Rewriting Theory for the Life Sciences: A Unifying Theory of CTMC Semantics

This page accompanies the paper with the title above, submitted to Theoretical Computer Science, with the code used to produce the results for the MØD section.

The Python code can be found here, and can be executed through the MØD wrapper script. Below are options for how to execute it manually. Besides printing data for the table in Appendix E, it will produce a PDF file with visualization of the rules and their composition. A pre-compiled version of this PDF can be found here.

Using the playground server

1. Download the code, calc.py
2. Paste it into the text field in the online playground.
3. Press "Run".
4. When finished the PDF with figures is available through the "Summary" link that appears.

Using a local installation of MØD

1. Install MØD through one of the methods described at http://jakobandersen.github.io/mod/installation.html (from source, Conda, or as a Docker image).
2. Download the code, calc.py
3. Run it with mod -f calc.py.
4. When finished the PDF with figures is available in summary/summary.pdf.