Preprint Review Version 1 Preserved in Portico This version is not peer-reviewed

Ten Quick Tips for Accurate Reconstruction of Prokaryotic and Eukaryotic Genome-Scale Metabolic Models

Gabriela Canto-Encalada
,
Jenna Armstrong
,
Carlos Focil-Espinosa4
,
Ademikanra Adekunle-Fiyin
,
Ila Peeler
,
William R. Gebbie
,
Julio Nunez-Garcia
,
Alexis Saldivar
ORCID logo ,
Diego Martinez
,
Cristal Zuniga
* ORCID logo
Version 1 : Received: 1 November 2023 / Approved: 7 November 2023 / Online: 7 November 2023 (14:59:34 CET)

How to cite: Canto-Encalada, G.; Armstrong, J.; Focil-Espinosa4, C.; Adekunle-Fiyin, A.; Peeler, I.; Gebbie, W.R.; Nunez-Garcia, J.; Saldivar, A.; Martinez, D.; Zuniga, C. Ten Quick Tips for Accurate Reconstruction of Prokaryotic and Eukaryotic Genome-Scale Metabolic Models. Preprints 2023, 2023110461. https://doi.org/10.20944/preprints202311.0461.v1 Canto-Encalada, G.; Armstrong, J.; Focil-Espinosa4, C.; Adekunle-Fiyin, A.; Peeler, I.; Gebbie, W.R.; Nunez-Garcia, J.; Saldivar, A.; Martinez, D.; Zuniga, C. Ten Quick Tips for Accurate Reconstruction of Prokaryotic and Eukaryotic Genome-Scale Metabolic Models. Preprints 2023, 2023110461. https://doi.org/10.20944/preprints202311.0461.v1

Abstract

Constraint-based metabolic modeling approaches have enhanced our knowledge and understanding of the metabolism of prokaryotes and eukaryotes. This approach highly depends on the reconstruction process of genome-scale metabolic models (Mmodels). M-models can guide effective experimental design and yield new insights into the function and control of biological systems. Despite the recent advances in the automated generation of draft metabolic network reconstructions, the manual curation of these networks remains a labor-intensive and challenging task. Thus, these ten quick tips for the manual curation process are essential for optimizing high-quality metabolic model generation in less time. This collection of tips describes in great detail the resources and methods to ensure successful reconstruction. Furthermore, it increases the scope of other protocols of metabolic modeling by including resources to reconstruct eukaryotic organisms. Thus, all tips are applicable to a wide range of eukaryotic organisms. We believe this manuscript will interest a broad audience and researchers from different disciplines, spanning from microbiology and systems biology to biotechnology.

Keywords

Genome-scale metabolic model reconstruction; manual curation; quick tips; systems biology

Subject

Biology and Life Sciences, Other

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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