Course Description


In order to systematically investigate biological systems, experimental and computational approaches can be combined. To understand a biological system, structural and dynamic properties can be represented in a computational model describing the entities involved and their interactions. This course aims at making students aware of formal and mathematically precise approaches to the faithful modeling of biological processes. In an interdisciplinary approach we will investigate how to construct and analyze such formal models using the framework of Petri nets. Biological case studies will be used as a guide to the modelling of biological phenomena.


  • becoming acquainted with uses of modelling techniques for biological research
  • gaining theoretical knowledge of the modelling framework of Petri nets
  • applying this knowledge to a small case study and report on their modeling approach
  • critically discussing academic papers

Set-up of the course:

This course is a combination of lectures, seminar sessions, and project work. After the introductory lectures and some practical sessions on using Petri net tools, groups will be formed to work on a project to model aspects of a given biological process using Petri nets.
Knowledge of Biology (the case studies) or Computer Science (Petri nets) is not a prerequisite.
Presence at all meetings is mandatory.
Note that there will be a maximum to the number of students that can participate; there will be a confirmation of enrollment at the second meeting.

The students' projects may serve as a stepping stone to a computer science master project.

Course material:

See the lectures content: Updates are announced during the course and will be available through Blackboard (this website links to relevant material there).