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A Graphical Representation for Biological Processes in the Stochastic Pi-calculus

Andrew Phillips, Luca Cardelli, and Giuseppe Castagna

Abstract

This paper presents a graphical representation for the stochastic pi-calculus, which builds on previous formal and informal notations. The graphical representation is used to model a couple of example biological systems, namely a bistable gene network and a mapk signalling cascade. One of the main benefits of the representation is its ability to highlight the existence of cycles, which are a key feature of many biological systems. Another benefit is its ability to animate interactions between system components, in order to clarify the overall system function. The graphical representation can also be used as a front end to a simulator for the stochastic pi-calculus. This complements the existing textual interface to the simulator, with a view to making modelling and simulation of biological systems more accessible to non computer scientists.

Details

Publication typeArticle
Published inTransactions in Computational Systems Biology
URLhttp://dx.doi.org/10.1007/11905455_7
Pages123–152
Volume4230
SeriesLNCS
PublisherSpringer
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