Documentation for PyCoMo
PyCoMo is a python 3 package for the creation and analysis of community metabolic models. More specifically, PyCoMo generates compartmentalized community metabolic models with a structure allowing simulations under fixed growth rate, but variable abundance profile, or fixed abundance profile and variable community growth rate. The community metabolic models generated by PyCoMo can switch between these two structures and retain the original reaction bounds of the input member models. As also all metabolites, reactions, genes and compartments are directly attributable to their member of origin, PyCoMo community metabolic models are fully reusable.
The community models can be analysed with PyCoMo to predict all feasible exchange metabolites and cross-feeding interactions, for the whole space of growth rate and abundance profiles. The community models are COBRApy models and can therefor be directly used by other COBRA methods. It is also possible to save and load the community models in SBML format, allowing to share and reuse the models built with PyCoMo.
The source code is available on GitHub. This is also the best place to let us know should you encounter problems!
Citing PyCoMo
Michael Predl, Marianne Mießkes, Thomas Rattei, Jürgen Zanghellini, PyCoMo: a python package for community metabolic model creation and analysis, Bioinformatics, Volume 40, Issue 4, April 2024, btae153, https://doi.org/10.1093/bioinformatics/btae153
Basics