Analysing formal models of genetic regulatory networks with delays

Int J Bioinform Res Appl. 2008;4(3):240-62. doi: 10.1504/IJBRA.2008.019573.

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.

MeSH terms

  • Algorithms*
  • Computer Simulation
  • Gene Expression Regulation / physiology*
  • Models, Biological*
  • Nonlinear Dynamics
  • Proteome / metabolism*
  • Signal Transduction / physiology*

Substances

  • Proteome