Semantics of Biological Regulatory Networks

Gilles Bernot (1) , Franck Cassez (2) , Jean-Paul Comet (1) , Franck Delaplace (1) , Céline Müller (1) , Olivier Roux (3)

1 IBISC - Informatique, Biologie Intégrative et Systèmes Complexes
2 IRCCyN - Institut de Recherche en Communications et en Cybernétique de Nantes
3 MeForBio

The aim of the paper is to revisit the model of Biological Regulatory Networks (BRN) which was proposed by René Thomas to model the interactions between a set of genes. We give a formal semantics for BRN in terms of transition systems which formalizes the evolution rules given by René Thomas. Then we show how to use this model to find interesting properties of a BRN like the set of stable states, cycles etc using tools for analyzing transition systems.

Domaines: Informatique; Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]; Informatique et théorie des jeux [cs.GT]; Modélisation et simulation; Physiologie [q-bio.TO]; Urologie et Néphrologie; Interactions cellulaires [q-bio.CB]

Gilles Bernot, Franck Cassez, Jean-Paul Comet, Franck Delaplace, Céline Müller, et al.. Semantics of Biological Regulatory Networks. Electronic Notes in Theoretical Computer Science, 2007, 180, pp.3--14. ⟨10.1016/j.entcs.2004.01.038⟩. ⟨hal-00339588⟩