MØD

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

Overview

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.

The package contains the following components.

• libMØD, shared library (mod)

  The main library.

• PyMØD, Python 3 module (mod)

  Python bindings for the library and extra functionality for easier usage of many features. It additionally include the submodule EpiM.

• PostMØD, Bash Script (mod_post)

  The post processor for compiling figures and summaries.

• The wrapper script, Bash Script (mod)

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

Contributors

• Jakob Lykke Andersen: main author.

• Nikolai Nøjgaard: author of EpiM.