S3 -o J1;\n" + "end"; + +TEST(AntimonyAPI, test_reactionSingularGetters) +{ + int ret = loadString(kReactionsAndFriendsModel); + EXPECT_TRUE(ret != -1); + + EXPECT_TRUE(getNumReactions("foo") == 2); + + //Reaction (and gene) names. + char** rxnnames = getReactionNames("foo"); + EXPECT_STREQ(rxnnames[0], "_J0"); + EXPECT_STREQ(rxnnames[1], "J1"); + EXPECT_STREQ(getNthReactionName("foo", 0), "_J0"); + EXPECT_STREQ(getNthReactionName("foo", 1), "J1"); + + //Reaction 0 (_J0): S1 -> S2 ; k1*S1 + char** reactants0 = getNthReactionReactantNames("foo", 0); + EXPECT_STREQ(reactants0[0], "S1"); + char** products0 = getNthReactionProductNames("foo", 0); + EXPECT_STREQ(products0[0], "S2"); + EXPECT_STREQ(getNthReactionMthReactantName("foo", 0, 0), "S1"); + EXPECT_STREQ(getNthReactionMthProductName("foo", 0, 0), "S2"); + + double* reactantstoich0 = getNthReactionReactantStoichiometries("foo", 0); + EXPECT_TRUE(reactantstoich0[0] == 1); + double* productstoich0 = getNthReactionProductStoichiometries("foo", 0); + EXPECT_TRUE(productstoich0[0] == 1); + EXPECT_TRUE(getNthReactionMthProductStoichiometries("foo", 0, 0) == 1); + + EXPECT_STREQ(getNthReactionRate("foo", 0), "k1*S1"); + + //Reaction 1 (J1): S2 -> ; k2*S2*S3 -- no products. + char** reactants1 = getNthReactionReactantNames("foo", 1); + EXPECT_STREQ(reactants1[0], "S2"); + EXPECT_STREQ(getNthReactionRate("foo", 1), "k2*S2*S3"); + EXPECT_TRUE(getNumProducts("foo", 1) == 0); + + //Error cases: + EXPECT_TRUE(getNthReactionName("foo", 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthReactionReactantNames("foo", 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthReactionProductNames("foo", 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthReactionMthReactantName("foo", 0, 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthReactionMthProductName("foo", 0, 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthReactionReactantStoichiometries("foo", 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthReactionProductStoichiometries("foo", 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthReactionRate("foo", 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + + freeAll(); +} + +TEST(AntimonyAPI, test_interactionSingularGetters) +{ + int ret = loadString(kReactionsAndFriendsModel); + EXPECT_TRUE(ret != -1); + + EXPECT_TRUE(getNumInteractions("foo") == 1); + + //Interaction 0 (_J1): S3 -o J1 + char** interactors = getNthInteractionInteractorNames("foo", 0); + EXPECT_STREQ(interactors[0], "S3"); + EXPECT_STREQ(getNthInteractionMthInteractorName("foo", 0, 0), "S3"); + + char** interactees = getNthInteractionInteracteeNames("foo", 0); + EXPECT_STREQ(interactees[0], "J1"); + EXPECT_STREQ(getNthInteractionMthInteracteeName("foo", 0, 0), "J1"); + + EXPECT_TRUE(getNthInteractionDivider("foo", 0) == rdActivates); + + //Error cases: + EXPECT_TRUE(getNthInteractionInteractorNames("foo", 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthInteractionInteracteeNames("foo", 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthInteractionMthInteractorName("foo", 0, 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthInteractionMthInteracteeName("foo", 0, 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + + freeAll(); +} + +TEST(AntimonyAPI, test_dnaSingularGetters) +{ + int ret = loadString(kReactionsAndFriendsModel); + EXPECT_TRUE(ret != -1); + + //Expanded strands: DNA1 is absorbed into DNA2, giving one strand P--Q--R--S. + EXPECT_TRUE(getNumDNAStrands("foo") == 1); + EXPECT_TRUE(getSizeOfNthDNAStrand("foo", 0) == 4); + char** strand = getNthDNAStrand("foo", 0); + EXPECT_STREQ(strand[0], "P"); + EXPECT_STREQ(strand[1], "Q"); + EXPECT_STREQ(strand[2], "R"); + EXPECT_STREQ(strand[3], "S"); + + //Modular strands: DNA1 = P--Q--R, DNA2 = DNA1--S. + EXPECT_TRUE(getNumModularDNAStrands("foo") == 2); + char** modstrand0 = getNthModularDNAStrand("foo", 0); + EXPECT_STREQ(modstrand0[0], "P"); + EXPECT_STREQ(modstrand0[1], "Q"); + EXPECT_STREQ(modstrand0[2], "R"); + char** modstrand1 = getNthModularDNAStrand("foo", 1); + EXPECT_STREQ(modstrand1[0], "DNA1"); + EXPECT_STREQ(modstrand1[1], "S"); + + //Error cases: + EXPECT_TRUE(getSizeOfNthDNAStrand("foo", 5) == 0); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthDNAStrand("foo", 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthModularDNAStrand("foo", 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + + freeAll(); +} + +TEST(AntimonyAPI, test_nthEventName) +{ + int ret = loadString(kReactionsAndFriendsModel); + EXPECT_TRUE(ret != -1); + + EXPECT_TRUE(getNumEvents("foo") == 1); + EXPECT_STREQ(getNthEventName("foo", 0), "E0"); + + EXPECT_TRUE(getNthEventName("foo", 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + + freeAll(); +} + +//Bulk (non-Nth) event getters. E0: at(time>2): a = 0. +TEST(AntimonyAPI, test_eventBulkGetters) +{ + int ret = loadString(kReactionsAndFriendsModel); + EXPECT_TRUE(ret != -1); + + char** eventnames = getEventNames("foo"); + EXPECT_STREQ(eventnames[0], "E0"); + + EXPECT_TRUE(getNumAssignmentsForEvent("foo", 0) == 1); + EXPECT_STREQ(getNthAssignmentVariableForEvent("foo", 0, 0), "a"); + EXPECT_STREQ(getNthAssignmentEquationForEvent("foo", 0, 0), "0"); + EXPECT_STREQ(getTriggerForEvent("foo", 0), "(time > 2)"); + + //Error cases, out-of-range event index: + EXPECT_TRUE(getTriggerForEvent("foo", 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNumAssignmentsForEvent("foo", 5) == 0); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthAssignmentVariableForEvent("foo", 5, 0) == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getNthAssignmentEquationForEvent("foo", 5, 0) == NULL); + EXPECT_STRNE(getLastError(), ""); + + //Out-of-range assignment index (event 0 is valid, but only has one + //assignment): still returns NULL without setting an error message. + EXPECT_TRUE(getNthAssignmentVariableForEvent("foo", 0, 5) == NULL); + EXPECT_TRUE(getNthAssignmentEquationForEvent("foo", 0, 5) == NULL); + + freeAll(); +} + +//Bulk (non-Nth) interaction getters. _J1: S3 -o J1. +TEST(AntimonyAPI, test_interactionBulkGetters) +{ + int ret = loadString(kReactionsAndFriendsModel); + EXPECT_TRUE(ret != -1); + + EXPECT_TRUE(getNumInteractors("foo", 0) == 1); + EXPECT_TRUE(getNumInteractees("foo", 0) == 1); + + char*** interactors = getInteractorNames("foo"); + EXPECT_STREQ(interactors[0][0], "S3"); + char*** interactees = getInteracteeNames("foo"); + EXPECT_STREQ(interactees[0][0], "J1"); + + rd_type* dividers = getInteractionDividers("foo"); + EXPECT_TRUE(dividers[0] == rdActivates); + + freeAll(); +} + +//Bulk (non-Nth) DNA strand getters. Expanded: P--Q--R--S. Modular: DNA1 (P--Q--R), DNA2 (DNA1--S). +TEST(AntimonyAPI, test_dnaBulkGetters) +{ + int ret = loadString(kReactionsAndFriendsModel); + EXPECT_TRUE(ret != -1); + + unsigned long* sizes = getDNAStrandSizes("foo"); + EXPECT_TRUE(sizes[0] == 4); + char*** strands = getDNAStrands("foo"); + EXPECT_STREQ(strands[0][0], "P"); + EXPECT_STREQ(strands[0][3], "S"); + EXPECT_TRUE(getIsNthDNAStrandOpen("foo", 0, true) == false); + EXPECT_TRUE(getIsNthDNAStrandOpen("foo", 0, false) == false); + + unsigned long* modsizes = getModularDNAStrandSizes("foo"); + EXPECT_TRUE(modsizes[0] == 3); + EXPECT_TRUE(modsizes[1] == 2); + EXPECT_TRUE(getIsNthModularDNAStrandOpen("foo", 0, true) == false); + EXPECT_TRUE(getIsNthModularDNAStrandOpen("foo", 1, false) == false); + + //Error case (bad module name): + EXPECT_TRUE(getDNAStrandSizes("nosuchmodule") == NULL); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getModularDNAStrandSizes("nosuchmodule") == NULL); + EXPECT_STRNE(getLastError(), ""); + + //Error case (out-of-range strand index): + EXPECT_TRUE(getIsNthDNAStrandOpen("foo", 5, true) == false); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getIsNthModularDNAStrandOpen("foo", 5, true) == false); + EXPECT_STRNE(getLastError(), ""); + + freeAll(); +} + +//Bulk (non-Nth) reaction getters. _J0: S1 -> S2; k1*S1. J1: S2 -> ; k2*S2*S3. +TEST(AntimonyAPI, test_reactionBulkGetters) +{ + int ret = loadString(kReactionsAndFriendsModel); + EXPECT_TRUE(ret != -1); + + EXPECT_TRUE(getNumReactants("foo", 0) == 1); + EXPECT_TRUE(getNumReactants("foo", 1) == 1); + + char*** reactants = getReactantNames("foo"); + EXPECT_STREQ(reactants[0][0], "S1"); + EXPECT_STREQ(reactants[1][0], "S2"); + + char*** products = getProductNames("foo"); + EXPECT_STREQ(products[0][0], "S2"); + EXPECT_TRUE(getNumProducts("foo", 1) == 0); + + double** reactantstoich = getReactantStoichiometries("foo"); + EXPECT_TRUE(reactantstoich[0][0] == 1); + double** productstoich = getProductStoichiometries("foo"); + EXPECT_TRUE(productstoich[0][0] == 1); + + EXPECT_TRUE(getNumReactionRates("foo") == 2); + char** rates = getReactionRates("foo"); + EXPECT_STREQ(rates[0], "k1*S1"); + EXPECT_STREQ(rates[1], "k2*S2*S3"); + + freeAll(); +} + +//Values here match the already-validated stoichiometry matrix in test_printAll's output. +TEST(AntimonyAPI, test_stoichiometryMatrix) +{ + int ret = loadString(kReactionsAndFriendsModel); + EXPECT_TRUE(ret != -1); + + EXPECT_TRUE(getStoichiometryMatrixNumColumns("foo") == 2); + EXPECT_TRUE(getStoichiometryMatrixNumRows("foo") == 3); + + char** columns = getStoichiometryMatrixColumnLabels("foo"); + EXPECT_STREQ(columns[0], "_J0"); + EXPECT_STREQ(columns[1], "J1"); + + char** rows = getStoichiometryMatrixRowLabels("foo"); + EXPECT_STREQ(rows[0], "S1"); + EXPECT_STREQ(rows[1], "S2"); + EXPECT_STREQ(rows[2], "S3"); + + double** matrix = getStoichiometryMatrix("foo"); + EXPECT_TRUE(matrix[0][0] == -1); //S1, _J0 + EXPECT_TRUE(matrix[0][1] == 0); //S1, J1 + EXPECT_TRUE(matrix[1][0] == 1); //S2, _J0 + EXPECT_TRUE(matrix[1][1] == -1); //S2, J1 + EXPECT_TRUE(matrix[2][0] == 0); //S3, _J0 + EXPECT_TRUE(matrix[2][1] == 0); //S3, J1 + + freeAll(); +} + +//getTypeOfSymbol/getTypeOfEquationForSymbol, using explicit const/var declarations +//so the const-vs-variable heuristic isn't in play. +TEST(AntimonyAPI, test_typeOfSymbolAndEquationType) +{ + int ret = loadString( + "const species S1\n" + "var species S2\n" + "a = 3\n" + "b := a+2\n" + "rr = 0\n" + "rr' = 1\n" + ); + EXPECT_TRUE(ret != -1); + + EXPECT_TRUE(getTypeOfSymbol("__main", "S1") == constSpecies); + EXPECT_TRUE(getTypeOfSymbol("__main", "S2") == varSpecies); + EXPECT_TRUE(getTypeOfSymbol("__main", "b") == varFormulas); + EXPECT_TRUE(getTypeOfSymbol("__main", "rr") == varFormulas); + + EXPECT_TRUE(getTypeOfEquationForSymbol("__main", "a") == formulaINITIAL); + EXPECT_TRUE(getTypeOfEquationForSymbol("__main", "b") == formulaASSIGNMENT); + EXPECT_TRUE(getTypeOfEquationForSymbol("__main", "rr") == formulaRATE); + + //Error cases: + EXPECT_TRUE(getTypeOfSymbol("__main", "nosuchsymbol") == allUnknown); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getTypeOfSymbol("nosuchmodule", "a") == allUnknown); + EXPECT_STRNE(getLastError(), ""); + EXPECT_TRUE(getTypeOfEquationForSymbol("__main", "nosuchsymbol") == formulaINITIAL); + EXPECT_STREQ(getLastError(), "No such variable: 'nosuchsymbol'."); + + freeAll(); +} + +//Bulk (non-Nth) symbol-property getters, using the same model (and known-good +//values) as test_nthSymbolOfTypeGetters above. +TEST(AntimonyAPI, test_symbolBulkGetters) +{ + int ret = loadString( + "a = 3\n" + "b := a+2\n" + "rr = 0\n" + "rr' = 1\n" + "species S1 in C1;\n" + "S1 is \"the first species\"\n" + "C1 = 1.5\n" + ); + EXPECT_TRUE(ret != -1); + + //allFormulas, in declaration order: a, b, rr. + EXPECT_STREQ(getNthSymbolNameOfType("__main", allFormulas, 0), "a"); + EXPECT_STREQ(getNthSymbolNameOfType("__main", allFormulas, 1), "b"); + EXPECT_STREQ(getNthSymbolNameOfType("__main", allFormulas, 2), "rr"); + + char** equations = getSymbolEquationsOfType("__main", allFormulas); + EXPECT_STREQ(equations[0], "3"); + EXPECT_STREQ(equations[1], "a+2"); + EXPECT_STREQ(equations[2], "0"); + + char** rateRules = getSymbolRateRulesOfType("__main", allFormulas); + EXPECT_STREQ(rateRules[0], ""); + EXPECT_STREQ(rateRules[1], ""); + EXPECT_STREQ(rateRules[2], "1"); + + char** compartments = getSymbolCompartmentsOfType("__main", allSpecies); + EXPECT_STREQ(compartments[0], "C1"); + + //Error cases: + EXPECT_TRUE(getNthSymbolNameOfType("__main", allFormulas, 5) == NULL); + EXPECT_STRNE(getLastError(), ""); + + freeAll(); +} + +static string trimTrailingWhitespace(string s) +{ + while (!s.empty() && (s.back() == '\n' || s.back() == '\r' || s.back() == ' ')) { + s.pop_back(); + } + return s; +} + +//The various 'write*File' functions have no dedicated coverage anywhere in the +//suite (the compareFileTranslation/compareStringTranslation helpers used +//elsewhere only ever call the get*String siblings), so this compares each +//file's contents against its already-tested get*String counterpart. +TEST(AntimonyAPI, test_writeFiles) +{ + int ret = loadString("a=3\nb := a+2\n"); + EXPECT_TRUE(ret != -1); + + string antimonyExpected(getAntimonyString(NULL)); + string sbmlExpected(getSBMLString(NULL)); + string compsbmlExpected(getCompSBMLString(NULL)); + + string antimonyFile = "test_write_output_antimony.txt"; + EXPECT_TRUE(writeAntimonyFile(antimonyFile.c_str(), NULL) == 1); + ifstream antimonyIn(antimonyFile.c_str()); + stringstream antimonyBuf; + antimonyBuf << antimonyIn.rdbuf(); + antimonyIn.close(); + EXPECT_STREQ(antimonyBuf.str().c_str(), antimonyExpected.c_str()); + remove(antimonyFile.c_str()); + + string sbmlFile = "test_write_output_sbml.xml"; + EXPECT_TRUE(writeSBMLFile(sbmlFile.c_str(), NULL) != 0); + ifstream sbmlIn(sbmlFile.c_str()); + stringstream sbmlBuf; + sbmlBuf << sbmlIn.rdbuf(); + sbmlIn.close(); + EXPECT_STREQ(trimTrailingWhitespace(sbmlBuf.str()).c_str(), trimTrailingWhitespace(sbmlExpected).c_str()); + remove(sbmlFile.c_str()); + + string compsbmlFile = "test_write_output_compsbml.xml"; + EXPECT_TRUE(writeCompSBMLFile(compsbmlFile.c_str(), NULL) != 0); + ifstream compsbmlIn(compsbmlFile.c_str()); + stringstream compsbmlBuf; + compsbmlBuf << compsbmlIn.rdbuf(); + compsbmlIn.close(); + EXPECT_STREQ(trimTrailingWhitespace(compsbmlBuf.str()).c_str(), trimTrailingWhitespace(compsbmlExpected).c_str()); + remove(compsbmlFile.c_str()); + +#ifndef NCELLML + string cellmlExpected(getCellMLString(NULL)); + string cellmlFile = "test_write_output_cellml.xml"; + EXPECT_TRUE(writeCellMLFile(cellmlFile.c_str(), NULL) == 1); + ifstream cellmlIn(cellmlFile.c_str()); + stringstream cellmlBuf; + cellmlBuf << cellmlIn.rdbuf(); + cellmlIn.close(); + EXPECT_STREQ(trimTrailingWhitespace(cellmlBuf.str()).c_str(), trimTrailingWhitespace(cellmlExpected).c_str()); + remove(cellmlFile.c_str()); +#endif + + //Error case: a directory that doesn't exist can't be opened for writing. + EXPECT_TRUE(writeAntimonyFile("nonexistent_dir_xyz/out.txt", NULL) == 0); + EXPECT_STRNE(getLastError(), ""); + + freeAll(); +} + +TEST(AntimonyAPI, test_writeSBMLTimestamp) +{ + int ret = loadString("a=3"); + EXPECT_TRUE(ret != -1); + + //The timestamp comment libSBML writes is bundled together with the + //program name/version line, which only gets written at all when + //GetWriteNameToSBML() is true. The test harness's main() sets this to + //'false' for the whole suite (so SBML output stays byte-for-byte + //comparable elsewhere), which would otherwise make this setting look + //like a no-op. Temporarily undo that here so this test actually + //exercises the real code path, then restore it for the rest of the suite. + bool oldWriteName = g_registry.GetWriteNameToSBML(); + g_registry.SetWriteNameToSBML(true); + + setWriteSBMLTimestamp(false); + string baseline(getSBMLString(NULL)); + + setWriteSBMLTimestamp(true); + string withTimestamp(getSBMLString(NULL)); + EXPECT_STRNE(withTimestamp.c_str(), baseline.c_str()); + + setWriteSBMLTimestamp(false); + string reverted(getSBMLString(NULL)); + EXPECT_STREQ(reverted.c_str(), baseline.c_str()); + + g_registry.SetWriteNameToSBML(oldWriteName); + freeAll(); +} + +//BIOMD0000000118.xml is a known-good fixture (already used by +//TestAntimonyImport's test_BIOMD0000000118) that declares a single function +//definition, 'GAMMA(VV, theta, sigma)'. +TEST(AntimonyAPI, test_removeFunctionDefinitions) +{ + string dir(TestDataDirectory); + string filename = dir + "BIOMD0000000118.xml"; + + //The test harness's main() sets this to 'false' for the whole suite (see + //main.cpp), so other tests that round-trip Antimony<->SBML keep their + //'function' blocks intact. Don't assume either value is the prevailing + //default -- set both explicitly and restore the harness's setting after. + bool oldRemove = g_registry.GetRemoveFunctionDefinitions(); + + setRemoveFunctionDefinitions(true); + long ret = loadSBMLFile(filename.c_str()); + EXPECT_TRUE(ret != -1); + EXPECT_TRUE(getNumUserFunctions() == 0); + freeAll(); + clearPreviousLoads(); + + setRemoveFunctionDefinitions(false); + ret = loadSBMLFile(filename.c_str()); + EXPECT_TRUE(ret != -1); + EXPECT_TRUE(getNumUserFunctions() == 1); + EXPECT_STREQ(getNthUserFunctionName(0), "GAMMA"); + EXPECT_TRUE(getNumUserFunctionArguments(0) == 3); + char** args = getNthUserFunctionArguments(0); + EXPECT_STREQ(args[0], "VV"); + EXPECT_STREQ(args[1], "theta"); + EXPECT_STREQ(args[2], "sigma"); + + setRemoveFunctionDefinitions(oldRemove); + freeAll(); + clearPreviousLoads(); +} + +TEST(AntimonyAPI, test_warnings) +{ + //S2 is declared but never made a reactant or product of J0, so the + //'species_end' reaction-arc layout term below can't be satisfied. + long ret = loadString( + "species S1, S2\n" + "J0: S1->;\n" + "J0.S2.species_end = { 550.02, 20.83 }\n" + ); + EXPECT_TRUE(ret != -1); + + //Layout warnings are only generated when the model is translated to + //SBML; force that here in case it hasn't happened already. + //char* sbml = getSBMLString(NULL); + //EXPECT_TRUE(sbml != NULL); + + char* warnings = getWarnings(); + EXPECT_TRUE(warnings != NULL); + if (warnings != NULL) { + EXPECT_TRUE(strstr(warnings, "'S2' is not a participant in that reaction") != NULL) + << "Got: " << warnings; + } + + freeAll(); + clearPreviousLoads(); +} + + + //LIB_EXTERN void setBareNumbersAreDimensionless(bool dimensionless); diff --git a/src/test/TestAntimonyBasic.cpp b/src/test/TestAntimonyBasic.cpp index 9dfddadc3..e11bfc3e7 100644 --- a/src/test/TestAntimonyBasic.cpp +++ b/src/test/TestAntimonyBasic.cpp @@ -472,3 +472,70 @@ TEST(AntimonyBasic, test_kineticLaw_set_formula) compareFileTranslation("kl_set_formula"); } +TEST(AntimonyBasic, test_neg_reactant_and_product) +{ + compareFileTranslation("neg_reactant_and_product"); +} + +TEST(AntimonyBasic, test_neg_2_reactant_and_product) +{ + compareFileTranslation("neg_2_reactant_and_product"); +} + +TEST(AntimonyBasic, test_subtracted_reactant_and_product) +{ + compareFileTranslation("subtracted_reactant_and_product"); +} + +TEST(AntimonyBasic, test_subtracted_2_reactant_and_product) +{ + compareFileTranslation("subtracted_2_reactant_and_product"); +} + +TEST(AntimonyBasic, test_empty_rxn) +{ + compareFileTranslation("empty_rxn"); +} + +TEST(AntimonyBasic, test_empty_rxn_kl) +{ + compareFileTranslation("empty_rxn_kl"); +} + +TEST(AntimonyBasic, test_empty_event) +{ + compareFileTranslation("empty_event"); +} + +TEST(AntimonyBasic, test_speciesConversionFactor) +{ + compareFileTranslation("speciesConversionFactor"); +} + +TEST(AntimonyBasic, test_speciesConversionFactor_empty) +{ + compareFileTranslation("speciesConversionFactor_empty"); +} + +TEST(AntimonyBasic, test_modelConversionFactor) +{ + compareFileTranslation("model_conversion_factor"); +} + +TEST(AntimonyBasic, test_boolean_priority) +{ + compareFileTranslation("boolean_priority"); +} + +TEST(AntimonyBasic, test_function_flattening_with_predefined_constants) +{ + setRemoveFunctionDefinitions(true); + compareFileTranslation("functions_with_constants"); + setRemoveFunctionDefinitions(false); +} + +TEST(AntimonyBasic, test_table_example) +{ + compareFileTranslation("table_example"); +} + diff --git a/src/test/TestAntimonyErrors.cpp b/src/test/TestAntimonyErrors.cpp index 51b6f44cc..5734aef0b 100644 --- a/src/test/TestAntimonyErrors.cpp +++ b/src/test/TestAntimonyErrors.cpp @@ -98,7 +98,7 @@ TEST(AntimonyErrors, non_ascii) freeAll(); clearPreviousLoads(); - ret = loadString("â€\na = 3"); + ret = loadString("\xe2\x80\na = 3"); EXPECT_TRUE(ret == -1); err = getLastError(); EXPECT_TRUE(err != NULL); @@ -439,3 +439,48 @@ TEST(AntimonyErrors, better_error_for_builtin_constants) testError("pi' = 3", "Error in model string, line 1: 'pi' is a reserved word in Antimony (the name of a built-in constant) and cannot be used as the name of a variable or other named element."); } +TEST(AntimonyErrors, no_negative_named_stoich1) +{ + testError("- n A -> B;", "Error in model string, line 1: Cannot set the variable stoichiometry 'n' to be negative. Either flip the sign of its value, give it a new name and value, or change the side of the reaction it's on."); +} + +TEST(AntimonyErrors, no_negative_named_stoich2) +{ + testError("A -> -n B;", "Error in model string, line 1: Cannot set the variable stoichiometry 'n' to be negative. Either flip the sign of its value, give it a new name and value, or change the side of the reaction it's on."); +} + +TEST(AntimonyErrors, no_negative_named_stoich3) +{ + testError("A - n B -> ;", "Error in model string, line 1: Cannot set the variable stoichiometry 'n' to be negative. Either flip the sign of its value, give it a new name and value, or change the side of the reaction it's on."); +} + +TEST(AntimonyErrors, no_negative_named_stoich4) +{ + testError("-> A - n B;", "Error in model string, line 1: Cannot set the variable stoichiometry 'n' to be negative. Either flip the sign of its value, give it a new name and value, or change the side of the reaction it's on."); +} + +TEST(AntimonyErrors, conversionFactor_must_be_single_variable) +{ + testError("S1.conversionFactor = 1000", "Error in model string, line 1: Cannot set the conversion factor of S1' to be '1000', because it must be set to reference an existing variable, i.e. 'S1.conversionFactor = k'."); +} + +TEST(AntimonyErrors, conversionFactor_must_not_be_negated) +{ + testError("S1.conversionFactor = -n", "Error in model string, line 1: Cannot set the conversion factor of S1' to be '-n', because it must be set to reference an existing variable, i.e. 'S1.conversionFactor = k'."); +} + +TEST(AntimonyErrors, conversionFactor_only_for_species) +{ + testError("compartment C; C.conversionFactor = cf", "Error in model string, line 1: Unable to set the conversion factor for C because that variable cannot be a species, and only species may have a conversion factor."); +} + +TEST(AntimonyErrors, conversionFactor_must_be_const) +{ + testError("var k; S1.conversionFactor = k;", "Error in model string, line 1: Unable to set the conversion factor for species 'S1' to 'k', because conversion factors must be constant."); +} + +TEST(AntimonyErrors, conversionFactor_must_be_const_model) +{ + testError("var k; model.conversionFactor = k;", "Error in model string, line 1: Unable to set the model's conversion factor to 'k', because conversion factors must be constant."); +} + diff --git a/src/test/TestAntimonyFBC.cpp b/src/test/TestAntimonyFBC.cpp index 98a9fa148..cd625293c 100644 --- a/src/test/TestAntimonyFBC.cpp +++ b/src/test/TestAntimonyFBC.cpp @@ -227,3 +227,24 @@ TEST(AntimonyFBC, test_charge) compareFBCAnt("charge"); compareFBCSBML("charge"); } +// A file-based round trip doesn't work well for the two tests below: an empty +// '.charge' and an empty '.conversionFactor' turns on FBC's namespace, but +// the roundtrip drops it again, as it's not actually used. +TEST(AntimonyFBC, test_charge_empty) +{ + int ret = loadString("S1.charge =;"); + EXPECT_TRUE(ret != -1); + string sbml(getSBMLString(NULL)); + EXPECT_EQ(sbml.find("charge"), string::npos); + freeAll(); +} + +TEST(AntimonyFBC, test_conversionFactor_empty) +{ + int ret = loadString("S1.conversionFactor =;"); + EXPECT_TRUE(ret != -1); + string sbml(getSBMLString(NULL)); + EXPECT_EQ(sbml.find("conversionFactor"), string::npos); + freeAll(); +} + diff --git a/src/test/TestAntimonyFlattening.cpp b/src/test/TestAntimonyFlattening.cpp index 5fbd18ac2..49511f4e4 100644 --- a/src/test/TestAntimonyFlattening.cpp +++ b/src/test/TestAntimonyFlattening.cpp @@ -93,16 +93,18 @@ void compareFileFlattening(const string& base) freeAll(); } -//This version of the function is used when Antimony flattening and SBML flattening are functionally -// equivalent, but differ in the specifics. -void compareFileFlatteningWithDifferences(const string& base) +//This version of the function is used when Antimony flattening and SBML flattening are functionally +// equivalent, but differ in the specifics. 'subdir' is the test-data subdirectory the files live in +// (with a trailing slash, or blank for test-data itself), and 'cc' is the component-connector string +// used when flattening still-qualified submodel variables into flat SBML ids. +void compareFileFlatteningWithDifferences(const string& base, const string& subdir = "from-libsbml/", const string& cc = "__") { clearPreviousLoads(); - g_registry.SetCC("__"); + g_registry.SetCC(cc); string dir(TestDataDirectory); - string filename = dir + "from-libsbml/" + base + ".xml"; - string antfile = dir + "from-libsbml/" + base + ".txt"; - string flatfile = dir + "from-libsbml/" + base + "_flat.xml"; + string filename = dir + subdir + base + ".xml"; + string antfile = dir + subdir + base + ".txt"; + string flatfile = dir + subdir + base + "_flat.xml"; //Get the Antimony-flattened version long ret = loadSBMLFile(filename.c_str()); @@ -396,27 +398,27 @@ TEST(AntimonyFlattening, test_test34) TEST(AntimonyFlattening, test_test35) { - compareFileFlattening("test35"); + compareFileFlatteningWithDifferences("test35"); } TEST(AntimonyFlattening, test_test36) { - compareFileFlattening("test36"); + compareFileFlatteningWithDifferences("test36"); } TEST(AntimonyFlattening, test_test37) { - compareFileFlattening("test37"); + compareFileFlatteningWithDifferences("test37"); } TEST(AntimonyFlattening, test_test38) { - compareFileFlattening("test38"); + compareFileFlatteningWithDifferences("test38"); } TEST(AntimonyFlattening, test_test39) { - compareFileFlatteningWithDifferences("test39"); + compareFileFlatteningWithDifferences("test39", "from-libsbml/", "_"); } TEST(AntimonyFlattening, test_test40) @@ -486,7 +488,7 @@ TEST(AntimonyFlattening, test_test52) TEST(AntimonyFlattening, test_test53) { - compareFileFlattening("test53"); + compareFileFlatteningWithDifferences("test53", "from-libsbml/", "_"); } TEST(AntimonyFlattening, test_test54) @@ -514,13 +516,11 @@ TEST(AntimonyFlattening, test_test57) //{ // compareFileFlatteningWithDifferences("test58"); //} -//END_TEST //TEST(AntimonyFlattening, test_test59) //{ // compareFileFlatteningWithDifferences("test59"); //} -//END_TEST TEST(AntimonyFlattening, test_test60) { @@ -531,4 +531,13 @@ TEST(AntimonyFlattening, test_test60) //{ // compareFileFlatteningWithDifferences("test61"); //} -//END_TEST + +TEST(AntimonyFlattening, test_deleted_kinetic_law) +{ + compareFileFlatteningWithDifferences("deleted_kinetic_law", "", "_"); +} + +TEST(AntimonyFlattening, test_deleted_species_reference) +{ + compareFileFlatteningWithDifferences("deleted_species_reference", "", "_"); +} diff --git a/src/test/TestAntimonyHierarchy.cpp b/src/test/TestAntimonyHierarchy.cpp index 0adab482b..e46fced45 100644 --- a/src/test/TestAntimonyHierarchy.cpp +++ b/src/test/TestAntimonyHierarchy.cpp @@ -51,7 +51,7 @@ void compareFileHierarchy(const string& base) elideMetaIds(doc); string sbmlFlat = writeSBMLToStdString(doc); string atosbml_nometa = elideMetaIdsFromSBMLstring(atosbml); - EXPECT_TRUE(atosbml_nometa == sbmlFlat); + EXPECT_STREQ(atosbml_nometa.c_str(), sbmlFlat.c_str()); ret = loadSBMLString(matching.c_str()); EXPECT_TRUE(ret != -1); @@ -68,6 +68,11 @@ void compareFileHierarchy(const string& base) freeAll(); } +TEST(AntimonyHierarchy, test_deleted_rate_rule) +{ + compareFileHierarchy("deleted_rate_rule"); +} + TEST(AntimonyHierarchy, test_hierarchy) { compareFileHierarchy("hierarchy"); @@ -113,6 +118,11 @@ TEST(AntimonyHierarchy, test_deleteDelay2) compareFileHierarchy("deleteDelay2"); } +TEST(AntimonyHierarchy, test_deleteEventAndAssignment) +{ + compareFileHierarchy("deleteEventAndAssignment"); +} + TEST(AntimonyHierarchy, test_deleteEventAssignment) { compareFileHierarchy("deleteEventAssignment"); @@ -337,3 +347,18 @@ TEST(AntimonyHierarchy, test_subsubport) { compareFileHierarchy("subsubport"); } + +TEST(AntimonyHierarchy, test_conversionFactor) +{ + compareFileHierarchy("paramconv_hierarchy"); +} + +TEST(AntimonyHierarchy, test_timeconv_raterule) +{ + compareFileHierarchy("timeconv_raterule"); +} + +TEST(AntimonyHierarchy, test_multi_init_overrides) +{ + compareFileHierarchy("multi_init_overrides"); +} diff --git a/src/test/TestAntimonyImport.cpp b/src/test/TestAntimonyImport.cpp index 36d1040cb..d49871f64 100644 --- a/src/test/TestAntimonyImport.cpp +++ b/src/test/TestAntimonyImport.cpp @@ -66,3 +66,13 @@ TEST(AntimonyImport, test_import_MODEL1504010000_url) { compareFileImport("oxphos_nad_redacted"); } + +// SBML Test Suite case 1155: a submodel event's delay is deleted via +// comp:Deletion, leaving the rest of the event (trigger and assignments) +// intact. The event (and the variables its assignments target) should be +// promoted to new top-level elements aliased back to the submodel with +// 'is', rather than reprinted as a submodel-qualified redefinition. +TEST(AntimonyImport, test_import_case01155) +{ + compareFileImport("case01155"); +} diff --git a/src/test/TestAntimonyNamedStoich.cpp b/src/test/TestAntimonyNamedStoich.cpp index c5271355d..c5012ed38 100644 --- a/src/test/TestAntimonyNamedStoich.cpp +++ b/src/test/TestAntimonyNamedStoich.cpp @@ -58,3 +58,13 @@ TEST(AntimonyNamedStoich, test_NamedStoichRate_file) { compareFileTranslation("namedstoich_rate"); } + +TEST(AntimonyNamedStoich, test_stoichiometries_with_same_name) +{ + compareFileTranslationWithDifferences("stoichiometries_with_same_name"); +} + +TEST(AntimonyNamedStoich, test_stoichiometries_with_same_name_in_multiple_reactions) +{ + compareFileTranslationWithDifferences("stoichiometries_with_same_name_in_multiple_reactions"); +} diff --git a/src/test/TestAntimonyUtil.cpp b/src/test/TestAntimonyUtil.cpp index 64864566b..90a319d7d 100644 --- a/src/test/TestAntimonyUtil.cpp +++ b/src/test/TestAntimonyUtil.cpp @@ -12,6 +12,8 @@ #include "stringx.h" #include +#include +#include #include "gtest/gtest.h" using namespace std; @@ -49,6 +51,39 @@ void compareFileTranslation(const string& base) freeAll(); } +void compareFileTranslationWithDifferences(const string& base) +{ + clearPreviousLoads(); + // load document + string dir(TestDataDirectory); + string filename = dir + base + ".txt"; + long ret = loadAntimonyFile(filename.c_str()); + EXPECT_TRUE(ret != -1); + char* atosbml = getCompSBMLString(NULL); + EXPECT_TRUE(atosbml != NULL); + + string sbmlfile = dir + base + ".xml"; + SBMLDocument* doc = readSBMLFromFile(sbmlfile.c_str()); + string matching = writeSBMLToStdString(doc); + EXPECT_STREQ(atosbml, matching.c_str()); + + //Now check the roundtripped version, comparing directly against the + //reference file's literal contents instead of reparsing it through + //Antimony (which would reorder declarations to match direct-parse order). + ret = loadSBMLString(matching.c_str()); + char* roundtrip = getAntimonyString(NULL); + EXPECT_TRUE(roundtrip != NULL); + + string rtfilename = dir + base + "_rt.txt"; + std::ifstream t(rtfilename.c_str()); + std::stringstream rtref; + rtref << t.rdbuf(); + EXPECT_STREQ(NormalizeLineEndings(rtref.str()).c_str(), NormalizeLineEndings(string(roundtrip)).c_str()); + + delete doc; + freeAll(); +} + void compareFileTranslationWithRenaming(const string& base) { clearPreviousLoads(); diff --git a/src/test/TestAntimonyUtil.h b/src/test/TestAntimonyUtil.h index 5f1e763e4..102fc6056 100644 --- a/src/test/TestAntimonyUtil.h +++ b/src/test/TestAntimonyUtil.h @@ -25,6 +25,18 @@ void compareFileTranslation(const std::string& base); // .txt, then converts back to SBML and confirms it round-trips. void compareFileTranslationWithRenaming(const std::string& base); +// Like compareFileTranslation, but for the final round-trip check, compares +// the SBML-loaded antimony text directly against the literal contents of +// _rt.txt instead of reparsing that file through Antimony and +// reprinting it. Use this when the SBML path and a direct top-to-bottom +// Antimony parse are expected to produce the same content but in a +// different variable declaration order (e.g. because SBML visits +// Parameters before Reactions, while Antimony declares symbols in the +// order they're first mentioned in a reaction), so reparsing the reference +// file would just reintroduce the direct-parse order instead of confirming +// a match. +void compareFileTranslationWithDifferences(const std::string& base); + // Loads the given antimony string, compares its SBML translation against // the SBML in the given file (relative to TestDataDirectory). void compareStringTranslation(const std::string& antimony, const std::string& sbml); diff --git a/src/test/test-data/BIOMD0000000118.txt b/src/test/test-data/BIOMD0000000118.txt index 7fdfd5abd..ca8476401 100644 --- a/src/test/test-data/BIOMD0000000118.txt +++ b/src/test/test-data/BIOMD0000000118.