Stochastic Calculus of Wrapped Compartments

Abstract

The Calculus of Wrapped Compartments (CWC) is a variant of the Calculus of Looping Sequences (CLS). While keeping the same expressiveness, CWC strongly simplifies the development of automatic tools for the analysis of biological systems. The main simplification consists in the removal of the sequencing operator, thus lightening the formal treatment of the patterns to be matched in a term (whose complexity in CLS is strongly affected by the variables matching in the sequences). We define a stochastic semantics for this new calculus. As an application we model the interaction between macrophages and apoptotic neutrophils and a mechanism of gene regulation in E.Coli

On Designing Multicore-Aware Simulators for Biological Systems

“…The idea of Gillespie's algorithm is that a rate constant is associated with each considered chemical reaction. Such a constant is obtained by multiplying the kinetic constant of the reaction by the number of possible combinations of reactants that may occur in the system (thus modelling the law of mass action, but more flexible approaches are also considered in the literature [9]). The resulting rate is then used as the parameter of an exponential distribution modelling the time spent between two occurrences of the considered chemical reaction.…”

“…The Calculus of labelled Wrapped Compartments (CWC) (see [9], [11]) is based on a nested structure of ambients delimited by membranes with specific proprieties. Biological entities like cells, bacteria and their interactions can be easily described in CWC.…”

“…Among other formalisms, the Calculus of Wrapped Compartments (CWC) [9] is a recently proposed rewriting-based language for the representation and simulation of biological systems. It has been designed with the aim of simplifying the development of efficient implementations, while keeping the same expressiveness of other more complex languages.…”

On Parallelizing On-Line Statistics for Stochastic Biological Simulations

“…The Calculus of labelled Wrapped Compartments (CWC) [5,2] has been designed to describe biological entities (like cells and bacteria) by means of a nested structure of ambients delimited by membranes.…”

“…In [2] we presented a highly parallelized simulator for the Calculus of Wrapped Compartments (CWC) [5] which exploits, in an efficient way, the multi-core architecture using the FastFlow programming framework [8]. The framework relies on selective memory [1], i.e.…”