Delays in Biological Regulatory Networks

Jamil Ahmad (1) , Adrien Richard (2) , Gilles Bernot (2) , Jean-Paul Comet (2) , Olivier Roux (3)

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

In this article, we propose a refinement of the modeling of genetic regulatory networks based on the approach of René Thomas. The notion of delays of activation/inhibition are added in order to specify which variable is faster affected by a change of its regulators. The formalism of linear hybrid automata is well suited to allow such refinement. We then use HyTech for two purposes: (1) to find automatically all paths from a specified initial state to another one and (2) to synthesize co nstraints on the delay parameters in order to follow any specific path.

Domains: Programming Languages [cs.PL]; Web; Software Engineering [cs.SE]; Multiagent Systems [cs.MA]

Jamil Ahmad, Adrien Richard, Gilles Bernot, Jean-Paul Comet, Olivier Roux. Delays in Biological Regulatory Networks. Proceedings of the 2nd International Workshop on Bioinformatics Research and Applications, 2006, United Kingdom. pp.887--894, ⟨10.1007/11758525_118⟩. ⟨hal-00341972⟩