12/02/2019 - 13/02/2019

EMBL Heidelberg
Meyerhofstraße 1
Heidelberg, Germany

Intermediate Linux Command Line & Basic Scripting

Code: shellscripting-2019
Price: 30 EUR pro Platz (VAT excl.)
Location: EMBL
Available seats: 30


Date, Time and Venue:

The course will take place on February 13, 9:30 am to 17:00 pm at the EMBL ATC computer training lab.

About the Course:

This course will teach you the basics of the most powerful aspects of command line computing on Linux operating systems and other Unix environments such as Mac OS X. Knowing how to quickly and specifically access information from huge files, customise your working environment, and write scripts to make your analyses automated and flexible, is extremely valuable and powerful for modern biological research. The skills that you learn on this course could save you a huge amount of time in the future, as well as ensuring that your research is more reproducible by making it easy to maintain consistency across the analysis of many samples.

This course is aimed at users who have basic knowledge of Linux commands (man, cd, pwd, cp, rm, mkdir, cat, less, grep, head, ssh etc.), perhaps from attending the other Bio-IT course, “Introduction to Linux Command Line”.

If you don’t have prior knowledge of these commands, please attend the introductory course taking place on February 12.

The course material covers:

  • advanced methods for extracting and working with data from text files (gzip, tar, grep, cut, sort, sed, awk)
  • setting and working with the environment and shell variables
  • the basics of scriptwriting in bash
  • Script syntax will focus on bash.

Maximum capacity for the course is 30 participants and registration is required to secure a place.

Course Fee:

EMBL Bio-IT will offer the course for free to all EMBL members.

External participants will be charged with a course fee of 30 Euros (to cover the lunch and infrastructure related cost). The invoice details will be shared via email.

Cancellation and No-Show:

Registration can be canceled free of charge until Friday 8th February 2019.

All participants will be charged a cancellation fee (if canceled after 8th Feb 2019) or no-show fee of 30 Euros. For EMBL members, this charge will be made to their group budget.


Please register by visiting EMBL Bio-IT’s official announcement page

If you have any questions, please contact Malvika Sharan and Toby Hodges by emailing