Department of Pathology, University of Cambridge, Cambridge, United Kingdom.
Department of Computer Science, University of Oxford, Oxford, United Kingdom.
PLoS Comput Biol. 2020 Mar 9;16(3):e1007651. doi: 10.1371/journal.pcbi.1007651. eCollection 2020 Mar.
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.
生物系统由随时间改变其行为（和相互作用）并与附近其他组件协调的组件组成。这种行为的复杂性加上庞大的状态空间，使得创建简洁的数学模型变得困难，这些模型难以扩展或修改。本文介绍了 Beacon 演算，这是一种专为简化建模交互生物组件任务而设计的过程代数。通过创建 DNA 复制动力学、DNA 甲基化损伤响应中的基因表达动力学以及多部位磷酸化开关的模型，展示了其广度。通过使 DNA 复制模型适应进一步包括文献中两个感兴趣的主题：合作起始点火和复制叉障碍，展示了这些模型的灵活性。Beacon 演算由开源模拟器 bcs（https://github.com/MBoemo/bcs.git）提供支持，允许用户开发和模拟自己的模型。
