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Admission requirements

Not applicable.


In order 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 interactions.

This course aims at making students aware of formal and mathematically precise approaches to the faithful modeling of biological processes. In an interdisciplinary approach we will investigate how to construct and analyze such formal models using the frameworks of Boolean Networks and Petri nets. Biological case studies will be used as a guide to the modelling of biological phenomena.

This course is a combination of lectures and project work. After the introductory lectures and some practical sessions on using Boolean Network and Petri Net tools, groups will be formed to work on a project to model aspects of a given biological process. Knowledge of Biology (the case studies) or Computer Science (Boolean Network and Petri Nets) is not a prerequisite. Presence at all meetings is mandatory.

Course objectives

  • becoming acquainted with uses of modelling techniques for biological research

  • gaining theoretical knowledge of the modelling framework of Boolean Networks and Petri nets


The most recent timetable can be found at the Computer Science (MSc) student website.

Mode of instruction

  • Lectures

  • Case study sessions

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

Course load

Hours of study: 168 (= 6 EC)
Lectures: 48
Presentation and preparations: 30
Practical work: 30
Report: 60

Assessment method

Grading is based on:

  • presence, assignments completion and active participation in discussion (10%)

  • contribution to a project: modeling, presentation, report (90%)

The final mark is the weighted average of the above as indicated.

Reading list

  • Systems biology - a textbook.

  • An Introduction to Systems Biology--Design Principles of Biological Circuits.

  • Modeling in Systems Biology – The Petri Net Approach.

  • Additional Materials that 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.


Lecturer: dr. Lu Cao