Modelling Biological Compartments in Bio-PEPA

Compartments and membranes play an important role in cell biology. Therefore it is highly desirable to be able to represent them in modelling languages for biology. Bio-PEPA is a language for the modelling and analysis of biochemical networks; in its present version compartments can be defined but they are only used as labels to express the location of molecular species.In this work we present an extension of Bio-PEPA with some features in order to represent more details about locations of species and reactions. With the term location we mean either a membrane or a compartment. We describe how models involving compartments and membranes can be expressed in the language and, consequently, analysed. We limit our attention to static locations (i.e. with a fixed structure) whose size can depend on time. We illustrate our approach via a classical model used to represent intracellular Ca2+ oscillations.