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. 2019 Jul 1;35(13):2332-2334.
doi: 10.1093/bioinformatics/bty941.

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

Federico Baldini  1 , Almut Heinken  1 , Laurent Heirendt  1 , Stefania Magnusdottir  1 , Ronan M T Fleming  1   2 , Ines Thiele  1
Affiliations

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

Federico Baldini et al. Bioinformatics. .

Abstract

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.

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Figures

Fig. 1.
Fig. 1.
Overview of the Microbiome Modeling Toolbox. (A) Pairwise modeling of microbe–microbe and host–microbe interactions. (B) Microbial community modeling
See this image and copyright information in PMC

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