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

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


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 The application is implemented in Java with bundles available for MS Windows and Macintosh OS X.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Factual
  • Genome
  • Metabolism*
  • Models, Biological*
  • Software*
  • Systems Biology / methods