FORMAL METHODS FOR COMPUTATIONAL SYSTEMS BIOLOGY

Abstract

This paper reports on our experience in modelling whole cells with process calculi. We followed a holistic approach, aiming at investigating the behaviour of biological objects at the system level, in particular of a hypothetical and a of real prokaryote. These cells, namely VICE and Escherichia coli, have been specified through the pi-calculus, endowed with a stochastic semantics. We describe a couple of variants of the pi-calculus and briefly survey three interpreters of it, with increasing efficiency. We show how the usage of tools based on process calculi greatly helped us in designing the virtual cell VICE, and in comparing it with other prposals. The main properties of the in silico experiments on VICE and on Escherichia coli are then discussed and shown in agreement with those of real prokaryoptes acting in vivo/vitro.