Translating SBML Models into the Stochastic pi-Calculus for Stochastic Simulation
نویسندگان
چکیده
This paper addresses the translation of Systems Biology MarkUp Language (SBML) Level 2 models of network of biochemical reactions to the Biochemical Stochastic π-calculus (SPI). SBML is XML-based formalism for systems biology, while SPI can describe the concurrency of the different interactions occurring in a network of biochemical stochastic reactions. SPI models can be used for simulation by available computer packages. We present the approach followed in designing a software tool for working biologists that parses an SBML model and performs the unsupervised translation into the process algebra model. To test the correctness of the translation process we present the results obtained by performing simulations of a translated simplified circadian clock model, comparing our results with that obtained with the original differential equation model.
منابع مشابه
Design and Implementation of a Tool for Translating SBML into the Biochemical Stochastic π - calculus
Motivation: 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 rep...
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