Efficient stochastic simulation of biological systems with multiple variable volumes

DOI10.1016/J.ENTCS.2007.12.012MaRDI QIDQ2870307zbMATH OpenOpenAlexFDO

Authors Cristian Versari, Nadia Busi

Publication date 17 January 2014

Published in Electronic Notes in Theoretical Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.entcs.2007.12.012

zbMATH Keywords

\(\pi\)-calculusprocess calculistochastic simulation

Mathematics Subject Classification ID

Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.) (68Q85) Probability in computer science (algorithm analysis, random structures, phase transitions, etc.) (68Q87) Systems biology, networks (92C42)

Recommendations

• Stochastic biological modelling in the presence of multiple compartments
• A Stochastic Pi Calculus for Concurrent Objects
• Stochastic simulation of multiple process calculi for biology
• Simulation techniques for the calculus of wrapped compartments
• Application of a stochastic name-passing calculus to representation and simulation of molecular processes

Cites work

• A calculus of mobile processes. I
• A calculus of mobile processes. II
• A Core Calculus for a Comparative Analysis of Bio-inspired Calculi
• A Stochastic Pi Calculus for Concurrent Objects
• Application of a stochastic name-passing calculus to representation and simulation of molecular processes
• BioAmbients: an abstraction for biological compartments
• Computational Methods in Systems Biology
• Computational methods in systems biology. International conference CMSB 2004, Paris, France, May 26--28, 2004. Revised selected papers.
• Formal molecular biology
• scientific article; zbMATH DE number 1296290 (Why is no real title available?)
• scientific article; zbMATH DE number 2059568 (Why is no real title available?)
• Priority in process algebra.

Cited in

(7)

• Stochastic biological modelling in the presence of multiple compartments
• Constructing and visualizing chemical reaction networks from pi-calculus models
• Modelling biological compartments in bio-PEPA
• A framework for modelling and simulating networks of cells
• The estimation of probability distribution of SDE by only one sample trajectory
• \textsf{CoBiC}: context-dependent bioambient calculus
• The stochastic evolution of a protocell: the Gillespie algorithm in a dynamically varying volume

Describes a project that uses

Uses Software

• SpiCO

This page was built for publication: Efficient stochastic simulation of biological systems with multiple variable volumes

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2870307)