Bioinformatics with Linux and Python

  • 20 February - 03 March 2023
  • Mornings 9:00-12:30
  • Online
  • Methodology
  • 1.5 ECTS

Course description

Linux and Python, a dynamic, readable programming language, is a popular combination for all types of bioinformatics work, from simple one-off scripts to large, complex software projects. This workshop is aimed at complete beginners and assumes no prior programming experience. It gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. The workshop is structured so that the parts of the language most useful for bioinformatics are introduced as early as possible, and that students can start writing plausibly-useful programs after the first few sessions. After completing the workshop, students should be in a position to (1) apply the skills they have learned to tackling problems in their own research and (2) continue their Linux and Python education in a self-directed way.

Course programme (subject to small changes):

Session 1 – connecting to the server and basic Linux commands Session 2 – assembling Linux commands into pipelines Session 3 – introduction to bash scripting and variables Session 4 – biological pipelines and data formats Session 5 – introduction to Python, text and files Session 6 – lists and loops in Python Session 7 – conditions in Python Session 8 – writing functions in Python Session 9 – paired data and dicts in Python Session 10 – programming workshop: develop you own ideas

Course organisation

Course coordinator (for more information)

Elackiya Sithamparanathan, e-mail:, tel: +31 (0) 6 8731 6681

Course fee

  • WUR PhDs with TSP: €260 (early bird) / €310 (regular)
  • SENSE PhDs with TSP: €520 (early bird) / €570 (regular)
  • All other PhD candidates: €560 (early bird) / €610 (regular)
  • Staff of WUR Graduate Schools including Postdocs / graduate schools mentioned above: €560 (early bird) / €610 (regular)
  • All others: €600 (early bird) / €650 (regular)


  • Early bird registration deadline: 20 January 2023
  • Regular registration deadline: 1 February 2023
  • Go to registration form

N.B.: This course gives priority to VLAG and WIMEK PhD candidates due to the limited space available.

Former occurrences of this course

10-21 May 2021   |   16-20 March 2020

  • WIMEK and VLAG, Wageningen University
  • Yearly
  • Dr. Martin Jones (founder of Python for Biologists)
  • 12-15 participants
  • Entree level programming. No modelling skills are needed. However, this course is heavy on bioinformatics and programming, so the interest to improve your modelling and programming skills is a requirement.