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

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Date
2022-02-14
Authors
Heinken, Almut
Thiele, Ines
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Oxford University Press
Published Version
10.1093/bioinformatics/btac082
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Abstract
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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Keywords
Microbiome Modelling Toolbox , COBRA Toolbox , Constraint-Based Reconstruction and Analysis (COBRA)
Citation
Heinken, 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/btac082
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https://hdl.handle.net/10468/13175
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APC Microbiome Ireland - Journal Articles
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© 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.