Andrew Phillips and Luca Cardelli
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 Mapk signalling cascade and an evolved gene network. One of the main benefits of the representation is its ability to clearly highlight the existence of cycles, which are a key aspect of many biological systems. Another advantage is its ability to animate interactions between biological system components, in order to clarify the overall system function. The paper also shows how the graphical representation can be used as a front end to a stochastic simulator for the pi-calculus, in order to allow the direct simulation of graphical models. This complements the existing textual interface of the simulator, with a view to making modelling and simulation of biological systems more accessible to non computer scientists.
In Concurrent Models in Molecular Biology