www.prismmodelchecker.org
[MDPR16] Chunyan Mu, Peter Dittrich, David Parker and Jonathan E. Rowe. Formal Quantitative Analysis of Reaction Networks Using Chemical Organisation Theory. In Proc. 14th International Conference on Computational Methods in Systems Biology (CMSB'16), volume 9859 of LNCS, pages 232-251, Springer. September 2016. [pdf] [bib] [Develops techniques for analysing reaction networks using chemical organisation theory, implemented in an extension of PRISM.]
Downloads:  pdf pdf (574 KB)  bib bib
Notes: The original publication is available at www.springerlink.com.
Abstract. Chemical organisation theory is a framework developed to simplify the analysis of long-term behaviour of chemical systems. In this paper, we build on these ideas to develop novel techniques for formal quantitative analysis of chemical reaction networks, using discrete stochastic models represented as continuous-time Markov chains. We propose methods to identify organisations, to study quantitative properties regarding movement between these organisations and to construct an organisation-based coarse graining of the model that can be used to approximate the behaviour of the original reaction network.

Publications