---
# System prepended metadata

title: Wintersemester 21
tags: [General information, Beuth]

---

###### tags: `General information` `Beuth`
# Wintersemester 21

**We always meet on Zoom**
Topic: WBi- Seq
Time: This is a recurring meeting Meet anytime
Join Zoom Meeting
https://tu-dresden.zoom.us/j/89620214178?pwd=RnN2QmhUb3R5WmZzd3p4Y3JJVFZsZz09
Meeting ID: 896 2021 4178
Passcode: 8erlinHT!

*************************
# General Information

Dear students,

This will be our primary point of contact for links, documents, shared information etc. 

Each day has a separate section, you can all add information and edit (-> so do not delete anything!). 

LG, Helena 


## Participants
*please add your Matrikelnummer, I will need it*
Benjamin	Jädicke	s87299@bht-berlin.de MN:933151		
Björn	Dierkes	s86720@bht-berlin.de (Martrikelnummer: 929463)		
Carolin	Dunker	s87114@bht-berlin.de	MN: 932319	
Christien	Splettstößer	s41124@bht-berlin.de MN: 904277		
Christopher	Hartl	s85354@bht-berlin.de (Matrikelnummer: 925477) 
Edis	Dukadjinac	s87360@bht-berlin.de (916209)		
Fabiana	Salm	s33223@bht-berlin.de		
Francesca Katharina	Hoffmann	s85943@bht-berlin.de MN: 915404		
Friederike Elisabeth	Herrmann	s85337@bht-berlin.de (926085)	
Giuliano	Ballacchino	s85447@bht-berlin.de    Matrikelnummer: 925606	
Gona	Berisha	s87113@bht-berlin.de (Matrikelnummer: 932321)	
Gülnihal	Inci	s87361@bht-berlin.de (MN:930845)		
Jennifer	Mik	s84023@bht-berlin.de (Matrikelnummer:903838)		
Jianjun	Yang	s85650@bht-berlin.de (Matrikelnummer:925894)		
Julia	Gruebner	s84219@bht-berlin.de	(869892)	
Katarina	Markovic	s89064@bht-berlin.de (930908)		
Miriam	Merget	s85473@bht-berlin.de (Matrikelnummer: 925105)		
Miriam Rebecca	Ermer	s87115@bht-berlin.de	(932320)	
Alicia	Oberländer	s83996@bht-berlin.de		911422




## Did you already take Bachelor course Bioinformatics?**
*add your name here*
Francesca Hoffmann (yes)
Katarina Markovic (no, I did not)
Edis Dukadjinac
Friederike Herrmann (no, I did not)
Christien Splettstößer (no, I did not)
Jianjun Yang (no, i did not)
Gona Berisha (No, I didnt)
Miriam Ermer (No, I didnt)
Carolin Dunker (No, I didnt)
Alicia Oberländer (No,I didn't)
Giuliano (Bachelor and Master I)
Björn Dierkes (No, I did not)
Gülnihal Inci (Yes)
Jennifer Mik (yes)
Christopher Hartl (No, I did not)


## Course outline
**Week 1**
Monday - Friday course days 
Friday 26th, 2PM Online tools for making visualizations

**Week 2**
complete tasks week 1, no in person time

**Week 3**
Monday-Friday course days 
Friday 10th, 2PM Introdcution to making figures with Inkscape (= open, free version of illustrator)

**Week 4**
compelte tasks week 2, 
Abgabe: Friday 17th


## Abgabe 
December, 17th Friday 
- Moodle-Abgabe: each student submits their work, if you worked in teams each team member submits 
- Mini-Paper
- Feedback from Helena until early Jan
- Time for improvements until Jan 15th 

** Mini Paper: 
The content of each unit is relevant to the grade, as a small publication will be written from all units at the end of the course. We will learn step by step how a publication is structured. In each unit, we will explain which component is to be included in the publication. After one week an intermediate status of the research is presented. At the end of the course your write up a little article. 


