PyCoMo: a python package for community metabolic model creation and analysis

Michael Predl, Marianne Mießkes, Thomas Rattei (Corresponding author), Jürgen Zanghellini (Corresponding author)

Publications: Contribution to journalArticlePeer Reviewed

Abstract

SUMMARY: PyCoMo is a python package for quick and easy generation of genome-scale compartmentalized community metabolic models that are compliant with current openCOBRA file formats. The resulting models can be used to predict (i) the maximum growth rate at a given abundance profile, (ii) the feasible community compositions at a given growth rate, and (iii) all exchange metabolites and cross-feeding interactions in a community metabolic model independent of the abundance profile; we demonstrate PyCoMo's capability by analysing methane production in a previously published simplified biogas community metabolic model.

AVAILABILITY AND IMPLEMENTATION: PyCoMo is freely available under an MIT licence at http://github.com/univieCUBE/PyCoMo, the Python Package Index, and Zenodo.

Original languageEnglish
Article numberbtae153
JournalBioinformatics (Oxford, England)
Volume40
Issue number4
DOIs
Publication statusPublished - 1 Apr 2024

Austrian Fields of Science 2012

  • 106005 Bioinformatics

Keywords

  • Software
  • Genome

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