26/06/2017 - 28/06/2017

IPMB, Heidelberg University
Im Neuenheimer Feld 364
Heidelberg, Germany

Introduction to Linux and Version Control

Code: 2017-Linux-GIT
Price: 90 EUR pro Platz (VAT excl.)
Location: IPMB, Heidelberg University
Available seats: 30



June 26 – June 28

Start time: 09:30 am (every day)

End time: 17:00 pm (except on the June 28 the course finishes at 14:30 pm)


Linux is an operating system with a powerful command line interface that is widely used for biological data analysis and in server and cluster systems. A knowledge and understanding of how to interact effectively with the command line is essential when using many popular bioinformatics software packages, efficiently performing repetitive computational tasks, and working in high-performance computing cluster environments.

Course contents:

–    Basic commands of Linux/shell (one day)
–    Principle of shell scripting (one day)
–    Using git for version control (half day)
–    Optional supervised practice (half day)
At the end of the course, the participants will be able to understand (and modify) the scripts they are using (and which they probably have received from someone else).
Learning goals:

This course aims to teach basic commands and shell scripting to the life scientists who wish to carry out repeated tasks to deal with biological data.

The goal of the course is to enable participants:
–    to use the shell interactively
–    to understand and modify given scripts
–    to write their own scripts


We do not expect the participants to have any prior knowledge with scripting or version control. This is a course for the researchers who wish to automate their tasks such as dealing with a large number of files to carry out identical or similar analysis using computers.

Course tutors:

Frank Thommen

Jules Kerssemakers

Johannes Werner

Malvika Sharan

Konrad Zych

Course Schedule:


9:30-11:00 Linux-1 (basic for absolute beginners)

11:00-11:15 Coffee Break

11:15-12:30 Linux-2

12:30-13:30 Lunch Break

13:30-15:00 Linux-3

15:00-15:30 Coffee Break/discuss with trainers

15:30-17:00 Linux-4


9:30-11:00 Git – 1

11:00-11:15 Coffee Break

11:15-12:30 Git – 2

12:30-13:30 Lunch Break

13:30-15:00 Linux-5

15:00-15:30 Coffee Break/discuss with trainers

15:30-17:00 Linux-6


9:30-11:00 Review

11:00-11:15 Coffee Break

11:15-12:30 work on your own data

12:30-13:00 Wrap-up and feedback

13:00-14:30 Lunch and End of the course