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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 biological processes or Petri Nets is not a prerequisite for this course.


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 modelling of biological phenomena.

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

Course objectives

  • becoming acquainted with uses of modelling techniques for biological research

  • gaining theoretical knowledge of the modelling framework of Petri nets

  • critically discussing academic papers


The most recent timetable can be found at the students' website.

Mode of instruction

  • Lectures

  • Seminar sessions

  • Presentation of own work (including a written report following a template)

Course Load

Hours of study: 168 (= 6 EC)
Lectures: 26
Literature research: 26
Presentation and preparations: 26
Practical work: 30
Report: 60

Assessment method

Grading is based on:

  • presence and active participation (10%)

  • participation in discussions within the group of relevant literature (10%)

  • contribution to a project: modeling, presentation, report (80%)

The final mark is the weighted average of the above as indicated, but under the addional condition that both

  • the result for the first 20% (two bullets)

  • and the result for the last 80% (bullet)
    are sufficient (at least 5.5).

Reading list

  • Will be announced during the course.


  • You have to sign up for courses and exams (including retakes) in uSis. Check this link for information about how to register for courses.

Contact information

Lecturers: dr. Jetty Kleijn & prof.dr. ir. Fons Verbeek
Course website: Bio-Modeling and Petri Nets