Modeling static biological compartments with beta-binders

Abstract

We investigate the modeling of biological systems with static compartments through Beta-binders, a recently developed process calculus. Biological entities are represented as bio-processes and the calculus is extended with the notion of compartment. Entities can either be internal to compartments or reside on compartment borders. Movement in and out of compartments is requested by internal objects and mediated by border objects. The extended calculus is equipped with the notion of locality, and various kinds of relations between actions are defined. Moreover, we compare our proposal with similar formalisms and we show how to use the proposed calculus for modeling and analyzing the cAMP-signaling pathway in OSNs. © Springer-Verlag Berlin Heidelberg 2007.