Adding two new presentations

_materials/1_introduction.html

@@ -262,36 +262,3 @@
 <img src="/images/protocols/beer-data-analysis/krona.png" width="400">
 
 ---
-
-### Schedule
-
-
-#### Part 1
-- 10 min Social introduction
-- 25 min Introduction Presentation
-- 40 min Lab safety and Lab exercises
-    - Pipetting
-    - Centrifuge
-    - Vortex Mixer
-- 10 min Introduction to the DNA extraction
-- ** 30 min Hands-on 1: Beer preparation **
-- Break 45 min
-- ** 60 min Hands-on 2: Beer preparation **
-- Break 15 min
-- ** 60 min Hands-on 3: DNA Extraction **
-- Break 15 min
-- 10 min Introduction to Lirbary Preparation
-- ** 30 min Hands-on 4: Lirbary Preparation **
-- 10 min Introduction to Nanopore Sequencing
-- ** 60 min Hands-on 5: Sequencing **
-- 10 min Final Words and Clean Up
-
----
-
-### Schedule
-
-#### Part 2
-- 20 min Bioinformatics Introduction
-- 20 min Galaxy Introduction
-- ** 30 min Hands-on 1: Data Analyis **
-- 30 min Question and Feedback Round

_materials/2_nanopore_sequencing.html

@@ -1,6 +1,6 @@
 ---
 layout: slides
-title: "What is Nanopore-Sequencing?"
+title: "What is Nanopore Sequencing?"
 ---
 
 ![](/images/materials/introduction/protocol_sequencing.png)
@@ -17,16 +17,17 @@
 ### How to Read DNA
 
 
-[Video](https://nanoporetech.com/applications/dna-nanopore-sequencing)
+<iframe src="https://player.vimeo.com/video/337258910" width="640" height="360" frameborder="0" allow="autoplay; fullscreen" allowfullscreen></iframe>
+<p><a href="https://vimeo.com/337258910">Animation: Nanopore sequencing</a> from <a href="https://vimeo.com/user5318092">Oxford Nanopore</a> on <a href="https://vimeo.com">Vimeo</a>.</p>
 
 ---
 
 ### Ingredients
 
 
-- **Fragmentation Mix (FRA):** Ligases (Exonucleases) to cut DNA into shorter pieces. Will cut at certain sequences.
-- **Rapid Sequencing Adapter (RAP):** Ligation of adapters to the DNA fragments (leader and hairpin adapter). The leader adapter will allow the DNA to dock to the nanopore. The hairpin adapter is then for the complement strand.
-- **Flush Tether (FLT):** Guides the motorprotein to the pores.
-- **Seqeuncing Buffer (SQB):** For the ionic current.
-- **Flush Buffer (FB):** For washing.
-- **Loading Beads (LB):** To increase the molecular weight of the DNA. Helps to suck the DNA from the loading port into the flowcell.
+- **Fragmentation Mix (FRA):** to cut DNA into shorter pieces.
+- **Rapid Sequencing Adapter (RAP):** to allow the DNA to dock to the nanopore.
+- **Flush Tether (FLT):** to guide the motorprotein to the pores.
+- **Seqeuncing Buffer (SQB):** to create our ionic current.
+- **Flush Buffer (FB):** to wash.
+- **Loading Beads (LB):** to suck the DNA from the loading port into the flowcell.

_materials/3_bioinformatics.html

@@ -11,7 +11,7 @@
 
 ### Where can you find Bioinformatics?
 
-#### Chemistry, Biology, Physics: Creating Software for Devices
+Chemistry, Biology, Physics: Creating Software for Devices
 
 <img src="/images/materials/introduction/evolution_seq_technologies.svg" width="400">
 <img src="/images/materials/bioinformatics/Blood_Glucose_Testing.jpeg" width="200">
@@ -20,23 +20,23 @@
 
 ### Where can you find Bioinformatics?
 
-#### Chemistry, Biology, Physics: Analysis of Sequence Data
+Chemistry, Biology, Physics: Analysis of Sequence Data
 
 ![](/images/materials/introduction/evolution_seq_technologies.svg)
 
 ---
 
 ### Where can you find Bioinformatics?
 
-#### Chemistry, Biology, Physics: Analysis of Image Data
+Chemistry, Biology, Physics: Analysis of Image Data
 
-<img src="/images/protocols/beer-data-analysis/krona.png" width="400">
+<img src="/images/materials/bioinformatics/cell_image.jpg" width="400">
 
 ---
 
 ### Where can you find Bioinformatics?
 
-#### Mathematics: Computer Science, Algorithms
+Mathematics, Statistics: Computer Science, Algorithms
 
 <img src="/images/materials/bioinformatics/AI.png" width="400">
 
@@ -82,10 +82,26 @@
 - **Line 1:** Read ID
 - **Line 2:** Sequence
 - **Line 3:** Additional Information
-- **Line 4:** Quality String; ASCII formated q-scores.
+- **Line 4:** Quality String
 
 ---
 
 ### Interpreted Data: Kraken
 
 ![](/images/materials/bioinformatics/3.svg)
+
+---
+
+### Interpreted Data: Kraken
+
+<img src="/images/protocols/beer-data-analysis/krona.png" width="400">
+
+---
+
+### Interpreted Data: Kraken
+
+|Taxon	| Read number |
+|-------|-------------|
+| d__Eukaryota |	2053 |
+| d__Eukaryota,k__Fungi |	2053 |
+|d__Eukaryota,k__Fungi,p__Ascomycota	|	2049	|

_materials/4_nanopore_sequencing_extended.html

@@ -1,6 +1,18 @@
 ---
 layout: slides
-title: "Further Imformation about Nanopore-Sequencing"
+title: "Further Information about Nanopore Sequencing"
+---
+
+### Ingredients
+
+
+- **Fragmentation Mix (FRA):** Ligases (Exonucleases) to cut DNA into shorter pieces. Will cut at certain sequences.
+- **Rapid Sequencing Adapter (RAP):** Ligation of adapters to the DNA fragments (leader and hairpin adapter). The leader adapter will allow the DNA to dock to the nanopore. The hairpin adapter is then for the complement strand.
+- **Flush Tether (FLT):** Guides the motorprotein to the pores.
+- **Seqeuncing Buffer (SQB):** For the ionic current.
+- **Flush Buffer (FB):** For washing.
+- **Loading Beads (LB):** To increase the molecular weight of the DNA. Helps to suck the DNA from the loading port into the flowcell.
+
 ---
 
 ### Technical Remarks
@@ -10,8 +22,8 @@
 - The nanopore itself is strong enough to open up the ds. A helicase is not necessary.
 - The MinION has 4 pores for 512 channels (in total 2048 pores).
 - During the sequencing the MinION uses only one pore per channel. Every hour the lane will be checked and perhaps the MinION swaps to a different pore.
-- The quality of the reads decreases at the end of a read like in Illumina Sequencing.
-- Average length 2-10 kb reads. Error Rate 15-40%.
+- The quality of the reads not decreases at the end of a read like in Illumina Sequencing.
+- Average length 2-10 kb reads. Error Rate 15-40% (which comes mostly from the basecalling).
 - Change between template and complement strand is recognized by a specific signal of a site located in the hairpin adapter.
 - [Literature](https://www.researchgate.net/publication/317848322_Nanopore_sequencing_data_analysis_state_of_the_art_applications_and_challenges)