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

Abstract

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