MØD

This is the documentation for the MØD software package. The sources can be found in the GitHub repository: http://github.com/jakobandersen/mod. For additional information see the webpage: http://mod.imada.sdu.dk.

If you use MØD in your research you may want to cite [AFMS-MØD], and other relevant publications, depending on the components used. A discussion of rule-based modelling of chemistry can be found in [AFMS-Levels]. See References for a full list of publications.

The package contains the following components.

• libMØD, a C++ shared library (mod)

  The main library.

• PyMØD, a Python module (mod)

  Python bindings for the library and extra functionality for easier usage of many features.

• PostMØD, a Bash script (mod_post)

  The post-processor for compiling figures and summaries.

• The Wrapper Script, a Bash script (mod)

  A convenience wrapper for invoking python3 with user-supplied code. The wrapper handles output and invokes the post-processor. Additionally, it can run python3 through gdb and/or valgrind (either normal memcheck or callgrind).

Contents

• 1. Installation
• 2. Compiling from Source
• 3. libMØD
• 4. PyMØD
• 5. PostMØD
• 6. The Wrapper Script
• 7. Graph, Rule, and Molecule Model
• 8. Data Formats
• 9. Derivation Graph Strategies
• 10. Examples
• 11. Known Issues
• 12. Changes
• 13. References

Contributors

• Jakob Lykke Andersen: main author.

• Nikolai Nøjgaard: author of EpiM which was a Python module of MØD (see [AHMNP-EpiM]).