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

View ORCID ProfileMichael A. Boemo, View ORCID ProfileLuca Cardelli, View ORCID ProfileConrad A. Nieduszynski
doi: https://doi.org/10.1101/579029
Michael A. Boemo
1Department of Pathology, University of Cambridge
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  • For correspondence: mb915@cam.ac.uk
Luca Cardelli
2Department of Computer Science, University of Oxford
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Conrad A. Nieduszynski
3Genome Damage and Stability Centre, University of Sussex
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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.

Author summary Simulating a model of a biological system can suggest ideas for future experiments and help ensure that conclusions about a mechanism are consistent with data. The Beacon Calculus is a new language that makes modelling simple by allowing users to simulate a biological system in only a few lines of code. This simplicity is critical as it allows users the freedom to come up with new ideas and rapidly test them. Models written in the Beacon Calculus are also easy to modify and extend, allowing users to add new features to the model or incorporate it into a larger biological system. We demonstrate the breadth of applications in this paper by applying the Beacon Calculus to DNA replication and DNA damage repair, both of which have implications for genome stability and cancer. We also apply it to multisite phosphorylation, which is important for cellular signalling. To enable users to create their own models, we created the open-source Beacon Calculus simulator bcs (https://github.com/MBoemo/bcs.git) which is easy to install and is well-supported by documentation and examples.

Footnotes

  • https://github.com/MBoemo/bcs.git

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted November 26, 2019.
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The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems
Michael A. Boemo, Luca Cardelli, Conrad A. Nieduszynski
bioRxiv 579029; doi: https://doi.org/10.1101/579029
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The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems
Michael A. Boemo, Luca Cardelli, Conrad A. Nieduszynski
bioRxiv 579029; doi: https://doi.org/10.1101/579029

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