Topology-based abstraction of complex biological systems: application to the Golgi apparatus.

Many complex cellular processes involve major changes in topology and geometry. We have developed a method using topology-based geometric modelling in which the edge labels of an n-dimensional generalized map (a subclass of graphs) represent the relations between neighbouring biological compartments. We illustrate our method using two topological models of the Golgi apparatus.

Analysing gene regulatory networks by both constraint programming and model-checking.

In this article, we propose a formal method to analyse gene regulatory networks (GRN). The dynamics of such systems is often described by an ordinary differential equation system, but has also been abstracted into a discrete transition system. This modeling depends on parameters for which different values are possible.

Symbolic modeling of genetic regulatory networks.

Understanding the functioning of genetic regulatory networks supposes a modeling of biological processes in order to simulate behaviors and to reason on the model. Unfortunately, the modeling task is confronted to incomplete knowledge about the system. To deal with this problem we propose a methodology that uses the qualitative approach developed by Thomas.