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

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Book cover Bacterial Molecular Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 804))

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.

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Acknowledgments

This work was partially supported by the FCT program (PhD grant SFRH/BD/32965/2006 to PTM). BB and HdJ were supported by the European commission under project COBIOS (FP6-2005-NEST-PATH-COM/043379). HdJ, JG, and DR were supported by the European commission under project EC-MOAN (FP6-2005-NEST-PATH-COM/043235).

Author information

Authors and Affiliations

  1. INRIA Paris – Rocquencourt, Domaine de Voluceau, Le Chesnay, France

    Grégory Batt

  2. Genostar, Montbonnot, France

    Bruno Besson & Pierre-Emmanuel Ciron

  3. INRIA Rhône-Alpes, Montbonnot, St. Ismier, France

    Hidde de Jong, Estelle Dumas, Regis Monte, Pedro T. Monteiro, Michel Page, François Rechenmann & Delphine Ropers

  4. Laboratoire Adaptation et Pathogénie des Microorganismes (CNRS UMR 5163), Bâtiment Jean Roget, Faculté de Médecine-Pharmacie, Université Joseph Fourier, La Tronche, France

    Johannes Geiselmann

Authors
  1. Grégory Batt
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  2. Bruno Besson
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  3. Pierre-Emmanuel Ciron
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  4. Hidde de Jong
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  5. Estelle Dumas
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  6. Johannes Geiselmann
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  7. Regis Monte
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  8. Pedro T. Monteiro
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  9. Michel Page
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  10. François Rechenmann
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  11. Delphine Ropers
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Corresponding author

Correspondence to Hidde de Jong .

Editor information

Editors and Affiliations

  1. Labo. Bioinformatique des, Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, bd. du Triomphe, Bruxelles, 1050, Belgium

    Jacques van Helden

  2. Labo. Bioinformatique des, Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Bvd. du Triomphe, Bruxelles, 1050, Belgium

    Ariane Toussaint

  3. INSERM 1024, Institut de Biologie de l'Ecole Normale, rue d'Ulm 46, Paris, 75230, France

    Denis Thieffry

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Batt, G. et al. (2012). Genetic Network Analyzer: A Tool for the Qualitative Modeling and Simulation of Bacterial Regulatory Networks. In: van Helden, J., Toussaint, A., Thieffry, D. (eds) Bacterial Molecular Networks. Methods in Molecular Biology, vol 804. Springer, New York, NY. https://doi.org/10.1007/978-1-61779-361-5_22

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  • DOI: https://doi.org/10.1007/978-1-61779-361-5_22

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  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-61779-360-8

  • Online ISBN: 978-1-61779-361-5

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