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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 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 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.

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

  • translating a biological case study (a process) into a formal and executable model

  • presenting the approach followed


The most recent timetable can be found at the LIACS website

Mode of instruction

  • Lectures

  • Computer practical

  • Seminar sessions

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

Assessment method

Grading is based on

  • presence and active participation (10%)

  • Petri Nets assignments (10%)

  • participation in presentations/discussions within the group of relevant literature (20%)

  • contribution to a project: modeling, presentation, report (60%)

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

  • the result for the first 40% (three bullets)

  • and the result for the last 60% (bullet) mentioned
    should be sufficient (at least 5.5).

Reading list

Literature will be provided during the course.


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

Contact information

Study coordinator Computer Science, Riet Derogee


Bio-modeling and Petri Nets