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

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 signaling 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.