Issue No. 01 - January-March (2008 vol. 5)
A translation of SBML (Systems Biology Markup Language) into a process algebra is proposed in order to allow the formal specification, the simulation and the formal analysis of biological models. Beta-binders, a language with a quantitative stochastic extension, is chosen for the translation. The proposed translation focuses on the main components of SBML models, as species and reactions. Furthermore, it satisfies the compositional property, i.e. the translation of the whole model is obtained by composing the translation of the subcomponents. An automatic translator tool of SBML models into Beta-binders has been implemented as well. Finally, the translation of a simple model is reported.
Process algebras, biological systems, modeling, Systems Biology Markup Language (SBML), translation tool, systems biology
P. Quaglia, F. Ciocchetta and C. Priami, "An Automatic Translation of SBML into Beta-Binders," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 5, no. , pp. 80-90, 2007.