Network modelling

With the great advances in molecular biology, genomics and functional genomics, regulatory and signalling networks are being uncovered, opening the way for a better understanding of how cellular processes are controlled. Molecular pathways interplay and operate at diverse levels (transcription and translation of the genetic material, protein modifications, etc.). The complexity of these networks call for the development of dedicated mathematical and computational models. In this context, our goal is to develop generic tools to model and analyse large signalling and regulatory networks. For this purpose, we mainly rely on a qualitative modelling framework combining the generalised logical formalism, cellular automata and Petri nets. Our research goes mainly along three lines. First, we devise new methods to efficiently analyse properties of biological relevance in discrete models. Second, methodological advances are made available in the form of novel computational tools or as new functionalities of GINsim, our software tool for logical modelling (http://ginsim.org). Finally, in a close collaboration with biologists, methodological developments are motivated by and challenged with real case applications, specifying and analysing models of networks involved in processes of interest (cell proliferation, differentiation, etc.)