Beacon Calculus Simulator (bcs)

Contents:

• Installation
• Quickstart
• Formatting
• Processes
• The System Line
• Communication
• Built-in Functions
• Simulation
• Plotting
• Examples

Overview

The Beacon Calculus is a process algebra designed to make modelling biological systems fast, intuitive, and accessible. It was designed with two main aims in mind: It should be possible to represent complex systems with minimal amounts of code, and models should be very easy to expand and modify. Once models are written in the Beacon Calculus, they can be simulated with the Beacon Calculus Simulator (bcs) software detailed here . Users interested in an introduction to the Beacon Calculus should first look through the corresponding methods publication which introduces the language by way of examples. A more formal description of the language and semantics is presented in the supplemental information of that publication. This page aims to catalogue the features of both the language and the software for reference.

Publications

Please cite the following publication if you use the Beacon Calculus for your research:

Boemo, M.A., Cardelli, L., Nieduszynski, C.A. (2020) The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems. PLoS Computational Biology 16:e1007651. [Journal DOI] [bioRxiv]

Bugs, Questions, and Comments

Should any bugs arise or if you have any questions about usage, please raise a GitHub issue. For more detailed discussions about collaborations or the Beacon Calculus, the bcs software, or the documentation, please Email Michael Boemo at mb915@cam.ac.uk.