Title: Modelling of biological networks
Lecturer: Claudine CHAOUIYA CHANTEGREL (Ecole Superieure d'Ingenieurs de Luminy, Marseille, France)
February 27-28, 2006; 17:00-20:00, Classroom 21 of Ada Byron Building
Abstract: Biological networks are found at the core of all biological functions, from biochemical pathways to cell communication processes and gene regulation mechanisms. When facing a complex interaction network, the biologist needs new means to check the coherence of tentative models with the observed dynamics, to better understand the logics of the interactions and to simulate the system behaviour for various kinds of perturbations. In this respect, Petri Nets (PNs) and their extensions constitute a promising framework for the modelling, analysis and simulation of biological networks. In the first part, I will briefly introduce some generalities on biological networks (metabolic pathways, signalling pathways and gene regulation networks), what their components are, the nature of the interactions between components, the different levels of abstraction to be considered, etc. Then I will focus on Petri net qualitative modelling of metabolic networks, illustrating through a simple example. In the second part, I will present the "logical" approach for the modelling of regulatory networks originally developed by R. Thomas. Illustration will be provided with biological applications and demonstrations with GINsim (the software developed in our group to support the modelling, simulation and analysis of gene networks). I will introduce our systematic rewriting rules to get standard Petri net models from logical regulatory graphs. This procedure will be illustrated with the same biological applications as previously and the resulting analyses will be detailed.