diff --git a/.github/workflows/schedule-validate.yml b/.github/workflows/schedule-validate.yml new file mode 100644 index 0000000..01b8c1a --- /dev/null +++ b/.github/workflows/schedule-validate.yml @@ -0,0 +1,38 @@ +# Validate MMED's schedule data (#54) with the SHARED validator, via pre-commit. +# +# MMED keeps its own schedule data in _data/schedule/mmed/.yml. The validation +# logic (schema, referential checks, role tokens) lives once in ICI3D.github.io and is +# pulled in as a pinned pre-commit hook (.pre-commit-config.yaml) — the SAME hook +# contributors run locally with `pre-commit install`. People records still come from +# the ICI3D.github.io submodule for now (see the hook's --people-dir). +name: Validate schedule data + +on: + pull_request: + paths: + - '_data/schedule/**' + - '.pre-commit-config.yaml' + push: + branches: ['gh-pages'] + paths: + - '_data/schedule/**' + - '.pre-commit-config.yaml' + workflow_dispatch: + +permissions: + contents: read + +jobs: + validate: + runs-on: ubuntu-latest + steps: + - name: Checkout (with the ICI3D.github.io submodule = shared people records) + uses: actions/checkout@v4 + with: + submodules: recursive + - uses: actions/setup-python@v5 + with: + python-version: '3.11' + - uses: pre-commit/action@v3.0.1 + with: + extra_args: validate-schedule --all-files diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..b8845fc --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,19 @@ +# Validate MMED's schedule data against the shared, versioned ICI3D schema. +# +# The validator, JSON Schema, and role vocabulary live once in ICI3D.github.io and +# are pulled in here as a pinned pre-commit hook (no vendoring). Contributors get the +# same check CI runs, locally on every commit: +# +# pip install pre-commit && pre-commit install +# +# Instructor keys resolve against the shared people records from the ICI3D.github.io +# submodule (--people-dir), the same records the Jekyll build reads. When MMED owns +# its own _data/team, drop the submodule and the --people-dir override. +repos: + # INTERIM: points at the fork branch until ICI3D/ICI3D.github.io#59 merges; then + # flip repo -> https://github.com/ICI3D/ICI3D.github.io and rev -> the merge sha/tag. + - repo: https://github.com/WestonVoglesonger/ICI3D.github.io + rev: 271a817244057f0b90fb64a2724e645b20827099 + hooks: + - id: validate-schedule + args: [--people-dir, ICI3D.github.io/_data/team] diff --git a/_data/schedule/mmed/2025.yml b/_data/schedule/mmed/2025.yml new file mode 100644 index 0000000..5046d90 --- /dev/null +++ b/_data/schedule/mmed/2025.yml @@ -0,0 +1,1651 @@ +clinic: mmed +year: 2025 +status: published +title: MMED 2025 +timezone: Africa/Johannesburg +display_timezones: +- Africa/Johannesburg +tracks: +- main +- Section 1 +- Section 2 +locations: + main-hall: Main Hall + comp-lab: Comp. Lab + group-breakouts: Group Breakouts + lobby: Lobby + sections: Section 1 / Section 2 +meal_defaults: + breakfast: + start: '07:45' + end: '08:15' + dinner: + start: '18:00' + end: '18:30' +weeks: +- title: 'Week 0: MMED Foundations' + collapsible: true + open: false + days: + - date: '2025-06-09' + label: Day 1 (Monday, 9 June) + sessions: + - start: '09:00' + end: '09:20' + kind: organizing + track: main + title: Introductions, Overview + instructors: + - everyone + location: main-hall + links: + - text: Introductions, Overview + url: https://docs.google.com/presentation/d/1g7F4kTMvPGq1NobmcAtLj_amwjV76MrFGRrJNURISBM + - start: '09:20' + end: '10:30' + kind: discussion + track: main + title: Public health, epidemiology, and infectious disease modelling + instructors: + - pearson + location: main-hall + links: + - text: Public health, epidemiology, and infectious disease modelling + url: https://docs.google.com/presentation/d/1Cxt6ZtRCalcu0iV0pX9fwDaW7DeNYi9Zgg58vUD5EfA + - start: '10:30' + end: '11:00' + kind: coffee + track: main + - start: '11:00' + end: '12:00' + kind: lecture + track: main + title: Introduction to infectious disease dynamics, Part I + instructors: + - mthombothi + location: main-hall + links: + - text: Introduction to infectious disease dynamics, Part I + url: https://drive.google.com/file/d/1nbtUAtmsc1SEbKq3-3YAz83_T2q1lYM0 + - start: '12:00' + end: '13:00' + kind: lecture + track: main + title: Simple Models + instructors: + - pearson + location: main-hall + links: + - text: Simple Models + url: https://docs.google.com/presentation/d/1tFHnRbpf-KBbA_k301pA3WAlS3FbhKlardRRb6jbis4 + - start: '13:00' + end: '14:00' + kind: meal + meal: lunch + track: main + - start: '14:00' + end: '15:30' + kind: computer-session + track: main + title: 'Tutorial 1: Introduction to R and Epidemic curves' + instructors: + - Tutors + location: comp-lab + links: + - text: 'Tutorial 1: Introduction to R and Epidemic curves' + url: https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_RTutorial_1.R + - start: '15:30' + end: '16:00' + kind: break + track: main + - start: '16:00' + end: '17:00' + kind: computer-session + track: main + title: Tutorial 1 cont. + instructors: + - Tutors + location: comp-lab + links: + - text: Tutorial 1 cont. + url: https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_RTutorial_1.R + - start: '17:00' + end: '17:45' + kind: discussion + track: main + title: How to read a scientific paper + instructors: + - pearson + location: main-hall + links: + - text: How to read a scientific paper + url: ../MedPH/How_to_read_exRabies.pdf + notes: + - '[Reference Paper](https://doi.org/10.1371/journal.pbio.1000053)' + - start: '17:45' + end: '18:00' + kind: organizing + track: main + title: Introduction to projects + instructors: + - pearson + location: main-hall + links: + - text: Introduction to projects + url: ../tutorials/pilotproject + notes: + - '[Project Groups](https://docs.google.com/spreadsheets/d/1gLfek_HAcFw-B1raWN6ZPZH_MHC4gtE88sjIf-jaIkc)' + links: + - text: End of Day Questions + url: https://forms.gle/wFNTAMsQU7JEQWrU9 + notes: + - text: Faculty meeting and dinner in E313 from 16h30; be sure to save food for late arrivals once + known + shadow: true + - date: '2025-06-10' + label: Day 2 + sessions: + - start: '08:30' + end: '09:00' + kind: activity + track: main + title: Reading time for a scientific paper + links: + - text: Reading time for a scientific paper + url: https://doi.org/10.1371/journal.pbio.1000053 + - start: '09:00' + end: '10:30' + kind: lecture + track: main + title: Introduction to infectious disease dynamics, Part II + instructors: + - mthombothi + location: main-hall + links: + - text: Introduction to infectious disease dynamics, Part II + url: https://drive.google.com/file/d/1SzQnv9haPgZ_o10GbGDT4nmoOvBeVU_T + notes: + - '["The" R0 paper](https://link.springer.com/article/10.1007/bf00178324) (might need [unpaywall](https://unpaywall.org/products/extension) + or similar tools to access)' + - start: '10:30' + end: '11:00' + kind: coffee + track: main + - start: '11:00' + end: '12:00' + kind: lecture + track: main + title: Dynamics of directly transmitted pathogens + instructors: + - pearson + location: main-hall + links: + - text: Dynamics of directly transmitted pathogens + url: https://docs.google.com/presentation/d/1zFQVS4gHNyfFPXKuz8BIvweMzWQNf6c9 + - start: '12:00' + end: '13:00' + kind: computer-session + track: main + title: 'Tutorial 2: More on Vectors, Data Frames, and Functions, and SEIR' + instructors: + - Tutors + location: comp-lab + links: + - text: 'Tutorial 2: More on Vectors, Data Frames, and Functions' + url: https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_RTutorial_2.R + - text: SEIR + url: https://raw.githubusercontent.com/ICI3D/RTutorials/master/seir.R + - start: '13:00' + end: '14:00' + kind: meal + meal: lunch + track: main + - start: '14:00' + end: '15:30' + kind: computer-session + track: main + title: Tutorial 2 & benchmark questions, and SEIR & Benchmark questions + instructors: + - Tutors + location: comp-lab + links: + - text: Tutorial 2 & benchmark questions + url: https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_RTutorial_2.R + - text: SEIR & Benchmark questions + url: https://raw.githubusercontent.com/ICI3D/RTutorials/master/seir.R + - start: '15:30' + end: '16:00' + kind: break + track: main + - start: '16:00' + end: '18:00' + kind: group-work + track: main + title: Project development + location: group-breakouts + links: + - text: Project development + url: ../tutorials/pilotproject + links: + - text: End of Day Questions + url: https://forms.gle/cWeCsKXKX6GSWSnk8 + - date: '2025-06-11' + label: Day 3 + sessions: + - start: '08:30' + end: '09:30' + kind: group-work + track: main + title: Project development + location: group-breakouts + links: + - text: Project development + url: ../tutorials/pilotproject + notes: + - 'from 08h30, each group will check in with Carl (odd, in 105) or Zinhle (even, lobby): 08h30 1 + and 2, 08h50 3 and 4, 09h10 5 and 6' + - '[Project Groups](https://docs.google.com/spreadsheets/d/1gLfek_HAcFw-B1raWN6ZPZH_MHC4gtE88sjIf-jaIkc)' + - start: '09:30' + end: '10:30' + kind: discussion + track: main + title: How did you read a scientific paper? + instructors: + - pearson + location: comp-lab + notes: + - '[Reference Paper](https://doi.org/10.1371/journal.pbio.1000053)' + - start: '10:30' + end: '11:00' + kind: coffee + track: main + - start: '11:00' + end: '11:45' + kind: lecture + track: main + title: 'Study Design and Analysis in Epidemiology: Where does modeling fit?' + instructors: + - pearson + location: main-hall + links: + - text: 'Study Design and Analysis in Epidemiology: Where does modeling fit?' + url: https://docs.google.com/presentation/d/15-i4vcP9oIOm3eKfqQs4O2Y7BSce1PI8 + - start: '11:45' + end: '13:00' + kind: computer-session + track: main + title: 'Lab 3: Study Design in Epidemiology' + instructors: + - Tutors + location: comp-lab + links: + - text: 'Lab 3: Study Design in Epidemiology' + url: https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_Lab_EpiStudyDesign.R + - start: '13:00' + end: '14:00' + kind: meal + meal: lunch + track: main + - start: '14:00' + end: '15:30' + kind: computer-session + track: main + title: Binomial Distribution Tutorial + instructors: + - Tutors + location: comp-lab + links: + - text: Binomial Distribution Tutorial + url: https://raw.githubusercontent.com/ICI3D/RTutorials/master/binomialDistribution.R + - start: '15:30' + end: '16:00' + kind: break + track: main + - start: '16:00' + end: '18:00' + kind: group-work + track: main + title: Project development + location: group-breakouts + links: + - text: Project development + url: ../tutorials/pilotproject + links: + - text: End of Day Questions + url: https://forms.gle/zrD8asaQy6UVP4F68 + - date: '2025-06-12' + label: Day 4 + sessions: + - start: '08:30' + end: '09:15' + kind: lecture + track: main + title: 'Study Design and Analysis, part II: RCT’s' + instructors: + - pearson + location: