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Q/A: Sun CTO Sees Genomics Rising


Sun Microsystems has pushed full speed ahead into the life sciences market, partnering with various genomics and bioinformatics firms, including CuraGen, DoubleTwist, Incogen, InforMax, Lion Bioscience, and Rosetta Inpharmatics. Greg Papadopoulos, senior vice president and CTO of Sun, has been instrumental in bringing attention to genomics. GT’s Meredith Salisbury had this exchange with Papadopoulos over e-mail.

What do you see as the greatest needs and opportunities in genomic and proteomic computing?

Papadopoulos: Genomics requires high-throughput computing, the processing of billions of data points to identify patterns through iterative analyses. In contrast, proteomics first and foremost requires powerful solutions for analyzing protein-folding, modeling in 3-D, and rendering rich graphics. However, proteomics will soon require that these analyses be conducted in a high-throughput manner to address the enormous problem of identifying which proteins interact with other proteins and how.

I see tremendous opportunities for hardware companies to design technologies that satisfy both high-throughput and high-performance computing. Everything from enterprise servers and massive storage arrays to small compute farms, workstations, and desktop Web clients will be needed to satisfy discovery informatics. The scientific community will also undoubtedly look to software companies to develop advanced algorithms for accelerating data processing, as well as sophisticated visualization packages to study graphics-rich data forms.

On a higher level, genomic and proteomic computing present not just technical needs and opportunities, but a challenge: to harness the power of computational science to drive discoveries that will positively impact people.

Sun’s chief scientist, Bill Joy, has publicly expressed reservations about the “new Pandora’s box of genetics, nanotechnology, and robotics.” Does Sun have any policies aimed at stemming what Joy sees as the potentially adverse effects of the genomics revolution?

Papadopoulos: Bill Joy, as a brilliant innovator himself, has a deep insight into the potential of technology as well as the knowledge to recognize how that potential can be distorted by a few misguided individuals. This is the red flag that he raises, that the masses are growing increasingly dependent on a select few to govern them and to advance science and technology on their behalf.

Of all the markets Sun serves, where does life sciences rank in terms of dollars? Where do you think it will rank five years from now?

Papadopoulos: Life science is a relatively new market for Sun. Compared to other markets such as telecommunications and finance, which are more established for Sun, life sciences revenues are much lower. However, given the pace at which this market is moving, I don’t expect that to be the case five years from now. Industry analysts predict a $3 billion to $5-billion-plus biotech market within the next five years. We expect that to translate into tremendous opportunities for large-scale systems vendors.

What was the most interesting outcome of Sun’s Informatics Advisory Council Summit last fall?

Papadopoulos: Perhaps the most interesting aspect of the summit was the level of openness, camaraderie, and frankness. Here was a group of brilliant scientists and IT specialists from academia to industry having friendly conversations with each other and their competitors, all talking about how they can work together toward an “informatics utopia” — a plug’n’play world where everyone’s data and analysis tools are fully compatible. The participants were collectively geared towards the altruistic goal of accelerating discovery to improve the quality of life on this planet. Incredible. And that they wanted Sun to work with them to do this? I’m honestly flattered and look forward to serving this community.


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