The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems.

PLoS Computational Biology
Michael A. BoemoConrad A. Nieduszynski

Abstract

Biological systems are made up of components that change their actions (and interactions) over time and coordinate with other components nearby. Together with a large state space, the complexity of this behaviour can make it difficult to create concise mathematical models that can be easily extended or modified. This paper introduces the Beacon Calculus, a process algebra designed to simplify the task of modelling interacting biological components. Its breadth is demonstrated by creating models of DNA replication dynamics, the gene expression dynamics in response to DNA methylation damage, and a multisite phosphorylation switch. The flexibility of these models is shown by adapting the DNA replication model to further include two topics of interest from the literature: cooperative origin firing and replication fork barriers. The Beacon Calculus is supported with the open-source simulator bcs (https://github.com/MBoemo/bcs.git) to allow users to develop and simulate their own models.

References

Mar 27, 2001·Pacific Symposium on Biocomputing·A RegevE Shapiro
Dec 17, 2002·Oncogene·Barbara Sedgwick, Tomas Lindahl
Oct 1, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jeremy Gunawardena
Oct 28, 2005·Molecular Biology of the Cell·Prasanta K PatelNicholas Rhind
Dec 19, 2007·The Journal of Continuing Education in the Health Professions·Gabrielle M Kane
May 15, 2009·The FEBS Journal·Carlos Salazar, Thomas Höfer
Jun 19, 2009·Nature·Matthew Thomson, Jeremy Gunawardena
May 12, 2010·Nucleic Acids Research·Alessandro P S de MouraConrad A Nieduszynski
Mar 1, 2011·Biophysical Journal·Omer DushekVahid Shahrezaei
Oct 19, 2011·BMC Systems Biology·Carsten MausAdelinde M Uhrmacher
Nov 29, 2011·Nucleic Acids Research·Cheuk C SiowConrad A Nieduszynski
Jan 13, 2012·Nature Reviews. Cancer·Dragony FuLeona D Samson
Jan 31, 2012·Nature Methods·Bastian R AngermannMartin Meier-Schellersheim
Oct 11, 2012·Immunological Reviews·Omer DushekP Anton van der Merwe
Feb 21, 2013·Molecular Systems Biology·Carlos F LopezPeter K Sorger
Mar 20, 2013·Bioinformatics·Fengkai ZhangMartin Meier-Schellersheim
Oct 4, 2013·Nucleic Acids Research·Carolin A MüllerConrad A Nieduszynski
Dec 3, 2014·Trends in Biochemical Sciences·James E Ferrell, Sang Hoon Ha
May 23, 2015·Nature Reviews. Molecular Cell Biology·Michalis FragkosMarcel Méchali
Oct 30, 2016·Bioinformatics·Leonard A HarrisJames R Faeder
Jun 29, 2018·Bioinformatics·Pierre BoutillierWalter Fontana

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Citations

Aug 6, 2021·PLoS Computational Biology·Kai BuddeAdelinde M Uhrmacher

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Software Mentioned

Bio
PEPA Eclipse plug
Beacon Calculus
PRISM
CCS
Rules
PEPA workbench
BioNetGen
bcs
PEPA

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