isrene (pronounced "is-reen") is a Python package for creating dynamic models of metabolic isotopologue reaction networks.
Writing up the equations for a dynamic model of metabolic stable isotope labeling experiments can be tedious and error-prone. isrene aims to make this process easier by providing a Python interface for:
- specifying metabolic reaction networks in terms of reaction patterns (rule-based models) describing stoichiometry, reversibility, kinetics, and atom mappings
- specifying isotopic tracers
- conveniently specifying observation functions for mass spectrometry measurements
- exporting the rule-based model to SBML-multi
- generating the full species/reaction network from the rule-based formulation and exporting it to core-SBML
isrene is not yet available on PyPI. To install, clone this repository and run pip install . from the root directory.
Check out the examples at examples/ to get started.
So far, only example notebooks and in-source documentation are available.
Note that isrene has not been thoroughly tested and is still under development. Use with caution.
In particular, there is insufficient error checking, and certain assumptions are made on the uniqueness of identifiers and combinations thereof.
If you are interested in a collaboration to apply or extend this package, please contact the author.