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Logical Modelling of Gene Regulatory Networks with GINsim

  • Claudine ChaouiyaEmail author
  • Aurélien Naldi
  • Denis Thieffry
Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 804)

Abstract

Discrete mathematical formalisms are well adapted to model large biological networks, for which detailed kinetic data are scarce. This chapter introduces the reader to a well-established qualitative (logical) framework for the modelling of regulatory networks. Relying on GINsim, a software implementing this logical formalism, we guide the reader step by step towards the definition and the analysis of a simple model of the lysis–lysogeny decision in the bacteriophage λ.

Key words

Networks Logical modelling Qualitative analysis Graph Regulatory circuit Dynamical simulation 
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Notes

Acknowledgments

A.N. has been supported by a PhD grant from the French Ministry of Research and Technology. This project was further supported by research grants from the EU FP6 (DIAMONDS STREP) and FP7 (APOSYS large scale project) programs, and by the Belgian Science Policy Office (IAP BioMaGNet).

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Claudine Chaouiya
    • 1
    Email author
  • Aurélien Naldi
    • 2
  • Denis Thieffry
    • 3
  1. 1.Instituto Gulbenkian de CiênciaOeirasPortugal
  2. 2.TAGC, INSERM U928MarseilleFrance
  3. 3.Institut de Biologie de l’Ecole Normale Supérieure (IBENS), UMR ENS, CNRS 8197, INSERM 1024ParisFrance

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