Detailed information about the course

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Computer Skills for Biological Research: Introduction to GNU/Linux and Bash Scripting


23 - 27 August 2021

Responsable de l'activité

Mathias Currat


Dr Mathias Currat, University of Geneva
Dr Jose Manuel Nunes, University of Geneva


Dr Mathias Currat, University of Geneva
Dr Jose Manuel Nunes, University of Geneva


This course intends to present useful computer tools and techniques for young researchers in biology that substantially extend basic computer knowledge acquired at undergraduate levels. The course concentrates on GNU/Linux environment and tools because it is powerful, free and easy to install in any kind of computer. Moreover, most of the computer clusters available for scientists run Linux.

The course is intended for beginners and for more advanced people, its level of complexity increasing through the four days. Basic knowledge in computing and programming is a plus but is not mandatory. The first part of the course will consist in learning the basic of GNU/Linux: installation of the environment, useful shell commands to work with text files, simple command lines and the use of regular expressions, pipes, and short scripts. The second part will consist in developing more complex scripts, as well as exercises using a computer cluster.

Upon conclusion of the course the attendees are expected to be able to:

  • use comfortably GNU/Linux workstations environments
  • work with shells and write shell scripts,
  • manipulate data files and perform file format conversions,
  • be able to read and write simple regular expressions,
  • use GNU/Linux computer clusters.

The training will provide a minimal theoretical basis in each of the topics listed below and concentrate on practical aspects through numerous applications. It will confer a working autonomy to solve problems while handling data and conducting data analyses pertinent to the researcher in biology.



Topics covered include:

1. GNU/Linux workstation, shell and command line utilities

2. Programming in the shell

3. Regular expressions

4. Working with computer clusters


University of Geneva


Full attendance and active participation




23 - 27.08.2021




At the Unoversity of Geneva, or online, depending upon the current sanitary situation




Marta Bellone






PhD students of the DPEE are eligible for the reimbursement of incurred travel expenses by train (half-fare card, and 2nd class).

The online reimbursement system is now in place, so once the course is over you will be able to request the reimbursement via MyCUSO, without sending the paperwork to me. More information: Reimbursement


In case of onsite teaching, please contact the coordinator of the doctoral program (ecologie-evolution(at) BEFORE the beginning of the course. NO reimbursement of accommodation without the coordinator of the doctoral program agreement prior of the course. In case of overnight stay, please post the original tickets and original bills along with the reimbursement form to:

Marta Bellone
Doctoral Program in Ecology and Evolution
Department of Biology
University of Fribourg
Chemin du Musée 10
CH-1700 Fribourg

NO reimbursement of meal expenses


Through your myCUSO account!

Deadline to register: 08.08.2021

Priority is given to DPEE PhD students until 15 July 2021. After this deadline, first comes, first serves!

Registration Fees:

In case of cancellations, before the deadline: free
Late cancellations or no-show: Administrative fee of 50 CHF will be demanded
Other participants: please contact the program coordinator at ecologie-evolution(at)



Deadline for registration 08.08.2021
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