Section: Research Program

Logical Paradigm for Systems Biology

Our group was among the first ones in 2002 to apply model-checking methods to systems biology in order to reason on large molecular interaction networks, such as Kohn's map of the mammalian cell cycle (800 reactions over 500 molecules) (N. Chabrier-Rivier, M. Chiaverini, V. Danos, F. Fages, V. Schächter. Modeling and querying biochemical interaction networks. Theoretical Computer Science, 325(1):25–44, 2004.). The logical paradigm for systems biology that we have subsequently developped for quantitative models can be summarized by the following identifications :

biological model = transition system,

biological property = temporal logic formula,

model validation = model-checking,

model inference = constraint solving.

In particular, the definition of a continuous satisfaction degree for first-order temporal logic formulae with constraints over the reals, was the key to generalize this approach to quantitative models, opening up the field of model-checking to model optimization. This line of research continues with the development of patterns with efficient solvers and their generalization to handle stochastic effects.