Molecular Cell Physiology, Vrije University Amsterdam

Amsterdam, The Netherlands

General information

The Molecular Cell Physiology research group at VU University examines how the interaction of macromolecules gives rise to life, to the functioning of living organisms. The research group develops and implements Systems Biology in the context of microbiology, medical biology and biotechnology.



The group is developing the 4M (Make Me My Model) platform which aims at providing dynamic network modelling and model analysis services. It will make you your model such that you can run it, use it to make predictions of the schemes you have in mind and compare them with your experimental results.


Technologies offered for the Open Call

- Building the network diagram for modelled process in SBML format (Systems Biology Markup
  Language) with CellDesigner, an open source software
- Converting network diagram into a first dynamic model in COPASI, an open source software
- Fitting the dynamic model to experimental data
- Model analysis, e.g. sensitivity analysis, looking for network targets, metabolic control analysis
- Model refinement and tuning with available datasets



Example of a Dynamic network model: simulation of emergent behavior - stress and distress

Additional resources offered for the Open Call

- Teaching to build dynamic models and use Flux Balance Analysis
- Promotion of standardized SB model representation (SBGN format), modelling (SBML format) and
  live model repository (JWS-Online)
- Support with classical systems biological tools (e.g. COPASI, CellDesigner)


Access modalities

Virtual access


Scientific and technical requirements

The planned modeling work must be feasible in terms of the number of modelled interactions in the modelled network (normally 10-100 interactions in the dynamic model).



Scientific contact: Hans V. Westerhoff 
Technical contact: Alexey Kolodkin