************************

# Mon, Nov 22 2021
## participants
1. Francesca Hoffmann
2. Giuliano Ballacchino
3. Friederike Herrmann
4. Christopher Hartl 
5. Miriam Ermer
6. Katarina Markovic
7. Carolin Dunker
8. Gona Berisha
9. Edis Dukadjinac
10. Benjamin Jädicke
11. Jianjun Yang
12. Christien Splettstößer
13. Alicia Oberländer
14. Miriam Merget
15. Björn Dierkes 
16. Fabiana Salm
17. Jennifer Mik
18. Gülnihal Inci
19. Julia Gruebner


## Schedule: 
13:00 **Welcome** 
- Organisation, Participants, HackMD
- Introduction to topic
- Breakout room: say hello to class mates
- Who wants to work in a team, who wants to work individually?
- Start with exercises
- 16:00 meet Helena in teams of 2-4 
    - 16:00 name & name
    - 16:10 another name
    - 16:20
    - 16:30
    - 16:40 
    - 16:50

## hackMD
hackMD tutorial https://hackmd.io/c/tutorials/%2Fs%2Ftutorials

## Team organisation
1. Christopher Hartl, Katarina Markovic: p53
1. Miriam Merget & Christien Splettstößer: ACE2
1. Giuliano Ballacchino & Alicia Oberländer: CAR 
1. Friederike Herrmann, Francesca Hoffmann:FUS
1. Jennifer Mik: ACTB
1. Benjamin J, Gülnihal Inci: ADH
1. Gona Berisha , Miriam Ermer: TNF
1. Jianjun Yang: TBB3
1. Björn Dierkes, Julia Gruebner: FBN1
1. Carolin Dunker: Occludin 
1. Edis Dukadjinac Myoglobin
1. Fabiana Salm: HBA


Possibly interesting Proteins to work with
* TBB3
* ACTB
* ACE2
* KINH
* FUS
* MYG1
* GLCNE
* MYH2
* RCC1
* ADH
* HBA


## Questions

## Slides, Materials 
https://www.dropbox.com/s/br98zraya0mcymg/Unit1.pdf?dl=0

## Links 
https://www.youtube.com/watch?v=gG7uCskUOrA 

The Simple Club: 
https://www.youtube.com/watch?v=Fy_3gpIkoNs
https://www.youtube.com/watch?v=HSdK7l9Qk1w
https://www.youtube.com/watch?v=3wFfj6D0_nQ



************************

# Tue, Nov 23 2021
## participants
1. Miriam Ermer
2. Gona Berisha
3. Giuliano Ballacchino
4. Alicia Oberländer (missing)
5. Gülnihal Inci
6. Christien Splettstößer
7. Carolin Dunker
8. Katarina Markovic
9. Benjamin Jädicke
10. Miriam Merget
11. Friederike Herrmann
12. Christopher Hartl
13. Jianjun Yang
14. Fabiana Salm
15. Jennifer Mik
16. Edis Dukadjinac
17. Björn Dierkes 
18. Julia Gruebner
19. Francesca Hoffmann
## Schedule: 
13:00 **Welcome** 
- Welcome, questions
- Continue Unit 1: Exercise 4, write an introduction 
- 
- ~~Upload introcution~~ too little time?
- Outlook for Day 3/4/5

16:00 
- Questions? Reserve a slot to ask YOUR question regarding your protein, Pubmed/EuropePMC, general 
    - 16:00 Friederike + Francesca 
    - 16:10
    - 16:20

## HOMEWORK
Write 5 "Big picture"-sentences (first sentence of the opening paragraph) for the your protein/topic of interest. (Open-ended question, Bold statement, Quote, Personal Story, Imagine a brighter future).

Share the best of them tomorrow in class and comment what you like and maybe why the other examples did not work. 
Get feedback from peers. 

