A calculus for modelling, simulating and analysing compartmentalized biological systems

This paper introduces Process Calculus, a special modeling language designed for encoding and calculating the behaviors of compartmentalized biological systems. The formalism combines, in a unified framework, two successful computational paradigms - process algebras and membrane systems. The goal of Protein Calculus is to provide a formal tool for transforming collected information from in vivo experiments into coded definition of the different types of proteins, complexes of proteins, and membrane-organized systems of such entities. Using this encoded information as input, our calculus computes, in silico, the possible behaviors of a living system.