PyCoMo: a python package for community metabolic model creation and analysis
- Author(s)
- Michael Predl, Marianne Mießkes, Thomas Rattei, Jürgen Zanghellini
- 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 github.com/univieCUBE/PyCoMo, the Python Package Index, and Zenodo.
- Organisation(s)
- Department of Microbiology and Ecosystem Science, Department of Analytical Chemistry
- External organisation(s)
- acib – Austrian Centre of Industrial Biotechnology, Doctoral School in Microbiology and Environmental Science
- Journal
- Bioinformatics (Oxford, England)
- Volume
- 40
- ISSN
- 1367-4803
- DOI
- https://doi.org/10.1093/bioinformatics/btae153
- Publication date
- 04-2024
- Peer reviewed
- Yes
- Austrian Fields of Science 2012
- 106005 Bioinformatics
- Keywords
- ASJC Scopus subject areas
- Computational Mathematics, Molecular Biology, Biochemistry, Statistics and Probability, Computer Science Applications, Computational Theory and Mathematics
- Portal url
- https://ucris.univie.ac.at/portal/en/publications/pycomo-a-python-package-for-community-metabolic-model-creation-and-analysis(41ab7827-51d0-4e0a-b4e8-4f1f73272d2c).html