TOKYO--Systems installed recently at the supercomputing facility of the Human Genome Center here make the center one of the largest configurations for genome analysis in the world, according to Toshihisa Takagi, a professor at the center. Leased at a monthly cost of 100 million yen, the equipment includes two 128-processor Cray Origin2000 systems, a Hitachi SR2201, and a Sun Ultra Enterprize 10000.
The center, housed at the University of Tokyo's Institute of Medical Science, is part of the Japanese Ministry of Education's Human Genome Project, which employs 130 students and researchers, including 18 faculty members and about 30 information science specialists.
The Origin2000 servers are the largest publicly funded, shared-memory systems specifically dedicated to genome structure analysis, according to Silicon Graphics (SGI) and its supercomputing subsidiary Cray Research, the vendors of the hardware.
SGI Biology Market Manager Juli Nash called the center's purchase "an absolutely tremendous investment by the Japanese government in the genome industry."
Especially remarkable, Nash said, is the government support for genomics information technology. "I'm very encouraged by the investment because it's an area that has not been traditionally directly well funded throughout the world," Nash told BioInform. "The level of support for the information structure--for the systems that will support existing genome scientists and the growth of the genome industry--is extraordinary," she said.
That sort of investment, of course, means big business for computer makers like SGI. Just to support Japan's genome installations, Nihon Silicon Graphics Cray maintains a 20-person genome task force here of hardware, software, and applications engineers and marketing support, Nash said. "We have staff onsite at the genome centers physically supporting the installations, keeping the web site up and all the production databases running, and learning about technology so we can reinvest it in our knowledge base."
The new systems will enable the center to apply real-time visualization, multimedia technology, and supercomputing to genomic analysis, according to SGI. Nash said the Japanese team here has made a significant investment in the area of visualization strategies for genome sciences. "They are the leaders in bringing visualization technology to the genome industry," she commented.
Importance of visualization technology
Visualization strategization is becoming one of the more active areas of research in genome sciences, according to Nash. As an increasing number of installations start to prepare themselves for managing terabytes of data, "finding a way to build visual exploration technology so you can actually navigate all of that complexity of information is very important," Nash explained.
The variety of data being stored--compound data, gene data, small molecules, and information about how genes are related to diseases--and the need to develop correlations, to understand how genes are related to disease, which genes can produce which proteins, and how those proteins interact with small molecules, make visualization technology imperative, Nash claimed. "Bringing visualization to any decisionmaking process can have significant impact. It's important with large volumes of data that may be stored as chemical compounds, or gene structures, or information about disease to be able to bring that together visually so that you can communicate, learn more, make better decisions about it."
Takagi told BioInform the center has not yet applied visualization technology to functional genomics, and that until the entire genome is sequenced, visualization and multimedia technologies will not be used directly in the Human Genome Project. "However, they are useful in analyzing functions of proteins and interactions between multiple genes," he said.
When such creative software work is undertaken, it will require the most powerful systems architectures to support the development of new software technology, said Nash.
Takagi said the computer installations will also enable the center to provide improved computer services for the domestic and international genome research community. Scientists at the center, together with those at the Institute for Chemical Research at Kyoto University, which installed one of the Cray 128-processor devices at its supercomputer laboratory last year, operate the GenomeNet Database Service at http://www.genome.ad.jp, and the Human Genome Center Homepage at http://www.hgc.ims.u-tokyo.ac.jp.
The wide-area computer network includes database systems developed by HGC, Japanese research groups and other public sources.