Constraint-based modelling: introduction and advanced topics

Date & location

25-29 November 2019, Leiden University

Gorlaeus Building, Einsteinweg 55, 2333 CC Leiden (25 – 28 November: room DM0.21, 29 November room LMUY 04.28).

Course coordinators

Ronan Fleming (Leiden University), Brett Oliver (VU University Amsterdam)

Course credits


Course overview

Constraint-based modelling is a powerful modeling methodology that is being used to model a diverse range of biological phenomena. These include both fundamental and applied questions relevant to biotechnology, microbiology and medicine. Central to constraint-based modelling is the use of genome-scale reconstructions that represent particular cellular functions as a biochemical reaction network. In this course, you will be introduced to:

  • the principles of constraint-based reconstruction and analysis (COBRA)
  • the underlying mathematical foundations of constraint-based modeling
  • methods for integration of omics data with constraint-based models
  • basic and advanced methods for interrogating models and interpreting results
  • open source COBRA software, including the COBRA Toolbox
  • standards for reconstruction and model sharing
  • example applications to biomedicine and biotechnology

The course is structured into both lectures and practical sessions so that theory can be illustrated with biologically motivated computational examples.

NB: For practical sessions, participants require their own laptop with MATLAB and the COBRA Toolbox pre-installed (See for instructions). Here you can find a student license for MATLAB.

Free 30 day MATLAB trial:

Course programme

Click here to view the draft course programme


Target audience

Constraint-based modeling is a rapidly growing field that is being used in both fundamental and applied research and biotechnology. It sits at the intersection between quantitative modeling, bioinformatics and cellular physiology, and as such, is an example of systems biology at work.

While participants would benefit from some knowledge of either quantitative modeling, bioinformatics or metabolism this is not required. This includes, for example, scientists working in a laboratory and wanting to learn more about building or using genome-scale models, as well as those who have used some basic COBRA methodologies, but want to know how else it can be applied to their research.

Learning outcomes

  • Introduction to COBRA
  • Proficiency with the COBRA Toolbox
  • Familiarity with typical applications of constraint-based modeling in biomedicine and biotechnology

More information

For more information about the course you can contact Ronan Fleming, or Brett Oliver.


The registration fees for this 5-day course are:

  • PhD student: 400 euro (excl. VAT)
  • Academic researcher (PI/Postdoc): 600 euro (excl. VAT)
  • Industry: 900 euros (excl.VAT)

The course fee includes:

  • Course material
  • Catering: coffee, tea and lunch will be provided.

Registration is closed.