An Algorithm for Qualitative Simulation of Gene Regulatory Networks with Steep Sigmoidal Response Functions

A specific class of ODEs has been shown to be adequate to describe the essential features of the complex dynamics of Gene-Regulatory Networks (GRN). But, the effective exploitation of such models to predict the dynamics of specific GRNs by classical numerical schemes is greatly hampered by the current lack of precise and quantitative information on regulation mechanisms and kinetic parameters. Due to the size and complexity of large GRNs, classical qualitative analysis could be very hard, or even impracticable, to be carried out by hand, and conventional qualitative simulation approaches rapidly lead to an exponential growth of the generated behavior tree that, besides all possible sound behaviors, may also contain spurious ones. This paper discusses the work-in-progress of a research effort aiming at the design and implementation of a computational framework for qualitative simulation of the dynamics of a class of ODE models of GRNs. The algorithm we propose results from a set of sy...

• Type: Conference
• Year: 2008
• Where: AB
• Authors: Liliana Ironi, Luigi Panzeri, Erik Plahte
• Keywords: AB 2008, Classical Qualitative Analysis, Computational Biology, Qualitative Simulation, Singular Perturbation Analysis