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



Lang EN Workshop language is English

Dr Mathias Currat, UNIGE


Dr Mathias Currat, UNIGE
Dr Jose Manuel Nunes, UNIGE


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: GNU/Linux workstation, shell and command line utilities; Programming in the shell; Regular expressions; Working with computer clusters.





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