Examples

New users are encouraged to look in the bcs/tests directory, which contains dozens of very simple models with the expected output and behaviour described in the comments.

We included examples from different fields of biology in the main Beacon Calculus manuscript, which are:

• simple reaction between two chemical species (see section “Language Overview”),
• DNA replication in S. cerevisiae (see section “DNA Replication”),
• a population of cells responding to methylation damage (see section “Cellular Response to DNA Damage”),
• receptor multisite phosphorylation and ultrasensitivity (see section “Multisite Phosphorylation”),
• kinesin stepping down a microtubule (see Supplemental Information).

Full source code is provided for each of these examples, along with a line-by-line description of the processes and expected behaviour of the model. For convenience, the source code for these models are provided in the bcs/examples directory, along with python scripts that create plots similar to those in the manuscript.

As we develop more applications and examples over time, we will post them here.