Sandro Stucki

Deriving rate equations for site graph rewriting systems

Vincent Danos, Russ Harmer, Ricardo Honorato-Zimmer, and Sandro Stucki. To appear in Proceedings of the 4th International Workshop on Static Analysis and Systems Biology (SASB '13), in ENTCS.


We introduce a side-effect-free calculus for stochastic site graph rewriting using action scripts to specify rewrite rules. We derive a differential semantics for sets of such rewrite rules and associated observable graphs in the form of a system of ODEs describing the dynamics of the observables on average. We show how to construct subsets of these ODEs that correspond to the rate equations of particular rewriting systems expressed in our framework.