The SEED database also contains a large number of genomescale metabolic models, including 14 published models [28] and approximately 11,000 models generated from the annotated genomes stored in the SEED [29] . The Metabolic Modeling and FBA Server also provides the user with an API to remotely obtain a list of the models in the SEED and to download data on the compounds and reactions in each SEED model. The server returns the following data for each reaction in a specified model: (i) all data from the SEED biochemistry database, (ii) a list of the genes associated with each reaction in the model in a format that captures how the protein products encoded by the genes function to catalyze the reaction (as either independent enzymes or multienzyme complexes), and (iii) a list of compartments in the model where the reaction takes place and the directionality/ reversibility of the reaction in each compartment. For the model compounds, the server returns the data from the SEED Figure 2 . Entities and relationships in the SEED. The entities (boxes) are connected to each other by a series of relationships (diamonds) that describe how the two entities relate. To move from one entity (e.g., ''Identifier'') to another (e.g., ''DNA Sequence''), the series of connections shown by the gray arrow is made. This way, any entity can be connected, either directly or indirectly, to any other entity. doi:10.1371/journal.pone.0048053.g002 biochemistry database. As with the biochemistry data, all the model data in the server are accessible either via Perl programs or the API.