One notion that emerged at Xconomy’s event in San Diego last week was that biomedical informatics might have a promising role to play in the region’s economic future. There is no consensus on this as yet, as Luke discovered when he talked with Illumina CEO Jay Flatley.

Among the true believers is UC San Diego’s Lucila Ohno-Machado. No surprises there—since last year, she has been director of biomedical informatics at the medical school. Before arriving in San Diego, she was director of the Harvard-MIT-Tufts-Boston University biomedical informatics training program.

We caught up with her this week via e-mail to find out more about the technology, what it means for the U.S. health care system, and the role she sees for San Diego’s innovation community.

Xconomy: What is biomedical informatics?

Lucila Ohno-Machado: Biomedical informatics is a scientific discipline focused on the development of new algorithms and/or new approaches to organize, visualize, and interpret health-related data in order to promote health and alleviate the burden of disease. The discipline is placed at the intersection of health sciences, biology, computer science, and statistics.

San Diego is in a unique position due to the accumulation of human talent, high-tech companies, and a collective interest in improving healthcare for all. It has all the ingredients to become the number one biomedical informatics center in the country.

X: How is it different from computational biology, which we’ve also been hearing a lot about?

LOM: Computational biology usually relates to the development and application of algorithms and computational strategies to analyze biological data at the molecular level. In biomedical informatics, we develop new algorithms and systems that relate to the full spectrum of data: from molecular to individual to population levels. We often refer to bio-, clinical- or public health-informatics for algorithmic developments and strategies targeting … Next Page »

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After establishing himself as a leading expert on computing and information technology, including the Internet and World Wide Web, Larry Smarr left the comfort of a job that was tailored for him at the University of Illinois, Urbana-Champaign, for a position in San Diego that offered an even better fit. In 2000, Smarr was hired as a professor of computer science and engineering at UC San Diego—and almost exactly nine years ago, he was named the founding director of the California Institute for Telecommunications and Information Technology.

Today, Smarr (who also is a San Diego Xconomist) describes the institute, pronounced “Cal-IT-squared” (and known in official shorthand as Calit2), as a framework for collaboration among students and researchers throughout the University of California system, as well as industry. In the first half of this two-part article, Smarr and I discussed his role in the development of the Internet and the factors that help encourage technology innovation. Because the institute emphasizes and encourages cross-disciplinary research, Smarr refers to Calit2’s affiliated centers as “loci for innovation,” with federal funding totaling more than $400 million since 2000.

As a researcher, Smarr also has continued working to develop technologies that combine optical networks, supercomputing, and grid technologies for use in the next-generation Internet. He views Calit2 as a “time machine” because the advanced capabilities of the institute’s high-performance network enable researchers to develop software applications five or 10 years before they can be deployed commercially. That’s something that could be true of any academic research center, although innovations developed for the Internet may stand in a class by themselves. (Smarr talks about the path forward and four big ideas in Part 2 of my story here.)

Smarr, who turns 61 on Oct. 16, traces the origins of the Internet to the early 1970s and the technical work done by Vint Cerf, Leonard Kleinrock, Robert Kahn, and others on the ARPAnet, the computer network developed by the Pentagon’s Advanced Research Projects Agency. By the mid-1980s, though, Smarr’s own career became intertwined with the development of the Internet. He was named in 1985 as founding director of the National Center for Supercomputing Applications, or NCSA, at the University of Illinois at Urbana-Champaign. During his tenure over the next 15 years, NCSA researchers, including Marc Andreessen, developed the first graphical Web browser (Mosaic) and technology that formed the basis of the popular Web server now known as Apache.

Because of the work done at the NCSA, which later became part of the National Computational Science Alliance, Smarr says he came to view … Next Page »

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The San Diego Supercomputer Center at U.C. San Diego today named UCSD astrophysicist Michael L. Norman as interim director. Norman replaces Fran Berman, a specialist in grid computing (and San Diego Xconomist), who has served as the center’s director since 2001. Berman plans to join the Rensselaer Polytechnic Institute as vice president of research, effective Aug. 1. Norman, a UCSD distinguished professor of physics, was appointed as the center’s chief scientific officer a year ago. The university says it plans to name a permanent director at a later date.

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UC San Diego says it has established a center for next-generation digital media with a gift from IBM (NYSE: IBM)—a high-performance IBM System z mainframe computer. In a statement, UCSD says IBM made the center possible through a shared university research award that includes the z mainframe, valued at about $2.2 million. The center, which will be housed at the San Diego Supercomputer Center, is dedicated to inventing the next generation of virtual worlds, multiple player online games, and high-fidelity digital cinema. UCSD says the center initially will focus on new production platforms for digital cinema through existing relationships with Hollywood studios.

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The new five-story building that doubles the size of the San Diego Supercomputer Center is more than just concrete, steel, and glass. As Fran Berman, SDSC director (and an Xconomist) said yesterday, the new building also represents the next generation in supercomputing—and she wants to ensure that San Diego’s emerging companies feel like they’re part of the family.

Berman ostensibly was hosting a dedication ceremony for the SDSC’s $44 million expansion. But the event included breakfast for more than 100 local technology executives, venture capital partners, and others to explain how supercomputing is crunching massive amounts of data to analyze Medicare fraud, cancer cells, earthquakes, and climate change.

Such research may not necessarily be useful to the venture community, but biotech and information technology startups increasingly need such capabilities, especially in digital storage and data mining, and to analyze complex models and simulations.

Today “SDSC sees its role as a partner and pathfinder with the research and education community to harness the power of cyberinfrastructure to adderess science and society’s most critical problems,” Berman said.

The supercomputer center, which was founded on the UCSD campus 23 years ago, now boasts that it has more archival storage capacity than any other academic institution in the world, about 25 petabytes (25 thousand trillion bytes). That’s about 1,000 times the digital plain-text equivalent of the printed collection in the Library of Congress.

The new building also houses some of the first optical networking equipment to be connected to the TeraGrid, a next-generation Internet for scientific research funded by the National Science Foundation.

“I have a number of models where we could work with industry,” said Ron Hawkins, SDSC’s director of industry relations.

The center could conduct sponsored research to address specific questions a company may have, Hawkins said. SDSC researchers also can do “high-end consulting” on corporate projects, or the center can simply offer access to its computational resources.

As one industry consultant noted, however, the programming required to solve complex problems on high-performance computers can be extremely expensive.

“Parallel processing is a specialized field, so, yes, it requires specialized expertise,” Hawkins acknowledged. “But the computing world and the IT world is going to parallel processing, so it’s only appropriate for us to work with industry to bring them along.”

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