{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T15:35:44Z","timestamp":1774625744130,"version":"3.50.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T00:00:00Z","timestamp":1763424000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Helmholtz School for Data Science in Life, Earth and Energy"},{"DOI":"10.13039\/501100001656","name":"Helmholtz Association of German Research Centres","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001656","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>13C-based metabolic flux analysis is a cornerstone of quantitative systems biology, yet its increasing data complexity and methodological diversity place high demands on simulation software. We introduce 13CFLUX(v3), a third-generation simulation platform that combines a high-performance C++ engine with a convenient Python interface. The software delivers substantial performance gains across isotopically stationary and nonstationary analysis workflows, while remaining flexible to accommodate diverse labeling strategies and analytical platforms. Its open-source availability facilitates seamless integration into computational ecosystems and community-driven extension. By supporting multi-experiment integration, multi-tracer studies, and advanced statistical inference such as Bayesian analysis, 13CFLUX provides a robust and extensible framework for modern fluxomics research.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Sources and containers are provided at https:\/\/jugit.fz-juelich.de\/IBG-1\/ModSim\/Fluxomics\/13CFLUX, and scripts to replicate results in the supplementary data at https:\/\/github.com\/JuBiotech\/Supplement-to-Stratmann-et-al.-Bioinformatics-2025.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf630","type":"journal-article","created":{"date-parts":[[2025,11,15]],"date-time":"2025-11-15T12:59:43Z","timestamp":1763211583000},"source":"Crossref","is-referenced-by-count":1,"title":["13CFLUX - third-generation high-performance engine for isotopically (non)stationary 13C metabolic flux analysis"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8391-3398","authenticated-orcid":false,"given":"Anton","family":"Stratmann","sequence":"first","affiliation":[{"name":"Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum J\u00fclich GmbH , 52425 J\u00fclich,","place":["Germany"]},{"name":"Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University , 52062 Aachen,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5383-3415","authenticated-orcid":false,"given":"Martin","family":"Bey\u00df","sequence":"additional","affiliation":[{"name":"Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum J\u00fclich GmbH , 52425 J\u00fclich,","place":["Germany"]},{"name":"Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University , 52062 Aachen,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5026-1546","authenticated-orcid":false,"given":"Johann F","family":"Jadebeck","sequence":"additional","affiliation":[{"name":"Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum J\u00fclich GmbH , 52425 J\u00fclich,","place":["Germany"]},{"name":"Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University , 52062 Aachen,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8501-0694","authenticated-orcid":false,"given":"Wolfgang","family":"Wiechert","sequence":"additional","affiliation":[{"name":"Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum J\u00fclich GmbH , 52425 J\u00fclich,","place":["Germany"]},{"name":"Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University , 52062 Aachen,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5407-2275","authenticated-orcid":false,"given":"Katharina","family":"N\u00f6h","sequence":"additional","affiliation":[{"name":"Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum J\u00fclich 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