Stochastic Calculus of Wrapped Compartments

TL;DR

This paper introduces a stochastic version of the Calculus of Wrapped Compartments (CWC), simplifying biological system modeling and analysis by removing sequencing operators, and demonstrates its application in biological interactions and gene regulation.

Contribution

It presents a stochastic semantics for CWC, enhancing its utility for biological modeling by simplifying formal treatment and enabling stochastic analysis.

Findings

Successfully modeled macrophage-neutrophil interactions

Captured gene regulation mechanisms in E.Coli

Provided a stochastic framework for biological systems

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.