Community standards to facilitate development and address challenges in metabolic modeling

Maureen A. Carey, Andreas Dräger, Moritz E. Beber, Jason A. Papin*, James T. Yurkovich*

*Corresponding author for this work

Research output: Contribution to journalComment/debateResearchpeer-review

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Abstract

Standardization of data and models facilitates effective communication, especially in computational systems biology. However, both the development and consistent use of standards and resources remain challenging. As a result, the amount, quality, and format of the information contained within systems biology models are not consistent and therefore present challenges for widespread use and communication. Here, we focused on these standards, resources, and challenges in the field of constraint-based metabolic modeling by conducting a community-wide survey. We used this feedback to (i) outline the major challenges that our field faces and to propose solutions and (ii) identify a set of features that defines what a “gold standard” metabolic network reconstruction looks like concerning content, annotation, and simulation capabilities. We anticipate that this community-driven outline will help the long-term development of community-inspired resources as well as produce high-quality, accessible models within our field. More broadly, we hope that these efforts can serve as blueprints for other computational modeling communities to ensure the continued development of both practical, usable standards and reproducible, knowledge-rich models.

Original languageEnglish
Article numbere9235
JournalMolecular Systems Biology
Volume16
Issue number8
Number of pages9
ISSN1744-4292
DOIs
Publication statusPublished - 2020

Bibliographical note

This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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