Metingear: a development environment for annotating genome-scale metabolic models

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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.


Source code, binaries, documentation and tutorials are freely available at The application is implemented in Java with bundles available for MS Windows and Macintosh OS X.


Supplementary information:

Supplementary data are available at Bioinformatics online.

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