TY - JOUR
T1 - The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems
AU - Boemo, Michael A.
AU - Cardelli, Luca
AU - Nieduszynski, Conrad A.
N1 - 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.
PY - 2020/3/9
Y1 - 2020/3/9
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85082143018&partnerID=8YFLogxK
U2 - 10.1371/journal.pcbi.1007651
DO - 10.1371/journal.pcbi.1007651
M3 - Article
C2 - 32150540
AN - SCOPUS:85082143018
VL - 16
JO - PLoS Computational Biology
JF - PLoS Computational Biology
SN - 1553-734X
IS - 3
M1 - e1007651
ER -