Biochemical reaction rules with constraints

Abstract. We propose React(C), an expressive programming language for stochastic modeling and simulation in systems biology that is based on biochemical reactions with constraints. We prove that React(C) can express the stochastic pi-calculus, in contrast to previous rule-based pro-gramming languages, and further illustrate the high expressiveness of React(C). We present a stochastic simulator for React(C) independently of the choice of the constraint language C. Our simulator decides for a given reaction rule whether it can be applied to the current biochemical solution. We show that this decision problem is NP-complete for arbi-trary constraint systems C and that it can be solved in polynomial time for rules of bounded arity. In practice, we propose to solve this problem by constraint programming.