title: Genetic network analyzer: a tool for the qualitative modeling and simulation of bacterial regulatory networks.
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.
authors.affiliation: INRIA Paris - Rocquencourt, Domaine de Voluceau, Le Chesnay, France.
authors.forename: Grégory
authors.initials: G
authors.lastname: Batt
authors.forename: Bruno
authors.initials: B
authors.lastname: Besson
authors.forename: Pierre-Emmanuel
authors.initials: PE
authors.lastname: Ciron
authors.forename: Hidde
authors.initials: H
authors.lastname: de Jong
authors.forename: Estelle
authors.initials: E
authors.lastname: Dumas
authors.forename: Johannes
authors.initials: J
authors.lastname: Geiselmann
authors.forename: Regis
authors.initials: R
authors.lastname: Monte
authors.forename: Pedro T
authors.initials: PT
authors.lastname: Monteiro
authors.forename: Michel
authors.initials: M
authors.lastname: Page
authors.forename: François
authors.initials: F
authors.lastname: Rechenmann
authors.forename: Delphine
authors.initials: D
authors.lastname: Ropers
mesh_terms: D001419:Bacteria / Q000235:genetics*; D003198:Computer Simulation; D053263:Gene Regulatory Networks / Q000235:genetics*; D055641:Mathematical Concepts; D008957:Models, Genetic; D012984:Software; D049490:Systems Biology / Q000379:methods*