Section: New Results

Rule-based Modeling with Arithmetics

 

Counters in Kappa: Semantics, Simulation, and Static Analysis.

Participants : Pierre Boutillier, Ioana Cristescu, Jérôme Feret.

 

Site-graph rewriting languages, such as Kappa or BNGL, offer parsimonious ways to describe highly combinatorial systems of mechanistic interactions among proteins. These systems may be then simulated efficiently. Yet, the modeling mechanisms that involve counting (a number of phosphorylated sites for instance) require an exponential number of rules in Kappa. In BNGL, updating the set of the potential applications of rules in the current state of the system comes down to the sub-graph isomorphism problem (which is NP-complete).

In [14], we extend Kappa to deal both parsimoniously and efficiently with counters. We propose a single push-out semantics for Kappa with counters. We show how to compile Kappa with counters into Kappa without counters (without requiring an exponential number of rules). We design a static analysis, based on affine relationships, to identify the meaning of counters and bound their ranges accordingly.