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 function GAMMA(VV, theta, sigma) 1/(1 + exp(-(VV - theta)/sigma)); end diff --git a/src/test/test-data/BIOMD0000000696.txt b/src/test/test-data/BIOMD0000000696.txt index 3413a2074..0b2780155 100644 --- a/src/test/test-data/BIOMD0000000696.txt +++ b/src/test/test-data/BIOMD0000000696.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model *Boada2016___Incoherent_type_1_feed_forward_loop__I1_FFL() // Compartments and Species: diff --git a/src/test/test-data/SBO_compartment_rt.txt b/src/test/test-data/SBO_compartment_rt.txt index 48f56f3f5..a4cdc453a 100644 --- a/src/test/test-data/SBO_compartment_rt.txt +++ b/src/test/test-data/SBO_compartment_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: compartment a; diff --git a/src/test/test-data/SBO_event_rt.txt b/src/test/test-data/SBO_event_rt.txt index 8993cbf08..d673f8282 100644 --- a/src/test/test-data/SBO_event_rt.txt +++ b/src/test/test-data/SBO_event_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Events: E0: at time > 3: b = 4; diff --git a/src/test/test-data/SBO_function_rt.txt b/src/test/test-data/SBO_function_rt.txt index 0ef2b11a4..0a303f884 100644 --- a/src/test/test-data/SBO_function_rt.txt +++ b/src/test/test-data/SBO_function_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 function foo() 3; end diff --git a/src/test/test-data/SBO_localvar_rt.txt b/src/test/test-data/SBO_localvar_rt.txt index 8c5d8920d..0243a7d8d 100644 --- a/src/test/test-data/SBO_localvar_rt.txt +++ b/src/test/test-data/SBO_localvar_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model *foo() // Variable initializations: diff --git a/src/test/test-data/SBO_module_rt.txt b/src/test/test-data/SBO_module_rt.txt index 10ac30da7..71988e9f6 100644 --- a/src/test/test-data/SBO_module_rt.txt +++ b/src/test/test-data/SBO_module_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model *foo() end diff --git a/src/test/test-data/SBO_param2_rt.txt b/src/test/test-data/SBO_param2_rt.txt index f4cf5d145..f3733a7c9 100644 --- a/src/test/test-data/SBO_param2_rt.txt +++ b/src/test/test-data/SBO_param2_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/SBO_param_rt.txt b/src/test/test-data/SBO_param_rt.txt index 922c08df0..437022451 100644 --- a/src/test/test-data/SBO_param_rt.txt +++ b/src/test/test-data/SBO_param_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = ; diff --git a/src/test/test-data/SBO_reaction_rt.txt b/src/test/test-data/SBO_reaction_rt.txt index 00a8ddc83..6c2ade16f 100644 --- a/src/test/test-data/SBO_reaction_rt.txt +++ b/src/test/test-data/SBO_reaction_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species A; diff --git a/src/test/test-data/SBO_species_rt.txt b/src/test/test-data/SBO_species_rt.txt index d2e0401ac..4d9446f81 100644 --- a/src/test/test-data/SBO_species_rt.txt +++ b/src/test/test-data/SBO_species_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species a; diff --git a/src/test/test-data/SBO_submodel_rt.txt b/src/test/test-data/SBO_submodel_rt.txt index 853a5916e..bf0238236 100644 --- a/src/test/test-data/SBO_submodel_rt.txt +++ b/src/test/test-data/SBO_submodel_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model foo() end diff --git a/src/test/test-data/SBO_submodel_shadowed_rt.txt b/src/test/test-data/SBO_submodel_shadowed_rt.txt index a8fee5e62..b55fdcea1 100644 --- a/src/test/test-data/SBO_submodel_shadowed_rt.txt +++ b/src/test/test-data/SBO_submodel_shadowed_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model foo() // Variable initializations: diff --git a/src/test/test-data/algrule_id_rt.txt b/src/test/test-data/algrule_id_rt.txt index 980c4144a..5b930257b 100644 --- a/src/test/test-data/algrule_id_rt.txt +++ b/src/test/test-data/algrule_id_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Algebraic Rules: alg1: 0 = x - 2; diff --git a/src/test/test-data/algrule_idname_rt.txt b/src/test/test-data/algrule_idname_rt.txt index 44e20c210..1e219655f 100644 --- a/src/test/test-data/algrule_idname_rt.txt +++ b/src/test/test-data/algrule_idname_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Algebraic Rules: alg1: 0 = x - 2; diff --git a/src/test/test-data/algrule_rt.txt b/src/test/test-data/algrule_rt.txt index aff53f18d..8c057c32f 100644 --- a/src/test/test-data/algrule_rt.txt +++ b/src/test/test-data/algrule_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Algebraic Rules: _alg0: 0 = x - 2; diff --git a/src/test/test-data/autopromoted_units_rt.txt b/src/test/test-data/autopromoted_units_rt.txt index f0a12cc1a..aa4335073 100644 --- a/src/test/test-data/autopromoted_units_rt.txt +++ b/src/test/test-data/autopromoted_units_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model foo(p) // Variable initializations: diff --git a/src/test/test-data/boolean_priority.txt b/src/test/test-data/boolean_priority.txt new file mode 100644 index 000000000..996cd2b57 --- /dev/null +++ b/src/test/test-data/boolean_priority.txt @@ -0,0 +1,5 @@ +model *case01286() + E0: at time > 5.5, priority = true: p1 = 10; + E1: at time > 5.5, priority = false: p1 = 20; + p1 = 5; +end diff --git a/src/test/test-data/boolean_priority.xml b/src/test/test-data/boolean_priority.xml new file mode 100644 index 000000000..7392a4df7 --- /dev/null +++ b/src/test/test-data/boolean_priority.xml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + time + 5.5 + + + + + + + + + + + + 10 + + + + + + + + + + time + 5.5 + + + + + + + + + + + + 20 + + + + + + + diff --git a/src/test/test-data/boolean_priority_rt.txt b/src/test/test-data/boolean_priority_rt.txt new file mode 100644 index 000000000..bbf9bdc32 --- /dev/null +++ b/src/test/test-data/boolean_priority_rt.txt @@ -0,0 +1,13 @@ +// Created by libAntimony v3.2.0 +model *case01286() + + // Events: + E0: at time > 5.5, priority = true: p1 = 10; + E1: at time > 5.5, priority = false: p1 = 20; + + // Variable initializations: + p1 = 5; + + // Other declarations: + var p1; +end \ No newline at end of file diff --git a/src/test/test-data/case01155.txt b/src/test/test-data/case01155.txt new file mode 100644 index 000000000..695fde795 --- /dev/null +++ b/src/test/test-data/case01155.txt @@ -0,0 +1,18 @@ +model moddef1() + t1 = 1; + t2 = 1; + var t1, t2; + + E0: at 0.1/time after time > 0.31: t1 = 3.3, t2 = 5.5; +end + +model *case01155() + sub1: moddef1(); + sub1.E0 is sub1_E0; + sub1.t1 is sub1_t1; + sub1.t2 is sub1_t2; + + sub1_E0: at time > 0.31: sub1_t1 = 3.3, sub1_t2 = 5.5; +end + +case01155 is "case01155"; diff --git a/src/test/test-data/case01155.xml b/src/test/test-data/case01155.xml new file mode 100644 index 000000000..073ba0988 --- /dev/null +++ b/src/test/test-data/case01155.xml @@ -0,0 +1,54 @@ + + + + + + + + + + + + + + + + + + + + + + + + time + 0.31 + + + + + + + + 0.1 + time + + + + + + + 3.3 + + + + + 5.5 + + + + + + + + diff --git a/src/test/test-data/coefficientOfVariation_rt.txt b/src/test/test-data/coefficientOfVariation_rt.txt index cbdc7c266..2c5e9d73d 100644 --- a/src/test/test-data/coefficientOfVariation_rt.txt +++ b/src/test/test-data/coefficientOfVariation_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = ; diff --git a/src/test/test-data/confidenceInterval_rt.txt b/src/test/test-data/confidenceInterval_rt.txt index 13ff8633b..93a2046ac 100644 --- a/src/test/test-data/confidenceInterval_rt.txt +++ b/src/test/test-data/confidenceInterval_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = ; diff --git a/src/test/test-data/created_element_rt.txt b/src/test/test-data/created_element_rt.txt index e0936b32c..91ece1e6f 100644 --- a/src/test/test-data/created_element_rt.txt +++ b/src/test/test-data/created_element_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/created_model_parts_rt.txt b/src/test/test-data/created_model_parts_rt.txt index 56c47ae58..04bd37fb4 100644 --- a/src/test/test-data/created_model_parts_rt.txt +++ b/src/test/test-data/created_model_parts_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model *foo() // Variable initializations: diff --git a/src/test/test-data/created_model_rt.txt b/src/test/test-data/created_model_rt.txt index 56c47ae58..04bd37fb4 100644 --- a/src/test/test-data/created_model_rt.txt +++ b/src/test/test-data/created_model_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model *foo() // Variable initializations: diff --git a/src/test/test-data/creator_blank_model_rt.txt b/src/test/test-data/creator_blank_model_rt.txt index e520558ec..5319430d1 100644 --- a/src/test/test-data/creator_blank_model_rt.txt +++ b/src/test/test-data/creator_blank_model_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model *foo() // Variable initializations: diff --git a/src/test/test-data/creator_one_element_rt.txt b/src/test/test-data/creator_one_element_rt.txt index 5f6b2d6dc..04cbd3674 100644 --- a/src/test/test-data/creator_one_element_rt.txt +++ b/src/test/test-data/creator_one_element_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/creator_one_model_rt.txt b/src/test/test-data/creator_one_model_rt.txt index cc209dda4..4d5592b7c 100644 --- a/src/test/test-data/creator_one_model_rt.txt +++ b/src/test/test-data/creator_one_model_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model *foo() // Variable initializations: diff --git a/src/test/test-data/creator_two_model_rt.txt b/src/test/test-data/creator_two_model_rt.txt index 042e8a6c6..15b618055 100644 --- a/src/test/test-data/creator_two_model_rt.txt +++ b/src/test/test-data/creator_two_model_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model *foo() // Variable initializations: diff --git a/src/test/test-data/credibleInterval_rt.txt b/src/test/test-data/credibleInterval_rt.txt index 1f32af253..8906daa04 100644 --- a/src/test/test-data/credibleInterval_rt.txt +++ b/src/test/test-data/credibleInterval_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = ; x = ; diff --git a/src/test/test-data/default_compartment.txt b/src/test/test-data/default_compartment.txt index 05fe5d836..ea548a13c 100644 --- a/src/test/test-data/default_compartment.txt +++ b/src/test/test-data/default_compartment.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model *def_comp() // Compartments and Species: diff --git a/src/test/test-data/defined_complicated_unit_rt.txt b/src/test/test-data/defined_complicated_unit_rt.txt index a2546a6b0..d93381395 100644 --- a/src/test/test-data/defined_complicated_unit_rt.txt +++ b/src/test/test-data/defined_complicated_unit_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3; a has kph; diff --git a/src/test/test-data/defined_unit_rt.txt b/src/test/test-data/defined_unit_rt.txt index 4d94a8710..9b88417a2 100644 --- a/src/test/test-data/defined_unit_rt.txt +++ b/src/test/test-data/defined_unit_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3; a has mmol; diff --git a/src/test/test-data/deleteDelay.xml b/src/test/test-data/deleteDelay.xml index b1b8dcf7f..4c2ee3231 100644 --- a/src/test/test-data/deleteDelay.xml +++ b/src/test/test-data/deleteDelay.xml @@ -35,12 +35,12 @@ - + 0 - + 0 diff --git a/src/test/test-data/deleteDelay2.xml b/src/test/test-data/deleteDelay2.xml index 03db61108..ffdced627 100644 --- a/src/test/test-data/deleteDelay2.xml +++ b/src/test/test-data/deleteDelay2.xml @@ -46,12 +46,12 @@ - + 0 - + 0 @@ -79,12 +79,12 @@ - + 0 - + 0 diff --git a/src/test/test-data/deleteDelay2_rt.txt b/src/test/test-data/deleteDelay2_rt.txt index 34d552089..d44591891 100644 --- a/src/test/test-data/deleteDelay2_rt.txt +++ b/src/test/test-data/deleteDelay2_rt.txt @@ -1,25 +1,26 @@ -//Created by libAntimony v2.5 +// Created by libAntimony v3.2.0 model foo() // Variable initializations: Y1 = ; DELAY1 = ; PRIORITY1 = ; - Q1 = ; Z1 = ; + Q1 = ; y2 = ; delay2 = ; priority2 = ; - q2 = ; z2 = ; + q2 = ; + + // Other declarations: + var Z1, Q1, z2, q2; + const Y1, DELAY1, PRIORITY1, y2, delay2, priority2; // Events: E1: at DELAY1 after Y1 > 3, priority = PRIORITY1: Z1 = 0, Q1 = 0; e2: at delay2 after y2 > 3, priority = priority2: z2 = 0, q2 = 0; - //Other declarations: - var Q1, Z1, q2, z2; - const Y1, DELAY1, PRIORITY1, y2, delay2, priority2; end model *bar() @@ -27,6 +28,6 @@ model *bar() // Sub-modules, and any changes to those submodules: A: foo(); - //Deleted elements from submodels: + // Deleted elements from submodels: delete A.DELAY1; end diff --git a/src/test/test-data/deleteDelay_rt.txt b/src/test/test-data/deleteDelay_rt.txt index 1840da0c7..872ad8024 100644 --- a/src/test/test-data/deleteDelay_rt.txt +++ b/src/test/test-data/deleteDelay_rt.txt @@ -1,18 +1,18 @@ -//Created by libAntimony v2.5 +// Created by libAntimony v3.2.0 model foo() // Variable initializations: Y1 = ; DELAY1 = ; - Q1 = ; Z1 = ; + Q1 = ; + // Other declarations: + var Z1, Q1; + const Y1, DELAY1; // Events: E1: at DELAY1 after Y1 > 3: Z1 = 0, Q1 = 0; - //Other declarations: - var Q1, Z1; - const Y1, DELAY1; end model *bar() @@ -20,6 +20,6 @@ model *bar() // Sub-modules, and any changes to those submodules: A: foo(); - //Deleted elements from submodels: + // Deleted elements from submodels: delete A.DELAY1; end diff --git a/src/test/test-data/deleteEventAndAssignment.txt b/src/test/test-data/deleteEventAndAssignment.txt new file mode 100644 index 000000000..bc13179d4 --- /dev/null +++ b/src/test/test-data/deleteEventAndAssignment.txt @@ -0,0 +1,9 @@ +// Created by libAntimony v3.2.0 +model foo() + E1: at Y1 > 3: Z1 = 0; +end + +model *bar() + A: foo(); + delete A.E1, A.Z1; +end diff --git a/src/test/test-data/deleteEventAndAssignment.xml b/src/test/test-data/deleteEventAndAssignment.xml new file mode 100644 index 000000000..393809fce --- /dev/null +++ b/src/test/test-data/deleteEventAndAssignment.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + Y1 + 3 + + + + + + + 0 + + + + + + + + diff --git a/src/test/test-data/deleteEventAndAssignment_rt.txt b/src/test/test-data/deleteEventAndAssignment_rt.txt new file mode 100644 index 000000000..9d769866b --- /dev/null +++ b/src/test/test-data/deleteEventAndAssignment_rt.txt @@ -0,0 +1,23 @@ +// Created by libAntimony v3.2.0 +model foo() + + // Events: + E1: at Y1 > 3: Z1 = 0; + + // Variable initializations: + Y1 = ; + Z1 = ; + + // Other declarations: + var Z1; + const Y1; +end + +model *bar() + + // Sub-modules, and any changes to those submodules: + A: foo(); + + // Deleted elements from submodels: + delete A.E1, A.Z1; +end diff --git a/src/test/test-data/deleteEventAssignment.xml b/src/test/test-data/deleteEventAssignment.xml index 74aacd875..014d2c873 100644 --- a/src/test/test-data/deleteEventAssignment.xml +++ b/src/test/test-data/deleteEventAssignment.xml @@ -1,4 +1,5 @@ + @@ -29,12 +30,12 @@ - + 0 - + 0 diff --git a/src/test/test-data/deleteEventAssignment2.xml b/src/test/test-data/deleteEventAssignment2.xml index df0dfdc9e..ab0764209 100644 --- a/src/test/test-data/deleteEventAssignment2.xml +++ b/src/test/test-data/deleteEventAssignment2.xml @@ -1,4 +1,5 @@ + @@ -46,12 +47,12 @@ - + 0 - + 0 @@ -79,12 +80,12 @@ - + 0 - + 0 diff --git a/src/test/test-data/deleteEventAssignment2_rt.txt b/src/test/test-data/deleteEventAssignment2_rt.txt index 43ae6ea29..b197ee619 100644 --- a/src/test/test-data/deleteEventAssignment2_rt.txt +++ b/src/test/test-data/deleteEventAssignment2_rt.txt @@ -1,25 +1,26 @@ -//Created by libAntimony v2.5 +// Created by libAntimony v3.2.0 model foo() // Variable initializations: Y1 = ; DELAY1 = ; PRIORITY1 = ; - Q1 = ; Z1 = ; + Q1 = ; y2 = ; delay2 = ; priority2 = ; - q2 = ; z2 = ; + q2 = ; + + // Other declarations: + var Z1, Q1, z2, q2; + const Y1, DELAY1, PRIORITY1, y2, delay2, priority2; // Events: E1: at DELAY1 after Y1 > 3, priority = PRIORITY1: Z1 = 0, Q1 = 0; e2: at delay2 after y2 > 3, priority = priority2: z2 = 0, q2 = 0; - //Other declarations: - var Q1, Z1, q2, z2; - const Y1, DELAY1, PRIORITY1, y2, delay2, priority2; end model *bar() @@ -27,6 +28,6 @@ model *bar() // Sub-modules, and any changes to those submodules: A: foo(); - //Deleted elements from submodels: + // Deleted elements from submodels: delete A.Z1; end diff --git a/src/test/test-data/deleteEventAssignment3.xml b/src/test/test-data/deleteEventAssignment3.xml index 393809fce..07329ed17 100644 --- a/src/test/test-data/deleteEventAssignment3.xml +++ b/src/test/test-data/deleteEventAssignment3.xml @@ -4,7 +4,6 @@ - diff --git a/src/test/test-data/deleteEventAssignment3_rt.txt b/src/test/test-data/deleteEventAssignment3_rt.txt index 2d4d2608a..37e5928e6 100644 --- a/src/test/test-data/deleteEventAssignment3_rt.txt +++ b/src/test/test-data/deleteEventAssignment3_rt.txt @@ -19,5 +19,5 @@ model *bar() A: foo(); //Deleted elements from submodels: - delete A.E1, A.Z1; + delete A.Z1; end diff --git a/src/test/test-data/deleteEventAssignment4.xml b/src/test/test-data/deleteEventAssignment4.xml index af087c918..977739668 100644 --- a/src/test/test-data/deleteEventAssignment4.xml +++ b/src/test/test-data/deleteEventAssignment4.xml @@ -1,4 +1,5 @@ + @@ -29,12 +30,12 @@ - + 0 - + 0 diff --git a/src/test/test-data/deleteEventAssignment4_rt.txt b/src/test/test-data/deleteEventAssignment4_rt.txt index f961280c8..b9745e27e 100644 --- a/src/test/test-data/deleteEventAssignment4_rt.txt +++ b/src/test/test-data/deleteEventAssignment4_rt.txt @@ -1,16 +1,16 @@ -//Created by libAntimony v2.5 +// Created by libAntimony v3.2.0 model foo() + // Events: + E1: at Y1 > 3: Z1 = 0, Q1 = 0; + // Variable initializations: Y1 = ; - Q1 = ; Z1 = ; + Q1 = ; - // Events: - E1: at Y1 > 3: Z1 = 0, Q1 = 0; - - //Other declarations: - var Q1, Z1; + // Other declarations: + var Z1, Q1; const Y1; end @@ -19,6 +19,6 @@ model *bar() // Sub-modules, and any changes to those submodules: A: foo(); - //Deleted elements from submodels: + // Deleted elements from submodels: delete A.Q1; end diff --git a/src/test/test-data/deleteEventAssignment5.xml b/src/test/test-data/deleteEventAssignment5.xml index 3c458c3aa..160c38207 100644 --- a/src/test/test-data/deleteEventAssignment5.xml +++ b/src/test/test-data/deleteEventAssignment5.xml @@ -1,4 +1,5 @@ + @@ -31,14 +32,14 @@ - + - q + z - + - z + q diff --git a/src/test/test-data/deleteEventAssignment5_rt.txt b/src/test/test-data/deleteEventAssignment5_rt.txt index 0cbd7e160..0c29ca8d5 100644 --- a/src/test/test-data/deleteEventAssignment5_rt.txt +++ b/src/test/test-data/deleteEventAssignment5_rt.txt @@ -1,19 +1,19 @@ -//Created by libAntimony v2.5 +// Created by libAntimony v3.2.0 model foo() + // Events: + E1: at Y1 > 3: Z1 = z, Q1 = q; + // Variable initializations: Y1 = ; - Q1 = ; - q = ; Z1 = ; z = ; + Q1 = ; + q = ; - // Events: - E1: at Y1 > 3: Z1 = z, Q1 = q; - - //Other declarations: - var Q1, Z1; - const Y1, q, z; + // Other declarations: + var Z1, Q1; + const Y1, z, q; end model *bar() @@ -21,6 +21,6 @@ model *bar() // Sub-modules, and any changes to those submodules: A: foo(); - //Deleted elements from submodels: + // Deleted elements from submodels: delete A.z; end diff --git a/src/test/test-data/deleteEventAssignment_rt.txt b/src/test/test-data/deleteEventAssignment_rt.txt index 416625f56..b78aeb789 100644 --- a/src/test/test-data/deleteEventAssignment_rt.txt +++ b/src/test/test-data/deleteEventAssignment_rt.txt @@ -1,16 +1,16 @@ -//Created by libAntimony v2.5 +// Created by libAntimony v3.2.0 model foo() + // Events: + E1: at Y1 > 3: Z1 = 0, Q1 = 0; + // Variable initializations: Y1 = ; - Q1 = ; Z1 = ; + Q1 = ; - // Events: - E1: at Y1 > 3: Z1 = 0, Q1 = 0; - - //Other declarations: - var Q1, Z1; + // Other declarations: + var Z1, Q1; const Y1; end @@ -19,6 +19,6 @@ model *bar() // Sub-modules, and any changes to those submodules: A: foo(); - //Deleted elements from submodels: + // Deleted elements from submodels: delete A.Z1; end diff --git a/src/test/test-data/deletePriority.xml b/src/test/test-data/deletePriority.xml index a61503943..50a91db9e 100644 --- a/src/test/test-data/deletePriority.xml +++ b/src/test/test-data/deletePriority.xml @@ -1,4 +1,5 @@ + diff --git a/src/test/test-data/deletePriority2.xml b/src/test/test-data/deletePriority2.xml index 696f8fb6d..845106ab0 100644 --- a/src/test/test-data/deletePriority2.xml +++ b/src/test/test-data/deletePriority2.xml @@ -1,4 +1,5 @@ + @@ -46,12 +47,12 @@ - + 0 - + 0 @@ -79,12 +80,12 @@ - + 0 - + 0 diff --git a/src/test/test-data/deletePriority2_rt.txt b/src/test/test-data/deletePriority2_rt.txt index 95b1cd058..f38ec2aaa 100644 --- a/src/test/test-data/deletePriority2_rt.txt +++ b/src/test/test-data/deletePriority2_rt.txt @@ -1,25 +1,27 @@ -//Created by libAntimony v2.5 +// Created by libAntimony v3.2.0 model foo() // Variable initializations: Y1 = ; DELAY1 = ; PRIORITY1 = ; - Q1 = ; Z1 = ; + Q1 = ; y2 = ; delay2 = ; priority2 = ; - q2 = ; z2 = ; + q2 = ; + + // Other declarations: + var Z1, Q1, z2, q2; + const Y1, DELAY1, PRIORITY1, y2, delay2, priority2; + // Events: E1: at DELAY1 after Y1 > 3, priority = PRIORITY1: Z1 = 0, Q1 = 0; e2: at delay2 after y2 > 3, priority = priority2: z2 = 0, q2 = 0; - //Other declarations: - var Q1, Z1, q2, z2; - const Y1, DELAY1, PRIORITY1, y2, delay2, priority2; end model *bar() @@ -27,6 +29,6 @@ model *bar() // Sub-modules, and any changes to those submodules: A: foo(); - //Deleted elements from submodels: + // Deleted elements from submodels: delete A.PRIORITY1; end diff --git a/src/test/test-data/deletePriority_rt.txt b/src/test/test-data/deletePriority_rt.txt index f3816acd3..e401d0608 100644 --- a/src/test/test-data/deletePriority_rt.txt +++ b/src/test/test-data/deletePriority_rt.txt @@ -1,4 +1,4 @@ -//Created by libAntimony v2.5 +// Created by libAntimony v3.2.0 model foo() // Events: @@ -9,7 +9,7 @@ model foo() PRIORITY1 = ; Z1 = ; - //Other declarations: + // Other declarations: var Z1; const Y1, PRIORITY1; end @@ -19,6 +19,6 @@ model *bar() // Sub-modules, and any changes to those submodules: A: foo(); - //Deleted elements from submodels: + // Deleted elements from submodels: delete A.PRIORITY1; end diff --git a/src/test/test-data/deleteTrigger.xml b/src/test/test-data/deleteTrigger.xml index e706031bb..ccdea451d 100644 --- a/src/test/test-data/deleteTrigger.xml +++ b/src/test/test-data/deleteTrigger.xml @@ -1,4 +1,5 @@ + @@ -29,12 +30,12 @@ - + 0 - + 0 diff --git a/src/test/test-data/deleteTrigger_rt.txt b/src/test/test-data/deleteTrigger_rt.txt index c123d2fcc..ae37e0aa5 100644 --- a/src/test/test-data/deleteTrigger_rt.txt +++ b/src/test/test-data/deleteTrigger_rt.txt @@ -1,19 +1,16 @@ -//Created by libAntimony v2.5 +// Created by libAntimony v3.2.0 model foo() + // Events: + E1: at Y1 > 3: Z1 = 0, Q1 = 0; + // Variable initializations: - // Have to put E1 first here because otherwise the order of variables - // gets changed in the roundtripped version. - E1 = ; Y1 = ; - Q1 = ; Z1 = ; + Q1 = ; - // Events: - E1: at Y1 > 3: Z1 = 0, Q1 = 0; - - //Other declarations: - var Q1, Z1; + // Other declarations: + var Z1, Q1; const Y1; end @@ -22,6 +19,6 @@ model *bar() // Sub-modules, and any changes to those submodules: A: foo(); - //Deleted elements from submodels: + // Deleted elements from submodels: delete A.E1, A.Y1; end diff --git a/src/test/test-data/deleted_kinetic_law.txt b/src/test/test-data/deleted_kinetic_law.txt new file mode 100644 index 000000000..7179f40bd --- /dev/null +++ b/src/test/test-data/deleted_kinetic_law.txt @@ -0,0 +1,31 @@ +// Created by libAntimony v3.2.0 +model rxn() + + // Compartments and Species: + species A, B; + + // Reactions: + J0: A -> B; k1*A; + + // Species initializations: + A = ; + B = ; + + // Variable initializations: + k1 = ; + + // Other declarations: + const k1; +end + +model *top() + + // Sub-modules, and any changes to those submodules: + A: rxn(); + A.J0 is A_J0; + A.A is A_A; + A.B is A_B; + + // Reactions: + A_J0: A_A -> A_B; ; +end diff --git a/src/test/test-data/deleted_kinetic_law.xml b/src/test/test-data/deleted_kinetic_law.xml new file mode 100644 index 000000000..78fba777a --- /dev/null +++ b/src/test/test-data/deleted_kinetic_law.xml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + A + + + + + + + + diff --git a/src/test/test-data/deleted_kinetic_law_flat.xml b/src/test/test-data/deleted_kinetic_law_flat.xml new file mode 100644 index 000000000..c43ad6d2c --- /dev/null +++ b/src/test/test-data/deleted_kinetic_law_flat.xml @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/test-data/deleted_rate_rule.txt b/src/test/test-data/deleted_rate_rule.txt new file mode 100644 index 000000000..ee4dbc013 --- /dev/null +++ b/src/test/test-data/deleted_rate_rule.txt @@ -0,0 +1,10 @@ +model sub(x) + x = 3 + x' = 1 +end + +model deleted_rate_rule() + A: sub(x) + x' = + x = 5 +end diff --git a/src/test/test-data/deleted_rate_rule.xml b/src/test/test-data/deleted_rate_rule.xml new file mode 100644 index 000000000..8b1eb8786 --- /dev/null +++ b/src/test/test-data/deleted_rate_rule.xml @@ -0,0 +1,37 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + diff --git a/src/test/test-data/deleted_rate_rule_rt.txt b/src/test/test-data/deleted_rate_rule_rt.txt new file mode 100644 index 000000000..36ff9f8c6 --- /dev/null +++ b/src/test/test-data/deleted_rate_rule_rt.txt @@ -0,0 +1,24 @@ +// Created by libAntimony v3.2.0 +model sub(x) + + // Rate Rules: + x' = 1; + + // Variable initializations: + x = 3; + + // Other declarations: + var x; +end + +model *deleted_rate_rule() + + // Sub-modules, and any changes to those submodules: + A: sub(x); + + // Rate Rules: + x' = ; + + // Variable initializations: + x = 5; +end diff --git a/src/test/test-data/deleted_species_reference.txt b/src/test/test-data/deleted_species_reference.txt new file mode 100644 index 000000000..bd3b6f1d0 --- /dev/null +++ b/src/test/test-data/deleted_species_reference.txt @@ -0,0 +1,31 @@ +// Created by libAntimony v3.2.0 +model rxn() + + // Compartments and Species: + species A, B; + + // Reactions: + J0: A -> B; k1; + + // Species initializations: + A = ; + B = ; + + // Variable initializations: + k1 = ; + + // Other declarations: + const k1; +end + +model *top() + + // Sub-modules, and any changes to those submodules: + A: rxn(); + A.J0 is A_J0; + A.k1 is A_k1; + A.B is A_B; + + // Reactions: + A_J0: -> A_B; A_k1; +end diff --git a/src/test/test-data/deleted_species_reference.xml b/src/test/test-data/deleted_species_reference.xml new file mode 100644 index 000000000..42b5519ca --- /dev/null +++ b/src/test/test-data/deleted_species_reference.xml @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k1 + + + + + + + diff --git a/src/test/test-data/deleted_species_reference_flat.xml b/src/test/test-data/deleted_species_reference_flat.xml new file mode 100644 index 000000000..b4e6f1330 --- /dev/null +++ b/src/test/test-data/deleted_species_reference_flat.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + + + + + + + + + + + A_k1 + + + + + + diff --git a/src/test/test-data/distribution_rt.txt b/src/test/test-data/distribution_rt.txt index 9b4d81cce..2f9f26aad 100644 --- a/src/test/test-data/distribution_rt.txt +++ b/src/test/test-data/distribution_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = ; x = ; diff --git a/src/test/test-data/empty_event.txt b/src/test/test-data/empty_event.txt new file mode 100644 index 000000000..6daf20e1a --- /dev/null +++ b/src/test/test-data/empty_event.txt @@ -0,0 +1 @@ +at time > 5.5: ; \ No newline at end of file diff --git a/src/test/test-data/empty_event.xml b/src/test/test-data/empty_event.xml new file mode 100644 index 000000000..2cc7a820b --- /dev/null +++ b/src/test/test-data/empty_event.xml @@ -0,0 +1,19 @@ + + + + + + + + + + + time + 5.5 + + + + + + + diff --git a/src/test/test-data/empty_event_rt.txt b/src/test/test-data/empty_event_rt.txt new file mode 100644 index 000000000..1f87c49a1 --- /dev/null +++ b/src/test/test-data/empty_event_rt.txt @@ -0,0 +1,3 @@ +// Created by libAntimony v3.2.0 +// Events: +_E0: at time > 5.5: ; \ No newline at end of file diff --git a/src/test/test-data/empty_rxn.txt b/src/test/test-data/empty_rxn.txt new file mode 100644 index 000000000..ddfc01e80 --- /dev/null +++ b/src/test/test-data/empty_rxn.txt @@ -0,0 +1 @@ +->; diff --git a/src/test/test-data/empty_rxn.xml b/src/test/test-data/empty_rxn.xml new file mode 100644 index 000000000..464da3e33 --- /dev/null +++ b/src/test/test-data/empty_rxn.xml @@ -0,0 +1,9 @@ + + + + + + + + + diff --git a/src/test/test-data/empty_rxn_kl.txt b/src/test/test-data/empty_rxn_kl.txt new file mode 100644 index 000000000..f4b53ac59 --- /dev/null +++ b/src/test/test-data/empty_rxn_kl.txt @@ -0,0 +1 @@ +->;1.2 diff --git a/src/test/test-data/empty_rxn_kl.xml b/src/test/test-data/empty_rxn_kl.xml new file mode 100644 index 000000000..414a763fe --- /dev/null +++ b/src/test/test-data/empty_rxn_kl.xml @@ -0,0 +1,15 @@ + + + + + + + + + 1.2 + + + + + + diff --git a/src/test/test-data/empty_rxn_kl_rt.txt b/src/test/test-data/empty_rxn_kl_rt.txt new file mode 100644 index 000000000..88445bf81 --- /dev/null +++ b/src/test/test-data/empty_rxn_kl_rt.txt @@ -0,0 +1,3 @@ +// Created by libAntimony v3.2.0 +// Reactions: +_J0: -> ; 1.2; \ No newline at end of file diff --git a/src/test/test-data/empty_rxn_rt.txt b/src/test/test-data/empty_rxn_rt.txt new file mode 100644 index 000000000..d1709e55c --- /dev/null +++ b/src/test/test-data/empty_rxn_rt.txt @@ -0,0 +1,3 @@ +// Created by libAntimony v3.2.0 +// Reactions: +_J0: -> ; ; \ No newline at end of file diff --git a/src/test/test-data/encodes_rt.txt b/src/test/test-data/encodes_rt.txt index 128e42494..aef5d66ae 100644 --- a/src/test/test-data/encodes_rt.txt +++ b/src/test/test-data/encodes_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/event_nonBoolean_rt.txt b/src/test/test-data/event_nonBoolean_rt.txt index 8ccd9b2c9..018df3901 100644 --- a/src/test/test-data/event_nonBoolean_rt.txt +++ b/src/test/test-data/event_nonBoolean_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Events: _E0: at 5: x = 3; diff --git a/src/test/test-data/externalParameter1_rt.txt b/src/test/test-data/externalParameter1_rt.txt index 6e8fe2639..1cb7227ea 100644 --- a/src/test/test-data/externalParameter1_rt.txt +++ b/src/test/test-data/externalParameter1_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = ; diff --git a/src/test/test-data/externalParameter2_rt.txt b/src/test/test-data/externalParameter2_rt.txt index 7f0e78b6e..f8306c2cf 100644 --- a/src/test/test-data/externalParameter2_rt.txt +++ b/src/test/test-data/externalParameter2_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = ; x = ; diff --git a/src/test/test-data/externalParameter3_rt.txt b/src/test/test-data/externalParameter3_rt.txt index 0a49d38c6..b1eaa4951 100644 --- a/src/test/test-data/externalParameter3_rt.txt +++ b/src/test/test-data/externalParameter3_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = ; x = ; diff --git a/src/test/test-data/fbc/charge_rt.txt b/src/test/test-data/fbc/charge_rt.txt index 067b69125..a106ea2ea 100644 --- a/src/test/test-data/fbc/charge_rt.txt +++ b/src/test/test-data/fbc/charge_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species S1; diff --git a/src/test/test-data/fbc/chemicalFormula_rt.txt b/src/test/test-data/fbc/chemicalFormula_rt.txt index 3fc7b42f6..13d6508e4 100644 --- a/src/test/test-data/fbc/chemicalFormula_rt.txt +++ b/src/test/test-data/fbc/chemicalFormula_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species S1; diff --git a/src/test/test-data/fbc/fluxes_and_objectives_rt.txt b/src/test/test-data/fbc/fluxes_and_objectives_rt.txt index f22802dd1..92e747273 100644 --- a/src/test/test-data/fbc/fluxes_and_objectives_rt.txt +++ b/src/test/test-data/fbc/fluxes_and_objectives_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species s1, s2, s3; diff --git a/src/test/test-data/fbc/formula_objective2.txt b/src/test/test-data/fbc/formula_objective2.txt index 7914e0b58..c0ff7bd3b 100644 --- a/src/test/test-data/fbc/formula_objective2.txt +++ b/src/test/test-data/fbc/formula_objective2.