This group is a subgroup of Life Sciences.
Coordinator of this subgroup: Jan van Schuppen
Theory development for problems of modeling, system identification, system reduction, and control of large biochemical reaction systems. Examples are the metabolic network of Trypanosoma brucei and a genetic network of Escherichia coli.
Researchers
- Dirk De Vos (as of 1 February 2009)
- Hanna Hardin
- Jana Nveemcova
- Jan van Schuppen
- System reduction of metabolic reaction networks
Period: From 1 April 2005 till 15 May 2009.
Researchers
Hanna M. Hardin, Jan H. van Schuppen, and Hans V. Westerhoff (VU.FALW)
Project description
The problem is to reduce a biochemical reaction system in the form of a differential equation with inputs and outputs to a system of lower complexity. The biochemical reaction system of glycolysis in yeast has been used as an example.
Financial support: NWO.CLS1.
Cooperation: CWI.MAS1. - Biomathematics in mass spectroscopy based proteomics for identification and modeling of protein networks
Period: 1 November 2006 till 1 April 2010.
Researchers
Dirk De Vos and Jan H. van Schuppen
Project description
Modeling and system identification of protein networks.
The example of the GATA1 network in red blood cell development is a primarily example.
Financial support: NBIC.
Cooperation: Frank Grosveld and Sjaak Philipsen (Erasmus University - Medical Center). - Realization and control of rational systems
Period: 1 November 2005 till 1 November 2009.
Researchers
Jana Nemcova and Jan H. van Schuppen
Project description
When does an input-output map have a realization as a rational system? When has such a realization a minimal dimension? What is the relation between minimal realizations? What are necesary and sufficient conditions for structural identifability?
An example used is the peptide chain network.
Financial support: NWO.EW.
Cooperation: Dr. M. Petreczky (TUE/CWI). - System reduction of genetic networks
Period: 1 February 2007 till 1 February 2010.
Researchers
Jan van Schuppen
Project description
How to reduce large biochemical reaction systems describing a genetic network by one of smaller complexity? Ammonium assimilation in Esscherichia coli has been investigated for system reduction. Abstraction of systems to automata is also investigated.
Financial support: European Commission (Project EC-MOAN).
Cooperation: INRIA Grenoble (Hidde de Jong, Delphine Ropers), and Mazaryk University Brno (Lubos Brim, David Safranek), and Vrije Universiteit (Fred Boogerd, Frank Bruggeman, Hans V. Westerhoff).
