nl en



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 several 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

  • Understand the concept of systems biology and bio-modeling.

  • Understand network motifs in systems biology.

  • Apply bio-modeling tools: Boolean Networks and Petri Nets to model real biological studies.

  • Evaluate the network created by bio-modeling tools.


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

You will find the timetables for all courses and degree programmes of Leiden University in the tool MyTimetable (login). Any teaching activities that you have sucessfully registered for in MyStudyMap will automatically be displayed in MyTimeTable. Any timetables that you add manually, will be saved and automatically displayed the next time you sign in.

MyTimetable allows you to integrate your timetable with your calendar apps such as Outlook, Google Calendar, Apple Calendar and other calendar apps on your smartphone. Any timetable changes will be automatically synced with your calendar. If you wish, you can also receive an email notification of the change. You can turn notifications on in ‘Settings’ (after login).

For more information, watch the video or go the the 'help-page' in MyTimetable. Please note: Joint Degree students Leiden/Delft have to merge their two different timetables into one. This video explains how to do this.

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%) * kick-off presentation (10%) * final presentation (15%) * final report (65%)

The final mark is the weighted average of the above as indicated.
If an assignment or a presentation is not completed, the resulting grade is a 0. There will be no retakes for the assignments and the presentations. The retake for the final report is an one-time resubmission with an improved version. The final grade can only be sufficient if the weighted average grade is at least a 5.5.

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.


From the academic year 2022-2023 on every student has to register for courses with the new enrollment tool MyStudyMap. There are two registration periods per year: registration for the fall semester opens in July and registration for the spring semester opens in December. Please see this page for more information.

Please note that it is compulsory to both preregister and confirm your participation for every exam and retake. Not being registered for a course means that you are not allowed to participate in the final exam of the course. Confirming your exam participation is possible until ten days before the exam.

Extensive FAQ's on MyStudymap can be found here.


Lecturer: dr. Lu Cao