With the vast speed and minimal costs of modern sequencing technology, new demands are being placed on the bioinformatics pipelines used to analyze sequence data [1] . Modern bioinformatics must be high throughput and high volume with a strong emphasis on comparative genomics, and the SEED family of resources for genome interpretation and analysis were specifically constructed to embody these characteristics [15] . The SEED resources are built upon the organization of biology into a modular set of subsystems, each describing a specific biological functionality (e.g., flagellar motility or histidine biosynthesis) [16] . Subsystems-based technologies were developed in the SEED with the view that the interpretation of one genome can be made more efficient and consistent if hundreds of genomes are simultaneously annotated in one subsystem at a time [16, 17] . The SEED Project, a multi-institutional effort coordinated by the Fellowship for Interpretation of Genomes (FIG) and Argonne National Laboratory, began with the ambitious goal of consistently annotating 1,000 genomes (http://theseed.org/wiki/ Annotating_1000_genomes); today, over 50,000 viral and prokaryotic genomes have been annotated by the subsystems technology. More recently, the SEED Project has been expanded to include the capacity to automatically generate genome-scale metabolic models based on SEED annotations of genome sequences, and the Model SEED system developed from this pipeline has now been applied to construct metabolic models for thousands of genomes [18, 19, 20] . The SEED family of resources now collectively serves as a repository for almost 5,000 distinct complete prokaryotic genomes, associated with approximately 30,000 annotations, 11,000 metabolic models, 178,000 protein families, 10,250 functional roles, and 1,060 subsystems.