Title: Analysing formal models of genetic regulatory networks with delays

Authors: Jamil Ahmad, Olivier Roux, Gilles Bernot, Jean-Paul Comet, Adrien Richard

Addresses: IRCCyN UMR CNRS 6597, BP 92101, 1 rue de la Noe, 44321 Nantes Cedex 3, France. ' IRCCyN UMR CNRS 6597, BP 92101, 1 rue de la Noe, 44321 Nantes Cedex 3, France. ' Laboratoire I3S, (UNSA & CNRS UMR 6070), Les Algorithmes, bat. Euclide B, BP.121, 06903 Sophia Antipolis Cedex, France. ' Laboratoire I3S, (UNSA & CNRS UMR 6070), Les Algorithmes, bat. Euclide B, BP.121, 06903 Sophia Antipolis Cedex, France. ' Laboratoire I3S, (UNSA & CNRS UMR 6070), Les Algorithmes, bat. Euclide B, BP.121, 06903 Sophia Antipolis Cedex, France

Abstract: In this paper, we propose a refinement of the modelling of biological regulatory networks based on the discrete approach of Rene Thomas. We refine and automatise the use of delays of activation/inhibition in order to specify which variable is more quickly 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: to find automatically all paths from a specified initial state to another one; to synthesise constraints on the delay parameters in order to follow any specific path.

Keywords: genetic regulatory networks; gene networks; modelling; delays; path algorithm; hyTech; cycles; constraints; bioinformatics; genetics; biological regulatory networks.

DOI: 10.1504/IJBRA.2008.019573

International Journal of Bioinformatics Research and Applications, 2008 Vol.4 No.3, pp.240 - 262

Available online: 17 Jul 2008 *

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