{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T16:38:09Z","timestamp":1776271089646,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2022,2,14]],"date-time":"2022-02-14T00:00:00Z","timestamp":1644796800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"European Research Council (ERC) under the European Union\u2019s Horizon 2020 Research"},{"name":"Innovation Programme","award":["757922"],"award-info":[{"award-number":["757922"]}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["1RF1AG058942-01"],"award-info":[{"award-number":["1RF1AG058942-01"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["1U19AG063744-01"],"award-info":[{"award-number":["1U19AG063744-01"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,4,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Constraint-Based Reconstruction and Analysis (COBRA) is a widely used approach\u00a0for the interrogation and stratification of microbiome samples, yet applications to large-scale cohorts are hampered by limited scalability and efficiency of simulations.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We substantially improved the computation speed and scalability of a previous implementation for the construction and interrogation of personalized constraint-based microbiome models as well as implemented additional functionalities for analysis and visualization.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Microbiome Modelling Toolbox and tutorials are freely available as part of the COBRA Toolbox at https:\/\/git.io\/microbiomeModelingToolbox.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac082","type":"journal-article","created":{"date-parts":[[2022,2,8]],"date-time":"2022-02-08T12:11:05Z","timestamp":1644322265000},"page":"2367-2368","source":"Crossref","is-referenced-by-count":51,"title":["Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities"],"prefix":"10.1093","volume":"38","author":[{"given":"Almut","family":"Heinken","sequence":"first","affiliation":[{"name":"School of Medicine, National University of Galway , Galway, Ireland"},{"name":"Ryan Institute, National University of Galway , Galway, Ireland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8071-7110","authenticated-orcid":false,"given":"Ines","family":"Thiele","sequence":"additional","affiliation":[{"name":"School of Medicine, National University of Galway , Galway, Ireland"},{"name":"Ryan Institute, National University of Galway , Galway, Ireland"},{"name":"Division of Microbiology, National University of Galway , Galway, Ireland"},{"name":"APC Microbiome Ireland, University College Cork , Cork, Ireland"}]}],"member":"286","published-online":{"date-parts":[[2022,2,14]]},"reference":[{"key":"2023020109023337400_btac082-B1","doi-asserted-by":"crossref","first-page":"2332","DOI":"10.1093\/bioinformatics\/bty941","article-title":"The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities","volume":"35","author":"Baldini","year":"2019","journal-title":"Bioinformatics"},{"key":"2023020109023337400_btac082-B2","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1186\/1471-2105-11-489","article-title":"Computationally efficient flux variability analysis","volume":"11","author":"Gudmundsson","year":"2010","journal-title":"BMC Bioinform"},{"key":"2023020109023337400_btac082-B3","doi-asserted-by":"crossref","DOI":"10.1101\/2020.11.09.375451","article-title":"AGORA2: large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities","author":"Heinken","year":"2020"},{"key":"2023020109023337400_btac082-B4","doi-asserted-by":"crossref","first-page":"100346","DOI":"10.1016\/j.coisb.2021.05.007","article-title":"Advances in constraint-based modelling of microbial communities","volume":"27","author":"Heinken","year":"2021","journal-title":"Curr. 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