The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems.
Publication Date
2020-03Journal Title
PLoS Comput Biol
ISSN
1553-734X
Publisher
Public Library of Science (PLoS)
Volume
16
Issue
3
Pages
e1007651
Language
eng
Type
Article
This Version
AM
Physical Medium
Electronic-eCollection
Metadata
Show full item recordCitation
Boemo, M., Cardelli, L., & Nieduszynski, C. A. (2020). The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems.. PLoS Comput Biol, 16 (3), e1007651. 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
DNA Damage, Computational Biology, DNA Replication, Phosphorylation, Models, Theoretical, Models, Biological, Computer Simulation
Sponsorship
Royal Society Grant RP\R\180001
Start-up funds from the Department of Pathology, University of Cambridge
St. Cross, University of Oxford Emanoel Lee Junior Research Fellowship
Identifiers
External DOI: https://doi.org/10.1371/journal.pcbi.1007651
This record's URL: https://www.repository.cam.ac.uk/handle/1810/301283
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