A simple calculus for proteins and cells
The use of process calculi to represent biological systems has led to the design of different formalisms Such as brane calculi and K-calculus. Both have proved to be useful to model different types of biological systems. As an attempt to unify the formalisms, we introduce the bio kappa-calculus, a simple Calculus for describing proteins and cells, in which bonds are represented by means of shared names and interactions are modelled at the domain level. In bio kappa-calculus, protein-protein interactions have to be at most binary and cell interactions have to fit with sort constraints. In this contribution we define the semantics of bio kappa-calculus, analyse its properties, discuss the expressivity of the calculus by modelling two significant examples - a signalling pathway and a virus infection - and study an implementation in Milner's pi-calculus. (C) 2008 Elsevier B.V. All rights reserved.
systems biology process algebra signal transduction pathways