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Bio-modeling and Petri Nets


Admission requirements

Bachelor degree in Computer Science, Biology, Biomedical Science, LST or Pharmaceutical Science, or currently enrolled in the Master Bio-Informatics. Note that knowledge of both biological processes and the Petri Nets framework is not a prerequisite for taking the course.


Experimental and computational approaches can be combined to systematically investigate biological systems. 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 modelling of biological processes. In an interdisciplinary approach we will investigate how to construct and analyse such models using the framework of the modelling technique Petri nets and related tools. Biological case studies will be used as a guide to the modelling of biological phenomena.

This course is a combination of lectures, seminar sessions with student presentations, practical assignments and project work. After a few introductory lectures and two practical sessions on using Petri Net tools, groups will be formed to work on small projects in which they will model aspects of a 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.
The students’ projects may serve as a stepping stone to a computer science master project. All information on the course can be found at

Course objectives

  • becoming acquainted with uses of modelling techniques for biological research

  • gaining theoretical knowledge of the modelling framework of Petri nets

  • critically presenting and discussing academic papers

  • being able to use the Petri net modelling tool to construct, simulate and analyse Petri net models

  • translating a biological case study (a process) into a theoretical and a practical model


The most recent timetable can be found at the LIACS website

Mode of instruction

  • Lectures

  • Computer practical

  • Seminar sessions

  • Presentation of own work

Assessment method

Grading is based on

  • participation in seminar discussions (10%)

  • practical exercises (10%)

  • individual presentation of a journal paper (20%)

  • and individual contribution to a group project (60%)

Reading list

Papers will be provided during the course. No textbook is used.


You have to sign up for classes and examinations (including resits) in uSis. Check this link for more information and activity codes.

There is a limited capacity for students from outside the master Computer Science programme. Please contact the study advisor.

Contact information

Study coordinator Computer Science, Riet Derogee


For more details and a description in English, see the website