Design and implementation of a tool for translating SBML into the biochemical stochastic pi-calculus.

Abstract

SBML is becoming a standard 'de-facto' to represent and store biological models. Although SBML is very useful in defining ways of exchanging and storing biological information, it is not formal enough to allow direct translation into non ambiguous formal representation languages to perform analysis and simulation of models. We here suggest to map SBML models into process calculi representations. We implemented and validated a tool that translates SBML descriptions into stochastic pi-calculus specifications. Source code is freely available for academic use by contacting the authors.