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NY Academic Consortium Petitions State for Cash to Create Computational Biology Cluster

Seven New York universities have joined forces to convince the state to fund their project to transform the New York into a cluster for computational biology.
The consortium, together with a summit slated to take place this month, are two of three moves taking place that aim to knit New York’s far-flung biotech sites into a cohesive cluster — a longtime promise of officials and life sciences leaders that until now has gone unfulfilled.
The universities have formed a consortium that is seeking $8 million a year from the state for at least the next three years to help it develop a computational biology network using supercomputers situated at the State University of New York at Stony Brook and Rensselaer Polytechnic Institute.
“What we’re looking for is operating support from the state of New York to make [supercomputers] more easily available [and] easier to use for corporate users,” said Robert McGrath, provost and vice president for Brookhaven Laboratory affairs at SUNY Stony Brook.
“We’re also looking to provide the support staff that would allow others to have efficient access to the machines, and … have some regional centers around New York state where computational support people could provide face-to-face interaction [with] researchers,” he added.
Stony Brook and RPI have formed the consortium along with Columbia University, Cornell University, New York University, SUNY Albany, and SUNY Buffalo.
The consortium is also looking to expand its membership to biotech and high-tech businesses, starting with industry contacts it plans to develop at the Life Sciences Summit, to be held June 14 in Huntington, NY, and organized by the Long Island Life Sciences Initiative. LILSI itself expects to play a role in the consortium, but details aren’t expected to be finalized until after the summit, executive director Joseph Scaduto said.
Organizers of the summit and the consortium hope to coalesce New York’s disparate biotech sites into a cohesive cluster. Some time this month, Spitzer is due to meet a delegation of life science industry leaders and advocates led by the New York Biotechnology Association. At deadline, the date had yet to be set.
Nathan Tinker, NYBA’s executive director, said the computational biology initiative would be one of several for which industry leaders would seek Spitzer’s support. Other areas include workforce development, business development, and a job attraction and retention effort.
“From the industry side, [the consortium] really creates the opportunity for New York businesses and biotech companies to have a new resource for quickly and efficiently moving through a broad range of molecules in order to find the most suitable ones for potential clinical trials and marketing,” Tinker said. “The ability to have that sort of resource nearby is key. One thing that’s always a challenge for emerging biotech companies is instrumentation you can get to locally.”
The consortium would link IBM Blue Gene supercomputer systems at Stony Brook and RPI, with a combined potential of processing more than 200 trillion computations per second. Stony Brook’s IBM Blue Gene/L system has been installed at Brookhaven National Laboratory and cost $26 million secured for the school last year by state Assemblyman Marc Alessi, Democrat of Manor Park.
“We clearly envision scientific as well as some commercial use,” said Wolf von Maltzahn, RPI’s acting vice president for research and a professor of biomedical engineering.
“If you combined the two supercomputers plus large computational centers that exist throughout the state, if you think about what you could do with that system as a whole, it’s quite impressive,” von Maltzahn added. “We need to pave the way so that researchers at any one of those member institutions can think big, really, really big about what huge problems can we address using this resource. We all think there’s tremendous potential. How we develop that potential is up to all of us.”
Biocomputation and bioinformatics is one of several specialties where RPI has developed three-person faculty teams, or “constellations,” as recommended by its 2000 Rensselaer Plan. Over the past two years, RPI has hired Angel Garcia from Sandia National Laboratory to run the program and added a second professional this year. A third is yet to be hired.
New York already has a stake in supercomputing at RPI. The institute, the state, and IBM agreed last year to split the cost of the $100 million Computational Center of Nanotechnology Innovations, set to open this year within RPI’s 450-acre, 13-building, 425,000-square-foot technology portion of Rensselaer Technology Park in North Greenbush.
Over the next five years RPI will spend $34 million and IBM and the state $33 million each on CCNI. IBM’s share includes part of the cost of the supercomputer, which CCNI will run.
The platform is currently being installed and “should be up and running in about two weeks,” von Maltzahn said.
In return, the three partners agreed to 20 percent shares of supercomputer use. The remaining 40 percent has til now been set aside for corporate partners working with CCNI. Whether members of the new consortium could be included has yet to be explored, von Maltzahn said.
RPI hopes the consortium can also facilitate supercomputing by researchers at several centers at its Troy campus near Albany, including the Center for Biotechnology and Interdisciplinary Research, the Rensselaer Exploratory Center for Cheminformatics Research, and the Center for Bioinformatics, a joint venture with the Wadsworth Center public health lab of New York state’s Department of Health.
Over time, Stony Brook’s McGrath said, the universities within the consortium would hammer out agreements with businesses, either individually or collectively. McGrath said he also hoped to build support within SUNY, and had discussed the idea with former chancellor John Ryan, who resigned May 31.

