In silico life: constraint-based modelling at genome scale


Monday 9 May 2016 –Wednesday 11 May 2016


Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands


Bas Teusink and Brett Olivier


Speakers (academia)
Dr. Filipe Branco dos Santos (UVA)
Prof. Frank Bruggeman (VU)
Dr. Richard Notebaart (RUMC)
Dr. Peter Schaap (WUR)
Prof. Bas Teusink (VU)
Dr. Katy Wolstencroft (LIACS)

Speakers (industry)
Dr. Ahmad Zeidan (Chr. Hansen)
Dr. Zheng Zhao (DSM)

Genome annotation: Jasper Koehorst (WUR)
Modelling with FAME: Dr Brett Olivier (VU)


Constraint-based modelling is a powerful modelling 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 a genome-scale reconstructions (GSR’s) that maps out the metabolism of a cell as a biochemical reaction network.

In this course you will be introduced to:

  • techniques for the construction of a working GSR: tools, tricks and pitfalls
  • the underlying mathematical definition and description of a constraint-based model
  • methods for interrogating models and interpreting results, such as Flux Balance Analysis and Flux Variability Analysis
  • software and standards

The preliminary course structure will be to divide each day into both lectures and practical sessions so that learned theory can immediately be applied in silico.

Target Audience

Constraint-based modelling is a rapidly growing field that is being use in both fundamental and applied research and biotechnology. It sits at the intersection between quantitative metabolic modelling, 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 modelling, bioinformatics or microbial physiology 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 basic FBA, but want to know how else it can be applied to their research.


CMD course2
  1. The first lecture (green slots) in the morning are longer 90 minutes while the second are 75
  2. Red practical sessions are on day one and two and a session on “models as data” on day 3.
  3. Yellow is coffee/lunch/social