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Bio-Modeling with Petri Nets

Vak 2011-2012

Admission requirements

Bachelor in Biology/LST/BFW/CS. Or admitted in the BioInformatics program.


Experimental and computational approaches can be combined to systematically investigate biological systems. To understand a biological system, structural and dynamic properties have to be represented by a 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 analyze such models using the framework of the modeling technique Petri nets and related tools. The infection process and granuloma formation of the Mycobacterium marinum pathogenesis, will serve as (one of the) case study and guide to understanding of modeling of biological phenomena.

This course is a combination of lectures, a students’ seminar, practical assignments, and project work. After a few introductory lectures and an inventory of the class (number, interests, background), groups will be formed to work on small projects in which they will model aspects of a biological process using Petri nets. The process of Mycobacterium infection and granuloma formation is a case that is still under study in which different levels of representation – molecular, cellular and tissue level – can be modeled dealing with the organism and its organ systems down through gene expression patterns and cell-to-cell signaling.

Students’ presence at all meetings is mandatory. The students’ projects may serve as stepping stone to a computer science master project.

Learning goals

Course objectives:
Learning to model a problem from the bio-domain in a modeling domain, e.g. a Petri Net.

Final qualifications:
Having obtained in depth knowledge of abstracting features from processes into computational models.


Time table is published on the website
1st lecture February 7th 15.45-17.30; then weekly according to schedule.
Project presentations are scheduled in May.

Mode of instruction

This course is a combination of lectures, a students’ seminar, practical assignments, and project work.

Assessment method

Participation in the lectures is mandatory. Each of the students works out an assignment, presents progress and this project assignment is concluded with a report and the outcome of the assignment. Both are presented to the course administration and assessed for the final mark.


Blackboard is not used for this course.
There is a website that holds all information required.

Reading list

Papers are provided by the course administration. The papers that are directly relevant to the introductory part of the course are provided via the website.


Registration is dealt with through the website
Registration is open for a limited time.
Alternatively, contact the course administration for information.

Exchange and Study Abroad students, please see the Prospective students website for more information on how to apply.

Contact information

Dr. H. Kleijn, or Dr Ir FJ Verbeek,


A flyer is available from the website.