With a 14 GB database, the Department of Energy Human Genome Project (HGP) at Los Alamos National Laboratory unquestionably qualifies for the "heavy computing" label. According to DB Administrator Robert Sutherland, the database has doubled in size every 15 months since 1989 when sequencing work began. The Los Alamos HGP relies on Sun technology to keep itself up and running.

The main file server and Sybase database engine is a SPARCR processor-based server running the SolarisTM Operating System (Solaris OS) (SPARCR Platform Edition). Workstation power is supplied by SPARC processor-based workstations and HyperSPARCR machines running the Solaris OS.

"We use the power of Sun for major relational database crunching -- formatting, incorporating, analyzing and assimilating data from outside sources," states Sutherland. "Our whole Center, roughly 65 people, uses Solaris OS. The Solaris OS is stable and it's easy to work with," he added.

Sutherland observes that the system at Los Alamos is constantly evolving, and the stability of the Solaris OS helps keep work moving smoothly and saves time as his team makes enhancements to the computing environment. "Solaris stays stable as we add hardware and different machine types. That helps us in overall maintenance and keeping down the time needed to deal with administrative issues," said Sutherland.

Because so much work in gene mapping and sequencing is breaking new ground, Sutherland and his team write almost all of their own applications software, relying heavily on Sun JavaTM System C 6 Update 2 and Sun JavaTM System C++.

"Most everything that we build and program, if we can't do it in 2-3 months it's not worth doing," said Sutherland. "We depend on WorkShop for C and C++, and we're starting to move into JavaTM technology now."

The HGP includes projects at universities, three DOE Genome Centers at the National Laboratories, and other research organizations. The ability to upload data from other HGP labs and analyze and incorporate it in an ad hoc way is crucial to the work at Los Alamos, according to Sutherland.

"Throughout the genome community, all of the largest databases are running Solaris, including Johns Hopkins' Genome Database (GDB) in Baltimore, Maryland; the Genome Sequencing Database (GSDB) in Santa Fe, New Mexico; GenBank at NIH in Bethesda, Maryland; and facilities in Japan and Australia," said Sutherland. All these facilities are linked by Sun technology through the Internet.

"Bioinformatics is a very information-rich environment, and the genome community has very much embraced the worldwide Web," Sutherland said. "All the genome data, public and private, is accessible on the Web, from all different labs, including Los Alamos. Los Alamos maintains three Web sites, all on Sun machines running Solaris." [...read more...]

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