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

Accepted version
Peer-reviewed

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Authors

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.

Description

Keywords

Computational Biology, Computer Simulation, DNA Damage, DNA Replication, Models, Biological, Models, Theoretical, Phosphorylation

Journal Title

PLoS Comput Biol

Conference Name

Journal ISSN

1553-734X
1553-7358

Volume Title

16

Publisher

Public Library of Science (PLoS)

Rights

All rights reserved
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