The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities.

Motivation: The application of constraint-based modeling to functionally analyze metagenomic data has been limited so far, partially due to the absence of suitable toolboxes.
Results: To address this gap, we created a comprehensive toolbox to model (i) microbe-microbe and host-microbe metabolic interactions, and (ii) microbial communities using microbial genome-scale metabolic reconstructions and metagenomic data. The Microbiome Modeling Toolbox extends the functionality of the constraint-based reconstruction and analysis toolbox.
Availability and Implementation: The Microbiome Modeling Toolbox and the tutorials at https://git.io/microbiomeModelingToolbox.
(© The Author(s) 2018. Published by Oxford University Press.)