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The Scripps Genome Center has a cluster system containing nine Sun servers and five Apple servers, for a total of 58 processors and over 200 gigabytes of RAM. RAID disk arrays provide an additional 17 terabytes of storage. Backups of the data are performed regularly and stored in a tape library.

Two TimeLogic DeCypher Engines, combined with TimeLogic's Tera-BLAST software, perform BLAST searches with run times comparable to those of clusters containing hundreds of CPUs.

All hardware is interconnected by gigabit Ethernet, via a dedicated CISCO switch, with router boards connected to the University of California, San Diego's Internet backbone and also directly to external links via a T1 line to provide redundancy.