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.
© The Author(s) 2022. Published by Oxford University Press.