Summary. P systems are a biologically inspired model introduced by Gheorghe Păun with the aim of representing the structure and the functioning of the cell. P systems are usually equipped with the maximal parallelism semantics; however, since their introduction, some alternative semantics have been proposed and investigated. We propose a semantics that describes the causal dependencies occurring between the reactions of a P system. We investigate the basic properties that are satisfied by such a semantics. The notion of causality turns out to be quite relevant for biological systems, as it permits to point out which events occurring in a biological pathway are necessary for another event to happen. 1

Abstract. In this chapter we introduce process algebras, a class of formal modelling techniques developed in theoretical computer science, and discuss their use within systems biology. These formalisms have a number of attractive features which make them ideal candidates to be intermediate, formal, compositional representations of biological systems. As we will show, when modelling is carried out at a suitable level of abstraction, the constructed model can be amenable to analysis using a variety of different approaches, encompassing both individualsbased stochastic simulation and population-based ordinary differential equations. We focus particularly on Bio-PEPA, a recently defined extension of the PEPA stochastic process algebra, which has features to capture both stoichiometry and general kinetic laws. We present the definition of the language, some equivalence relations and the mappings to underlying mathematical models for analysis. We demonstrate the use of Bio-PEPA on two biological examples.

Summary. Brane Calculi are a family of biologically inspired process calculi, proposed in [6] to model the interactions of dynamically nested membranes. We propose a semantics that describes the causal dependencies occurring between the reactions of a system described in Brane Calculi. We investigate the basic properties that are satisfied by such a semantics. The notion of causality turns out to be quite relevant for biological systems, as it permits to point out which events occurring in a biological pathway are necessary for another event to happen. 1