The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems
Publication Date
2020-03-09Journal Title
PLOS Computational Biology
ISSN
1553-734X
Publisher
Public Library of Science
Volume
16
Issue
3
Language
en
Type
Article
This Version
VoR
Metadata
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Boemo, M. A., Cardelli, L., & Nieduszynski, C. A. (2020). The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems. PLOS Computational Biology, 16 (3) https://doi.org/10.1371/journal.pcbi.1007651
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.
Keywords
Research Article, Physical sciences, Biology and life sciences, Medicine and health sciences, Social sciences
Sponsorship
Biotechnology and Biological Sciences Research Council (BB/N016858/1)
Wellcome Trust (110064/Z/15/Z)
Identifiers
pcompbiol-d-19-00602
External DOI: https://doi.org/10.1371/journal.pcbi.1007651
This record's URL: https://www.repository.cam.ac.uk/handle/1810/303713
Rights
Attribution 4.0 International (CC BY 4.0)
Licence URL: https://creativecommons.org/licenses/by/4.0/
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