## Questions

## Slides, Materials 
https://www.dropbox.com/sh/8rmmytkivtlk2x8/AABbU6dQBSb3HJLVihlIupRGa?dl=0

## Links 


************************

# Wed, Nov 24 2021
## Participants

1. Gülnihal Inci
2. Gona Berisha
3. Carolin Dunker
4. Katarina Markovic
5. Björn Dierkes 
6. Christien Splettstößer
7. Giuliano Ballacchino
9. Miriam Merget
10. Benjamin Jädicke
11. Friederike Herrmann 
12. Alicia Oberländer
13. Jennifer Mik
14. Christopher Hartl
15. Miriam Ermer
16. Edis Dukadjinac
17. Francesca Hoffmann
18. Jianjun Yang
19. Julia Gruebner

## Schedule: 
13:00 **welcome** 
- Organisation, questions?
- BREAKOUT ROOMS (5/room): Homework from Day 2
- Introduction to sequences
- Exercises Unit 2

16:00 Questions? Pick a slot for yours
  - 16:00 Carolin Dunker
  - 16:10 Ben und Gülnihal
  - 16:20 Fabiana
  - 16:30 Chris & Katarina
  - 16:40
  - 16:50
 

## Questions



## Slides, Materials 
Handout Unit 2:
https://www.dropbox.com/sh/ofke99mi0jqitoj/AABaAuc4LVW4GEhZaQmZQz2ma?dl=0

Intro lecture, recorded:
https://youtu.be/x5HuhXHPrRs

## Links 
Download sequences, NCBI Tutorial 3 Min!
https://youtu.be/ZWnLyYKozaI

How to organise your sequences with a "Sequence  editor", tutorial for ApE - 3 parts, 5 minutes each
https://youtu.be/G-6jiKbZTcs
https://youtu.be/dNc_7Cg1qiI
https://youtu.be/h4PiBcnRP2k


************************

# Thur, Nov 25 2021
## Participants
1. Francesca Hoffmann
2. Carolin Dunker
3. Gona Berisha
4. Miriam Rebecca Ermer
5. Christopher Hartl
6. Christien Splettstößer
7. Miriam Merget
8. Gülnihal Inci
9. Björn Dierkes 
10. Katarina Markovic
11. Benjamin Jädicke
12. Alicia Oberländer 
13. Jianjun Yang
14. Friederike Herrmann 
15. Giuliano Ballacchino
16. Jennifer Mik
17. Fabiana Salm
18. Edis Dukadjinac
19. Julia Gruebner



## Schedule: 
13:00 **Welcome**
- Questions? 
- Contine Unit 2

16:00 maybe more questions? 
- 16:00
- 16:10 Gona und Miriam


## Slides, Materials 

## Links 
You find a paper from a previous year here. Marie dropped it into a public repository (i.e. open for everyone to see)
https://github.com/MarieKoehler/Bioinformatik/blob/main/WS2021%20Bioinformatik/BioinformatikMaster_GruppeJ_MarieK%C3%B6hler.pdf


## Questions

Could you perhaps go through Task 3 and 4 of Unit 2 with us using an example, please?

Explain the ORF please again. 



************************

# Fri, Nov 26 2021
## Participants
1. Francesca Hoffmann (absent)
2. Christopher Hartl (absent in the beginning)
3. Gona Berisha 
4. Miriam Ermer
5. Carolin Dunker
6. Benjamin Jädicke
7. Alicia Oberländer
8. Jianjun Yang
9. Giuliano Ballacchino (missing)
10. Katarina Markovic
11. Miriam Merget
12. Edis Dukadjinac
13. Fabiana Salm
14. Björn Dierkes
15. Jennifer Mik
16. Friederike Herrmann 
17. Gülnihal Inci
18. Christien Splettstößer
19. Julia Gruebner
## Schedule 
13:00 **Welcome** 
- Organisation & questions?
- Intro: Sequence comparisons

14:00 **DataViz HelpDesk**
- Tutorial for web-tools to create pretty data plots, by Joachim Goedhart, University of Amsterdam. Tools: https://lnkd.in/dEatTqze. 
Zoom link: https://tu-dresden.zoom.us/j/85843314580?pwd=NEtDZlFTOFpvM0xMSFpVRUJBUVZ0dz09
Meeting ID : 858 4331 4580
Passcode: Boxpl0t!