main-hall + links: + - text: 'Study Design and Analysis, part II: RCT’s' + url: https://docs.google.com/presentation/d/14Vv6XiQjOVgNjGU0vyLeYUFj-9Azf50y + notes: + - 'Side reading: [CDC on the Tuskegee Experiment](https://www.cdc.gov/tuskegee/timeline.htm), [Declaration + of Helsinki](https://www.wma.net/policies-post/wma-declaration-of-helsinki-ethical-principles-for-medical-research-involving-human-subjects/), + [Belmont Report](https://www.hhs.gov/ohrp/regulations-and-policy/belmont-report/index.html)' + - start: '09:15' + end: '10:30' + kind: computer-session + track: main + title: 'Lab 4: Study Design for Clinical Trials' + instructors: + - Tutors + location: comp-lab + links: + - text: 'Lab 4: Study Design for Clinical Trials' + url: https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_Lab_RCT.R + - start: '10:30' + end: '11:00' + kind: coffee + track: main + - start: '11:00' + end: '12:00' + kind: lecture + track: main + title: Transmission in Finite Populations + instructors: + - mthombothi + location: main-hall + links: + - text: Transmission in Finite Populations + url: https://drive.google.com/file/d/1mCqNCQ4Ak78uW6VUYyRRnN0p3Iv3zfEn + - start: '12:00' + end: '13:00' + kind: group-work + track: main + title: Project development, with progress checkin + location: comp-lab + links: + - text: Project development + url: ../tutorials/pilotproject + notes: + - All checkins in the lab. Odd groups check in with Carl, even with Zinhle. Be prepared to show + your draft report, slides, and poster. + - '[Project Groups](https://docs.google.com/spreadsheets/d/1gLfek_HAcFw-B1raWN6ZPZH_MHC4gtE88sjIf-jaIkc)' + - start: '13:00' + end: '14:00' + kind: activity + track: main + title: Lunch + - start: '14:00' + end: '15:30' + kind: group-work + track: main + title: Project development + links: + - text: Project development + url: ../tutorials/pilotproject + - start: '15:30' + end: '16:00' + kind: break + track: main + - start: '16:00' + end: '18:00' + kind: computer-session + track: main + title: 'If incomplete: review questions from Lab 4: Study Design for Clinical Trials , Tutorial + 3: Probability Distributions and Control Structures, and review questions . Otherwise Project + development' + instructors: + - Tutors + location: comp-lab + links: + - text: 'Lab 4: Study Design for Clinical Trials' + url: https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_Lab_RCT.R + - text: 'Tutorial 3: Probability Distributions and Control Structures, and review questions' + url: https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_RTutorial_3.R + - text: Project development + url: ../tutorials/pilotproject + links: + - text: Final Fundamentals Week Quiz (includes Qs from Friday) + url: https://forms.gle/Lrc1GcGbYcqDZZhZA + - date: '2025-06-13' + label: Day 5 + sessions: + - start: '08:30' + end: '09:30' + kind: lecture + track: main + title: Dynamics of vector-borne pathogens + instructors: + - mthombothi + location: main-hall + links: + - text: Dynamics of vector-borne pathogens + url: https://drive.google.com/file/d/1D5kCsgvKuA6VRTl-5kUZs6nJ3mWmcnSe + - start: '09:30' + end: '10:30' + kind: group-work + track: main + title: Final Group Work + location: group-breakouts + notes: + - submit slides to [Zinhle](mailto:zinhle@aims.ca.za) by 10h30 + - start: '10:30' + end: '11:00' + kind: coffee + track: main + - start: '11:00' + end: '13:00' + kind: group-work + track: main + title: Practice presentations and feedback + instructors: + - all + location: main-hall + notes: + - '**Aim** for: 6 minutes, 3-4 minutes for questions, 3-4 minutes for feedback; max 15 minutes' + - 'Groups: 11h00-11h15 4, 11h15-11h30 1, 11h30-11h45 3, 11h45-12h00 2, 12h00-12h15 5 (with 45 minute + buffer for overruns)' + - start: '13:00' + end: '14:00' + kind: meal + meal: lunch + track: main + - start: '14:00' + end: '15:00' + kind: group-work + track: main + title: Revisions + location: group-breakouts + - start: '15:00' + end: '15:30' + kind: discussion + track: main + title: Review / Preview + location: main-hall + - start: '15:30' + end: '16:00' + kind: break + track: main + - start: '16:00' + end: '18:00' + kind: group-work + track: main + title: 'Optional: re-present + re-feedback. Optional: poster feedback.' + location: main-hall +- title: 'Week 1: Meaningful Modeling of Epidemiological Data (MMED)' + collapsible: true + open: false + days: + - date: '2025-06-15' + label: Day 0 (Sunday, 15 June) + sessions: [] + notes: + - On arrival {{ org }} mentors and tutors will assist with direction to accommodations + - text: Faculty meeting and dinner in E313 from 16h30; be sure to save food for late arrivals once + known + shadow: true + - date: '2025-06-16' + label: Day 1 + sessions: + - start: '07:30' + end: '08:20' + kind: organizing + track: main + title: Registration + instructors: + - bruce + location: lobby + - start: '08:30' + end: '09:00' + kind: activity + track: main + title: Welcome and Motivation for Workshop + instructors: + - kassanjee + location: main-hall + links: + - text: Welcome and Motivation for Workshop + url: https://drive.google.com/file/d/15P91x6rYAw5JW0Yu74YwgDVAtXwNnAef + - start: '09:00' + end: '09:45' + kind: discussion + track: main + title: Public health, epidemiology, and models + instructors: + - pearson + location: main-hall + links: + - text: Public health, epidemiology, and models + url: https://docs.google.com/presentation/d/1LbeHeiB-JlZk1tQq7IjMwnuwXQF7SYZE + notes: + - text: 'Notes: Mutono' + shadow: true + - start: '09:45' + end: '10:00' + kind: activity + track: main + title: MMED roadmap and program overview + instructors: + - kassanjee + location: main-hall + links: + - text: MMED roadmap and program overview + url: ../roadmap + - start: '10:00' + end: '10:30' + kind: coffee + track: main + - start: '10:30' + end: '11:30' + kind: lecture + track: main + title: Introduction to dynamic modelling of infectious disease I + instructors: + - kassanjee + location: main-hall + links: + - text: Introduction to dynamic modelling of infectious disease I + url: https://drive.google.com/file/d/1z9fvgjnNkFOY0Q3fvis4qvk_71xJqBw8 + notes: + - text: 'Notes: Carl' + shadow: true + - start: '11:30' + end: '12:30' + kind: lecture + track: main + title: Introduction to infectious disease data + instructors: + - blumberg + location: main-hall + links: + - text: Introduction to infectious disease data + url: https://drive.google.com/file/d/1F3QSyDc0SnYBkkBfFdVHk6Cv2qKd_MJE + notes: + - text: 'Notes: Carl' + shadow: true + - start: '12:30' + end: '13:00' + kind: activity + track: main + title: faculty meeting + shadow: true + - start: '12:30' + end: '14:00' + kind: meal + meal: lunch + track: main + - start: '13:15' + end: '13:45' + kind: activity + track: main + title: (technical assistance for participants + notes: + - text: Led by Carl + shadow: true + - start: '14:00' + end: '15:00' + kind: lecture + track: main + title: Foundations of dynamical modelling + instructors: + - dushoff + location: main-hall + links: + - text: Foundations of dynamical modelling + url: https://drive.google.com/file/d/1_sa6YOal0UqElX3e-uQ6HZvYRfY_RIV8 + notes: + - text: 'Notes: Seth the Motivator' + shadow: true + - start: '15:00' + end: '15:30' + kind: computer-session + track: main + title: Dynamical fever exercise + instructors: + - nyamai + location: comp-lab + notes: + - Launch from R prompt with `ICI3D::dynamicalFever()` + - text: assisted by Seth, Carl, Jeremy, Martha + shadow: true + - text: Stanley should relax! + shadow: true + - start: '15:30' + end: '16:00' + kind: tea + track: main + title: (poster setup, group 1) + instructors: + - nyamai + - Mentors + location: main-hall + links: + - text: poster setup, group 1 + url: https://drive.google.com/drive/folders/19DlY2bPRbzAsHIux5nSeBibbCSXlKBrU + - start: '16:00' + end: '17:00' + kind: activity + track: main + title: Dynamical fever exercise, cont. + location: comp-lab + notes: + - '[Dynamical fever summary](https://docs.google.com/presentation/d/18POIDzoVrtrXAlZAYbJ9PiajPpssGu7i) + ({% include instructors people="nyamai" %}, {{ lab }})' + - start: '17:00' + end: '18:00' + kind: activity + track: main + title: Poster session 1 + location: main-hall + links: + - text: Poster session 1 + url: https://drive.google.com/drive/folders/19DlY2bPRbzAsHIux5nSeBibbCSXlKBrU + - start: '19:00' + end: '20:30' + kind: activity + track: main + title: Ice-breaker/Card games + instructors: + - bruce + location: main-hall + links: + - text: End of Day Questions + url: https://forms.gle/zkufuNG8PhfB2YEg9 + notes: + - text: 0730? whatsapp checkin + shadow: true + - date: '2025-06-17' + label: Day 2 + sessions: + - start: '08:30' + end: '09:15' + kind: activity + track: main + title: (Hidden) assumptions of simple ODE models + instructors: + - vanschalkwyk + location: main-hall + links: + - text: (Hidden) assumptions of simple ODE models + url: https://drive.google.com/file/d/1tYkR9t3bzmq1iD4fesaXzxgZIeJHWeTY + notes: + - text: note takers {% include instructors people="nyamai" %} + shadow: true + - start: '09:15' + end: '10:00' + kind: live-coding + track: main + title: Introduction to model implementation in R + instructors: + - kassanjee + location: main-hall + links: + - text: Introduction to model implementation in R + url: https://drive.google.com/file/d/1YTiZZGaW17Mx92hmJsCS2qV464wkxL9E + notes: + - '[Resulting Code](https://drive.google.com/file/d/1GFA1k7ckK5lvpml-05tW1u4xqE5EQrrJ)' + - text: 'Notes: Carl' + shadow: true + - start: '10:00' + end: '10:30' + kind: coffee + track: main + - start: '10:30' + end: '11:30' + kind: activity + track: main + title: 'R Tutorials: Lab 1 - ODE Models' + instructors: + - luka + location: comp-lab + links: + - text: R Tutorials + url: ../tutorials + - text: Lab 1 - ODE Models + url: https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_Lab_ODEmodels.R + notes: + - '[Lab 1 Summary](https://drive.google.com/file/d/1iHSjqrwj_LsK8pzAka_OZjepVaLGljH3)' + - start: '11:30' + end: '12:30' + kind: activity + track: main + title: Thinking about Data + instructors: + - nyamai + - Mentors + location: main-hall + links: + - text: Thinking about Data + url: https://docs.google.com/presentation/d/1zygkn_iRYJT4hVigEJuP3siy1GCGkgXX + notes: + - text: note takers Seth + shadow: true + - start: '12:30' + end: '14:00' + kind: meal + meal: lunch + track: main + - start: '14:00' + end: '15:00' + kind: lecture + track: main + title: Study design + instructors: + - kassanjee + location: main-hall + links: + - text: Study design + url: https://drive.google.com/file/d/1de7qMKvnC6djx6CJYIZ8slEt-LOD5-Rh + notes: + - text: 'note takers: Jonathan' + shadow: true + - start: '15:00' + end: '17:00' + kind: activity + track: main + title: '(with tea break) R Tutorials: Lab 4 - study design II & Tutorial 4 - Visualizing Infectious + Disease Data' + instructors: + - blumberg + - kassanjee + - Mentors + location: comp-lab + links: + - text: R Tutorials + url: ../tutorials + - text: Lab 4 - study design II + url: https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_Lab_RCT.R + - text: Tutorial 4 - Visualizing Infectious Disease Data + url: ../tutorials/visualizeData + notes: + - '[Study Design Slides](https://drive.google.com/file/d/1ZrNvXJeJMx8Ei-b4fopwYd_fNG5FAKbG)' + - '[Visualization Summary](https://drive.google.com/file/d/1I_waaz-S3S85s5G0z61ZrIwE-b99oU_N)' + - '[Lab 3 - study design I](https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_Lab_EpiStudyDesign.R) + may also be of interest, but is an own-time activity' + - start: '15:30' + end: '16:00' + kind: tea + track: main + title: (poster setup, group 2) + instructors: + - nyamai + - Mentors + location: main-hall + links: + - text: poster setup, group 2 + url: https://drive.google.com/drive/folders/19DlY2bPRbzAsHIux5nSeBibbCSXlKBrU + - start: '17:00' + end: '18:00' + kind: activity + track: main + title: Poster session 2 + location: main-hall + links: + - text: Poster session 2 + url: https://drive.google.com/drive/folders/19DlY2bPRbzAsHIux5nSeBibbCSXlKBrU + - start: '19:00' + end: '20:00' + kind: lecture + track: main + title: 'Guest Lecture: "Mathematical models of vector-borne diseases: from theory to research" Joseph + Challenger' + links: + - text: 'Guest Lecture: "Mathematical models of vector-borne diseases: from theory to research"' + url: https://docs.google.com/presentation/d/1Gb49d0V84EljTYoulxPQyuiwEEy2jRSV + - text: Joseph Challenger + url: https://scholar.google.com/citations?user=q3Inh-AAAAAJ&hl=en&oi=ao + notes: + - Moderator {% include instructors people="dushoff" %} + links: + - text: End of Day Questions + url: https://forms.gle/ioZ2PLLsjo9WsJH98 + notes: + - text: 0730? whatsapp checkin + shadow: true + - date: '2025-06-18' + label: Day 3 + sessions: + - start: '08:30' + end: '09:30' + kind: lecture + track: main + title: Consequences of heterogeneity and modelling options + instructors: + - dushoff + location: main-hall + notes: + - text: 'Notes: Seth' + shadow: true + - start: '09:30' + end: '11:00' + kind: computer-session + track: main + title: (with coffee break) Lab 2 - Consequences of heterogeneity + instructors: + - dushoff + location: comp-lab + notes: + - text: Mentors, Seth, Joe, CarL + shadow: true + - Download lab + and + supplementary functions + - '[Summary _updated_](https://drive.google.com/file/d/1rSE_99TIUySW-ra0iSb0muFCxR7KbyEb/view?usp=drive_link) + ({% include instructors people="dushoff" %})' + - start: '10:00' + end: '10:30' + kind: coffee + track: main + - start: '11:00' + end: '14:30' + kind: computer-session + track: main + title: 'Introduction to models and data: HIV in Harare' + instructors: + - kassanjee + - pearson + location: comp-lab + links: + - url: https://drive.google.com/file/d/1tFthcPurLo4zvs9j9huFEKJ4pueLICAx + notes: + - 'runs 11:00-14:30 with a lunch break; triaged from an undefined {{ mlect }} macro that rendered empty in the wall' + - text: 'Notes: Mutono' + shadow: true + - Launch from R prompt with `ICI3D::hivTutorial()` + - If you finish all five versions of the model for the Harare data before lunch, move on to working + on data from other countries. + - '**Additional info:** [Distributed Delay Models of Survival](../tutorials/distributedDelay.pdf) + (Boxcar Models) and [example script](https://www.dropbox.com/s/ykirgmodga2j7m9/distributed_delay_boxcar.R?dl=1)' + - text: '[Summary of Harare tutorial]() ({% include instructors people="pearson" %})' + shadow: true + - start: '12:30' + end: '13:00' + kind: activity + track: main + title: faculty meeting + shadow: true + - start: '12:30' + end: '14:00' + kind: meal + meal: lunch + track: main + - start: '14:30' + end: '15:30' + kind: discussion + track: main + title: Formulating research questions + instructors: + - vanschalkwyk + - blumberg + location: sections + notes: + - text: AIMS in main room assisted by Mutono + shadow: true + - text: Seth somewhere notes by Rehsma + shadow: true + - start: '15:30' + end: '16:00' + kind: tea + track: main + - start: '16:00' + end: '17:30' + kind: lecture + track: main + title: Introduction to statistical philosophy + instructors: + - dushoff + location: main-hall + links: + - text: Introduction to statistical philosophy + url: https://drive.google.com/file/d/199YBtpaM6Rl9-UitW7LCyX6OrFLnH1gp + notes: + - text: 'note takers: Cari' + shadow: true + - start: '17:30' + end: '18:00' + kind: activity + track: main + title: 'Projects: Topic Intro' + instructors: + - blumberg + location: main-hall + links: + - text: 'Projects: Topic Intro' + url: https://docs.google.com/presentation/d/1DzepzN9YnYyzhpiV4JKs6x10b2I6B5Pe + notes: + - text: 'note takers: Mutono' + shadow: true + - start: '19:00' + end: '20:00' + kind: activity + track: main + title: 'Optional: Tutorials catch-up' + instructors: + - Mentors + location: comp-lab + links: + - text: Tutorials + url: ../tutorials + links: + - text: End of Day Questions + url: https://forms.gle/K1hNVfazuXbWVvEbA + notes: + - text: 0730? whatsapp checkin + shadow: true + - date: '2025-06-19' + label: Day 4 + sessions: + - start: '08:30' + end: '10:00' + kind: discussion + track: main + title: Creating a model world to address a research question + instructors: + - blumberg + - nyamai + location: sections + notes: + - text: 'note takers: Cari, Jonathan' + shadow: true + - start: '10:00' + end: '10:30' + kind: coffee + track: main + - start: '10:30' + end: '11:15' + kind: lecture + track: main + title: Introduction to likelihood + instructors: + - vanschalkwyk + location: main-hall + links: + - text: Introduction to likelihood + url: https://drive.google.com/file/d/1cQqKXN9DqQ3a3v5HYraWbGOxPbzkGXgX + notes: + - text: 'note takers: Carl' + shadow: true + - start: '11:15' + end: '12:30' + kind: computer-session + track: main + title: Lab 5 - Introduction to likelihood + instructors: + - vanschalkwyk + - Mentors + location: comp-lab + links: + - text: Lab 5 - Introduction to likelihood + url: https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_Lab_introLikelihood.R + notes: + - text: 'helping: Jonathan, Seth, mentors' + shadow: true + - start: '12:30' + end: '13:00' + kind: activity + track: main + title: faculty meeting + shadow: true + - start: '12:30' + end: '14:00' + kind: meal + meal: lunch + track: main + - start: '14:00' + end: '15:30' + kind: live-coding + track: main + title: Participatory coding of a dynamical model + instructors: + - dushoff + location: main-hall + notes: + - '[This years code](https://github.com/ICI3D/RTutorials/blob/master/participatoryDynamics2025.R) + (past years generally available [here](https://github.com/ICI3D/RTutorials))' + - text: 'note takers: Carl' + shadow: true + - start: '15:30' + end: '16:00' + kind: tea + track: main + - start: '16:00' + end: '17:00' + kind: lecture + track: main + title: Introduction stochastic simulation models + instructors: + - kassanjee + location: main-hall + links: + - text: Introduction stochastic simulation models + url: https://drive.google.com/file/d/1zMJWRqbgHpT-PhE88qXmurhvHOh-rCth + notes: + - text: 'note takers: Carii' + shadow: true + - text: Drum on the drums; remind them about assessment + shadow: true + - start: '17:00' + end: '18:00' + kind: discussion + track: main + title: 'Exercise 1: Stochastic models' + instructors: + - kassanjee + location: comp-lab + links: + - text: 'Exercise 1: Stochastic models' + url: https://github.com/ICI3D/RTutorials/blob/master/ICI3D_Example_StochasticSpillover.R + notes: + - '[Summary](https://drive.google.com/file/d/12Km8PtWUdyHf4FQBSwZtDGAxfOc-76Fv)' + - text: 'Support: Mutono, Jonathan, Seth' + shadow: true + - start: '18:30' + end: '19:00' + kind: activity + track: main + title: Finish Model Diagram + - start: '19:00' + end: '21:00' + kind: social + track: main + title: Drumming + location: main-hall + links: + - text: End of Day Questions + url: https://forms.gle/WjMN2aD7HksgrZLv7 + notes: + - text: 0730? whatsapp checkin + shadow: true + - date: '2025-06-20' + label: Day 5 + sessions: + - start: '08:30' + end: '10:00' + kind: discussion + track: main + title: Description of proposed model and assumptions + instructors: + - nyamai + - vanschalkwyk + - blumberg + - Mentors + location: sections + notes: + - text: Telephone! + shadow: true + - text: 'note takers: Team, Reshma' + shadow: true + - start: '10:00' + end: '10:30' + kind: coffee + track: main + - start: '10:30' + end: '11:15' + kind: lecture + track: main + title: Fitting I + instructors: + - vanschalkwyk + location: main-hall + links: + - text: Fitting I + url: https://drive.google.com/file/d/1u0wD9ImMKiLtOvbbqQx7QkL3DNENZ_4f + notes: + - text: 'note takers: {% include instructors people="nyamai" %}' + shadow: true + - start: '11:15' + end: '12:15' + kind: activity + track: main + title: Mentor presentations + instructors: + - blumberg + location: main-hall + notes: + - text: We don't take formal notes here; you are requested to communicate privately with the mentors + shadow: true + - text: 'Seth: mention that lunch not served until 12:30' + shadow: true + - start: '12:15' + end: '12:45' + kind: activity + track: main + title: faculty meeting + shadow: true + - start: '12:15' + end: '13:45' + kind: meal + meal: lunch + track: main + title: (note slight shift) + - start: '13:45' + end: '15:00' + kind: computer-session + track: main + title: Lab 6 - MLE fitting of an SIR model to prevalence data + instructors: + - blumberg + location: comp-lab + links: + - text: Lab 6 - MLE fitting of an SIR model to prevalence data + url: https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_Lab_MLE_SIV_HIV.R + notes: + - text: Jonathan, Reshma, CarL, Carii, mentors + shadow: true + - '[Intro / Summary Slides](https://docs.google.com/presentation/d/1Yj0a1-2-1M8Cg0HH6PiPrc6cdKGGH1ru)' + - start: '15:00' + end: '15:30' + kind: activity + track: main + title: 'Projects: Topic Qs' + instructors: + - nyamai + location: main-hall + links: + - text: 'Projects: Topic Qs' + url: https://docs.google.com/presentation/d/1DzepzN9YnYyzhpiV4JKs6x10b2I6B5Pe + notes: + - text: 'note takers: Jonathan, Seth' + shadow: true + - start: '15:30' + end: '16:00' + kind: tea + track: main + - start: '16:00' + end: '17:00' + kind: activity + track: main + title: Mid-Clinic Feeback session + instructors: + - bruce + location: main-hall + - start: '17:00' + end: '18:00' + kind: activity + track: main + title: Optional catchup session + location: comp-lab + links: + - text: Optional catchup session + url: https://docs.google.com/forms/d/10c8MwOpJYpToRikrSXSHOWjKg80xduucFMKa9A4BDh0 + notes: + - Let the mentors know your questions + - start: '19:00' + end: '21:00' + kind: social + track: main + title: Movie Night + location: main-hall + notes: + - text: 'Project group: work on group assignments possibly calling on