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

MOTIVATION: 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...

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Detalles Bibliográficos
Autores principales: Heinken, Almut, Thiele, Ines
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9004645/
https://www.ncbi.nlm.nih.gov/pubmed/35157025
http://dx.doi.org/10.1093/bioinformatics/btac082
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author Heinken, Almut
Thiele, Ines
author_facet Heinken, Almut
Thiele, Ines
author_sort Heinken, Almut
collection PubMed
description MOTIVATION: 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.
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spelling pubmed-90046452022-04-13 Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities Heinken, Almut Thiele, Ines Bioinformatics Applications Note MOTIVATION: 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. Oxford University Press 2022-02-14 /pmc/articles/PMC9004645/ /pubmed/35157025 http://dx.doi.org/10.1093/bioinformatics/btac082 Text en © The Author(s) 2022. Published by Oxford University Press. https://creativecommons.org/licenses/by-nc/4.0/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. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Note
Heinken, Almut
Thiele, Ines
Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities
title Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities
title_full Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities
title_fullStr Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities
title_full_unstemmed Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities
title_short Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities
title_sort microbiome modelling toolbox 2.0: efficient, tractable modelling of microbiome communities
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9004645/
https://www.ncbi.nlm.nih.gov/pubmed/35157025
http://dx.doi.org/10.1093/bioinformatics/btac082
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