15:00 Exercises Unit 3
(continue at your pace also next week + Monday 6th)

16:00 Questions
- 16:00
- 16:10 Caro
- 16:20



## Questions

Caro: In a paper where I find listed mutations in the gene of my protein, they state the "nucleotide alterations" and the "amino acid alterations". But I don't understand what the letters and numbers exactly mean. Could cou help me understand this (I hope it is okay, that I attach the following image)?

![](https://i.imgur.com/qwaJzqE.png)
(taken from O’Driscoll (2017) *Am. J. Hum. Genet.* )

Ist es Möglich, dass Sie die Materialien für Woche 2 schon hochladen? 

++Unit 3, Excercise 1.5:++ Which proteins are you talking about here? The proteins from species mentioned in 1.4: Human, C.elegans and E.coli? What should we do when we don't have hits for E.coli and C.elegans in BLASTP?
++Unit 3, Excersie 1.4, point 2:++ I don't know about the others but I barely learned sth about Taxonomy. How can I interpret the list which is shown under the "taxonomy" tab in BLASTP, how can I see which is the "most distant sequence"?
++Unit 3, Excercise 2.2:++ Same here, I never worked with Phylogeny and don't have knowledge about it. So could you explain what you want in excercise 2.2 and maybe show examples?


## Slides, Materials 
https://www.dropbox.com/sh/x8ocgfjhzu6ogvm/AAD-L_n2mQY35oe5VsqbOfJ1a?dl=0

Watch me find homologs with ENSEMBL
https://www.loom.com/share/ffda5cb0a5934b538f88c88d70f10576

https://www.loom.com/share/f442e612e5d44660ba34f00cdd1da6b2
## Links 


# Week 2
Mon, Dec 6 
- Continue unit 3

Tue, Dec 7
- Presentation of project (Breakout rooms, flipped presentation)
- Gene Expression (Unit 4)

Wed, Dec 8
- R programmieren (Unit 5)

Thu, Dec 9 
- R programmieren (Unit 5) 

Fri, Dec 10 
- DataViz  (Unit 6)
Exercise DataViz Yenai, use tools from Joachim Goedhart

2PM: Tutorial Inkscape (aka free Illustrator)

# Mon, Dec 6th 2021
## Participants
1. Gona Berisha
2. Miriam Ermer 
3. Edis Dukadjinac (a bit later due to an appointment)
4. Miriam Merget
5. Christien Splettstößer
6. Carolin Dunker
7. Fabiana Salm
8. Björn Dierkes 
9. Katarina Markovic
10. Julia Gruebner
11. Benjamin Jädicke
12. Jianjun Yang
13. Alicia Oberländer
14. Giuliano Ballacchino 
15. Gülnihal Inci
16. Jennifer Mik (had to go earlier)
17. Christopher Hartl

## Schedule
14:00 Brief check in with Helena, open Zoom for group works
15:30 Helena, organisational questions
- Friederike, Fabiana: please add you matrikel #
- Report of units 1-3, what do I expect? 
- 
16:00 Questions Unit 3 

## Slides, Materials 
Phylogenetic trees explained": 
https://www.dropbox.com/s/q1esdprcp8vhjy3/MSA_PhylogeneticTrees.pdf?dl=0

## Links 



# Tue, Dec 7th 2021
## Participants
1. Miriam Ermer
2. Christien Splettstößer
3. Björn Dierkes 
4. Gona Berisha
5. Friederike Herrmann
6. Carolin Dunker
7. Christopher Hartl 
8. Katarina Markovic
9. Miriam Merget
10. Jianjun Yang
11. Benjamin Jädicke
12. Alicia Oberländer
13. Gülnihal Inci (leave a bit early today)
14. Francesca Hoffmann
15. Edis Dukadjinac
16. Jennifer Mik
17. Giuliano Ballaccchino
18. Julia Gruebner

## Schedule 
13:00 Welcome, Report: current state of research 
- Breakout rooms, 15 min:
1. Katarina, Giuliano, Edis 
1. Christopher, Miriam M
1. Christien, Alicia
1. Friederike, Jennifer
1. Francesca, Benjamin
1. Gülnihal, Gona
1. Miriam E, Jianjun
1. Björn, Carolin
1. Julia
2. Fabiana [not joined]

- Each person summarises the state of the other persons project in 2 minutes. Goal: really talk with each other and try to understand each other!