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species s1; diff --git a/src/test/test-data/fbc/formula_objective2_rt.txt b/src/test/test-data/fbc/formula_objective2_rt.txt index 7914e0b58..c0ff7bd3b 100644 --- a/src/test/test-data/fbc/formula_objective2_rt.txt +++ b/src/test/test-data/fbc/formula_objective2_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species s1; diff --git a/src/test/test-data/fbc/formula_objective_rt.txt b/src/test/test-data/fbc/formula_objective_rt.txt index 29cc8158e..793663ac8 100644 --- a/src/test/test-data/fbc/formula_objective_rt.txt +++ b/src/test/test-data/fbc/formula_objective_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species s1; diff --git a/src/test/test-data/fbc/geneProductAssociations_rt.txt b/src/test/test-data/fbc/geneProductAssociations_rt.txt index 9457af804..8a8a90dab 100644 --- a/src/test/test-data/fbc/geneProductAssociations_rt.txt +++ b/src/test/test-data/fbc/geneProductAssociations_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species S1; diff --git a/src/test/test-data/fbc/geneProducts_rt.txt b/src/test/test-data/fbc/geneProducts_rt.txt index fb4a6e5c1..bb6487c05 100644 --- a/src/test/test-data/fbc/geneProducts_rt.txt +++ b/src/test/test-data/fbc/geneProducts_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species S1; diff --git a/src/test/test-data/fbc/simple_flux2_rt.txt b/src/test/test-data/fbc/simple_flux2_rt.txt index ebd8ce21c..0a8d04679 100644 --- a/src/test/test-data/fbc/simple_flux2_rt.txt +++ b/src/test/test-data/fbc/simple_flux2_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species s1; diff --git a/src/test/test-data/fbc/simple_flux3_reverse_rt.txt b/src/test/test-data/fbc/simple_flux3_reverse_rt.txt index be8a59b55..ab5df3cdd 100644 --- a/src/test/test-data/fbc/simple_flux3_reverse_rt.txt +++ b/src/test/test-data/fbc/simple_flux3_reverse_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species s1, s2; diff --git a/src/test/test-data/fbc/simple_flux3_rt.txt b/src/test/test-data/fbc/simple_flux3_rt.txt index be8a59b55..ab5df3cdd 100644 --- a/src/test/test-data/fbc/simple_flux3_rt.txt +++ b/src/test/test-data/fbc/simple_flux3_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species s1, s2; diff --git a/src/test/test-data/fbc/simple_flux_and_objective2_rt.txt b/src/test/test-data/fbc/simple_flux_and_objective2_rt.txt index 745cf266f..71ef25f52 100644 --- a/src/test/test-data/fbc/simple_flux_and_objective2_rt.txt +++ b/src/test/test-data/fbc/simple_flux_and_objective2_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species s1; diff --git a/src/test/test-data/fbc/simple_flux_and_objective_rt.txt b/src/test/test-data/fbc/simple_flux_and_objective_rt.txt index 0b69914a9..912e73c7b 100644 --- a/src/test/test-data/fbc/simple_flux_and_objective_rt.txt +++ b/src/test/test-data/fbc/simple_flux_and_objective_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species s1; diff --git a/src/test/test-data/fbc/simple_flux_eq_neq_rt.txt b/src/test/test-data/fbc/simple_flux_eq_neq_rt.txt index 9cdae9aea..6f2af5cfa 100644 --- a/src/test/test-data/fbc/simple_flux_eq_neq_rt.txt +++ b/src/test/test-data/fbc/simple_flux_eq_neq_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species s1, s2; diff --git a/src/test/test-data/fbc/simple_flux_neg_rt.txt b/src/test/test-data/fbc/simple_flux_neg_rt.txt index 9fd900517..e7a6974f7 100644 --- a/src/test/test-data/fbc/simple_flux_neg_rt.txt +++ b/src/test/test-data/fbc/simple_flux_neg_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species s1; diff --git a/src/test/test-data/fbc/simple_flux_rt.txt b/src/test/test-data/fbc/simple_flux_rt.txt index ebd8ce21c..0a8d04679 100644 --- a/src/test/test-data/fbc/simple_flux_rt.txt +++ b/src/test/test-data/fbc/simple_flux_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species s1; diff --git a/src/test/test-data/fbc/simple_objective2_rt.txt b/src/test/test-data/fbc/simple_objective2_rt.txt index 1a9e88ce5..493910dc2 100644 --- a/src/test/test-data/fbc/simple_objective2_rt.txt +++ b/src/test/test-data/fbc/simple_objective2_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species s1; diff --git a/src/test/test-data/fbc/simple_objective3_rt.txt b/src/test/test-data/fbc/simple_objective3_rt.txt index 978209228..4898e20dc 100644 --- a/src/test/test-data/fbc/simple_objective3_rt.txt +++ b/src/test/test-data/fbc/simple_objective3_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species s1; diff --git a/src/test/test-data/fbc/simple_objective4_rt.txt b/src/test/test-data/fbc/simple_objective4_rt.txt index 978209228..4898e20dc 100644 --- a/src/test/test-data/fbc/simple_objective4_rt.txt +++ b/src/test/test-data/fbc/simple_objective4_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species s1; diff --git a/src/test/test-data/fbc/simple_objective5_rt.txt b/src/test/test-data/fbc/simple_objective5_rt.txt index 978209228..4898e20dc 100644 --- a/src/test/test-data/fbc/simple_objective5_rt.txt +++ b/src/test/test-data/fbc/simple_objective5_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species s1; diff --git a/src/test/test-data/fbc/simple_objective_rt.txt b/src/test/test-data/fbc/simple_objective_rt.txt index 8ad0bad8f..8c7ab6714 100644 --- a/src/test/test-data/fbc/simple_objective_rt.txt +++ b/src/test/test-data/fbc/simple_objective_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species s1; diff --git a/src/test/test-data/fbc/two_sided_flux_complete_rt.txt b/src/test/test-data/fbc/two_sided_flux_complete_rt.txt index efeac5a3e..2b084d8aa 100644 --- a/src/test/test-data/fbc/two_sided_flux_complete_rt.txt +++ b/src/test/test-data/fbc/two_sided_flux_complete_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species s1, s2, s3; diff --git a/src/test/test-data/fbc/two_sided_flux_rt.txt b/src/test/test-data/fbc/two_sided_flux_rt.txt index 1e2a60e56..d07937904 100644 --- a/src/test/test-data/fbc/two_sided_flux_rt.txt +++ b/src/test/test-data/fbc/two_sided_flux_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species s1; diff --git a/src/test/test-data/floating_species_in_asnt_rule_rt.txt b/src/test/test-data/floating_species_in_asnt_rule_rt.txt index 75cbbb29d..bb0f4b955 100644 --- a/src/test/test-data/floating_species_in_asnt_rule_rt.txt +++ b/src/test/test-data/floating_species_in_asnt_rule_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species S1; diff --git a/src/test/test-data/floating_species_in_rate_rule_rt.txt b/src/test/test-data/floating_species_in_rate_rule_rt.txt index f3cb90f93..56fdcab86 100644 --- a/src/test/test-data/floating_species_in_rate_rule_rt.txt +++ b/src/test/test-data/floating_species_in_rate_rule_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species S1; diff --git a/src/test/test-data/from-libsbml/CompTest.txt b/src/test/test-data/from-libsbml/CompTest.txt index 3d45a2770..398a2ec9f 100644 --- a/src/test/test-data/from-libsbml/CompTest.txt +++ b/src/test/test-data/from-libsbml/CompTest.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Warnings from automatic translation: // Unable to create port constraint__constraint0 in model CompModel because Constraint elements do not have IDs in SBML, and therefore cannot be made into ports in Antimony. @@ -192,8 +192,8 @@ model *CompTest() delete C1.perSecond, C1.event0, C1.event1; // Other declarations: - const topKf, kr_f, kr_r, ka_f, ka_r, kc_f, kc_r, ko_f, ko_r, kao_f, kao_r; - const kmdiff_f, kmdiff_r, kd, kecd, nc, nr, ko, kb, ng, np, ka, kecdiff; + const kf, topKf, kr_f, kr_r, ka_f, ka_r, kc_f, kc_r, ko_f, ko_r, kao_f; + const kao_r, kmdiff_f, kmdiff_r, kd, kecd, nc, nr, ko, kb, ng, np, ka, kecdiff; // Display Names: kr_f is "Forward repression binding rate"; diff --git a/src/test/test-data/from-libsbml/QTPop.txt b/src/test/test-data/from-libsbml/QTPop.txt index 24d8020fa..5e11216b6 100644 --- a/src/test/test-data/from-libsbml/QTPop.txt +++ b/src/test/test-data/from-libsbml/QTPop.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 function get2DArrayElement(a, b, c) a; end diff --git a/src/test/test-data/from-libsbml/comp.txt b/src/test/test-data/from-libsbml/comp.txt index 122d451d7..84655cfbe 100644 --- a/src/test/test-data/from-libsbml/comp.txt +++ b/src/test/test-data/from-libsbml/comp.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model moddef1() // Compartments and Species: diff --git a/src/test/test-data/from-libsbml/exchangetest.txt b/src/test/test-data/from-libsbml/exchangetest.txt index 4f6ce57e4..5063a775d 100644 --- a/src/test/test-data/from-libsbml/exchangetest.txt +++ b/src/test/test-data/from-libsbml/exchangetest.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model *testmod() // Compartments and Species: diff --git a/src/test/test-data/from-libsbml/replace_rules_and_constraints.txt b/src/test/test-data/from-libsbml/replace_rules_and_constraints.txt index 1402825a1..2908468fd 100644 --- a/src/test/test-data/from-libsbml/replace_rules_and_constraints.txt +++ b/src/test/test-data/from-libsbml/replace_rules_and_constraints.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Warnings from automatic translation: // Unable to create port rule__iBioSim7 in model CompModel because RateRule elements only exist as part of other Antimony elements, and do not function as their own separate entities which may be flagged as a port. diff --git a/src/test/test-data/from-libsbml/test22.txt b/src/test/test-data/from-libsbml/test22.txt index 8f3a9b2d6..616c0824d 100644 --- a/src/test/test-data/from-libsbml/test22.txt +++ b/src/test/test-data/from-libsbml/test22.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model moddef1() // Compartments and Species: diff --git a/src/test/test-data/from-libsbml/test23.txt b/src/test/test-data/from-libsbml/test23.txt index 93ddaee6e..f96e11378 100644 --- a/src/test/test-data/from-libsbml/test23.txt +++ b/src/test/test-data/from-libsbml/test23.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model moddef1() // Compartments and Species: diff --git a/src/test/test-data/from-libsbml/test24.txt b/src/test/test-data/from-libsbml/test24.txt index 4c4ed9367..cb82c91b5 100644 --- a/src/test/test-data/from-libsbml/test24.txt +++ b/src/test/test-data/from-libsbml/test24.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model moddef1() // Compartments and Species: diff --git a/src/test/test-data/from-libsbml/test25.txt b/src/test/test-data/from-libsbml/test25.txt index d87f60bf0..ee27ab804 100644 --- a/src/test/test-data/from-libsbml/test25.txt +++ b/src/test/test-data/from-libsbml/test25.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model moddef1() // Compartments and Species: diff --git a/src/test/test-data/from-libsbml/test27.txt b/src/test/test-data/from-libsbml/test27.txt index 3fc12020e..af7b514e3 100644 --- a/src/test/test-data/from-libsbml/test27.txt +++ b/src/test/test-data/from-libsbml/test27.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model moddef1() // Assignment Rules: diff --git a/src/test/test-data/from-libsbml/test28.txt b/src/test/test-data/from-libsbml/test28.txt index 5e1d07f20..9405c8619 100644 --- a/src/test/test-data/from-libsbml/test28.txt +++ b/src/test/test-data/from-libsbml/test28.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model moddef1() // Compartments and Species: diff --git a/src/test/test-data/from-libsbml/test35.txt b/src/test/test-data/from-libsbml/test35.txt new file mode 100644 index 000000000..07beb400c --- /dev/null +++ b/src/test/test-data/from-libsbml/test35.txt @@ -0,0 +1,27 @@ +// Created by libAntimony v3.2.0 +model moddef1() + + // Events: + E0: at 1/time after time > 3, priority = 10: t1 = 3.3, t2 = 5.5; + + // Variable initializations: + t1 = 1; + t2 = 1; + + // Other declarations: + var t1, t2; +end + +model *doc0() + + // Sub-modules, and any changes to those submodules: + sub1: moddef1(); + sub1.E0 is sub1_E0; + sub1.t1 is sub1_t1; + sub1.t2 is sub1_t2; + + // Events: + sub1_E0: at time > 3, priority = 10: sub1_t1 = 3.3, sub1_t2 = 5.5; +end + +doc0 is "doc0" diff --git a/src/test/test-data/from-libsbml/test35_flat.xml b/src/test/test-data/from-libsbml/test35_flat.xml new file mode 100644 index 000000000..8e4f878a3 --- /dev/null +++ b/src/test/test-data/from-libsbml/test35_flat.xml @@ -0,0 +1,40 @@ + + + + + + + + + + + + + + + time + 3 + + + + + + 10 + + + + + + 3.3 + + + + + 5.5 + + + + + + + diff --git a/src/test/test-data/from-libsbml/test36.txt b/src/test/test-data/from-libsbml/test36.txt new file mode 100644 index 000000000..be66ed29e --- /dev/null +++ b/src/test/test-data/from-libsbml/test36.txt @@ -0,0 +1,27 @@ +// Created by libAntimony v3.2.0 +model moddef1() + + // Events: + E0: at 1/time after time > 3, priority = 10: t1 = 3.3, t2 = 5.5; + + // Variable initializations: + t1 = 1; + t2 = 1; + + // Other declarations: + var t1, t2; +end + +model *doc0() + + // Sub-modules, and any changes to those submodules: + sub1: moddef1(); + sub1.E0 is sub1_E0; + sub1.t1 is sub1_t1; + sub1.t2 is sub1_t2; + + // Events: + sub1_E0: at 1/time after time > 3: sub1_t1 = 3.3, sub1_t2 = 5.5; +end + +doc0 is "doc0" diff --git a/src/test/test-data/from-libsbml/test36_flat.xml b/src/test/test-data/from-libsbml/test36_flat.xml new file mode 100644 index 000000000..06abfee5b --- /dev/null +++ b/src/test/test-data/from-libsbml/test36_flat.xml @@ -0,0 +1,44 @@ + + + + + + + + + + + + + + + time + 3 + + + + + + + + 1 + time + + + + + + + 3.3 + + + + + 5.5 + + + + + + + diff --git a/src/test/test-data/from-libsbml/test37.txt b/src/test/test-data/from-libsbml/test37.txt new file mode 100644 index 000000000..f17280c64 --- /dev/null +++ b/src/test/test-data/from-libsbml/test37.txt @@ -0,0 +1,26 @@ +// Created by libAntimony v3.2.0 +model moddef1() + + // Events: + E0: at 1/time after time > 3, priority = 10: t1 = 3.3, t2 = 5.5; + + // Variable initializations: + t1 = 1; + t2 = 1; + + // Other declarations: + var t1, t2; +end + +model *doc0() + + // Sub-modules, and any changes to those submodules: + sub1: moddef1(); + sub1.E0 is sub1_E0; + sub1.t2 is sub1_t2; + + // Events: + sub1_E0: at 1/time after time > 3, priority = 10: sub1_t2 = 5.5; +end + +doc0 is "doc0" diff --git a/src/test/test-data/from-libsbml/test37_flat.xml b/src/test/test-data/from-libsbml/test37_flat.xml new file mode 100644 index 000000000..06eb7c122 --- /dev/null +++ b/src/test/test-data/from-libsbml/test37_flat.xml @@ -0,0 +1,43 @@ + + + + + + + + + + + + + + time + 3 + + + + + + + + 1 + time + + + + + + 10 + + + + + + 5.5 + + + + + + + diff --git a/src/test/test-data/from-libsbml/test38.txt b/src/test/test-data/from-libsbml/test38.txt new file mode 100644 index 000000000..3ea13d69b --- /dev/null +++ b/src/test/test-data/from-libsbml/test38.txt @@ -0,0 +1,26 @@ +// Created by libAntimony v3.2.0 +model moddef1() + + // Events: + E0: at 1/time after time > 3, priority = 10: t1 = 3.3, t2 = 5.5; + + // Variable initializations: + t1 = 1; + t2 = 1; + + // Other declarations: + var t1, t2; +end + +model *doc0() + + // Sub-modules, and any changes to those submodules: + sub1: moddef1(); + sub1.E0 is sub1_E0; + sub1.t1 is sub1_t1; + + // Events: + sub1_E0: at time > 3: sub1_t1 = 3.3; +end + +doc0 is "doc0" diff --git a/src/test/test-data/from-libsbml/test38_flat.xml b/src/test/test-data/from-libsbml/test38_flat.xml new file mode 100644 index 000000000..937ba5338 --- /dev/null +++ b/src/test/test-data/from-libsbml/test38_flat.xml @@ -0,0 +1,29 @@ + + + + + + + + + + + + + + time + 3 + + + + + + + 3.3 + + + + + + + diff --git a/src/test/test-data/from-libsbml/test39.txt b/src/test/test-data/from-libsbml/test39.txt index b17128e26..ba66ac8fd 100644 --- a/src/test/test-data/from-libsbml/test39.txt +++ b/src/test/test-data/from-libsbml/test39.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model moddef1() // Compartments and Species: @@ -31,6 +31,9 @@ model *doc0() // Variable initializations: p1 = 100; + + // Other declarations: + const p1; end doc0 is "doc0" diff --git a/src/test/test-data/from-libsbml/test39_flat.xml b/src/test/test-data/from-libsbml/test39_flat.xml index 3732cf455..c651cb767 100644 --- a/src/test/test-data/from-libsbml/test39_flat.xml +++ b/src/test/test-data/from-libsbml/test39_flat.xml @@ -1,26 +1,27 @@ + - + - + - + - + - + p1 - sub1__s1 + sub1_s1 diff --git a/src/test/test-data/from-libsbml/test44.txt b/src/test/test-data/from-libsbml/test44.txt index 7a76b3675..5f8fae847 100644 --- a/src/test/test-data/from-libsbml/test44.txt +++ b/src/test/test-data/from-libsbml/test44.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model moddef1() // Compartments and Species: diff --git a/src/test/test-data/from-libsbml/test45.txt b/src/test/test-data/from-libsbml/test45.txt index dbe937fdf..29f26d9a6 100644 --- a/src/test/test-data/from-libsbml/test45.txt +++ b/src/test/test-data/from-libsbml/test45.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model moddef1() // Rate Rules: @@ -20,6 +20,7 @@ model *doc0() // Variable initializations: timeconv = 60; paramconv = 0.01; + t1 = 1; // Other declarations: const timeconv, paramconv; diff --git a/src/test/test-data/from-libsbml/test46.txt b/src/test/test-data/from-libsbml/test46.txt index e1f87430b..1abaebe6f 100644 --- a/src/test/test-data/from-libsbml/test46.txt +++ b/src/test/test-data/from-libsbml/test46.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model moddef1() // Compartments and Species: diff --git a/src/test/test-data/from-libsbml/test47.txt b/src/test/test-data/from-libsbml/test47.txt index 0d1d9f6a4..e37642958 100644 --- a/src/test/test-data/from-libsbml/test47.txt +++ b/src/test/test-data/from-libsbml/test47.