Working group: "Computational Biology"

2011, the 9th of November

Russ Harmer

Title: Constraining rule-based dynamics with types.


A generalized framework of site graphs is introduced in order to provide the first fully semantic definition of the side-effect-free core of the rule-based language Kappa. This formalization allows for the use of types either to confirm that a rule respects a certain invariant or to guide a restricted refinement process that allows us to constrain its run-time applicability.