Practical Introduction to Computer science for biologists and biochemists

This course is open to Master students from the Bioinformatics Master Program of Université Lyon 1, especially to those with an initial training in Biology or Biochemistry. It is coordinated by Carole Knibbe and Arnaud Mary. In this course, students learn:

  • how all types of information (text, images...) are encoded with bytes,
  • how to interact with Linux, both with the graphical interface and the command line,
  • how to activate the Linux firewall,
  • how to make backups of their data on Linux,
  • how to write a simple Shell script,
  • what is a relational database,
  • in which situtations a relational database is a better option to store data than a set of text or Excel files,
  • how to write simple SQL requests to retrieve information from a relational database,
  • what is an algorithm and what are the main control statements (if-then-else, loops...),
  • how to implement simple algorithms in Python,
  • how to divide a program into several functions,
  • what are the main data structures in Python (lists, dictionaries...),
  • how to design a static web page with HTML,
  • how to use CSS to make a static web page responsive (nice looking on all devices including smartphones).

The algorithmics + Python part is a customized version of the interactive tutorial on interactivepython.org, which was itself based on the open source book How to think like a computer scientist by Downey et al.

This course is worth 2 ECTS credits. It is part of larger module called "Basic skills for molecular bionformatics" (6 ECTS credits in total), which also involves basic notions in biochemistry and basic usage of bioinformatic tools.