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Bacterial Molecular Networks

Volume 804 of the series Methods in Molecular Biology pp 463-479

Date:

Logical Modelling of Gene Regulatory Networks with GINsim

  • Claudine ChaouiyaAffiliated withInstituto Gulbenkian de Ciência Email author 
  • , Aurélien NaldiAffiliated withTAGC, INSERM U928
  • , Denis ThieffryAffiliated withInstitut de Biologie de l’Ecole Normale Supérieure (IBENS), UMR ENS, CNRS 8197, INSERM 1024

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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