Evidence map›Paper›PMID 42008579›Full record

ArticlePLoS computational biology2026

A standardized workflow for kinetic metabolic model curation and dissemination.

Margaret Cook, Stella Anastasakis, Adel Heydarabadipour, Janis Shin, Diego Alba Burbano, James M Carothers, Herbert M Sauro

Abstract read
In one paragraph

Article in PLoS computational biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Margaret CookMolecular Engineering and Sciences Institute, University of Washington, Seattle, Washington, United States of America.ORCID https://orcid.org/0000-0003-4210-6885
Stella AnastasakisDepartment of Chemical Engineering, University of Washington, Seattle, Washington, United States of America.ORCID https://orcid.org/0009-0000-9171-396X
Adel HeydarabadipourDepartment of Bioengineering, University of Washington, Seattle, Washington, United States of America.
Janis ShinMolecular Engineering and Sciences Institute, University of Washington, Seattle, Washington, United States of America.
Diego Alba BurbanoDepartment of Chemical Engineering, University of Washington, Seattle, Washington, United States of America.
James M CarothersDepartment of Chemical Engineering, University of Washington, Seattle, Washington, United States of America.
Herbert M SauroDepartment of Bioengineering, University of Washington, Seattle, Washington, United States of America.ORCID https://orcid.org/0000-0002-3659-6817

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

Data CurationMetabolic Networks and PathwaysModels, BiologicalWorkflowComputational BiologyKineticsReproducibility of ResultsSoftwareSystems Biology

Identifiers

PMID42008579
PMCPMC13132423

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.