Modelling biological and ecological systems with the Calculus of Wrapped Compartments

The modelling and analysis of biological systems has deep roots in mathematics, specifically in the field of Ordinary Differential Equations. Alternative approaches based on formal calculi, often derived from process algebras or term rewriting systems, provide a quite complementary way to analyse the behaviour of biological systems. These calculi allow coping in a natural way with notions like compartments and membranes, which are not easy to handle with purely numerical approaches and are often based on stochastic simulation methods. This work will examine the modelling of biological and ecological systems with the Calculus of Wrapped Compartments. The Calculus of Wrapped Compartments is a framework based on stochastic multiset rewriting in a compartmentalised setting used for the description of biological and ecological systems. We provide an extended presentation of the Calculus of Wrapped Compartments, sketch a few modelling guidelines to encode biological and ecological interactions and present two extended applications in biology and ecology.