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Online Course – 1st Edition

Introduction to Bash applied to Bioinformatics

October 17th-20th, 2022


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This course will be delivered live online

Online live sessions from 15:00 to 18:00 (Madrid time zone).

Live sessions will be recorded. Recordings will be made available to participants for a limited period of time. However, attendance to the live sessions is required.

Course Introduction to Bash for Bioinformatics

Course overview:

Bash is the universal base programming language of bioinformatics. It is the basic structure for any current bioinformatics analysis, from the most basic to the most advanced computational biology pipelines. This course is oriented to researchers who want to start performing their own bioinformatics analyses, from a very basic level.

The course will cover brief introductions to the different functions, their applications, large text file processing tools, and finally some applied problems. Also, hands-on sessions with will be run to put into practice the knowledge acquired after each session. In brief, if you want to overcome the fear of facing a “black terminal screen”, this course is for you!

Course Requirements

All participants must have a personal computer. If your computer is Windows we will send you instructions about how to install a terminal in it. Webcam and headphones are strongly recommended, and a good internet connection.




October 17th-20th, 2022

Schedule and Course length

Online live sessions from Monday 17th to Thursday 20th, 2022, from 15:00 to 18:00 (Madrid time zone).

14 hours live online.

Live sessions will be recorded. However, attendance to the live sessions is required.




Places are limited to 18 participants and will be occupied by strict registration order.

Participants who have completed the course will receive a certificate at the end.

Juan Rodriguez Instructor Transmitting Science

Dr. Juan Rodríguez

GLOBE Institute


Haris Saslis coordinator for Transmitting Science

Dr. Haris Saslis
Transmitting Science


  • Introduction to the Linux Operating System
  • General basics
  • First contact with the shell (Bash Terminal)
  • Basic system commands
  • File system
  • Why Bash for Bioinformatics?
  • Introduction to Bash
  • Text editors
  • Working with text files
    • sed and awk as file processing tools
    • Quick commands (“one-liners”)
  • My first bash script
    • Variables
    • Loops and conditionals (for, if, while)
  • Bash applied to solve common problems in bioinformatics
    • Problem 1
    • Problem 2
    • Problem 3
    • Problem 4
  • Good practices and structure of the programs.


  • Course Fee
  • Early bird (until September 30th, 2022):
  • 256 €
    (208.8 € for Ambassador Institutions)
  • Regular (after September 30th, 2022):
  • 310 €
    (248 € for Ambassador Institutions)
  • This includes course material (VAT included).
    After registration you will receive confirmation of your acceptance in the course. Payment is not required during registration.

You can check the list of Ambassador Institutions. If you want your institution to become a Transmitting Science Ambassador please contact us at communication@transmittingscience.com


Discounts are not cumulative and apply only on the Course Fee. We offer the possibility of paying in two instalments (contact courses@transmittingscience.com).

Former participants will have a 5 % discount on the Course Fee.

20 % discount on the Course Fee is offered for members of some organizations (Ambassador Institutions). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).

Unemployed scientists living in Spain may benefit from a 40 % discount on the Course Fee. If you would like to enquire about this discount, please contact the course coordinator. That would apply for a maximum of 2 places and they will be covered by strict registration order.