Section: New Results

Petri Net Analysis of Biochemical Networks

Participants : François Fages, Thierry Martinez, Faten Nabli, Sylvain Soliman.

Bridging the gap between quantitative and qualitative models, Petri nets (also known as place/transition graphs) have recently emerged as a promising tool for modeling and analysis of biochemical networks. In [14] , we present a method to compute the minimal siphons and traps of a Petri net as a Constraint Satisfaction Problem (CSP). In our case, siphons and traps are purely structural properties that brings us information about the persistence of some molecular species. We present a constraint program that finds minimal siphons and traps containing specific set of places in a Petri net. This method is compared on models of the biomodels.net repository with other methods based on Mixed Integer Linear Programming (MILP) and Boolean Satisfiability (SAT). The flexibility brought by constraint programming, for instance in the declarative choice of variable enumeration heuristics, seems promising in further improving those results.