Frank Thommen (DKFZ) Jules Kerssemakers (DKFZ) Malvika Sharan (EMBL) Johannes Werner (DKFZ) (HD-HuB)

26-28 June, 2017 Location: Heidelberg Center for Human Bioinformatics (HD-HuB) Institute of Pharmacy and Molecular Biotechnology (IPMB) 5th floor, Im Neuenheimer Feld 364, 69120, Heidelberg

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 understend 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 large number of files to carry out identical or similar analysis using computers.

Programming; Command Line; Version Control; Bioinformatics; Data Analysis

Bash; Unix/Linux; shell, Git; GitHub

Malvika Sharan
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