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The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems
- Source :
- PLoS Computational Biology, PLoS Computational Biology, Vol 16, Iss 3, p e1007651 (2020)
- Publication Year :
- 2020
- Publisher :
- Public Library of Science (PLoS), 2020.
-
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.<br />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.
- Subjects :
- 0301 basic medicine
Computer science
Process calculus
Social Sciences
Biochemistry
Immune Receptors
Task (project management)
0302 clinical medicine
Calculus
Medicine and Health Sciences
Biochemical Simulations
State space
Psychology
Biology (General)
Post-Translational Modification
Phosphorylation
Language
0303 health sciences
Immune System Proteins
DNA methylation
Ecology
Mathematical model
FOS: Social sciences
Formal methods
Chromatin
Nucleic acids
Computational Theory and Mathematics
Modeling and Simulation
030220 oncology & carcinogenesis
Physical Sciences
Epigenetics
DNA modification
Chromatin modification
Research Article
Signal Transduction
Chromosome biology
DNA Replication
QH301-705.5
Immunology
FOS: Physical sciences
Models, Biological
Cellular and Molecular Neuroscience
03 medical and health sciences
Genetics
Computer Simulation
Molecular Biology
Ecology, Evolution, Behavior and Systematics
030304 developmental biology
Flexibility (engineering)
Biology and life sciences
Cognitive Psychology
Proteins
Computational Biology
DNA
Cell Biology
Models, Theoretical
Replication (computing)
T Cell Receptors
Task (computing)
030104 developmental biology
Fork (system call)
Cognitive Science
Gene expression
030217 neurology & neurosurgery
Mathematics
Neuroscience
DNA Damage
Subjects
Details
- Database :
- OpenAIRE
- Journal :
- PLoS Computational Biology, PLoS Computational Biology, Vol 16, Iss 3, p e1007651 (2020)
- Accession number :
- edsair.doi.dedup.....6e38e95c3903ac96245d211ee5353bb7
- Full Text :
- https://doi.org/10.17863/cam.48364