Course Materials

See this page for help with obtaining teaching material from GitLab and GitHub.

Bio-IT CoursesLSI-1_5

Follow the links below to access materials for Bio-IT courses. You might also be interested in our list of useful cheat sheets.

Introduction to Python Programming
Maintainer: Renato Alves previously Toby Hodges
homepage | pdf

Image Analysis with Python
Maintainer: Jonas Hartmann
homepage

Introduction to R Programming
Maintainer: Nicolas Descostes
homepage

Introduction to Linux Command Line
Maintainer: Renato Alves previously Toby Hodges
homepage | pdf

Intermediate Linux Command Line
Maintainer: Renato Alves previously Toby Hodges
homepage | pdf

Git Fundamentals
Maintainer: Renato Alves previously Toby Hodges
homepage | pdf

Introduction to Regular Expressions
Maintainer: Renato Alves previously Toby Hodges
homepage | repository

Scientific Data Management
Maintainer: Renato Alves previously Toby Hodges
homepage

Snakemake Training

Snakemake Example
Maintainer: Christian Arnold
homepage

Snakemake Tutorial
Maintainer: Thomas Schwarzl
homepage

Cluster Training

Introduction to High Performance Computing at EMBL
Maintainer: Mike Smith
course repository

Hands-On with the New EMBL HPC Cluster
Maintainer: Jure Pečar
slides

jug @ EMBL
Maintainer: Renato Alves
slides | repository

Wrapping tools with merit
Maintainer: Markus Fritz/GBCS
slides
merit repository

Singularity Training

Introduction to Container Computing with Singularity
Maintainer: Josep Moscardó
course repository

CSDA Courses

Biostatistical Basics
Maintainer: Sarah Kaspar
course home page

Older CSDA course materials can be found at Bernd Klaus's homepage. They include:

  • Introduction to R (using the tidyverse)
  • Data handling and graphics with R (using the tidyverse)
  • Exploratory data analysis and ggplot2
  • Statistical methods for bioinformatics
  • Hypothesis testing
  • Differential expression analysis of RNA-Seq data with DESeq2
  • Machine learning
  • Analysis of high throughput microscopy data

CBNA Courses

Materials from courses taught by the Centre for Biomolecular Network Analysis are available via the CBNA pages. Courses include:

  • Introduction to Network Biology
  • Cytoscape (introduction & intermediate)
  • Chromatin Signatures During Differentiation (EMBl course)
  • Networks and Pathways (EMBL-EBI course)
  • Integration of Transcriptome and Proteome (EMBL course)
  • From Beginner to Intermediate in 3 Days Omicron Workshop on Network Biology (Jagiellonian University, Collegium Medicum)
  • Intermediate Network Analysis - Automation and Scripting in Cytoscape and R iGraph

CBM Courses

Introduction to MATLAB
Maintainer: Eva Geissen
homepage

PreDoc Course

What is version control (with git)
Maintainer: Renato Alves
slides | repository

Introduction to Python
Maintainer: Renato Alves
slides | repository

Introduction to Python IO and plotting
Maintainer: Renato Alves
slides | repository