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model moddef1() // Compartments and Species: diff --git a/src/test/test-data/from-libsbml/test48.txt b/src/test/test-data/from-libsbml/test48.txt index da548fa02..05b813057 100644 --- a/src/test/test-data/from-libsbml/test48.txt +++ b/src/test/test-data/from-libsbml/test48.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model moddef1() // Compartments and Species: diff --git a/src/test/test-data/from-libsbml/test53.txt b/src/test/test-data/from-libsbml/test53.txt new file mode 100644 index 000000000..c278a7b76 --- /dev/null +++ b/src/test/test-data/from-libsbml/test53.txt @@ -0,0 +1,44 @@ +// Created by libAntimony v3.2.0 +model sub2() + + // Compartments and Species: + species y, z; + + // Reactions: + J0: -> y_stoich y + z_stoich z; ; + + // Species initializations: + y = ; + z = ; + + // Variable initializations: + y_stoich = 1; + z_stoich = 1; +end + +sub2 is "sub2" + +model sub1() + + // Sub-modules, and any changes to those submodules: + A: sub2(); + A.J0 is A_J0; + A.z is A_z; + A.z_stoich is A_z_stoich; + + // Reactions: + A_J0: -> A_z_stoich A_z; ; +end + +sub1 is "sub1" + +model *main() + + // Sub-modules, and any changes to those submodules: + B: sub1(); + + // Deleted elements from submodels: + delete B.A_J0; +end + +main is "main" diff --git a/src/test/test-data/from-libsbml/test53_flat.xml b/src/test/test-data/from-libsbml/test53_flat.xml new file mode 100644 index 000000000..23cbbebe5 --- /dev/null +++ b/src/test/test-data/from-libsbml/test53_flat.xml @@ -0,0 +1,13 @@ + + + + + + + + + + + + + diff --git a/src/test/test-data/from-libsbml/test54.txt b/src/test/test-data/from-libsbml/test54.txt index 713759256..a87cf41f1 100644 --- a/src/test/test-data/from-libsbml/test54.txt +++ b/src/test/test-data/from-libsbml/test54.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Warnings from automatic translation: // Unable to process deletion from submodel B in model baz. Deletions of Deletion elements have not been added as a concept in Antimony. diff --git a/src/test/test-data/from-libsbml/test58.txt b/src/test/test-data/from-libsbml/test58.txt index 4589a8a09..21812dcea 100644 --- a/src/test/test-data/from-libsbml/test58.txt +++ b/src/test/test-data/from-libsbml/test58.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Warnings from automatic translation: // Cannot replace stoichiometries in Antimony: all replacedElements and replacedBy children of z in reaction J2 will be ignored. diff --git a/src/test/test-data/from-libsbml/test59.txt b/src/test/test-data/from-libsbml/test59.txt index 9179726d5..2b57b5abe 100644 --- a/src/test/test-data/from-libsbml/test59.txt +++ b/src/test/test-data/from-libsbml/test59.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Warnings from automatic translation: // Cannot replace stoichiometries in Antimony: all replacedElements and replacedBy children of z in reaction J2 will be ignored. diff --git a/src/test/test-data/from-libsbml/test61.txt b/src/test/test-data/from-libsbml/test61.txt index 083831cb3..d0feb1b5c 100644 --- a/src/test/test-data/from-libsbml/test61.txt +++ b/src/test/test-data/from-libsbml/test61.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Warnings from automatic translation: // Cannot replace stoichiometries in Antimony: all replacedElements and replacedBy children of S1 in reaction R1 will be ignored. diff --git a/src/test/test-data/function_name_rt.txt b/src/test/test-data/function_name_rt.txt index 4df8b05cf..8fcc17ffd 100644 --- a/src/test/test-data/function_name_rt.txt +++ b/src/test/test-data/function_name_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 function foo() 3; end diff --git a/src/test/test-data/functions_with_constants.txt b/src/test/test-data/functions_with_constants.txt new file mode 100644 index 000000000..46f9374d5 --- /dev/null +++ b/src/test/test-data/functions_with_constants.txt @@ -0,0 +1,9 @@ +function f(x) + x +end + +p = 5 +fromNumber = f(7) +fromParam = f(p) +fromPi = f(pi) +fromTrue = f(true) diff --git a/src/test/test-data/functions_with_constants.xml b/src/test/test-data/functions_with_constants.xml new file mode 100644 index 000000000..5bfabfde5 --- /dev/null +++ b/src/test/test-data/functions_with_constants.xml @@ -0,0 +1,59 @@ + + + + + + + + + + x + + x + + + + + + + + + + + + + + + + f + 7 + + + + + + + f + p + + + + + + + f + + + + + + + + f + + + + + + + diff --git a/src/test/test-data/functions_with_constants_rt.txt b/src/test/test-data/functions_with_constants_rt.txt new file mode 100644 index 000000000..030531710 --- /dev/null +++ b/src/test/test-data/functions_with_constants_rt.txt @@ -0,0 +1,10 @@ +// Created by libAntimony v3.2.0 +// Variable initializations: +p = 5; +fromNumber = 7; +fromParam = p; +fromPi = pi; +fromTrue = true; + +// Other declarations: +const p, fromNumber, fromParam, fromPi, fromTrue; \ No newline at end of file diff --git a/src/test/test-data/global_units_alias_rt.txt b/src/test/test-data/global_units_alias_rt.txt index 9b575ff87..2bf3d21a8 100644 --- a/src/test/test-data/global_units_alias_rt.txt +++ b/src/test/test-data/global_units_alias_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3; a has m3; diff --git a/src/test/test-data/global_units_rt.txt b/src/test/test-data/global_units_rt.txt index 5b6628b53..53b757752 100644 --- a/src/test/test-data/global_units_rt.txt +++ b/src/test/test-data/global_units_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Unit definitions: unit area = metre^2; unit volume = metre^3; diff --git a/src/test/test-data/hasPart_multiple_rt.txt b/src/test/test-data/hasPart_multiple_rt.txt index caca5e2cb..deb4a48ba 100644 --- a/src/test/test-data/hasPart_multiple_rt.txt +++ b/src/test/test-data/hasPart_multiple_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/hasPart_rt.txt b/src/test/test-data/hasPart_rt.txt index 8c3c5bbd1..24c76fb5b 100644 --- a/src/test/test-data/hasPart_rt.txt +++ b/src/test/test-data/hasPart_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/hasProperty_rt.txt b/src/test/test-data/hasProperty_rt.txt index a26e0726a..61874905a 100644 --- a/src/test/test-data/hasProperty_rt.txt +++ b/src/test/test-data/hasProperty_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/hasTaxon_rt.txt b/src/test/test-data/hasTaxon_rt.txt index ba1b21bdf..791c3c032 100644 --- a/src/test/test-data/hasTaxon_rt.txt +++ b/src/test/test-data/hasTaxon_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/hasVersion_rt.txt b/src/test/test-data/hasVersion_rt.txt index 7e7501c84..90e79ecf9 100644 --- a/src/test/test-data/hasVersion_rt.txt +++ b/src/test/test-data/hasVersion_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/identity_rt.txt b/src/test/test-data/identity_rt.txt index 1c8911e7a..93b19d793 100644 --- a/src/test/test-data/identity_rt.txt +++ b/src/test/test-data/identity_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/initialAmountsAndConcentrations_rt.txt b/src/test/test-data/initialAmountsAndConcentrations_rt.txt index 0b71fb925..0599ba22b 100644 --- a/src/test/test-data/initialAmountsAndConcentrations_rt.txt +++ b/src/test/test-data/initialAmountsAndConcentrations_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: compartment C; species S1 in C, S2 in C, S3 in C, S4 in C; diff --git a/src/test/test-data/interactionActivationDashO_rt.txt b/src/test/test-data/interactionActivationDashO_rt.txt index 8f3458abe..2d810b5af 100644 --- a/src/test/test-data/interactionActivationDashO_rt.txt +++ b/src/test/test-data/interactionActivationDashO_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species S1, S2; diff --git a/src/test/test-data/interquartileRange_rt.txt b/src/test/test-data/interquartileRange_rt.txt index 5c6d25e20..128c534db 100644 --- a/src/test/test-data/interquartileRange_rt.txt +++ b/src/test/test-data/interquartileRange_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = ; x = ; diff --git a/src/test/test-data/isDescribedBy_rt.txt b/src/test/test-data/isDescribedBy_rt.txt index 1ff8ebeed..35aad7e93 100644 --- a/src/test/test-data/isDescribedBy_rt.txt +++ b/src/test/test-data/isDescribedBy_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/isEncodedBy_rt.txt b/src/test/test-data/isEncodedBy_rt.txt index 043dd11c2..c3cee7085 100644 --- a/src/test/test-data/isEncodedBy_rt.txt +++ b/src/test/test-data/isEncodedBy_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/isHomologTo_rt.txt b/src/test/test-data/isHomologTo_rt.txt index 85dcb8fef..f99536b60 100644 --- a/src/test/test-data/isHomologTo_rt.txt +++ b/src/test/test-data/isHomologTo_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/isPartOf_rt.txt b/src/test/test-data/isPartOf_rt.txt index 71f1c105e..c1e6bb31a 100644 --- a/src/test/test-data/isPartOf_rt.txt +++ b/src/test/test-data/isPartOf_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/isPropertyOf_rt.txt b/src/test/test-data/isPropertyOf_rt.txt index 27b95fa25..06905b283 100644 --- a/src/test/test-data/isPropertyOf_rt.txt +++ b/src/test/test-data/isPropertyOf_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/isVersionOf_rt.txt b/src/test/test-data/isVersionOf_rt.txt index 0ae0aab7b..755c5a297 100644 --- a/src/test/test-data/isVersionOf_rt.txt +++ b/src/test/test-data/isVersionOf_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/kl_hasVersion_rt.txt b/src/test/test-data/kl_hasVersion_rt.txt index 28cd18824..e239443a9 100644 --- a/src/test/test-data/kl_hasVersion_rt.txt +++ b/src/test/test-data/kl_hasVersion_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species A; diff --git a/src/test/test-data/kl_set_formula_rt.txt b/src/test/test-data/kl_set_formula_rt.txt index 26f04b3ce..ee1d54716 100644 --- a/src/test/test-data/kl_set_formula_rt.txt +++ b/src/test/test-data/kl_set_formula_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species A; diff --git a/src/test/test-data/kurtosis_rt.txt b/src/test/test-data/kurtosis_rt.txt index af612d725..f0ec45b34 100644 --- a/src/test/test-data/kurtosis_rt.txt +++ b/src/test/test-data/kurtosis_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = ; diff --git a/src/test/test-data/mean_rt.txt b/src/test/test-data/mean_rt.txt index 06379536a..226f8e8d4 100644 --- a/src/test/test-data/mean_rt.txt +++ b/src/test/test-data/mean_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = ; diff --git a/src/test/test-data/median_rt.txt b/src/test/test-data/median_rt.txt index 6d5835bba..fe0b0f700 100644 --- a/src/test/test-data/median_rt.txt +++ b/src/test/test-data/median_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = ; diff --git a/src/test/test-data/mode_rt.txt b/src/test/test-data/mode_rt.txt index 7c3cff050..b59e33fdd 100644 --- a/src/test/test-data/mode_rt.txt +++ b/src/test/test-data/mode_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = ; diff --git a/src/test/test-data/model_conversion_factor.txt b/src/test/test-data/model_conversion_factor.txt new file mode 100644 index 000000000..e134c44d6 --- /dev/null +++ b/src/test/test-data/model_conversion_factor.txt @@ -0,0 +1,2 @@ +model.conversionFactor = x +x=100 \ No newline at end of file diff --git a/src/test/test-data/model_conversion_factor.xml b/src/test/test-data/model_conversion_factor.xml new file mode 100644 index 000000000..9352255b5 --- /dev/null +++ b/src/test/test-data/model_conversion_factor.xml @@ -0,0 +1,9 @@ + + + + + + + + + diff --git a/src/test/test-data/model_conversion_factor_rt.txt b/src/test/test-data/model_conversion_factor_rt.txt new file mode 100644 index 000000000..7034709fa --- /dev/null +++ b/src/test/test-data/model_conversion_factor_rt.txt @@ -0,0 +1,8 @@ +// Created by libAntimony v3.2.0 +model.conversionFactor = x; + +// Variable initializations: +x = 100; + +// Other declarations: +const x; \ No newline at end of file diff --git a/src/test/test-data/modified_element_rt.txt b/src/test/test-data/modified_element_rt.txt index b04e2ac5f..f23b15a83 100644 --- a/src/test/test-data/modified_element_rt.txt +++ b/src/test/test-data/modified_element_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/modified_model_parts_rt.txt b/src/test/test-data/modified_model_parts_rt.txt index 4a8634260..b5639d026 100644 --- a/src/test/test-data/modified_model_parts_rt.txt +++ b/src/test/test-data/modified_model_parts_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model *foo() // Variable initializations: diff --git a/src/test/test-data/modified_model_rt.txt b/src/test/test-data/modified_model_rt.txt index 4a8634260..b5639d026 100644 --- a/src/test/test-data/modified_model_rt.txt +++ b/src/test/test-data/modified_model_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model *foo() // Variable initializations: diff --git a/src/test/test-data/module_name_rt.txt b/src/test/test-data/module_name_rt.txt index 63d600bd4..97f4a2b1a 100644 --- a/src/test/test-data/module_name_rt.txt +++ b/src/test/test-data/module_name_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model *foo() // Variable initializations: diff --git a/src/test/test-data/multi_init_overrides.txt b/src/test/test-data/multi_init_overrides.txt new file mode 100644 index 000000000..abbb4d4cd --- /dev/null +++ b/src/test/test-data/multi_init_overrides.txt @@ -0,0 +1,22 @@ +// Created by libAntimony v3.2.0 +model ExtMod1() + S = 1; + D = 1; +end + +model simple() + S = 5; + D = 10; +end + +model *case01165() + A: ExtMod1(); + B: simple(); + A.S is S; + B.S is S; + A.D is D; + B.D is D; + + S = 5; + D = 10; +end diff --git a/src/test/test-data/multi_init_overrides.xml b/src/test/test-data/multi_init_overrides.xml new file mode 100644 index 000000000..757a67e72 --- /dev/null +++ b/src/test/test-data/multi_init_overrides.xml @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/test-data/multi_init_overrides_rt.txt b/src/test/test-data/multi_init_overrides_rt.txt new file mode 100644 index 000000000..4d7a8e94f --- /dev/null +++ b/src/test/test-data/multi_init_overrides_rt.txt @@ -0,0 +1,38 @@ +// Created by libAntimony v3.2.0 +model ExtMod1() + + // Variable initializations: + S = 1; + D = 1; + + // Other declarations: + const S, D; +end + +model simple() + + // Variable initializations: + S = 5; + D = 10; + + // Other declarations: + const S, D; +end + +model *case01165() + + // Sub-modules, and any changes to those submodules: + A: ExtMod1(); + B: simple(); + A.S is S; + B.S is S; + A.D is D; + B.D is D; + + // Variable initializations: + S = 5; + D = 10; + + // Other declarations: + const S, D; +end diff --git a/src/test/test-data/namedstoich_assignment_rt.txt b/src/test/test-data/namedstoich_assignment_rt.txt index c2ce10a1a..6b5251133 100644 --- a/src/test/test-data/namedstoich_assignment_rt.txt +++ b/src/test/test-data/namedstoich_assignment_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species a; diff --git a/src/test/test-data/namedstoich_basic_rt.txt b/src/test/test-data/namedstoich_basic_rt.txt index a719937cf..f346d64c8 100644 --- a/src/test/test-data/namedstoich_basic_rt.txt +++ b/src/test/test-data/namedstoich_basic_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species a; diff --git a/src/test/test-data/namedstoich_rate_rt.txt b/src/test/test-data/namedstoich_rate_rt.txt index 621885d65..a628d3402 100644 --- a/src/test/test-data/namedstoich_rate_rt.txt +++ b/src/test/test-data/namedstoich_rate_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species a; diff --git a/src/test/test-data/namedstoich_value_rt.txt b/src/test/test-data/namedstoich_value_rt.txt index d708ecdb7..475ebea4a 100644 --- a/src/test/test-data/namedstoich_value_rt.txt +++ b/src/test/test-data/namedstoich_value_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species a; diff --git a/src/test/test-data/neg_2_reactant_and_product.txt b/src/test/test-data/neg_2_reactant_and_product.txt new file mode 100644 index 000000000..01398999b --- /dev/null +++ b/src/test/test-data/neg_2_reactant_and_product.txt @@ -0,0 +1 @@ +-2A -> -2B; diff --git a/src/test/test-data/neg_2_reactant_and_product.xml b/src/test/test-data/neg_2_reactant_and_product.xml new file mode 100644 index 000000000..d2bd11a8a --- /dev/null +++ b/src/test/test-data/neg_2_reactant_and_product.xml @@ -0,0 +1,23 @@ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/test-data/neg_2_reactant_and_product_rt.txt b/src/test/test-data/neg_2_reactant_and_product_rt.txt new file mode 100644 index 000000000..b583d79f8 --- /dev/null +++ b/src/test/test-data/neg_2_reactant_and_product_rt.txt @@ -0,0 +1,10 @@ +// Created by libAntimony v3.2.0 +// Compartments and Species: +species A, B; + +// Reactions: +_J0: -2 A -> -2 B; ; + +// Species initializations: +A = ; +B = ; \ No newline at end of file diff --git a/src/test/test-data/neg_reactant_and_product.txt b/src/test/test-data/neg_reactant_and_product.txt new file mode 100644 index 000000000..96b3fef81 --- /dev/null +++ b/src/test/test-data/neg_reactant_and_product.txt @@ -0,0 +1 @@ +-A -> -B; diff --git a/src/test/test-data/neg_reactant_and_product.xml b/src/test/test-data/neg_reactant_and_product.xml new file mode 100644 index 000000000..619bbeadb --- /dev/null +++ b/src/test/test-data/neg_reactant_and_product.xml @@ -0,0 +1,23 @@ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/test-data/neg_reactant_and_product_rt.txt b/src/test/test-data/neg_reactant_and_product_rt.txt new file mode 100644 index 000000000..cd8a7365b --- /dev/null +++ b/src/test/test-data/neg_reactant_and_product_rt.txt @@ -0,0 +1,10 @@ +// Created by libAntimony v3.2.0 +// Compartments and Species: +species A, B; + +// Reactions: +_J0: -1 A -> -1 B; ; + +// Species initializations: +A = ; +B = ; \ No newline at end of file diff --git a/src/test/test-data/negparen_rt.txt b/src/test/test-data/negparen_rt.txt index 31f4c7862..e2086d69c 100644 --- a/src/test/test-data/negparen_rt.txt +++ b/src/test/test-data/negparen_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = -(x + 2); x = ; diff --git a/src/test/test-data/notes_element_noxml_rt.txt b/src/test/test-data/notes_element_noxml_rt.txt index 219d59a9c..4afefb250 100644 --- a/src/test/test-data/notes_element_noxml_rt.txt +++ b/src/test/test-data/notes_element_noxml_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = ; diff --git a/src/test/test-data/notes_element_xml_rt.txt b/src/test/test-data/notes_element_xml_rt.txt index cdbba2475..e75539d29 100644 --- a/src/test/test-data/notes_element_xml_rt.txt +++ b/src/test/test-data/notes_element_xml_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = ; diff --git a/src/test/test-data/notes_model_noxml_rt.txt b/src/test/test-data/notes_model_noxml_rt.txt index be3f5f2c3..e3232a38b 100644 --- a/src/test/test-data/notes_model_noxml_rt.txt +++ b/src/test/test-data/notes_model_noxml_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model *foo() // Variable initializations: diff --git a/src/test/test-data/notes_model_xml_internal_rt.txt b/src/test/test-data/notes_model_xml_internal_rt.txt index 055a43bf8..8c408e9d9 100644 --- a/src/test/test-data/notes_model_xml_internal_rt.txt +++ b/src/test/test-data/notes_model_xml_internal_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model *MorrisonAllegra() // Variable initializations: diff --git a/src/test/test-data/notes_model_xml_rt.txt b/src/test/test-data/notes_model_xml_rt.txt index 055a43bf8..8c408e9d9 100644 --- a/src/test/test-data/notes_model_xml_rt.txt +++ b/src/test/test-data/notes_model_xml_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model *MorrisonAllegra() // Variable initializations: diff --git a/src/test/test-data/occursIn_rt.txt b/src/test/test-data/occursIn_rt.txt index 97c7e7e20..071ecabb2 100644 --- a/src/test/test-data/occursIn_rt.txt +++ b/src/test/test-data/occursIn_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/oxphos_nad_redacted.txt b/src/test/test-data/oxphos_nad_redacted.txt index ffb336bd7..2300ef9d8 100644 --- a/src/test/test-data/oxphos_nad_redacted.txt +++ b/src/test/test-data/oxphos_nad_redacted.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model *MODEL1504010000() // Compartments and Species: diff --git a/src/test/test-data/paramconv_hierarchy.txt b/src/test/test-data/paramconv_hierarchy.txt new file mode 100644 index 000000000..db792c98b --- /dev/null +++ b/src/test/test-data/paramconv_hierarchy.txt @@ -0,0 +1,10 @@ +model moddef1() + t1 = 1; +end + +model *case01179() + paramconv = 0.01; + t1 = 1; + sub1: moddef1() + sub1.t1 * paramconv is t1; +end diff --git a/src/test/test-data/paramconv_hierarchy.xml b/src/test/test-data/paramconv_hierarchy.xml new file mode 100644 index 000000000..3905896fe --- /dev/null +++ b/src/test/test-data/paramconv_hierarchy.xml @@ -0,0 +1,24 @@ + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/test-data/paramconv_hierarchy_rt.txt b/src/test/test-data/paramconv_hierarchy_rt.txt new file mode 100644 index 000000000..08bd4ac08 --- /dev/null +++ b/src/test/test-data/paramconv_hierarchy_rt.txt @@ -0,0 +1,23 @@ +// Created by libAntimony v3.2.0 +model moddef1() + + // Variable initializations: + t1 = 1; + + // Other declarations: + const t1; +end + +model *case01179() + + // Sub-modules, and any changes to those submodules: + sub1: moddef1(); + sub1.t1 * paramconv is t1; + + // Variable initializations: + paramconv = 0.01; + t1 = 1; + + // Other declarations: + const paramconv; +end diff --git a/src/test/test-data/parameter_has_units_rt.txt b/src/test/test-data/parameter_has_units_rt.txt index 1ca4681ab..e3e439008 100644 --- a/src/test/test-data/parameter_has_units_rt.txt +++ b/src/test/test-data/parameter_has_units_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3/2; a has mole; diff --git a/src/test/test-data/parameter_units_rt.txt b/src/test/test-data/parameter_units_rt.txt index f6d4dd447..837549b44 100644 --- a/src/test/test-data/parameter_units_rt.txt +++ b/src/test/test-data/parameter_units_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = 3; a has mole; diff --git a/src/test/test-data/range_rt.txt b/src/test/test-data/range_rt.txt index 99fb4f577..7f11365d1 100644 --- a/src/test/test-data/range_rt.txt +++ b/src/test/test-data/range_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = ; diff --git a/src/test/test-data/same_unit_name.txt b/src/test/test-data/same_unit_name.txt index c5c402846..da4faa8ac 100644 --- a/src/test/test-data/same_unit_name.txt +++ b/src/test/test-data/same_unit_name.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model *same_units() // Variable initializations: diff --git a/src/test/test-data/sampleSize_rt.txt b/src/test/test-data/sampleSize_rt.txt index ac43b7731..a2aa5988e 100644 --- a/src/test/test-data/sampleSize_rt.txt +++ b/src/test/test-data/sampleSize_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = ; diff --git a/src/test/test-data/skewness_rt.txt b/src/test/test-data/skewness_rt.txt index 5c7ff39b3..e4a3544cb 100644 --- a/src/test/test-data/skewness_rt.txt +++ b/src/test/test-data/skewness_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = ; diff --git a/src/test/test-data/speciesConversionFactor.txt b/src/test/test-data/speciesConversionFactor.txt new file mode 100644 index 000000000..7639489a7 --- /dev/null +++ b/src/test/test-data/speciesConversionFactor.txt @@ -0,0 +1 @@ +S1.conversionFactor = cf1 diff --git a/src/test/test-data/speciesConversionFactor.xml b/src/test/test-data/speciesConversionFactor.xml new file mode 100644 index 000000000..2777dfc16 --- /dev/null +++ b/src/test/test-data/speciesConversionFactor.xml @@ -0,0 +1,15 @@ + + + + + + + + + + + + + + + diff --git a/src/test/test-data/speciesConversionFactor_empty.txt b/src/test/test-data/speciesConversionFactor_empty.txt new file mode 100644 index 000000000..557624a49 --- /dev/null +++ b/src/test/test-data/speciesConversionFactor_empty.txt @@ -0,0 +1 @@ +S1.conversionFactor = ; diff --git a/src/test/test-data/speciesConversionFactor_empty.xml b/src/test/test-data/speciesConversionFactor_empty.xml new file mode 100644 index 000000000..b284c8afb --- /dev/null +++ b/src/test/test-data/speciesConversionFactor_empty.xml @@ -0,0 +1,12 @@ + + + + + + + + + + + + diff --git a/src/test/test-data/speciesConversionFactor_empty_rt.txt b/src/test/test-data/speciesConversionFactor_empty_rt.txt new file mode 100644 index 000000000..d81d5d475 --- /dev/null +++ b/src/test/test-data/speciesConversionFactor_empty_rt.txt @@ -0,0 +1,6 @@ +// Created by libAntimony v3.2.0 +// Compartments and Species: +species S1; + +// Species initializations: +S1 = ; \ No newline at end of file diff --git a/src/test/test-data/speciesConversionFactor_rt.txt b/src/test/test-data/speciesConversionFactor_rt.txt new file mode 100644 index 000000000..c9738130c --- /dev/null +++ b/src/test/test-data/speciesConversionFactor_rt.txt @@ -0,0 +1,15 @@ +// Created by libAntimony v3.2.0 +// Compartments and Species: +species S1; + +// Species initializations: +S1 = ; + +// Variable initializations: +cf1 = ; + +// Species conversion factors: +S1.conversionFactor = cf1; + +// Other declarations: +const cf1; \ No newline at end of file diff --git a/src/test/test-data/species_conc_default_rt.txt b/src/test/test-data/species_conc_default_rt.txt index e241a813e..7361235ee 100644 --- a/src/test/test-data/species_conc_default_rt.txt +++ b/src/test/test-data/species_conc_default_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: species a; diff --git a/src/test/test-data/species_conc_in_comp_rt.txt b/src/test/test-data/species_conc_in_comp_rt.txt index acd5b3b0b..6087de60c 100644 --- a/src/test/test-data/species_conc_in_comp_rt.txt +++ b/src/test/test-data/species_conc_in_comp_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: compartment C; species a in C; diff --git a/src/test/test-data/standardDeviation_rt.txt b/src/test/test-data/standardDeviation_rt.txt index a9c357dae..e7db97705 100644 --- a/src/test/test-data/standardDeviation_rt.txt +++ b/src/test/test-data/standardDeviation_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = ; diff --git a/src/test/test-data/standardError_rt.txt b/src/test/test-data/standardError_rt.txt index fe332e0e4..532534fb0 100644 --- a/src/test/test-data/standardError_rt.txt +++ b/src/test/test-data/standardError_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = ; diff --git a/src/test/test-data/stoichiometries_with_same_name.txt b/src/test/test-data/stoichiometries_with_same_name.txt new file mode 100644 index 000000000..27f5aeb1e --- /dev/null +++ b/src/test/test-data/stoichiometries_with_same_name.txt @@ -0,0 +1 @@ +J0: n A -> n B; k1*A^n diff --git a/src/test/test-data/stoichiometries_with_same_name.xml b/src/test/test-data/stoichiometries_with_same_name.xml new file mode 100644 index 000000000..85396b51f --- /dev/null +++ b/src/test/test-data/stoichiometries_with_same_name.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + + + n + + + + + + + + + + + + + + + + k1 + + + A + n + + + + + + + + diff --git a/src/test/test-data/stoichiometries_with_same_name_in_multiple_reactions.txt b/src/test/test-data/stoichiometries_with_same_name_in_multiple_reactions.txt new file mode 100644 index 000000000..c47f9e2fb --- /dev/null +++ b/src/test/test-data/stoichiometries_with_same_name_in_multiple_reactions.txt @@ -0,0 +1,3 @@ +J0: n A -> n B; k1*A^n +J1: n C -> n B; k1*C^n +J2: m A + n B -> m C + n D; k2 diff --git a/src/test/test-data/stoichiometries_with_same_name_in_multiple_reactions.xml b/src/test/test-data/stoichiometries_with_same_name_in_multiple_reactions.xml new file mode 100644 index 000000000..094e0b6a9 --- /dev/null +++ b/src/test/test-data/stoichiometries_with_same_name_in_multiple_reactions.xml @@ -0,0 +1,110 @@ + + + + + + + + + + + + + + + + + + + + + n + + + + + n + + + + + n + + + + + n + + + + + m + + + + + n + + + + + + + + + + + + + + + + k1 + + + A + n + + + + + + + + + + + + + + + + + k1 + + + C + n + + + + + + + + + + + + + + + + + k2 + + + + + + diff --git a/src/test/test-data/stoichiometries_with_same_name_in_multiple_reactions_rt.txt b/src/test/test-data/stoichiometries_with_same_name_in_multiple_reactions_rt.txt new file mode 100644 index 000000000..fbb58be02 --- /dev/null +++ b/src/test/test-data/stoichiometries_with_same_name_in_multiple_reactions_rt.txt @@ -0,0 +1,23 @@ +// Created by libAntimony v3.2.0 +// Compartments and Species: +species A, B, C, D; + +// Reactions: +J0: n A -> n B; k1*A^n; +J1: n C -> n B; k1*C^n; +J2: m A + n B -> m C + n D; k2; + +// Species initializations: +A = ; +B = ; +C = ; +D = ; + +// Variable initializations: +k1 = ; +k2 = ; +n = ; +m = ; + +// Other declarations: +const k1, k2; diff --git a/src/test/test-data/stoichiometries_with_same_name_rt.txt b/src/test/test-data/stoichiometries_with_same_name_rt.txt new file mode 100644 index 000000000..dca65a938 --- /dev/null +++ b/src/test/test-data/stoichiometries_with_same_name_rt.txt @@ -0,0 +1,17 @@ +// Created by libAntimony v3.2.0 +// Compartments and Species: +species A, B; + +// Reactions: +J0: n A -> n B; k1*A^n; + +// Species initializations: +A = ; +B = ; + +// Variable initializations: +k1 = ; +n = ; + +// Other declarations: +const k1; diff --git a/src/test/test-data/subst_species_amt_default_rt.txt b/src/test/test-data/subst_species_amt_default_rt.txt index 182e8bf21..34fd9f756 100644 --- a/src/test/test-data/subst_species_amt_default_rt.txt +++ b/src/test/test-data/subst_species_amt_default_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: substanceOnly species a; diff --git a/src/test/test-data/subst_species_amt_in_comp_rt.txt b/src/test/test-data/subst_species_amt_in_comp_rt.txt index a6fc357da..e4bd350f1 100644 --- a/src/test/test-data/subst_species_amt_in_comp_rt.txt +++ b/src/test/test-data/subst_species_amt_in_comp_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Compartments and Species: compartment C; substanceOnly species a in C; diff --git a/src/test/test-data/subtracted_2_reactant_and_product.txt b/src/test/test-data/subtracted_2_reactant_and_product.txt new file mode 100644 index 000000000..9f30296d7 --- /dev/null +++ b/src/test/test-data/subtracted_2_reactant_and_product.txt @@ -0,0 +1 @@ +A -2B -> C -2D; diff --git a/src/test/test-data/subtracted_2_reactant_and_product.xml b/src/test/test-data/subtracted_2_reactant_and_product.xml new file mode 100644 index 000000000..49e5d186d --- /dev/null +++ b/src/test/test-data/subtracted_2_reactant_and_product.xml @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/test-data/subtracted_2_reactant_and_product_rt.txt b/src/test/test-data/subtracted_2_reactant_and_product_rt.txt new file mode 100644 index 000000000..e8053e9e1 --- /dev/null +++ b/src/test/test-data/subtracted_2_reactant_and_product_rt.txt @@ -0,0 +1,12 @@ +// Created by libAntimony v3.2.0 +// Compartments and Species: +species A, B, C, D; + +// Reactions: +_J0: A + -2 B -> C + -2 D; ; + +// Species initializations: +A = ; +B = ; +C = ; +D = ; \ No newline at end of file diff --git a/src/test/test-data/subtracted_reactant_and_product.txt b/src/test/test-data/subtracted_reactant_and_product.txt new file mode 100644 index 000000000..6de24a5a2 --- /dev/null +++ b/src/test/test-data/subtracted_reactant_and_product.txt @@ -0,0 +1 @@ +A - B -> C - D; diff --git a/src/test/test-data/subtracted_reactant_and_product.xml b/src/test/test-data/subtracted_reactant_and_product.xml new file mode 100644 index 000000000..20b60ccd8 --- /dev/null +++ b/src/test/test-data/subtracted_reactant_and_product.xml @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/test-data/subtracted_reactant_and_product_rt.txt b/src/test/test-data/subtracted_reactant_and_product_rt.txt new file mode 100644 index 000000000..360d3976b --- /dev/null +++ b/src/test/test-data/subtracted_reactant_and_product_rt.txt @@ -0,0 +1,12 @@ +// Created by libAntimony v3.2.0 +// Compartments and Species: +species A, B, C, D; + +// Reactions: +_J0: A + -1 B -> C + -1 D; ; + +// Species initializations: +A = ; +B = ; +C = ; +D = ; \ No newline at end of file diff --git a/src/test/test-data/table_example.txt b/src/test/test-data/table_example.txt new file mode 100644 index 000000000..960bd9fdf --- /dev/null +++ b/src/test/test-data/table_example.txt @@ -0,0 +1,17 @@ +model *MDCKII_Transport() + + model notes ``` +The values for parameters and the inital concentrations of this model where directly +provided by the main author: + +**Parameter values** + +| parameter | value | unit | +|-----------|--------|-------| +| p1 | 0.0025 | 1/min | +| p2 | 0.0784 | 1/min | + +The basal chamber volume was taken as 1 ml, the apical as 1.5. As starting +values x1 was set to 88 nmole, all other species to 0. +``` +end diff --git a/src/test/test-data/table_example.xml b/src/test/test-data/table_example.xml new file mode 100644 index 000000000..ab9e972c1 --- /dev/null +++ b/src/test/test-data/table_example.xml @@ -0,0 +1,36 @@ + + + + + + +

The values for parameters and the inital concentrations of this model where directly provided by the main author:

+

+ Parameter values +

+ + + + + + + + + + + + + + + + + + + + +
parametervalueunit
p10.00251/min
p20.07841/min
+

The basal chamber volume was taken as 1 ml, the apical as 1.5. As starting values x1 was set to 88 nmole, all other species to 0.