“From the industry side, [the consortium] really creates the opportunity for New York businesses and biotech companies to have a new resource for quickly and efficiently moving through a broad range of molecules in order to find the most suitable ones for potential clinical trials and marketing.”

McGrath said computational biology could help the state’s life-science industry remain competitive with other states that have moved to establish themselves in the field. He cited Texas, where the University of Texas at San Antonio houses its two-year-old Computational Biology Initiative in a portion of the $83.7 million, 220,000-square-foot Biotechnology Science and Engineering building completed last year on UTSA’s campus at Loop 1604.
Meantime, Brown University in 2003 established a Center for Computational Molecular Biology using a $20 million gift from an anonymous Brown trustee.
Building an Empire
Though lagging the nation’s top biotech clusters of California’s Bay Area and the Boston-Cambridge region, New York has remained among the top 10 regions where bio companies have won venture capital funding.
Over the past decade, the state has fluctuated between a high of $135 million in eight deals in 2001 and a low of about $6 million in six deals in 2005, according to the quarterly MoneyTree Report by PricewaterhouseCoopers and the National Venture Capital Association.
And while 13 biotechs in New York state won a total $72 million in 2006, the first quarter saw a single VC winner from the Empire State: Cara Therapeutics, based in the New York City suburb of Tarrytown, captured $5 million in third-stage expansion financing. Cara is due to move later this year to Shelton, Conn.
On the brighter side, New York has seen biotech clusters emerge in Buffalo and Albany, as well as in New York City and nearby suburban counties that comprise the lower Hudson Valley region.
Those clusters have emerged separately, and with only spotty support from the state government. Under Spitzer’s predecessor George Pataki, the state joined Westchester County and Greenburgh town officials in crafting a combined $9 million in tax breaks that persuaded Regeneron Pharmaceuticals to stay in Tarrytown. Regeneron will occupy 194,000 square feet — all of one building and part of a second — within a $145 million, three-building, 360,000-square-foot expansion of The Landmark at Eastview, owned by BioMed Realty Trust.
In 2002, then-Governor Pataki and lawmakers also created six centers of excellence, including one in Buffalo, devoted to bioinformatics and life sciences. And his economic development agency, the Empire State Development Corp., joined the private nonprofit New York Economic Development Council and 13 other public agencies and private companies to launch “NY Loves Bio,” a biotech-specific job-attraction effort last fall.
But Pataki opposed in principle tailoring tax incentives similarly to biotechnology or other industries, long sought by the industry. And his plan last year to spend $200 million on academic research, including stem-cell research, failed on two fronts.
First, the state Charitable Asset Foundation objected to spending 60 percent of its $260 million to help fund the proposed Biotechnology and Biomedicine Research Initiative. The foundation was created through the proceeds of Empire Blue Cross Blue Shield converting from a nonprofit to a for-profit company. And a key Pataki political foe insisted the state spend $300 million on the research program.
Spitzer, who took office in January, has promised to grow biotech and other life sciences industries in New York. His first effort to fulfill that promise came in his first budget as governor. The $120.9 billion spending plan for the fiscal year that started April 1 included $100 million to create an Empire State Stem Cell Trust that would collect and distribute funds for stem-cell research. The trust would be run by a new Empire State Stem Cell Board within the state Department of Health. Spitzer has not yet named its members.
Spitzer and legislative leaders also agreed to dedicate $500 million to the fund over 10 years, or $50 million a year spread over 10 fiscal years starting in 2008-‘09. The $500 million would come from converting the nonprofit Health Insurance Plan of Greater New York to a for-profit company.
Another Spitzer idea has been to include a variety of science specialties within each of the existing centers of excellence, which Pataki envisioned as focusing exclusively on one or a few specialties in technology.
Asked whether those centers could also serve as the regional centers envisioned by the consortium, McGrath termed the idea “interesting” but said the consortium had yet to study it.

“To me, computational science is exactly the kind of thing that lends itself easily to integration [of multiple centers],” McGrath said. “To get things done, not everybody has to be sitting in the same room.”

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