14:00 Overview Gene Expression
14:30 - 17:00 time for exercises 

## Slides, Materials 
Exercises 
https://www.dropbox.com/s/qufikv0kzwg28ye/Unit%204.docx?dl=0

also posted above: phylogenetic trees:
https://www.dropbox.com/s/q1esdprcp8vhjy3/MSA_PhylogeneticTrees.pdf?dl=0

slide gene expression: 
https://www.dropbox.com/s/d12juyn3r94id9t/Gene_expression_EN.pdf?dl=0

## Links 


## Questions
- Phylogenetic trees vs Guidetree?
- Numbers next to the phylogenetic tree
- Do you want us to differentiate between discussion and results in the mini paper?
    - yes! But the discussion can be short (3 paragraphs: here I show this.... here I also show that... this means that next we can do that!) of course, since you do not have 3 years of data..   



# Wed, Dec 8th 2021
## Participants
1. Carolin Dunker (at the beginning)
2. Miriam Merget
3. Alicia Oberländer
4. Christien Splettstößer
4. Katarina Markovic
5. Christopher Hartl
6. Benjamin Jädicke
7. Francesca Hoffmann
8. Björn Dierkes 
9. Jianjun Yang
10. Giuliano Ballacchino
11. Friederike Herrmann 
12. Jennifer Mik
13. Edis Dukadjinac
14. Miriam Ermer (at the beginning)
15. Gülnihal Inci
16. Gona Berisha (a little late due to an appointment)
17. Julia Gruebner

## Schedule 
13:00 Introdciution to R and R Studio
I have no/little experience with R 
- Christopher Hartl (no experience)
- Björn Dierkes (no experience)
- Miriam Merget
- Gülnihal Inci
- Katarina Markovic (no experience)
- Jennifer Mik (no experience)
- Christien Splettstößer (no experience)
- Alicia Oberländer (no experience)
- Benjamin Jädicke
- Jianjun Yang (no experience)
- Julia Gruebner (none)
- Edis Dukadjinac (no experience)
- Giuliano Ballacchino (no experience)
- Francesca Hoffmann (no experience)


I know how to use R
- Gona Berisha (not an expert :))
- Carolin Dunker (its a loooooong time ago but same as Gona)
- Miriam Ermer (same like Gona and Caro we all in the same course)

## Question Unit4
* Miriam M.: What is the difference between TPM and FPKM Express value?

https://www.rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained/


## Slides, Materials 
https://www.dropbox.com/sh/5aes2pc0ac16dhk/AADXPpuJVDSyaPQJpHYvoJ-da?dl=0

## Links 

# Thu, Dec 9th 2021
## Participants
1. Katarina Markovic (possibly late at the beginning)
2. Francesca Hoffmann
3. Christopher Hartl 
4. Gona Berisha
5. Christien Splettstößer
6. Miriam Ermer
7. Carolin Dunker
8. Alicia Oberländer
9. Gülnihal Inci
10. Miriam Merget
11. Jianjun Yang
12. Björn Dierkes
13. Benjamin Jädicke 
14. Edis Dukadjinac
15. Jennifer Mik
16. Friederike Herrmann 
17. Giuliano Bllacchino
18. Julia Gruebner

##Question
can you show us how to do a bloxplot in R?

## Schedule 
13:00 unit descirtopn 

16:30 anyone has question? 
--> ==yes, Gona and Miriam have some==
AHH, just saw now, coming 

## Questions

**++Caro:++**
![](https://i.imgur.com/RtvabBJ.png)
phylogenetic tree:
(
NM_008756.2:0.16441,
NM_001003195.1:0.05804,
(
NM_001205254.2:0.00999,
XM_034959994.1:0.00913)
:0.09028);

--> Dont know what to do. Bei den anderen funktioniert es. Ich denke es liegt am phylogenetischen Tree (siehe oben)

Helena: Das sieht gut aus eigentlich. Man musste ja sich entscheiden was der root sein soll, hattest Du das gemacht?
das war das 'reroot' command. 

