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

Michael Predl; Marianne Mießkes; Thomas Rattei; Jürgen Zanghellini

doi:10.1093/bioinformatics/btae153

Titel

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

Autor*in

Michael Predl

Department für Mikrobiologie und Ökosystemforschung, Zentrum für Mikrobiologie und Umweltsystemwissenschaft, Universität Wien

Marianne Mießkes

Institut für Analytische Chemie, Fakultät für Chemie, Universität Wien

Thomas Rattei

Department für Mikrobiologie und Ökosystemforschung, Zentrum für Mikrobiologie und Umweltsystemwissenschaft, Universität Wien

... show all

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.

Objekt-Typ

journal article

Sprache

Englisch [eng]

Persistent identifier

phaidra.univie.ac.at/o:2068167

DOI

10.1093/bioinformatics/btae153

Erschienen in

Titel

Bioinformatics

Band