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# System prepended metadata

title: Bioinfo-Club

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# Bioinfo-Club

## Schedule
_please add new topics from the top_
- 2023-11-09: Max (Leipzig) about his project in NZ
- 2023-10-26: Max (Berlin) about data science of MD of GPCRs
- 2023-09-13: Christina intro ML and Pitfalls
- 2023-08-31: Chistiane about sex-based differences in gene expression
- 2023-07-06: Max (Leipzig) about CRISPR 
- 2023-06-22: Sascha about Docker
- 2023-06-08: Julie about Snakemake 
- 2023-05-23: Christopher about telomere repeats
- 2023-04-24: Sarah about new project
- 2023-04-04: First meeting again, Karl and general things

## General questions
### When do we want to meet? 
-  Every second week thursday at lunch time (12-13) 

### Wishes for future topics? 
- multi-omics (Tobias?)
- 

### Stuff i learned
- Christina:
    - splice-variant analysis with StringTie
    - web development with dash (python)
    - molecular mechanisms of tumorgenesis (mutations, altered pathways...)
    - survival analysis with kaplan-meier, cox-PH model, random survival forest, deep learning models (DeepSurv)
    - machine learning models, such as SVM, Random Forest, Neural Networks, regularization 
- Max: 
- Christopher:
- ...

## Interesting stuff, nice bioinfo links...

### Coding

#### A list of genome visualization tools: 
https://cmdcolin.github.io/awesome-genome-visualization/?latest=true
* Python package for genome visualization https://github.com/moshi4/pyGenomeViz

#### Docker and Snakemake

This is an example for CWL (and a bit subprocess🌚)
https://github.com/julie-tooi/baikal_amphipod_pipelines/tree/master

CWL documentation: https://www.commonwl.org/user_guide/

This is a Snakemake example: https://github.com/xamiiii/Led-Seq

Snakemake documentation with really nice tutorial: https://snakemake.readthedocs.io/en/stable/index.html

SnakeCharm for interested people🌚 https://plugins.jetbrains.com/plugin/11947-snakecharm


### Theory 