--> Ich hab es jetzt hinbekommen, aber nur unter Umständen indem ich das FASTA Dokument, dass ich mit R gespeichert habe, dubliziere, den Inhalt lösche und den Phylogenetischen Tree Code dort einfüge (und danach den suffix auf .nwk ändere). Dann funktioniert es. Wenn ich ein komplett neues Text-Dokument erstelle (ich benutze auch MacOS), und dort den Code einsetze, dann funktioniert es komischerweise nicht...

Helena: ich habe copy&paste von CLustalOmega gemacht. Ich finde es sehr komisch, dass man da keine .nwk Datei herunterladen kann... 

Miriam: Inwiefern copy&paste?
Bei ClustalOmega sieht man ja den Ohylogenetischen Tree und unter dem Tab 'Guidetree' den guidetree und 'Results Summary' konnte man den phylogenetischen Tree die Daten anklicken und das wird dann in einem neuen Browser Window angezeigt und daraus habe ich dann die Daten kopiert. Also NICHT den Text kopiert unter dem Phylo-Tree sondern tatsächlich das Dokument aufgemacht bei Results.
Evt ist das auch eine Lösung für @caro0310 ?


--> Caro an Miriam: hab ich beides ausprobier, beides nicht funktioniert. Funktioniert nur so wie oben beschrieben

:smirk: hauptsache es geht irgendwie... 

Habe es immer noch nicht geschafft.. aber ich arbeite dran :D
Gülnihal: hab ein ähnliches problem. wenn ich die datei als nwk. datei speichern will und dann in r offenen sagt r mir die datei kann nicht gelesen werden



## Slides, Materials 
2 exercises: 
- a little statistics in R --> just pretend this is something about your protein in the paper and include the histogram and t-test result
- make a fasta in R, use it for ClustalOmega, get the tree and create a beautiful tree in R
https://www.dropbox.com/sh/b935ms998eh8ulk/AAAQCpIk85OcATd5_t-2llpba?dl=0


**I forgot one info!!!** 
To save your plot you have 2 options: 1. in the tab "plots", you can usually use "save as" and chose PNG or PDF. 2. Alternatively you can also create your PDF as part of your R script! Add the commands below: 
#Create a pdf output file this will be saved into the same working directory 

```{r}
pdf("MyPhylotree.pdf") #this switches on the pdf writer
plot(reroot_Helena, node.depth = 1, tip.color = tipcol, edge.color = edgecol, main = "KIFAA protein similarity") #or whatever you have as final plot
dev.off() #this switches off the PDF writer
```

## Links 

# Fri, Dec 10th 2021
## Participants
1. Giuliano Ballacchino (Internet Breakdown of Vodafone)
2. Gona Berisha
3. Christien Splettstößer
4. Alicia Oberländer
5. Gülnihal Inci
6. Miriam Ermer
7. Christopher Hartl
8. Katarina Markovic
9. Francesca Hoffmann
10. Miriam Merget
11. Benjamin Jädicke
12. Jennifer Mik
13. Carolin Dunker
14. Friederike Herrmann
15. Edis Dukadjinac
16. Jianjun Yang




## Schedule 
-- we have to start later! --
14:00 DataViz Academy: 
Jerome Mutterer: Reproducible figures with inkscape, ImageJ and R
Scheduled: 10. Dec 2021 at 14:00 to 15:00
Topic: DataVis Help Desk 
https://tu-dresden.zoom.us/j/85843314580?pwd=NEtDZlFTOFpvM0xMSFpVRUJBUVZ0dz09
Meeting ID: 858 4331 4580

15:00 - 15:30 A few more tips for Data Visualization
- colors 
- how to make a boxplot with R

## Slides, Materials 
Slides dataviz
https://www.dropbox.com/s/353ibj5csxgb0pg/DataVisualization.pdf?dl=0


# Save & convert HackMD file
Use the ... symbol in the top left corner of the HackMD page. Then Download the .md file  
- the html file can be viewed in any browser window and view - it will look like the HackMD document but it will no longer be changable. 
- the .md file can be opend in RStudio!! 

