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By Jeff Moad

June 15, 2003 | Overcoming a funding controversy that arose when its original backer pulled a big chunk of promised financial support, Stanford University’s innovative, $150-million Bio-X interdisciplinary research project will move into its new 225,000-square-foot home this month.

Bio-X is the first of several recently funded bio-medical research initiatives setting up shop on major university campuses. Other sites include the Genome Sciences Research Building at Duke University and a new genome sciences research space planned at the University of Washington. Last January, the Massachusetts Institute of Technology launched its interdisciplinary program, the Computational and Systems Biology Initiative.

The Stanford Bio-X project, intended to foster collaborative projects involving researchers from Stanford’s various humanities and science disciplines, was launched in 1999 with the promise of a $150-million donation from Jim Clark, founder of Silicon Graphics Inc. and Netscape Communications. The project was threatened, however, when Clark pulled $60 million in August 2001 to protest President Bush’s decision to place limits on human embryonic stem cell research. Stanford, however, went ahead with Bio-X, supported by $60 million from a second, anonymous donor.

Donations are not only paying for construction of the James H. Clark Center for Biomedical Engineering and Sciences on the Stanford Campus, but also providing seed funding for 40 interdisciplinary research projects and supporting shared computing and lab technology facilities, many of which will be located at the Clark Center.

 The center will house 42 Stanford faculty members and provide space for 600 to 700 researchers and support staff, according to Matthew P. Scott, professor of developmental biology and genetics and chairman of the Bio-X Leadership Council. Scott, who was appointed chair of the Bio-X Leadership Council in 2002, is also an investigator with the Howard Hughes Medical Institute and has published work using genetics and molecular biology to identify and isolate components of gene regulation and signaling pathways. He was among the first to isolate homeotic genes.

 “[What’s] unique about the Clark Center is that it will have different people from different fields brought into close contact,” says Scott. “We want to make it a gathering place, a community center, in addition to a site for important research.”

Iceberg Cluster
Shared IT resources supported by Bio-X and located at the Clark Center will include a 602-processor, Linux-based computing cluster using Dell servers. Dubbed Iceberg, the cluster is the largest so far to run the open source, Rocks cluster management software program developed at the San Diego Supercomputer Center, according to Steve Jones, cluster operations manager. Generating 3.37 teraFLOPs (trillion floating-point operations per second) of processing power, the Iceberg cluster relies on 301 Dell 2650 nodes, each with dual Pentium 4, 2.8-gigahertz processors.

“Iceberg is certainly one of the largest bio-computational clusters out there right now,” says Jones. At present, the most pressing problem “is determining how to properly manage this kind of resource as we add users.”

The center will also house a 128-processor Origin 3800 shared-memory supercomputer from Silicon Graphics, which is being used for research in genomics, developmental and structural biology, and cardiovascular and musculoskeletal biomechanical modeling.

On the laboratory side, Bio-X resources are supporting a Cell Sciences Imaging Facility including confocal laser scanning devices and other advanced electron microscopy. The foundation of the Clark Center building, Scott says, was designed to produce low vibrations in order to enable advanced laser-based research. Other advanced lab technology funded by Bio-X includes a mass spectrometry laboratory including ion trap mass spectrometers and a tissue bank to support biomedical research.

In all, $7 million in Bio-X funding is going to support shared IT and lab technology centers. Another $3 million in Bio-X money is earmarked as seed funding for 40 interdisciplinary research projects that will be housed at the Clark Center and make use of Bio-X shared facilities. Only projects that include researchers from different disciplines were considered for Bio-X seed funding. One such project, headed by Michael Levitt, chair of computational structural biology at the Stanford School of Medicine and Vijay Pande, assistant professor of chemistry, is using Iceberg to simulate the kinetics and thermodynamics of proteins and nucleic acids. Pande says the Iceberg cluster has helped researchers directly simulate protein-folding dynamics.

“[Protein folding dynamics] has been the holy grail of computational biology for the last 30 years,” says Pande, “and it has applications in that several diseases, such as Mad Cow and Alzheimer’s, are thought to be linked to protein misfolding.”

Another Bio-X-funded project -- a collaboration between researchers from Stanford’s Medicine; Health, Research & Policy; and Chemistry departments -- is studying protein patterns and other  markers in blood serum in order to predict which patients may experience adverse reactions to radiation treatment (something that affects 1 in 20 patients, researchers say.)

A third protect involves researchers from Stanford’s ophthalmology and biochemistry disciplines who are developing artificial corneas using new types of polymers.

Clark’s decision to reduce his contribution never seriously threatened the Bio-X project, says Scott, but it did force a reduction in the number of research projects that could be funded. Still, Stanford understood and agreed with Clark’s motives, according to the BioX leadership chairman.

“We are all very concerned about limits on stem cell research because it can potentially play such a large role in regenerative medicine,” he says.

While Stanford is one of the first institutions to open a new research center devoted to interdisciplinary bioscience and engineering discovery, Scott acknowledged that several other universities are hot on Stanford’s heels. Besides Duke and the University of Washington, Princeton and MIT are making similar major investments. Why? Because, notes Scott, emerging bioscience fields like genomics are inherently interdisciplinary and so require new facilities and funding models.

“In genomics, for example, the drivers came from the world of enzymology, the world of machines that handle the automation of DNA for sequencing, and the world of machines for interpreting sequences,” Scott says. “Those are completely different worlds, but they came together. That’s happening in many areas. The experience of researchers is that the things they used to be able to do on their own are now more effectively done in an interdisciplinary way.”

For reprints and/or copyright permission, please contact Angela Parsons, 781.972.5467.