Software that simulates the behaviour of systems written in the Beacon Calculus. bcs is under development by the Boemo Group at the University of Cambridge.
Clone the bcs repository by running:
git clone https://github.com/MBoemo/bcs.gitThe bcs directory will appear in your current directory. bcs was written in C++11 and uses OpenMP for parallel processing, but these are standard on most systems; there are no other third party dependencies. Compile the latest version of bcs by running:
cd bcs
git checkout v1.0.1
makeThis will put the bcs executable into the bcs/bin directory. Development was done using gcc 5.4.0 on an Ubuntu 16.04 platform, and bcs was tested to compile and run on both OSX and Linux systems.
A manual for writing models in the Beacon Calculus and documentation for bcs is available at https://beacon-calculus-simulator.readthedocs.io. It includes:
- quick-start tutorials,
- a bank of examples,
- a full list of features.
Please cite the following publication if you use the Beacon Calculus for your research: Boemo MA, Cardelli L, Nieduszynski CA. The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems. PLoS Computational Biology 2020;16:e1007651. [bioRxiv] [Journal Link]
Should any bugs arise or if you have a question about usage, please raise a GitHub issue at https://github.com/MBoemo/bcs/issues. For more detailed discussions on the Beacon Calculus, the bcs software, the manual, or for collaborations, please Email mb915@cam.ac.uk.