Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities

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dc.contributor.authorHeinken, Almut
dc.contributor.authorThiele, Ines
dc.contributor.funderHorizon 2020en
dc.contributor.funderEuropean Research Councilen
dc.contributor.funderNational Institute on Agingen
dc.date.accessioned2022-05-13T09:26:30Z
dc.date.available2022-05-13T09:26:30Z
dc.date.issued2022-02-14
dc.description.abstractMotivation: Constraint-Based Reconstruction and Analysis (COBRA) is a widely used approach for the interrogation and stratification of microbiome samples, yet applications to large-scale cohorts are hampered by limited scalability and efficiency of simulations. Results: 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. Availability and implementation: Microbiome Modelling Toolbox and tutorials are freely available as part of the COBRA Toolbox at https://git.io/microbiomeModelingToolbox.en
dc.description.sponsorshipNational Institute on Aging (1RF1AG058942-01; 1U19AG063744-01)en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationHeinken, A. and Thiele, I. (2022) ‘Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities’, Bioinformatics, 38(8), pp. 2367–2368. doi: 10.1093/bioinformatics/btac082en
dc.identifier.doi10.1093/bioinformatics/btac082en
dc.identifier.eissn1460-2059
dc.identifier.endpage2368en
dc.identifier.issn1367-4803
dc.identifier.issued8en
dc.identifier.journaltitleBioinformaticsen
dc.identifier.startpage2367en
dc.identifier.urihttps://hdl.handle.net/10468/13175
dc.identifier.volume38en
dc.language.isoenen
dc.publisherOxford University Pressen
dc.relation.projectinfo:eu-repo/grantAgreement/EC/H2020::ERC::ERC-STG/757922/EU/Predicting the effects of gut microbiota and diet on an individual’s drug response and safety/BugTheDrugen
dc.rights© 2022, the Authors. Published by Oxford University Press. 2367 This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttps://creativecommons.org/licenses/by-nc/4.0/
dc.subjectMicrobiome Modelling Toolboxen
dc.subjectCOBRA Toolboxen
dc.subjectConstraint-Based Reconstruction and Analysis (COBRA)en
dc.titleMicrobiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communitiesen
dc.typeArticle (peer-reviewed)en
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