Sun Microsystems supercomputer to advance genomics

Sun Microsystems, Inc. and UW–Madison today, May 18, announced the expansion of a decade-long relationship enabling the campus to acquire a $2.5 million supercomputer for genetics research.

Popularly known as the Starfire server, the Sun Enterprise 10000 server has one of the largest shared memory systems in the world, as well as a massive processing capacity, making it one of the world’s leading supercomputers.

The Genome Center of Wisconsin, a research group steering genomics research projects on campus, will be starting pilot tests on the computer this month. The system will benefit researchers not only in genomics, but across the entire biotechnology spectrum at UW–Madison. UW–Madison will also be named a Sun Center of Excellence in Genomics, a designation that will pave the way for a continued research relationship between the two organizations.

“We’re very pleased to expand our relationship with UW–Madison into the genetics field,” says Georgi Johnson, business development manager, Global Education and Research at Sun Microsystems. “Partnering Sun’s strength in high-performance computing with Wisconsin’s leadership in biological sciences research will create many new opportunities for joint research.”

UW–Madison’s Genome Center of Wisconsin brings together a multi-disciplinary team of faculty who are developing tools to sequence the complete blueprints of life forms and determine the functions of genes. “Genomics is one of our growth areas and we expect to be a world leader,” adds Virginia Hinshaw, Graduate School dean and chief research officer. “This computer helps us move at the rapid pace that this field demands.”

Fred Blattner, a genetics professor and director of the genome center, says the new computer will add roughly 500 times more computational power to the center’s current fleet of computers – qualifying it as one of the 500 fastest computers in the world. “This is a field that produces tremendous amounts of data and enormous image files, so computer power is crucial to our task,” Blattner says. “This computer gives us the horsepower we need to make sense of genomes.”

One promising area of research at UW is bioinformatics – the process of deciphering the deluge of information coming from DNA sequencing. Computer tools will ultimately help scientists determine the functions of genes and the locations of genetic diseases.
More than a dozen researchers at UW–Madison have projects that will benefit from the computer, including:

• Plant pathologist Sally Leong and her team, who are working on a portion of the international rice genome project. Sequencing the rice genome is seen as a keystone to unlocking major agricultural benefits in food crops.
• David Schwartz, a professor of chemistry and biotechnology, who developed a unique way of viewing whole genomes called optical mapping.
• Virologist Ann Palmenberg who will use the computer in work involving RNA folding and viral structure.
• Computer scientists Mark Craven and Jude Shavlik, who are experts in “data mining” techniques that extract useful information from huge data streams.

UW-Madison’s status as a Sun Center of Excellence will build on a decade-long association between Sun and UW–Madison computer scientists to research parallel computer architecture. Additional financial support is being provided by the Graduate School, the Wisconsin Alumni Research Foundation, the School of Medicine and the College of Agricultural and Life Sciences.

Sun is a leading provider of open network computing solutions to colleges and universities around the world, powering academic research and high performance computing systems, campus administration, digital libraries and student instruction systems. In addition, Sun is committed to connecting the world students to the Internet, beginning with primary and secondary schools and extending to all levels of higher education.

For information about Sun in Education, please visit http://www.sun.com/edu.