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

Boemo, Michael A., Cardelli, Luca and Nieduszynski, Conrad A. ORCID: https://orcid.org/0000-0003-2001-076X (2020) The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems. PLoS Computational Biology, 16 (3). ISSN 1553-734X

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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.

Item Type: Article
Additional Information: Funding Information: This work was supported by Biotechnology and Biological Sciences Research Council (https://bbsrc.ukri.org/) grant BB/N016858/1 and Wellcome Trust (https://wellcome.ac.uk/) Investigator Award 110064/Z/15/Z to CAN. Additional funding and support is provided by the St. Cross College Emanoel Lee Junior Research Fellowship to MAB, as well as funds to MAB from the Department of Pathology, University of Cambridge. No funders had a role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Uncontrolled Keywords: ecology, evolution, behavior and systematics,modelling and simulation,ecology,molecular biology,genetics,cellular and molecular neuroscience,computational theory and mathematics ,/dk/atira/pure/subjectarea/asjc/1100/1105
Faculty \ School: Faculty of Science > School of Biological Sciences
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Depositing User: LivePure Connector
Date Deposited: 07 Sep 2022 14:31
Last Modified: 22 Sep 2022 18:34
URI: https://ueaeprints.uea.ac.uk/id/eprint/87850
DOI: 10.1371/journal.pcbi.1007651

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