Bio-Modeling and Petri Nets 2017-2018

BMPN is a course in the Master Computer Science and Advanced Data Analytics.
It targets students with a bachelor degree in Computer Science, Biology, LST or Pharmaceutical Sciences.
It is taught in the spring semester, Tuesday afternoons (February 6 - May 8, 2018).

ECTS: 6.0
Level: 500

Lecturers: Jetty Kleijn and Fons Verbeek
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 interaction. This course aims at making students aware of formal, mathematically precise, approaches to the faithful modeling of biological processes. In an interdisciplinary approach we will investigate how to construct and analyse such formal models using the framework of Petri nets. Biological case studies will be used as a guide to the modeling of biological phenomena.

Students are introduced to formal modeling techniques for biological research;
they acquire theoretical knowledge of the modeling framework of Petri nets;
learn how it may be used to model biological processes;
can apply this knowledge to a small case study and report on their modeling approach;
they can assess scientific literature on the topic.

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:
will be announced during the course.

Last update: September 5, 2017

For questions, remarks etc. contact: h.c.m.kleijn at