Causal π-Calculus for Biochemical Modelling

An increasing number of researchers is trying to define models of biochemical pathways via theoretical and technological tools, allowing biologists to simulate reactions before doing them in vitro. The advantages are obvious: a computation normally requires less time then a real experiment, simulation of reactions is cheaper than doing them effectively, and so on. The problem is to find a formal modelling language for systems biology that represents: • the ”actors” of the system (molecules, proteins, genes. . . ) at different level of abstraction; • the qualitative evolution of the system in terms of their reactions possibly expressing causality between reactans or reactions; • all the quantitative aspects of the pathways (quantity of reagents, temperature, reaction rates, . . . ) Recently Regev, Silvermann & Shapiro [8] proposed the π-calculus [3] as a qualitative model of biochemical pathways, seen as network of proteins. Then [6] use a stochastic variant of the π-calculus [5], yielding a language that permits to model also quantitative aspects of biochemical pathways. ∗The first three authors have been partially supported by UE project IST-32072-DEGAS within the FET initiative on Global Computing.