Working group: "Computational Biology"

2010, the 20th of April

Espen Højsgaard

Title: Simulating Biology with Bigraphs


The theory of bigraphs has been proposed as a formalism for modelling molecular biological systems with dynamic compartmentalization. For example, Damgaard et al. have used bigraphs to model the formation of clathrin-coated cytoplasmic vesicles, through budding from the plasma membrane (the cell-wall) [1].

Bigraphical Reactive Systems (BRSs) is a rule based model of concurrency developed by Milner [2], that in essence generalizes and unifies the connectivity of CCS with the spatiality of the ambient calculus in one framework. Many process calculi can be expressed as BRSs, such as CCS, pi calculus, ambient calculus, CSP, and kappa. Recently, Krivine et al. have equipped the theory with a stochastic semantics [3].

In this talk, I will give an introduction to bigraphs and BRSs and present ongoing work on implementing an efficient simulator for stochastic bigraphs.