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.