Python Programming with Application to Bioinformatics, 2 hp


National course open for PhD students (prioritized), postdocs, researchers and other employees in need of bioinformatic skills within all Swedish universities.

Description

This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are lead 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.

Important dates

Application open: October 26

Application deadline: December 4

Acceptance Confirmation: December 11

If you don’t receive information according to the dates above, contact education@scilifelab.uu.se.

Audience and Prerequisites

  • 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 course are available at SciLifeLab for it.
  • Bring your own laptop (Linux, or Mac) for the practical exercises. Otherwise, please contact us at education@scilifelab.uu.se before you apply.

Course content

Course webpage

During this course you will learn about:

  • 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 objectives

After the end of the course you should be 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)

Format

  • Presentations and demonstrations
  • Practical exercises (either in the lab with assistants or on your own).

Main teacher: Frédéric Haziza

Prior to the course, you can read a companion book “Programming Python”, or “Learning Python”. Such a book will also prove useful for your programming tasks, after the course is over. It is however not required, and material will be presented in class.

Course fee

A course fee of 1800 SEK will be invoiced to accepted participants (includes the study material, coffee, lunches and course dinner). NOTE – Uppsala University cannot invoice individuals.

Related courses

Perl Programming with Application to Bioinformatics, 2 hp

Selection criteria

Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.