Welcome to TRuML’s documentation!

TRuML is a Translator for Rule-based Modeling Languages. TRuML is designed to convert between systems biology models written in the Kappa or BioNetGen (BNGL) languages. While not all models can be converted between the two languages, most features of these languages are mutually compatible.

Contents:

• Installation
  • Installing from PyPI
  • Installing from source
• Tutorial
  • Converting from Kappa to BNGL
  • Converting from BNGL to Kappa
  • Verbose conversion
• Advanced concepts
  • Variables, parameters, and functions
  • Syntax joining molecules and molecularity
    • Kappa to BNGL
    • BNGL to Kappa
• TRuML Module References
  • TRuML main function (truml.truml)
  • TRuML model file readers (truml.readers)
  • TRuML semantic objects (truml.objects)
  • TRuML utility functions (truml.utils)
  • TRuML custom exceptions (truml.rbexceptions)
• External References

Indices and tables

• Index
• Module Index
• Search Page