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Bioinformatics 2005 21(Suppl 1):i19-i28; doi:10.1093/bioinformatics/bti1048
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli

Grégory Batt 1, Delphine Ropers 1, Hidde de Jong 1,*, Johannes Geiselmann 2, Radu Mateescu 1, Michel Page 1,3 and Dominique Schneider 2

1INRIA Rhône-Alpes Montbonnot, France
2Laboratoire Adaptation et Pathogénie des Microorganismes, CNRS UMR 5163, Université Joseph Fourier Grenoble, France
3Université Pierre Mendès France Grenoble, France

*To whom correspondence should be addressed.

Motivation: The modeling and simulation of genetic regulatory networks have created the need for tools for model validation. The main challenges of model validation are the achievement of a match between the precision of model predictions and experimental data, as well as the efficient and reliable comparison of the predictions and observations.

Results: We present an approach towards the validation of models of genetic regulatory networks addressing the above challenges. It combines a method for qualitative modeling and simulation with techniques for model checking, and is supported by a new version of the computer tool Genetic Network Analyzer (GNA). The model-validation approach has been applied to the analysis of the network controlling the nutritional stress response in Escherichia coli.

Availability: GNA and the model of the stress response network are available at http://www-helix.inrialpes.fr/gna

Contact: Hidde.de-Jong{at}inrialpes.fr

Received on January 15, 2005; accepted on March 27, 2005

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