Introduction
The Network-Based SEED API offers a framework that supports programmatic access to current SEED data. The system is distributed as a small set of Perl packages that the user downloads and installs locally. These packages define an API that the programmer uses to communicate over the network with the SEED environment maintained by the Fellowship for Interpretation of Genomes (FIG), Argonne National Lab (ANL) and the University of Chicago (UC). The distribution can be easily installed on a Mac or Unix-based system, and with a little extra effort, on a Windows machine. In addition to the packages that are used in constructing Perl programs, we offer a library of utility programs that offer predefined commands that can be used to extract data from the SEED.
The bulk of the functionality is offered via SAPserver.pm, a module that supports access to a database of genomic data that includes data on over a thousand genomes. The database is described abstractly via an Entity-Relationship model and is managed via metadata which makes it straightforward to extend the model, and is implemented via a standard relational database. We also offer:
- MODELserver.pm to support the construction and use of metabolic models and flux-based analysis,
- ANNOserver.pm to support annotation of DNA and protein sequences
- RASTserver.pm to support the submission of genomes to be annotated and the retrieval of the annotations.
