ArticleMolecular systems biology2020
Community standards to facilitate development and address challenges in metabolic modeling.
Article in Molecular systems biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- From FAIR to CURE: guidelines for computational models of biological systems.NPJ systems biology and applications · 2026Review
- MCC: automated mass and charge curation at the genome scale applied toMicrobiology spectrum · 2026Article
- Genome-scale metabolic model ofmSystems · 2025Article
- In silico encounters: harnessing metabolic modelling to understand plant-microbe interactions.FEMS microbiology reviews · 2025Review
- Exploring the metabolic profile of A. baumannii for antimicrobial development using genome-scale modeling.PLoS pathogens · 2024Article
- Genome-scale model ofMicrobiology spectrum · 2024Article
- The transition from genomics to phenomics in personalized population health.Nature reviews. Genetics · 2024Review
- Genome-scale flux balance analysis reveals redox trade-offs in the metabolism of the thermoacidophileFrontiers in systems biology · 2024Article
- Microbiome modeling: a beginner's guide.Frontiers in microbiology · 2024Review
- Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations.Briefings in bioinformatics · 2023Review
- An integrated systems biology approach reveals differences in formate metabolism in the genusiScience · 2023Article
- Standards, dissemination, and best practices in systems biology.Current opinion in biotechnology · 2023Review
- Reconciliation and evolution of Penicillium rubens genome-scale metabolic networks-What about specialised metabolism?PloS one · 2023Article
- Genome-scale metabolic models consistently predictFrontiers in bioinformatics · 2023Article
- Mycobacterial metabolic model development for drug target identification.GigaByte (Hong Kong, China) · 2023Article
- A Genome-Scale Metabolic Model ofMetabolites · 2022Article
- Genome-scale modeling of yeast metabolism: retrospectives and perspectives.FEMS yeast research · 2022Review
- Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models.PLoS computational biology · 2022Article
- eQuilibrator 3.0: a database solution for thermodynamic constant estimation.Nucleic acids research · 2022Article
- Elucidating Plant-Microbe-Environment Interactions Through Omics-Enabled Metabolic Modelling Using Synthetic Communities.Frontiers in plant science · 2022Article
Corrections and comments
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Authors and funding
5 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.