Skip to main content
Premium Trial:

Request an Annual Quote

Buffalo Bioinformatics COE s New Director Likely To Spark Cluster Envy among Peers

Premium

The director of the new Buffalo Center of Excellence in Bioinformatics is power hungry — for compute power, at least. With an additional $11 million in funding from New York State under its belt and plans for a new building on the table, the center is ready to take its first steps away from the drawing board.

But while many of the details of the center — including its temporary home —need to be worked out, newly appointed director Jeffrey Skolnick has made one key equipment decision: The center will have a huge amount of computational power on tap.

For his own research, the structure and function prediction of proteins, Skolnick said he plans to install a 10-teraflop, 4,000-plus-processor Linux cluster with 10 terabytes of storage. This will far exceed his current 1,040-processor cluster at the Donald Danforth Plant Science Center in St. Louis, where he is director of computational and structural biology. “It’s my expectation it will be, at least for a short period of time, the top personal cluster,” he said. “It gives a whole new meaning to the word ‘PC’.”

Skolnick said he is in the process of selecting a vendor for the mammoth cluster.

Offering resources of this scale may well be the strongest selling point to attract researchers to the new center, one of Skolnick’s first tasks on arrival. “I wouldn’t be shocked if … there are 10,000 processors running around the center of excellence in three or four years,” he said. But Skolnick reckons it might take up to four years to recruit the “world-class people” he’s seeking.

Last week, Governor Pataki announced $110 million in state support for a new facility in downtown Buffalo that will be shared by the center of excellence, Roswell Park Cancer Institute, and Hauptman-Woodward Medical Research Institute. Of the funding, $61 million — $11 million more than originally promised — is earmarked for the COE, a collaboration between the University of Buffalo, Roswell Park, and Hauptman-Woodward that is supported by several companies, the state of New York, and the federal government. Since it was announced at the beginning of last year, it has also attracted more than $150 million in private funding.

Skolnick was selected as the center’s first director last month. When he starts his appointment at the end of September, he will have 17 scientists from St. Louis in tow, and will begin the search process for the remaining ten faculty positions. Researchers will cover a range of research areas. “Basically it’s going to be a lot of systems biology,” he said, “because that’s where I believe the most exciting science is going to be happening in the next half decade or decade.”

Gradual growth may give the new facility’s builders a chance to keep up. Groundbreaking for the new 400,000-square-foot facility — 150,000 of which will house the center — is planned for the summer, Skolnick said. The facility is anticipated to be finished within three years. The bioinformatics group has been alloted 35,000 square feet and 5,000 square feet will be used for a shared computer room. One of the goals of the center will be to foster the commercialization of spin-off technologies, and 5,000 square feet of space in the new building will be set aside initially for startup companies.

So far the role of the center’s industrial partners — including Bristol-Myers Squibb, Pfizer, Hewlett-Packard, IBM, and Sun Microsystems — has been limited to providing infrastructure resources. But other types of collaborations that go beyond technology support are also evolving, Skolnick said, although details have yet to be decided.

Finally, the center will play a role in educating the next generation of bioinformaticists. Right from the start, this will include the training of postdoctoral fellows, Skolnick said, but within two years, he intends to expand an existing master’s program in bioinformatics at the University of Buffalo into a PhD program. In addition, there are plans in progress for summer internships for undergraduates.

Having built a similar bioinformatics center at the Danforth, albeit on a smaller scale, Skolnick is not daunted by his new job. “In some respects the situation in Buffalo is easier,” he commented. “There is already a significant infrastructure with the [UB] Center for Computational Research [and] the partnership of Hauptman-Woodard and Roswell Park and significant industrial support already in place.”

— JK

Filed under

The Scan

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.

Survey Sees Genetic Literacy on the Rise, Though Further Education Needed

Survey participants appear to have higher genetic familiarity, knowledge, and skills compared to 2013, though 'room for improvement' remains, an AJHG paper finds.

Study Reveals Molecular, Clinical Features in Colorectal Cancer Cases Involving Multiple Primary Tumors

Researchers compare mismatch repair, microsatellite instability, and tumor mutation burden patterns in synchronous multiple- or single primary colorectal cancers.

FarGen Phase One Sequences Exomes of Nearly 500 From Faroe Islands

The analysis in the European Journal of Human Genetics finds few rare variants and limited geographic structure among Faroese individuals.