Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities
Oxford University Press
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.
Microbiome Modelling Toolbox , COBRA Toolbox , Constraint-Based Reconstruction and Analysis (COBRA)
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
© 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.