Introduction to Linux Command Line & Basic Scripting

Malvika Sharan   2018-06-26   Comments Off on Introduction to Linux Command Line & Basic Scripting

Date(s) - 2018-06-26 - 2018-06-27
09:30 CEST - 16:30 CEST


  • Frank Thommen: DKFZ Heidelberg, Omics IT and Data Management Core Facility
  • Malvika Sharan: Bio-IT, EMBL-HD
  • Helpers (TBA)

Course Description

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. This course will be offered in collaboration with Omics IT and Data Management Core Facility of DKFZ Heidelberg.

Course Modules

  • Basic commands of Linux/shell
  • The principle of shell scripting

Course Outcome

This course will provide an introduction to the basic UNIX (linux/Mac OS X) commands and principle of scripting. By the end of the course the participants should be confident and competent in navigating around a linux filesystem, performing file operations and finding help on the commandline. With the scripting skills, the participants will be able to understand (and modify) the scripts they are using (and which they probably have received from someone else).

Learning Objectives

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 of 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.


Please register for the course here:

Please note that the maximum capacity for the course is 30 participants and registration is required to secure a place. If you have any questions, please contact Malvika Sharan.

Course Fee:

This course will be offered for free to all EMBL members.

The external participants will be charged with a course fee of 60 Euros (to cover the lunch and infrastructure related cost). The invoice details will be shared via email.

Cancellation and No-Show:

The registration can be canceled for the free of charge until June 18, 2018.

The participants will be charged a cancellation fee (if canceled after June 18, 2018) or no-show fee of 50 Euros. The invoice details will be shared via email.

About Malvika Sharan

I am a Community Outreach Coordinator for Bio-IT and Training Coordinator for ELIXIR Germany. Find me at EMBL-HD office 101 or at Bio-IT drop-in Sessions on Tuesdays 10:00-12:00 at the EMBL staff lounge. Contact Details: email -, Twitter -, GitHub -