experts' + shadow: true + links: + - text: End of Day Questions + url: https://forms.gle/55XBgBjKi34jFPVJ9 + notes: + - text: 0730? whatsapp checkin + shadow: true + - '**NO LATER THAN 1800: [Project selection form](https://docs.google.com/forms/d/1RJW6X5RFQ0ZdSu7cqe3T-SvNsoIksQFhpbaaXWCD9NY)**' + - date: '2025-06-21' + label: Day 6 + sessions: + - start: '09:00' + end: '10:30' + kind: live-coding + track: main + title: Participatory coding for stochastic model + instructors: + - pearson + location: main-hall + notes: + - text: 'note takers: Reshma' + shadow: true + - start: '10:30' + end: '11:00' + kind: coffee + track: main + - start: '11:00' + end: '11:30' + kind: activity + track: main + title: 'Projects: Group Assignments' + instructors: + - nyamai + location: comp-lab + links: + - text: 'Projects: Group Assignments' + url: https://docs.google.com/spreadsheets/d/1oYApOiOTl1C8M2E9QYEJjZeQCL1ErvWmSwrTD8B01AQ/ + - start: '11:30' + end: '12:30' + kind: activity + track: main + title: 'Optional: Tutorials catch-up or Project Group Work' + instructors: + - Mentors + location: comp-lab + links: + - text: Tutorials + url: ../tutorials + notes: + - text: 0730? whatsapp checkin + shadow: true + - '{{ sc }} Optional: Group Lunch at Kalky''s (costs covered)' + - text: 16h30 post-Kalky's all hands faculty meeting in E313; beverages provided + shadow: true + - date: '2025-06-22' + label: Day 7 + sessions: [] + notes: + - '{{ sc }} Social Outing: Cape Point National Park; depart 09h00 sharp' +- title: 'Week 2: MMED Project Focus' + collapsible: true + open: true + days: + - date: '2025-06-23' + label: Day 8 (Monday, 23 June) + sessions: + - start: '08:30' + end: '08:45' + kind: discussion + track: main + title: Feedback responses; Review Schedule & goals + instructors: + - kassanjee + location: main-hall + notes: + - text: 'Notes: Seth' + shadow: true + - start: '08:45' + end: '09:30' + kind: lecture + track: main + title: Life cycle of a modeling project + instructors: + - pearson + location: main-hall + links: + - text: Life cycle of a modeling project + url: https://docs.google.com/presentation/d/1QluWYDhtsHUZK4WSY_Ddq7u8tJe3pG7N + notes: + - text: 'note takers: Mutono, Joe' + shadow: true + - start: '09:30' + end: '10:00' + kind: group-work + track: main + title: First meeting of project groups + location: group-breakouts + links: + - text: project groups + url: https://docs.google.com/spreadsheets/d/1oYApOiOTl1C8M2E9QYEJjZeQCL1ErvWmSwrTD8B01AQ/ + - start: '10:00' + end: '10:30' + kind: coffee + track: main + - start: '10:30' + end: '11:30' + kind: activity + track: main + title: Introduction to github + instructors: + - pearson + - Mentors + location: comp-lab + links: + - text: Introduction to github + url: https://docs.google.com/presentation/d/1Y0pTtI3DPKuE6ZKJ_gyfutFnjTJy3VkD + notes: + - text: 'note takers: Cari' + shadow: true + - start: '11:30' + end: '12:30' + kind: group-work + track: main + title: MMED project work + location: group-breakouts + - start: '12:30' + end: '14:00' + kind: meal + meal: lunch + track: main + - start: '14:00' + end: '15:30' + kind: lecture + track: main + title: Likelihood fitting and dynamical models II + instructors: + - blumberg + location: main-hall + links: + - text: Likelihood fitting and dynamical models II + url: https://docs.google.com/presentation/d/1AdBlXce06jznzo1tyywdiwqNs_UZIN6P + notes: + - text: 'Notes: Cari, Jonathan' + shadow: true + - text: Announce github practice no need to sign up + shadow: true + - start: '15:30' + end: '16:00' + kind: tea + track: main + - start: '16:00' + end: '18:00' + kind: group-work + track: main + title: MMED project work + mentoring sessions + location: group-breakouts + links: + - text: mentoring sessions + url: https://docs.google.com/spreadsheets/d/1jzPPM6DxPewEEFea2nAPiadjunCzKu_dpwgoVei6658 + - start: '19:00' + end: '20:00' + kind: activity + track: main + title: 'Optional: Github practice and and trouble-shooting / tutorial catch-up' + instructors: + - pearson + - Mentors + location: comp-lab + links: + - text: End of Day Questions + url: https://forms.gle/ycGw6LvfUfqK3THw7 + - date: '2025-06-24' + label: Day 9 + sessions: + - start: '08:30' + end: '10:00' + kind: lecture + track: main + title: Introduction to Markov Chain Monte Carlo (MCMC) + instructors: + - pearson + location: main-hall + notes: + - text: Seth, Mutono + shadow: true + - start: '10:00' + end: '10:30' + kind: coffee + track: main + - start: '10:30' + end: '11:30' + kind: computer-session + track: main + title: Lab 7 & Lab 8 MCMC model fitting + instructors: + - pearson + - Mentors + location: comp-lab + links: + - text: Lab 7 + url: https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_Lab_MCMC-Binomial.R + - text: Lab 8 + url: https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_Lab_MCMC-SI_HIV.R + notes: + - text: Cari, Seth, Jonathan + shadow: true + - start: '11:30' + end: '12:30' + kind: group-work + track: main + title: MMED project work + location: group-breakouts + - start: '12:30' + end: '14:00' + kind: meal + meal: lunch + track: main + - start: '14:00' + end: '14:45' + kind: lecture + track: main + title: Data management and cleaning + instructors: + - nyamai + location: main-hall + links: + - text: Data management and cleaning + url: https://drive.google.com/file/d/1Ub-UmIWcCso-r6p_GZII3c5zigO4NL3Q + notes: + - text: 'Notes: Jonathan' + shadow: true + - start: '14:45' + end: '15:30' + kind: