Adding two new presentations

_materials/introduction.html → _materials/1_introduction.html

@@ -256,4 +256,42 @@
 
 ---
 
-### Data analysis
+### Data analysis
+
+<img src="/images/materials/bioinformatics/3.svg" width="400">
+<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

@@ -0,0 +1,32 @@
+---
+layout: slides
+title: "What is Nanopore-Sequencing?"
+---
+
+![](/images/materials/introduction/protocol_sequencing.png)
+
+---
+
+### How to Read DNA
+
+
+![](/images/materials/nanopore/1.svg)
+
+---
+
+### How to Read DNA
+
+
+[Video](https://nanoporetech.com/applications/dna-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.

_materials/3_bioinformatics.html

@@ -0,0 +1,91 @@
+---
+layout: slides
+title: "What is Bioinformatics?"
+---
+
+### Discuss: Where can you find Bioinformatics?
+
+![](/images/materials/bioinformatics/1.svg)
+
+---
+
+### Where can you find Bioinformatics?
+
+#### 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">
+
+---
+
+### Where can you find Bioinformatics?
+
+#### 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
+
+<img src="/images/protocols/beer-data-analysis/krona.png" width="400">
+
+---
+
+### Where can you find Bioinformatics?
+
+#### Mathematics: Computer Science, Algorithms
+
+<img src="/images/materials/bioinformatics/AI.png" width="400">
+
+---
+
+
+### Bioinformatics is the Bridge
+
+
+![](/images/materials/bioinformatics/2.svg)
+
+---
+
+### Discuss: What kind of data will we encounter?
+
+---
+
+### Types of Data We Will Have
+
+- **Raw Signal** (e.g., current/time-data of MinION)
+- **Sequence Data** (e.g., FASTQ data)
+- **Interpreted Data** (i.e., results of Kraken)
+
+---
+
+### Raw Signal Data
+
+![](/images/materials/nanopore/1.svg)
+
+
+---
+
+
+### Sequence Data: FASTQ Format
+
+```
+@SEQ_ID
+GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
++
+!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
+```
+
+- **Line 1:** Read ID
+- **Line 2:** Sequence
+- **Line 3:** Additional Information
+- **Line 4:** Quality String; ASCII formated q-scores.
+
+---
+
+### Interpreted Data: Kraken
+
+![](/images/materials/bioinformatics/3.svg)

_materials/4_nanopore_sequencing_extended.html

@@ -0,0 +1,42 @@
+---
+layout: slides
+title: "Further Imformation about Nanopore-Sequencing"
+---
+
+### Technical Remarks
+
+
+- Double strands are required for nanopore-sequencing, because single strands would stop at the point where you have your adapter (ds position).
+- 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%.
+- 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)
+
+---
+
+### Base Calling
+
+
+- Decoding the raw current signal into a base.
+- Long stretches of the same base might induce a higher error (e.g., Poly-A-Tail problem).
+
+---
+
+### RNA Sequencing
+
+
+- RNA sequencing is possible but so far you need to do a RNA PCR into ds strands (see technical remarks).
+- Also possible is the standard way of a reverse trascription into cDNA and then a cDNA PCR.
+
+---
+
+### Max Scan
+
+
+- It is the name for Nanopore's Current Checking.
+- It will automatically determine which pores has the best electric field.
+- Then the MinION will pick those pores for seqeuncing.
+- This feature is important, since the quality can change over time for the base calling of the each pore.