December 13-15, 2017 | CIBIO-InBIO, Vairão, Portugal


This practical course will let the users to learn some useful tricks for file handling through command line scripting. Everyday is more and more important having practice in installing software and be able to run it using high performance computing what means execute them through command line.
Some programs inputs/outputs are not 100% compatibles between them, or there are some particular necessities that we need to cover rather than the standards, so is in this scenario where the knowledge on basic scripting saves us enormous time.

The course will be focused on basic command line functions and redirections to other ones, as well as some clues of how to use ‘sed’ and ‘awk’ for quick file modifications. Finally an introduction to ‘Perl’ will be taught for making a bit more complex scripts.


Wednesday, Dec 13 (9:30-13:00 | 14:30-17:00)
0.- Basics on Linux. Command line and shortcuts for making easy work with plain text files.
1.- Sed and awk. Easy file modification from prompt.


Thursday, Dec 14 (9:30-13:00 | 14:30-17:00)
2.- Sed and awk. Exercises.
3.- Perl basics: Functions and nomenclature.


Friday, Dec 15 (9:30-13:00 | 14:30-17:00)
4.- Perl examples and exercises.

5.- Review of results and doubts.


Antonio Muñoz - CIBIO-InBIO | Bioinformatics


The course will be open to a maximum number of 25 participants.

All the participants will be required to have previously set a Unix system in their laptops (OSX or Linux).
Priority will be given to:
• 1st year and other PhD students attending the BIODIV Doctoral Program;
• PhD students attending other courses;
• Other post-graduate students and researchers.


Registration Deadline: October 22, 2017


Participation is free of charge for BIODIV students | 65 € (students) / 125 € (other participants).CIBIO-InBIO members will have an additional discount of 20%. Does not include lunch nor coffee breaks.
To apply, please send an e-mail accompanied by your short CV (max. two A4 pages) to Please refer your academic status (PhD student, MSc Student, Other) and the institution to which you are affiliated. BIODIV students should also mention which year of their PhD they are in. If you are interested in more than one course, you need to send a separate application for each of them. All applicants will be notified about whether they are accepted by October 29, 2017.


Please note that new rules apply for all BIODIV students.