DOE OSTI · 3364445
A standardized workflow for kinetic metabolic model curation and dissemination
Abstract
Kinetic metabolic models provide invaluable insights into cellular metabolism, supporting applications in synthetic biology, metabolic engineering, and systems biology. However, reproducibility and utility of these models hinge on clear and rigorous documentation, standardized annotation, and accessible visualization. This paper presents a workflow for building, annotating, visualizing, and sharing kinetic metabolic models. Our method integrates community standards and open-source tools to ensure reproducibility, interoperability, and user accessibility. This procedure enables researchers to produce reusable and well-documented kinetic models, advancing their role as powerful tools in metabolic research.
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Cook, Margaret [Univ. of Washington, Seattle, WA (United States)] (ORCID:0000000342106885), Anastasakis, Stella [Univ. of Washington, Seattle, WA (United States)] (ORCID:000900009171396X), Heydarabadipour, Adel [Univ. of Washington, Seattle, WA (United States)], Shin, Janis [Univ. of Washington, Seattle, WA (United States)], Burbano, Diego Alba [Univ. of Washington, Seattle, WA (United States)], Carothers, James M. [Univ. of Washington, Seattle, WA (United States)], Sauro, Herbert M. [Univ. of Washington, Seattle, WA (United States)] (ORCID:0000000236596817). 2026-04-20. A standardized workflow for kinetic metabolic model curation and dissemination. https://doi.org/10.1371/journal.pcbi.1014227
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