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On 10th Anniversary, VBI Envisions Doubling Its Operations in Coming Decade

By Alex Philippidis

NEW YORK (GenomeWeb News) — When Harold (Skip) Garner took the helm as executive director of the Virginia Bioinformatics Institute a year ago this month, he was challenged by Virginia Tech’s president, Charles Steger, to double VBI’s operations over the coming decade.

VBI has begun to do just that, Garner told GenomeWeb Daily News in a recent interview. The institute doesn’t have a choice, he added, given the need to analyze, and then act on the data gleaned through sequencing and imaging.

“You can do the math. That really means doubling the number of people, having plenty of space to do it [and] having plenty of money to do that," he said. "It won't be easy to double in size, but … we know that we're in demand. And we'll just have to gather the resources, [including] resources available from Virginia Tech to spur that growth, and that results in things like us winning $10.6 million contracts."

Garner spoke to GWDN after VBI announced it had been awarded a $10.6 million grant from NIH’s National Institute of Allergy and Infectious Diseases toward a new Center for Modeling Immunity to Enteric Pathogens.

The center will apply mathematical modeling and perform pre-clinical and clinical experiments designed to advance the study of immune responses to gut pathogens, with the goal of revealing how the immune system works when intestinal pathogens invade the human body. The center will be organized into four major areas: computational/mathematical model development, immunological experimentation, bioinformatics, and education.

"We want to use powerful computer simulations to uncover the mechanisms of action underlying immune responses to intestinal pathogens and accelerate the discovery of drug targets suitable for the prevention and treatment of diseases and disorders caused by gut pathogens, such as persistent diarrhea, gastric cancer, inflammation, and ulcers," Josep Bassaganya-Riera, principal investigator of the center, said in a statement.

Bassaganya-Riera is also an associate professor at VBI, and leader of the Nutritional Immunology and Molecular Medicine Group in VBI's CyberInfrastructure Division.

Potential drug targets, Garner said, “can be both things that could potentially target directly the pathogens themselves, with minimum interaction or zero interaction with the host … [and] drugs that could alter whole-cell presentations that limit the access of pathogens to host cells, and such.

“There are all kinds of possibilities. That’s the whole point," he said. "This is relatively new. There isn’t a particular target they’re going for right now, such as for example, a particular membrane protein or something like that. Hopefully that’s what will come of all of this.”

The new grant comes more than three months after VBI wrapped up the fiscal year with a surge in NIH funding due to the American Recovery and Reinvestment Act and a large one-time award from the agency. During the fiscal year 2010 ending June 30, VBI racked up $120.8 million, according to the institute's 2010 Annual Report from the Office of the Vice President for Research — up 28 percent from $94.7 million in fiscal 2009, and up 24 percent from $97.2 million in fiscal 2008.

The FY 2010 figure includes the largest-ever one-time federal award in the history of Virginia Tech — a five-year, $27,670,448 NIAID contract to the CyberInfrastructure Group to support infectious disease research worldwide, by integrating information on pathogens, providing resources and tools to scientists, and helping researchers analyze genomic, proteomic, and other data from infectious disease research.

It was extramural funding of a different sort — $12.3 million from the US tobacco settlement of 1998 that allowed VBI to open its doors in July 2000.

Since then, VBI has grown to 250 staffers – including about 50 faculty members – working at three facilities developed over two phases. VBI occupies a 130,000-square-foot facility on Virginia Tech’s Blacksburg, campus, as well as offices in the nearby Virginia Tech Corporate Research Center, and in Alexandria.

Garner told GWDN that VBI has plans for a third-phase facility, a $30 million, roughly 50,000-square-foot building that would link the institute’s two existing buildings, which now house a mix of computer space and wet laboratory space.

Unlike those buildings, Phase 3 will not contain new wet labs. “It will be dominated by much more computational space, and offices and bullpens necessary for large computational groups,” Garner said.

Garner said the Phase 3 building is needed to accommodate the professionals need to analyze the torrent of data VBI, like other institutions, is gathering through next-generation sequencing and a variety of imaging technologies.

"The analysis challenge to reduce that massive amount of data down to actionable knowledge is going up. And it requires bioinformatics, very high performance machines, and very high performance people," Garner said. "And so, this is an area that is growing, and people are recognizing it as such, and we are prepared, and we'll be responding."

VBI has begun a fundraising effort for the Phase 3 building. The institute sought stimulus funding for the Phase 3 building under the $814 billion American Recovery and Reinvestment Act, only to be turned down.

"It's designed and ready to go right now. It really depends on the finances of the state. My personal hope is that we'd be breaking ground within about a year,” Garner said.

The prospect of state funding is unknown, though Virginia is looking at several measures designed to grow its academic institutions specializing in life sciences research. A panel appointed by Gov. Robert McDonnell has issued preliminary recommendations — set to be formalized on Friday — that the state "transform academic institutions into economic engines" by creating academic-industry "Centers of Excellence" and awarding refundable R&D tax credits to companies using research developed at state universities.

While a state role in funding Phase 3 is foreseen, Garner said, private funding will prove even more important as VBI ramps up its science and hires new researchers.

"That really requires us to have philanthropic contributions, into which we're going to put considerable effort, given the fact that I think we have some very attractive and compelling stories for individuals and foundations to really help move their individual missions to advance healthcare, [and] to advance research science," Garner said.

VBI maintains a core laboratory for 'omics sciences that offers among its services genome sequencing using Illumina's platform and Roche's 454 GS FLX platform. It also offers genotyping, gene expression analysis, and proteomics. In addition, the institute runs a data analysis core, and a computational core consisting of two data centers with a combined 1,850 square feet; more than 2.65 terabytes of RAM; 1100 processor cores distributed across 220 servers and clusters; and more than 450 terabytes of disk storage.

The cores serve VBI's four research program areas: biosystems, which uses genomic and proteomic technologies to study host-pathogen environment interactions and inflammation; cyberinfrastructure to support bench-to-bedise health sciences activities; the network dynamics and simulation science laboratory, which uses interaction-based modeling and other methods and analyses to understand large biological, information, social, and technological systems; and medical informatics and systems, which focuses on human disease from an 'omics perspective.

VBI recently hired a new faculty member, Pawel Michalak, for its medical informatics and systems research program, created by Garner soon after his arrival at the institute last year. Another faculty member has not officially started at VBI but is expected to come on-board in the coming weeks.

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