Chapter

Programming Languages and Systems

Volume 6602 of the series Lecture Notes in Computer Science pp 338-357

Biochemical Reaction Rules with Constraints

  • Mathias JohnAffiliated withBioComputing, LIFL (CNRS UMR8022) & IRI (CNRS USR3078)University of Lille 1
  • , Cédric LhoussaineAffiliated withBioComputing, LIFL (CNRS UMR8022) & IRI (CNRS USR3078)University of Lille 1
  • , Joachim NiehrenAffiliated withBioComputing, LIFL (CNRS UMR8022) & IRI (CNRS USR3078)Inria
  • , Cristian VersariAffiliated withUniversity of Bologna

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 π-calculus, in contrast to previous rule-based programming 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 arbitrary 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.