Larcher, Roberto and Priami, Corrado (2008) From BlenX to chemical reactions via SBML. UNSPECIFIED. (Unpublished)

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Abstract

Recently process calculi have been used to model biological systems. We use the process calculi-based language BlenX to develop executable models starting from the composition of the description of the molecules involved in the system. BlenX programs can be run through a stochastic run-time that makes the molecules interact together, mimicking different kinds of reactions. The goal of the paper is to extract from BlenX programs a description of the same system based on chemical reactions that can be executed through chemical-based stochastic simulators. We present an algorithm that extracts the list of these reactions from the model definition given in BlenX. The translation is done without run- ning the system, but just analysing the model. The boxes in the BlenX models, used to represent molecules, often perform immediate actions (i.e. reactions with infinite rate) to change their internal state, some of which can be removed by the algorithm to optimize the model. The outcome of the algorithm is an SBML file that can be easily im- ported in SBML-supporting simulators that in some cases may run faster then executing BlenX programs due to model reduction and optimization. Furthermore, exporting our models in SBML allow us to share the models we develop in BlenX with the scientific community.

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