computer-session + track: main + title: 'Tutorial 5: Data cleaning, data' + instructors: + - bingham + location: comp-lab + links: + - text: 'Tutorial 5: Data cleaning' + url: https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_RTutorial_5_DataCleaning.R + - text: data + url: https://github.com/ICI3D/datasets/blob/master/dataCleaning/tutorial5.csv + notes: + - '[Summary]() ({% include instructors people="Mentors" %})' + - text: 'note takers: Mutono, Cari' + shadow: true + - start: '15:30' + end: '16:00' + kind: tea + track: main + - start: '16:00' + end: '18:00' + kind: group-work + track: main + title: MMED project work + mentoring sessions + location: group-breakouts + links: + - text: mentoring sessions + url: https://docs.google.com/spreadsheets/d/1jzPPM6DxPewEEFea2nAPiadjunCzKu_dpwgoVei6658 + - start: '19:00' + end: '20:00' + kind: activity + track: main + title: 'Optional: Github Trouble-shooting / tutorial catch-up' + instructors: + - Mentors + location: comp-lab + links: + - text: End of Day Questions + url: https://forms.gle/ydGJTpyQuBner1Wd7 + - date: '2025-06-25' + label: Day 10 + sessions: + - start: '08:30' + end: '09:30' + kind: lecture + track: main + title: Model assessment + instructors: + - dushoff + location: main-hall + links: + - text: Model assessment + url: https://drive.google.com/file/d/1qyncr5wiEdAaR6EP36M9MUYwh8Ktj_Xk + notes: + - text: 'Notes: Joe, Cari' + shadow: true + - start: '09:30' + end: '10:00' + kind: group-work + track: main + title: MMED project work + location: group-breakouts + - start: '10:00' + end: '10:30' + kind: coffee + track: main + - start: '10:30' + end: '11:00' + kind: group-work + track: main + title: MMED project work + location: group-breakouts + - start: '11:00' + end: '12:30' + kind: group-work + track: main + title: '**either** MMED project work **or** Analysis pipelines (resulting code)' + instructors: + - pearson + location: group-breakouts + notes: + - text: 'note takers: Carl' + shadow: true + - text: Get a more direct summary title for this + shadow: true + - start: '12:30' + end: '14:00' + kind: meal + meal: lunch + track: main + - start: '14:00' + end: '15:30' + kind: group-work + track: main + title: MMED project work + location: group-breakouts + - start: '15:30' + end: '16:00' + kind: tea + track: main + - start: '16:00' + end: '18:00' + kind: group-work + track: main + title: MMED project work + mentoring sessions + location: group-breakouts + links: + - text: mentoring sessions + url: https://docs.google.com/spreadsheets/d/1jzPPM6DxPewEEFea2nAPiadjunCzKu_dpwgoVei6658 + - start: '19:00' + end: '20:00' + kind: activity + track: main + title: 'Guest Lecture: Mmamapudi Kubjane' + location: main-hall + links: + - text: Mmamapudi Kubjane + url: https://www.ici3d.org/DAIDD/team/kubjane/ + links: + - text: End of Day Questions + url: https://forms.gle/MUPLB5WP9RUqWUA47 + - date: '2025-06-26' + label: Day 11 + sessions: + - start: '08:30' + end: '10:00' + kind: group-work + track: main + title: MMED project work + mentoring sessions + location: group-breakouts + links: + - text: mentoring sessions + url: https://docs.google.com/spreadsheets/d/1jzPPM6DxPewEEFea2nAPiadjunCzKu_dpwgoVei6658 + - start: '10:00' + end: '10:30' + kind: coffee + track: main + - start: '10:30' + end: '12:30' + kind: group-work + track: main + title: MMED project work + location: group-breakouts + - start: '12:30' + end: '14:00' + kind: meal + meal: lunch + track: main + - start: '14:00' + end: '15:30' + kind: group-work + track: main + title: '**either** MMED project work **or** Participatory coding for study design and simulation + based validation' + instructors: + - dushoff + location: main-hall + notes: + - text: 'note takers: {% include instructors people="pearson" %}' + shadow: true + - text: '[One-study code](https://github.com/ICI3D/RTutorials/blob/master/sampling_JD/study_design.R); + [Many-study code](https://github.com/ICI3D/RTutorials/blob/master/sampling_JD/study_design_rep.R)' + shadow: true + - start: '15:30' + end: '16:00' + kind: tea + track: main + - start: '16:00' + end: '17:30' + kind: discussion + track: main + title: Modelling for policy + instructors: + - blumberg + location: main-hall + notes: + - text: 'note takers: {% include instructors people="dushoff" %}' + shadow: true + - start: '19:00' + end: '20:00' + kind: activity + track: main + title: MMED project work + - date: '2025-06-27' + label: Day 12 + sessions: + - start: '08:30' + end: '12:30' + kind: group-work + track: main + title: MMED project work + location: group-breakouts + - start: '10:00' + end: '10:30' + kind: coffee + track: main + notes: + - 12h30 [Report due]() + - 13h00 [Presentations due]() + - start: '12:30' + end: '13:30' + kind: meal + meal: lunch + track: main + - start: '13:30' + end: '15:30' + kind: group-work + track: main + title: Project presentations + instructors: + - nyamai + location: main-hall + notes: + - text: 'note takers: {% include instructors people="dushoff" %}' + shadow: true + - start: '15:30' + end: '16:00' + kind: tea + track: main + - start: '16:00' + end: '17:00' + kind: discussion + track: main + title: Feedback session II + instructors: + - bruce + location: main-hall + - start: '17:15' + end: '17:45' + kind: activity + track: main + title: Closing Remarks + instructors: + - kassanjee + location: main-hall + notes: + - text: 'note takers: {% include instructors people="TBD" %}' + shadow: true