Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species
Journal article, 2021

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.

yeast species

genome-scale metabolic models

usability

interoperability

systems biology

accessibility

Author

Iván Domenzain Del Castillo Cerecer

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Feiran Li

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Eduard Kerkhoven

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Verena Siewers

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

FEMS Yeast Research

1567-1356 (ISSN) 1567-1364 (eISSN)

Vol. 21 1

Subject Categories

Other Computer and Information Science

Bioinformatics (Computational Biology)

Computer Systems

DOI

10.1093/femsyr/foab002

PubMed

33428734

More information

Latest update

4/30/2021