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The modelling and analysis of biological systems has deep roots inMathematics, specifically in the field of Ordinary Differential Equations.Alternative approaches based on formal calculi, often derived from processalgebras or term rewriting systems, provide a quite complementary way toanalyse the behaviour of biological systems. These calculi allow to cope in anatural way with notions like compartments and membranes, which are not easy(sometimes impossible) to handle with purely numerical approaches, and areoften based on stochastic simulation methods. The Calculus of WrappedCompartments is a framework based on stochastic multiset rewriting in acompartmentalised setting used for the description of biological and ecologicalsystems. We provide an extended presentation of the Calculus of WrappedCompartments, sketch a few modelling guidelines to encode biological andecological interactions, show how spatial properties can be handled within theframework and define a hybrid simulation algorithm. Several applications inBiology and Ecology are proposed as modelling case studies.

Modelling Biological and Ecological Systems with the Calculus of Wrapped Compartments