Convert from .md to e.g. .docx
1. Open command line
  - Mac und Linux: Terminal
  - Windows: Powershell

2. Find the folder in which your html document is saved to, move into that folder containing your .md document
(Pro-tip: this is faster if not a subfolder of a subfolder of a subfolder) 
View current folder: type `pwd` and press `Enter`
Show the content of current folder: type `ls` 
Change the folder: type`cd` ("change directory")
    Type `cd` followed by name of subfolder you want to move to 
    Type `cd ..` to move a folder up

3. Now execute pandoc 
The line should read pandoc, followed by the name of the file you want to convert, followed by the destination file you want to create. 

For word:
```
pandoc Name_of_File.md -s -o NewName.docx
```
for pdf: 
```
pandoc Name_of_File.md -s -o NewName.pdf
```
or if you downloaded the html: 
```
pandoc Name_of_File.html -s -o NewName.pdf
```

!!! if there is a empty space in your name you have to remove it/rename it before converting! 

4. Your word file or pdf will appear in the SAME folder as your template .md

     - `pandoc` calls the program
     - `Workshop-MD-Kurzanleitung.md` defines which is your template file
     - `-s` tells pandoc to create a "standalone document" 
     - `-o` means output
     -  `Workshop-MD-Kurzanleitung.docx` is the destination/output file and you give it the file format ending you need. 

More information about pandoc 
[Getting Started](https://pandoc.org/getting-started.html#)
[pandoc-Manual](https://pandoc.org/MANUAL.html)
or: google is your friend. 



# Abgabe, Coursework what counts?

## Questions before the 'Abgabe'
- no questions Monday 13 :)
- no questions Tuesday 14



## Information for Abgabe/coursework 
https://www.dropbox.com/sh/bnt113nehrqsypj/AAAEsGC0m3Kf_e01qbBHvq7Wa?dl=0

1. Do presentation Tuesday 7th Dec
2. Hand in the mini-paper 
max. 5 page writing including: 
- Introduction
- Methods (e.g. table with accesssion numbers "database")
- Results with figures
- Discussion (inlcuding a statement: what is next to answer the gap? More bioinformatics? Actual experiments?)
- References 
- Figures as many as you like WITH figure legend (Abbildungsdunterschrift)

3. Revision of the paper
You get a chance to improve the paper based on my comments. If you are happy as is you can also opt to not improve :smiley: 

## Zoom-office hour to discuss open questions
I will comment on questions you have on my feedback, I will not re-do the course :) 
Time: 
Wednesday, 26th January, 14:00 - 15:00, please sing in
* 14:00 Carolin Dunker
* 14:10 Gona Berisha and Miriam Ermer
* 14:20 Giuliano (Wednesday 26.01 or Friday 28.01 ???)
    * Wednesday 26th.. soryr! If you can only make it Friday let's talk about that (HKJ), best: send me Email.
* ...
* 
Can't make it on Wed? Propose an alternative time & I have a look in my calendar. 

==Question (Gona): Do you mean the 26th of January? The 28th is a Friday :)==
HKJ: yes, yes yes... I am busy Friday

## Dates
DATE: Hand in paper December 17th. 
VIA MOODLE

Alicia and Giuliano 23.12.21 -> Minipaper handed in by mail 
Gona und Miriam 19.12.21
Jianjun 22.12.21



Example: 

You find a paper from a previous year here. Marie dropped it into a public repository (i.e. open for everyone to see)
https://github.com/MarieKoehler/Bioinformatik/blob/main/WS2021%20Bioinformatik/BioinformatikMaster_GruppeJ_MarieK%C3%B6hler.pdf



