February 14, 2011

Sabine Peres (LRI)

In the available databases, biological processes are described from molecular and cellular points of view, but these descriptions are represented with text annotations that make difficult to handle them for computation. Consequently, there is an obvious need for formal descriptions of biological processes.
A formalism that uses the BioPsi concepts to model biological processes from molecular details to networks will be presented. This computational approach, based on elementary bricks of actions, allows us to calculate on biological functions (e.g. process comparison, mapping structure-function relationships, etc.). Its application will be illustrated with the functional description of the central carbon metabolism network. This computational approach is compatible with detailed biological knowledge and can be applied to different kinds of systems of simulation.