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. 2013 Sep 1;29(17):2213-5.
doi: 10.1093/bioinformatics/btt342. Epub 2013 Jun 13.

Metingear: A Development Environment for Annotating Genome-Scale Metabolic Models

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Free PMC article

Metingear: A Development Environment for Annotating Genome-Scale Metabolic Models

John W May et al. Bioinformatics. .
Free PMC article

Abstract

Genome-scale metabolic models often lack annotations that would allow them to be used for further analysis. Previous efforts have focused on associating metabolites in the model with a cross reference, but this can be problematic if the reference is not freely available, multiple resources are used or the metabolite is added from a literature review. Associating each metabolite with chemical structure provides unambiguous identification of the components and a more detailed view of the metabolism. We have developed an open-source desktop application that simplifies the process of adding database cross references and chemical structures to genome-scale metabolic models. Annotated models can be exported to the Systems Biology Markup Language open interchange format.

Availability: Source code, binaries, documentation and tutorials are freely available at http://johnmay.github.com/metingear. The application is implemented in Java with bundles available for MS Windows and Macintosh OS X.

Figures

Fig. 1.
Fig. 1.
Overview of the annotation procedures to attach a chemical structure. Each method indicates whether the process is entirely automated, requires manual user input or combines an automated process with minimal user input

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