Python programming with applications to bioinformatics – ONLINE

October 18, 2021 October 22, 2021

Python programming with applications to bioinformatics – ONLINE

October 18 @ 08:00 October 22 @ 17:00 CEST

National course open for PhD students, postdocs, researchers and other employees in need of fundamental Python skills within all Swedish universities.

Important dates

Application opens: June 21
Application closes: September 4
Confirmation to accepted students: September 8
Responsible teachers: Nina Norgren, Dimitris Bampalikis

If you do not receive information according to the above dates please contact: Nina Norgren (

Course fee

No course fee will be invoiced for online courses. However, if you accept a position at the course and do not participate (no-show) you will be invoiced 2000 SEK.
*Please note that NBIS cannot invoice individuals

Course description

This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are led through the core aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs from scratch and to customize more complex code to fit their needs.

Course content

  • Core concepts about Python syntax: Data types, blocks and indentation, variable scoping, iteration, functions, methods and arguments
  • Different ways to control program flow using loops and conditional tests
  • Regular expressions and pattern matching
  • Writing functions and best-practice ways of making them usable
  • Reading from and writing to files
  • Code packaging and Python libraries
  • How to work with biological data using external libraries.

Learning outcomes

  • Describe and apply basic concepts in Python, such as:
    • Loops
    • If/else statements
    • Functions
    • Reading/writing to files
  • Being able to edit and run Python code
  • Write file-processing Python programs that produce output to the terminal and/or external files
  • Create stand-alone python programs to process biological data
  • Know how to develop your skills in Python after the course (including debugging)


Presentations and demonstrations. Practical exercises (either in the lab with assistants or on your own). Presentations will be given online, mixed with exercises where teaching assistants will be available online to help with the exercises.

Entry requirements

The course is suitable for complete beginners and assumes no prior programming experience (beyond the ability to use a text editor). A very basic knowledge of UNIX would be an advantage, such as navigating through folders and issuing commands at a shell prompt. We will not teach UNIX in detail: Other courses are available at SciLifeLab for it. Make sure your laptop has python installed for the practical exercises.

Due to limited space the course can accommodate a maximum of 30 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.

Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits, however the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.

Last updated: 2021-06-02

Content Responsible: Maria Bäckström(