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Hybrid Modeling and Simulation of Genetic Regulatory Networks: A Qualitative Approach

  • Hidde de Jong
  • Jean-Luc Gouzé
  • Céline Hernandez
  • Michel Page
  • Tewfik Sari
  • Johannes Geiselmann
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2623)

Abstract

The study of genetic regulatory networks has received a major impetus from the recent development of experimental techniques allowing the measurement of patterns of gene expression in a massively parallel way. This experimental progress calls for the development of appropriate computer tools for the modeling and simulation of gene regulation processes. We present a method for the hybrid modeling and simulation of genetic regulatory networks, based on a class of piecewiselinear (PL) differential equations that has been well-studied in mathematical biology. Distinguishing characteristics of the method are that it makes qualitative predictions of the behavior of regulatory systems and that it deals with discontinuities in the right-hand side of the differential equations. The simulation method has been implemented in Java in the computer tool Genetic Network Analyzer (GNA). The method and the tool have been used to analyze several networks of biological interest, including the network underlying the initiation of sporulation in Bacillus subtilis.

Keywords

Regulatory Domain Qualitative Behavior Transition Graph Switching Domain Genetic Regulatory Network 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • Hidde de Jong
    • 1
  • Jean-Luc Gouzé
    • 2
  • Céline Hernandez
    • 3
  • Michel Page
    • 1
    • 4
  • Tewfik Sari
    • 5
  • Johannes Geiselmann
    • 6
  1. 1.Institut National de Recherche en Informatique et en Automatique (INRIA)Unité de recherche Rhône-AlpesSaint Ismier CedexFrance
  2. 2.Institut National de Recherche en Informatique et en Automatique (INRIA)Unité de recherche Sophia AntipolisFrance
  3. 3.Swiss Institute of Bioinformatics (SIB)GenevaSwitzerland
  4. 4.École Supérieure des AffairesUniversité Pierre Mendès FranceGrenobleFrance
  5. 5.Laboratoire de MathématiquesUniversité de Haute AlsaceMulhouseFrance
  6. 6.Laboratoire Plasticité et Expression des Génomes MicrobiensUniversité Joseph FourierGrenobleFrance

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