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Online Course – 1st Edition

Introduction to Bash for Bioinformatics

December 1st-4th, 2020

Statistics and Bioinformatics

Statistics and Bioinformatics

This course will be delivered ONLINE: 12 hours of online live lessons,  plus 9 hours of assignments. A good internet connection is required to follow the course.

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.




This course will be delivered online.

Please check the schedule for the live online part, and be aware that it is GMT+1.


December 1st-4th, 2020




21 hours Online.

This course is equivalent to 1 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.

The recognition of ECTS by other institutions depends on each university or school.


Places are limited to 16 participants and will be occupied by strict registration order. If the course fills up there will be an assistant instructor to help during the practise time.

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

Juan Rodriguez Instructor Transmitting Science

Dr. Juan Rodríguez



  • 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 October 31st, 2020):
  • 374 € *
    (299.2 € for Ambassador Institutions)
  • Regular (after October 31st, 2020):
  • 445 € *
    (356 € for Ambassador Institutions)
  • This includes the course material (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.

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


  • Tuesday to Friday (GMT+1):
    • 15:00 to 18:00 online live lessons.

The rest of the time will be taught with recorded classes and assignments, to be done between the live sessions.


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 the country were the course will be held, as well as PhD students based in that country without any grant or scholarship to develop their PhD, could benefit from a 40 % discount on the Course Fee. If you want to ask for this discount, please contact the course coordinator. That would apply for a maximum of 2 places and they will be covered by strict inscription order.


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