Abstract
This paper addresses the translation of Systems Biology Mark-Up Language (SBML) Level 2 models of network of biochemical reactions into 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.
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Eccher, C., Lecca, P. (2006). Translating SBML Models into the Stochastic π-Calculus for Stochastic Simulation. In: Priami, C., Ingólfsdóttir, A., Mishra, B., Riis Nielson, H. (eds) Transactions on Computational Systems Biology VII. Lecture Notes in Computer Science(), vol 4230. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11905455_4
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DOI: https://doi.org/10.1007/11905455_4
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