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Genetic Network Analyzer: A Tool for the Qualitative Modeling and Simulation of Bacterial Regulatory Networks

Grégory Batt 1 Bruno Besson 2 Pierre-Emmanuel Ciron 2 Hidde de Jong 3 Estelle Dumas 3 Johannes Geiselmann 3, 4 Regis Monte 2 Pedro T. Monteiro 3, 5 Michel Page 3 François Rechenmann 2, 3 Delphine Ropers 3
1 CONTRAINTES - Constraint programming
Inria Paris-Rocquencourt
2 Genostar
3 IBIS - Modeling, simulation, measurement, and control of bacterial regulatory networks
LAPM - Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble], Inria Grenoble - Rhône-Alpes, Institut Jean Roget
4 LAPM - Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble]
5 IST - Instituto Superior Técnico, Universidade Técnica de Lisboa
Abstract : Genetic Network Analyzer (GNA) is a tool for the qualitative modeling and simulation of gene regulatory networks, based on so-called piecewise-linear differential equation models. We describe the use of this tool in the context of the modeling of bacterial regulatory networks, notably the network of global regulators controlling the adaptation of Escherichia coli to carbon starvation conditions. We show how the modeler, by means of GNA, can define a regulatory network, build a model of the network, determine the steady states of the system, perform a qualitative simulation of the network dynamics, and analyze the simulation results using model-checking tools. The example illustrates the interest of qualitative approaches for the analysis of the dynamics of bacterial regulatory networks.
Keywords : Genetic Network Analyzer Qualitative modeling and simulation Gene regulatory networks Piecewise-linear differential equations Model checking Carbon starvation Escherichia coli
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https://hal.inria.fr/hal-00762122
Contributor : François Rechenmann Connect in order to contact the contributor
Submitted on : Thursday, December 6, 2012 - 2:52:27 PM
Last modification on : Friday, November 6, 2020 - 4:03:40 AM

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Grégory Batt, Bruno Besson, Pierre-Emmanuel Ciron, Hidde de Jong, Estelle Dumas, et al.. Genetic Network Analyzer: A Tool for the Qualitative Modeling and Simulation of Bacterial Regulatory Networks. Jacques van Helden, Ariane Toussaint, Denis Thieffry. Bacterial Molecular Networks Methods and Protocols, 804, Springer, pp.439-462, 2012, Methods in Molecular Biology,, 978-1-61779-361-5. ⟨10.1007/978-1-61779-361-5_22⟩. ⟨hal-00762122⟩

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