{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T23:22:32Z","timestamp":1778628152039,"version":"3.51.4"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2025,2,8]],"date-time":"2025-02-08T00:00:00Z","timestamp":1738972800000},"content-version":"vor","delay-in-days":7,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020 Programme"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,2,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Constraint-based metabolic models offer a scalable framework to investigate biological systems using optimality principles. Construction and simulation of detailed models that utilize multiple kinds of constraint systems pose a significant coding overhead, complicating implementation of new types of analyses. We present an improved version of the constraint-based metabolic modeling package COBREXA, which utilizes a hierarchical model construction framework that decouples the implemented analysis algorithms into independent, yet re-combinable, building blocks. By removing the need to re-implement modeling components, assembly of complex metabolic models is simplified, which we demonstrate on use-cases of resource-balanced models, and enzyme-constrained flux balance models of interacting bacterial communities. Notably, these models show improved predictive capabilities in both monoculture and community settings. In perspective, the re-usable model-building components in COBREXA 2 provide a sustainable way to handle increasingly complex models in constraint-based modeling.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>COBREXA 2 is available from https:\/\/github.com\/COBREXA\/COBREXA.jl, and from Julia package repositories. COBREXA 2 works on all major operating systems and computer architectures. Documentation is available at https:\/\/cobrexa.github.io\/COBREXA.jl\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf056","type":"journal-article","created":{"date-parts":[[2025,2,3]],"date-time":"2025-02-03T20:24:58Z","timestamp":1738614298000},"source":"Crossref","is-referenced-by-count":2,"title":["COBREXA 2: tidy and scalable construction of complex metabolic models"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7356-4075","authenticated-orcid":false,"given":"Miroslav","family":"Kratochv\u00edl","sequence":"first","affiliation":[{"name":"Luxembourg Centre for Systems Biomedicine, University of Luxembourg , Esch-sur-Alzette L-4362,","place":["Luxembourg"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4113-2590","authenticated-orcid":false,"given":"St Elmo","family":"Wilken","sequence":"additional","affiliation":[{"name":"Institute of Quantitative and Theoretical 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