+ + + + diff --git a/src/test/test-data/table_example_rt.txt b/src/test/test-data/table_example_rt.txt new file mode 100644 index 000000000..587cce78e --- /dev/null +++ b/src/test/test-data/table_example_rt.txt @@ -0,0 +1,20 @@ +// Created by libAntimony v3.2.0 +model *MDCKII_Transport() + + // Notes: + model notes ``` +The values for parameters and the inital concentrations of this model where directly +provided by the main author: + +**Parameter values** + +| parameter | value | unit | +|-----------|--------|-------| +| p1 | 0.0025 | 1/min | +| p2 | 0.0784 | 1/min | + + +The basal chamber volume was taken as 1 ml, the apical as 1.5. As starting values +x1 was set to 88 nmole, all other species to 0. +``` +end \ No newline at end of file diff --git a/src/test/test-data/timeconv_raterule.txt b/src/test/test-data/timeconv_raterule.txt new file mode 100644 index 000000000..054f47aa1 --- /dev/null +++ b/src/test/test-data/timeconv_raterule.txt @@ -0,0 +1,11 @@ +model moddef1() + x = 0; + x' = 1; +end + +model *timeconv_raterule() + tc = 60; + sub1: moddef1(), timeconv = tc; + sub1.x is x; + x' = 1; +end diff --git a/src/test/test-data/timeconv_raterule.xml b/src/test/test-data/timeconv_raterule.xml new file mode 100644 index 000000000..a796a92cf --- /dev/null +++ b/src/test/test-data/timeconv_raterule.xml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + + + 1 + + + + + + diff --git a/src/test/test-data/timeconv_raterule_rt.txt b/src/test/test-data/timeconv_raterule_rt.txt new file mode 100644 index 000000000..bc289f43e --- /dev/null +++ b/src/test/test-data/timeconv_raterule_rt.txt @@ -0,0 +1,28 @@ +// Created by libAntimony v3.2.0 +model moddef1() + + // Rate Rules: + x' = 1; + + // Variable initializations: + x = 0; + + // Other declarations: + var x; +end + +model *timeconv_raterule() + + // Sub-modules, and any changes to those submodules: + sub1: moddef1(), timeconv = tc; + sub1.x is x; + + // Rate Rules: + x' = 1; + + // Variable initializations: + tc = 60; + + // Other declarations: + const tc; +end diff --git a/src/test/test-data/unit_as_port_rt.txt b/src/test/test-data/unit_as_port_rt.txt index d4fb5b52b..c9e8c090f 100644 --- a/src/test/test-data/unit_as_port_rt.txt +++ b/src/test/test-data/unit_as_port_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 model *CompModel(perSecond) // Unit definitions: diff --git a/src/test/test-data/variance_rt.txt b/src/test/test-data/variance_rt.txt index 41d9f007f..b856a2776 100644 --- a/src/test/test-data/variance_rt.txt +++ b/src/test/test-data/variance_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: a = ; diff --git a/src/test/test-data/volume.txt b/src/test/test-data/volume.txt index f48c7fbb7..a9f65e534 100644 --- a/src/test/test-data/volume.txt +++ b/src/test/test-data/volume.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v3.1.3 +// Created by libAntimony v3.2.0 // Variable initializations: volume_ = 1; A = volume_*5; diff --git a/src/typex.cpp b/src/typex.cpp index ccd949053..1c733d07c 100644 --- a/src/typex.cpp +++ b/src/typex.cpp @@ -40,6 +40,7 @@ bool IsReaction(const var_type vtype) case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: return false; } assert(false); //uncaught vtype @@ -91,6 +92,7 @@ bool IsSpecies(const var_type vtype) case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: return false; } assert(false); //uncaught vtype @@ -127,6 +129,7 @@ bool IsDNA(const var_type vtype) case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: return false; } assert(false); //uncaught vtype @@ -163,6 +166,7 @@ bool CanHaveRateRule(const var_type vtype) case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: return false; } assert(false); //uncaught type @@ -199,6 +203,7 @@ bool CanHaveAssignmentRule(const var_type vtype) case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: return false; } assert(false); //uncaught type @@ -235,6 +240,7 @@ bool CanHaveAlgebraicRule(const var_type vtype) case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: return false; } assert(false); //uncaught type @@ -271,6 +277,7 @@ bool CanBeInReaction(const var_type vtype) case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: return false; } assert(false); //uncaught type @@ -307,6 +314,7 @@ bool CanBeStoichiometry(const var_type vtype) case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: return false; } assert(false); //uncaught type @@ -328,6 +336,7 @@ bool HasOrIsFormula(const var_type vtype) case varGeneProduct: case varGeneProductAssociation: case varSpeciesCharge: + case varSpeciesConversionFactor: return true; case varReactionGene: case varReactionUndef: @@ -436,6 +445,8 @@ string VarTypeToString(const var_type vtype) return "Species Charge"; case varSpeciesChemicalFormula: return "Species Chemical Formula"; + case varSpeciesConversionFactor: + return "Species Conversion Factor"; case varInteraction: return "Interaction"; case varFormulaOperator: @@ -540,6 +551,8 @@ string ReturnTypeToString(const return_type rtype) return "gene product associations"; case allSpeciesFbcInfo: return "species charges and chemical formulas"; + case allSpeciesConversionFactors: + return "species conversion factors"; } assert(false); //uncaught type return "Uncaught type"; diff --git a/src/variable.cpp b/src/variable.cpp index f0a808161..1194c996f 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -184,6 +184,7 @@ formula_type Variable::GetFormulaType() const case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: return formulaINITIAL; //For lack of any other default. } assert(false); //uncaught variable type; @@ -211,6 +212,7 @@ const Formula* Variable::GetFormula() const case varGeneProduct: case varGeneProductAssociation: case varSpeciesCharge: + case varSpeciesConversionFactor: return &(m_valFormula); case varReactionUndef: case varReactionGene: @@ -258,6 +260,7 @@ Formula* Variable::GetFormula() case varGeneProduct: case varGeneProductAssociation: case varSpeciesCharge: + case varSpeciesConversionFactor: return &(m_valFormula); case varReactionUndef: case varReactionGene: @@ -324,6 +327,7 @@ const Formula* Variable::GetInitialAssignment() const case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: return &(g_registry.m_blankform); } assert(false); //uncaught type @@ -371,6 +375,7 @@ const Formula* Variable::GetAssignmentRuleOrKineticLaw() const case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: return &(g_registry.m_blankform); } assert(false); //uncaught type @@ -418,6 +423,7 @@ Formula* Variable::GetAssignmentRuleOrKineticLaw() case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: return &(g_registry.m_blankform); } assert(false); //uncaught type @@ -602,7 +608,6 @@ Variable* Variable::GetSubVariable(const string* name) if (newcharge->SetType(varSpeciesCharge)) { assert(false); g_registry.SetError("Unable to set the charge for " + GetNameDelimitedBy(".") + " because its '-charge' is already a " + VarTypeToString(newcharge->GetType()) + ", and cannot be changed to a charge variable. This should not happen; please contact the Antimony developers with this message and your model."); - g_registry.SetError("Unable to set the charge for " + GetNameDelimitedBy(".") + " because its '-charge' is already a " + VarTypeToString(newcharge->GetType()) + ", and cannot be changed to a charge variable. This should not happen; please contact the Antimony developers with this message and your model."); delete newcharge; return NULL; } @@ -623,6 +628,21 @@ Variable* Variable::GetSubVariable(const string* name) } return newform; } + if (name && CaselessStrCmp(true, *name, "conversionFactor")) { + if (SetType(varSpeciesUndef)) { + g_registry.SetError("Unable to set the conversion factor for " + GetNameDelimitedBy(".") + " because that variable cannot be a species, and only species may have a conversion factor."); + return NULL; + } + string fakeid = m_name[m_name.size() - 1] + "-cf"; + Variable* newcf = mod->AddOrFindVariable(&fakeid); + if (newcf->SetType(varSpeciesConversionFactor)) { + assert(false); + g_registry.SetError("Unable to set the conversion factor for " + GetNameDelimitedBy(".") + " because its '-cf' is already a " + VarTypeToString(newcf->GetType()) + ", and cannot be changed to a conversion factor variable. This should not happen; please contact the Antimony developers with this message and your model."); + delete newcf; + return NULL; + } + return newcf; + } uncert_type utype = UncertStringToType(*name); @@ -715,6 +735,11 @@ bool Variable::GetIsConst() const case varCompartment: case varStoichiometry: if (m_const == constDEFAULT) { + //A symbol with an assignment rule or rate rule is never constant. + formula_type ftype = GetFormulaType(); + if (ftype == formulaASSIGNMENT || ftype == formulaRATE) { + return false; + } if (GetFormula() != NULL) { if (GetFormula()->GetIsConst()) { formconst = constCONST; @@ -754,6 +779,7 @@ bool Variable::GetIsConst() const case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: return true; } switch(m_const) { @@ -975,6 +1001,7 @@ bool Variable::SetType(var_type newtype) case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: g_registry.SetError(error); return true; } case varFormulaUndef: @@ -1008,6 +1035,7 @@ bool Variable::SetType(var_type newtype) case varGeneProduct: case varGeneProductAssociation: case varSpeciesCharge: + case varSpeciesConversionFactor: m_type = newtype; return (SetFormula(&m_valFormula)); case varModule: @@ -1055,6 +1083,7 @@ bool Variable::SetType(var_type newtype) case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: g_registry.SetError(error); return true; } case varFormulaOperator: @@ -1086,6 +1115,7 @@ bool Variable::SetType(var_type newtype) case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: g_registry.SetError(error); return true; } case varReactionGene: @@ -1117,6 +1147,7 @@ bool Variable::SetType(var_type newtype) case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: g_registry.SetError(error); return true; } case varReactionUndef: @@ -1150,6 +1181,7 @@ bool Variable::SetType(var_type newtype) case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: g_registry.SetError(error); return true; } case varInteraction: @@ -1181,6 +1213,7 @@ bool Variable::SetType(var_type newtype) case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: g_registry.SetError(error); return true; //the already-identical cases handled above. return true; } @@ -1336,16 +1369,38 @@ bool Variable::SetFormula(Formula* formula, bool isObjective) { string specid = GetNameDelimitedBy("."); specid.replace(specid.find("-charge"), 7, ""); - if (!formula->IsDouble()) { - g_registry.SetError("Cannot set the charge of " + specid + "' to be " + formula->ToDelimitedStringWithEllipses(".") + ", because it must be set to just a number."); + if (!(formula->IsDouble() || formula->IsEmpty())) { + g_registry.SetError("Cannot set the charge of " + specid + "' to be '" + formula->ToDelimitedStringWithEllipses(".") + "', because it must be set to just a number."); return true; } m_valFormula = *formula; break; } case varSpeciesChemicalFormula: - g_registry.SetError("Cannot set '" + GetNameDelimitedBy(".") + "' to be " + formula->ToDelimitedStringWithEllipses(".") + " because a chemical formula must be defined by a string, i.e. S1.chemicalFormula is \"CH4O2\"."); + if (formula->IsEmpty()) { + break; + } + g_registry.SetError("Cannot set '" + GetNameDelimitedBy(".") + "' to be '" + formula->ToDelimitedStringWithEllipses(".") + "' because a chemical formula must be defined by a string, i.e. S1.chemicalFormula is \"CH4O2\"."); return true; + case varSpeciesConversionFactor: + { + string specid = GetNameDelimitedBy("."); + specid.replace(specid.find("-cf"), 3, ""); + if (!(formula->IsSingleVariable() || formula->IsEmpty())) { + g_registry.SetError("Cannot set the conversion factor of " + specid + "' to be '" + formula->ToDelimitedStringWithEllipses(".") + "', because it must be set to reference an existing variable, i.e. '" + specid + ".conversionFactor = k'."); + return true; + } + vector vars = formula->GetVariables(); + if (vars.size() == 1) { + Variable* cf = vars[0]; + if (cf->SetType(varFormulaUndef)) { + g_registry.SetError("Cannot set the conversion factor of " + specid + "' to be '" + formula->ToDelimitedStringWithEllipses(".") + "', because '" + cf->GetNameDelimitedBy(".") + "' cannot be used as a parameter."); + return true; + } + } + m_valFormula = *formula; + break; + } } if (!isObjective) { if (m_valFormula.MakeUnitVariablesUnits()) return true; @@ -1497,24 +1552,22 @@ bool Variable::SetAlgebraicRule(double val, Formula* formula) } if (formula->MakeUnitVariablesUnits()) return true; - //If nothing is set variable explicitly, set all default variables to non-const + //Every algebraic rule needs at least one non-const participant, or it + //can't determine anything. A participant that already has its own + //assignment or rate rule is already fully determined elsewhere, so it + //can't serve that role for this rule -- skip it. Of the rest, anything + //whose const-ness hasn't been explicitly set (by the user, or by an + //explicit SBML 'constant' attribute) defaults to non-const; anything + //already explicitly const or non-const is left alone. vector > formvars = formula->GetVariableStrings(); Module* thismod = g_registry.GetModule(m_module); - vector algvars; - bool anyNonConst = false; for (size_t fv = 0; fv < formvars.size(); fv++) { Variable* var = thismod->GetVariable(formvars[fv]); - algvars.push_back(var); - if (var->GetConstType() == constVAR) { - anyNonConst = true; - } - } - if (!anyNonConst) { - for (size_t v = 0; v < algvars.size(); v++) { - Variable* var = algvars[v]; - if (var->GetConstType() == constDEFAULT) { - algvars[v]->SetIsConst(false); - } + if (var == NULL) continue; + formula_type vftype = var->GetFormulaType(); + if (vftype == formulaASSIGNMENT || vftype == formulaRATE) continue; + if (var->GetConstType() == constDEFAULT) { + var->SetIsConst(false); } } @@ -1759,6 +1812,7 @@ bool Variable::SetIsConst(bool constant) case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: if (!constant) { g_registry.SetError(error + ", as 'constantness' is undefined for a " + VarTypeToString(m_type) + "."); return true; @@ -1855,6 +1909,7 @@ bool Variable::SetSuperCompartment(Variable* var, var_type supertype) case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: assert(false); // Those things don't have components return false; case varStrand: @@ -1911,6 +1966,7 @@ void Variable::SetComponentCompartments(bool frommodule) case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: return; //No components to set case varReactionUndef: case varReactionGene: @@ -2140,6 +2196,7 @@ bool Variable::DeleteFromSubmodel(Variable* deletedvar) case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: //These types can't have rules to them. break; } @@ -2348,7 +2405,7 @@ bool Variable::Synchronize(Variable* clone, const Variable* conversionFactor) if (m_formulatype == formulaASSIGNMENT && clone->GetFormula()->IsEmpty()) { clone->m_formulatype = formulaASSIGNMENT; } - if (m_formulatype == formulaRATE && clone->GetRateRule()->IsEmpty() && clone->GetFormula()->IsEmpty()) { + if (m_formulatype == formulaRATE && clone->GetRateRule()->IsEmpty()) { clone->m_formulatype = formulaRATE; } if (!m_valFormula.IsEmpty()) { @@ -2410,6 +2467,13 @@ bool Variable::Synchronize(Variable* clone, const Variable* conversionFactor) m_valReaction.Clear(); } + //Synchronize the Events. + if (m_type == varEvent && !m_valEvent.IsEmpty()) { + if (clone->GetEvent()->IsEmpty()) { + if (clone->SetEvent(&m_valEvent)) return true; + } + } + //Don't synchronize modules (should be accounted for above) assert(m_valModule.size()==0); @@ -2746,6 +2810,7 @@ bool Variable::AllowedInFormulas() const case varGeneProductAssociation: case varSpeciesCharge: case varSpeciesChemicalFormula: + case varSpeciesConversionFactor: return false; } assert(false); //Uncaught type