Related Experiment Video
Updated: Dec 26, 2025

A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems
Michael A Boemo1, Luca Cardelli2, Conrad A Nieduszynski3
1Department of Pathology, University of Cambridge, Cambridge, United Kingdom.
None:
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.
Related Concept Videos
Fundamental Mathematical Principles in Pharmacokinetics: Calculus and Graphs
On the other hand, integral calculus focuses on...
Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
Synthetic Biology
Golden rice
Golden rice is a genetically modified...
Mechanistic Models: Compartment Models in Individual and Population Analysis
Mechanistic Models: Overview of Compartment Models
Methods of Documentation V: CBE
In CBE, healthcare professionals establish predefined standards of practice that define what constitutes...

