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

  • Grégory Batt
  • Bruno Besson
  • Pierre-Emmanuel Ciron
  • Hidde de Jong
  • Estelle Dumas
  • Johannes Geiselmann
  • Regis Monte
  • Pedro T. Monteiro
  • Michel Page
  • François Rechenmann
  • Delphine Ropers
Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

Genetic Network Analyzer Qualitative modeling and simulation Gene regulatory networks Piecewise-linear differential equations Model checking Carbon starvation Escherichia coli 

Notes

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).

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Grégory Batt
    • 1
  • Bruno Besson
    • 2
  • Pierre-Emmanuel Ciron
    • 2
  • Hidde de Jong
    • 3
  • Estelle Dumas
    • 3
  • Johannes Geiselmann
    • 4
  • Regis Monte
    • 3
  • Pedro T. Monteiro
    • 3
  • Michel Page
    • 3
  • François Rechenmann
    • 3
  • Delphine Ropers
    • 3
  1. 1.INRIA Paris – Rocquencourt, Domaine de VoluceauLe ChesnayFrance
  2. 2.GenostarMontbonnotFrance
  3. 3.INRIA Rhône-AlpesMontbonnot, St. IsmierFrance
  4. 4.Laboratoire Adaptation et Pathogénie des Microorganismes (CNRS UMR 5163), Bâtiment Jean Roget, Faculté de Médecine-PharmacieUniversité Joseph FourierLa TroncheFrance

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