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Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species.

Authors
  • Domenzain, Iván1, 2
  • Li, Feiran1, 2
  • Kerkhoven, Eduard J1, 2
  • Siewers, Verena1, 2
  • 1 Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden. , (Sweden)
  • 2 Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden. , (Sweden)
Type
Published Article
Journal
FEMS Yeast Research
Publisher
Oxford University Press
Publication Date
Mar 04, 2021
Volume
21
Issue
1
Identifiers
DOI: 10.1093/femsyr/foab002
PMID: 33428734
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

Metabolic network reconstructions have become an important tool for probing cellular metabolism in the field of systems biology. They are used as tools for quantitative prediction but also as scaffolds for further knowledge contextualization. The yeast Saccharomyces cerevisiae was one of the first organisms for which a genome-scale metabolic model (GEM) was reconstructed, in 2003, and since then 45 metabolic models have been developed for a wide variety of relevant yeasts species. A systematic evaluation of these models revealed that-despite this long modeling history-the sequential process of tracing model files, setting them up for basic simulation purposes and comparing them across species and even different versions, is still not a generalizable task. These findings call the yeast modeling community to comply to standard practices on model development and sharing in order to make GEMs accessible and useful for a wider public. © The Author(s) 2021. Published by Oxford University Press on behalf of FEMS.

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