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Download the PDF version of this article as it appeared in Projects in Scientific Computing, 2002.

Biomedical Supercomputing

In 1987, the PSC biomedical program became the first extramural biomedical supercomputing program in the country funded by NIH. Since then, with support from NIH's National Center for Research Resources, PSC has fostered exchange between PSC expertise in computational science and experts in biology and medicine to solve important problems in the life sciences.

						     Workshop attendees.

Developing Bioinformatics Programs
From July 8 to 19, PSC hosted 23 participants for a two-week course in the concepts and methods of "bioinformatics" — the field that marries information technology and the life sciences. Taught by PSC scientists, the course introduced the participants, from five colleges and universities, to the computational, mathematical and biological issues of this still-emerging field and prepared them to teach bioinformatics courses at their campuses.

PSC workshops and courses on computational biology have trained more than 2,000 researchers in the use of high-performance computing for biomedical research, in such areas as sequence analysis in genome research, the structure of proteins and DNA, and biological fluid dynamics. The National Human Genome Research Initiative this year renewed its decade-long support for PSC's workshop in Nucleic Acid and Protein Sequence Analysis. "Our training reaches hundreds of biomedical scientists each year," says biochemist David Deerfield, who directs the PSC program. "Techniques we've developed are helping scientists nationwide cope with the explosion of genome data."

Since its inception, PSC's biomedical program has provided computing resources for more than 800 biomedical research projects involving nearly 1,800 researchers in 43 states and the District of Columbia. Among these are several projects featured in this booklet (pp. 18-29, 44), including research by PSC scientists on an important enzyme mechanism.

In addition to training and access to computational resources, the biomedical group carries out research in structural biology, protein and nucleic-acid sequence analysis, computational neuroscience and microphysiology. Its researchers collaborate with scientists at many other institutions, including the University of Pittsburgh Medical School, Carnegie Mellon University, Scripps Research Institute, University of California at San Francisco, and Whitehead Institute.

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Networking the Future


Gwendolyn Huntoon

Director of the Quilt
In September 2001, Gwendolyn Huntoon, PSC assistant director for networking, agreed to serve as the first executive director of The Quilt, an effort of many U.S. regional networking organizations to promote and extend research network services. She has continued in her leadership role at PSC while taking responsibility, through The Quilt, to coordinate many groups nationwide in development of next-generation network technologies.

PSC's team of network engineers, the National Center for Network Engineering (NCNE), is one of the leading resources in the world for network know-how. They provide engineering consulting for advanced networking nationally, and they conduct seminars that disseminate knowledge to engineers around the country. Since 1998, when an NSF grant established NCNE, their training activities have reached more than 2,600 people. In projects such as Web100 and Net100, they're actively involved in developing technologies that will define networks of the future.

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Getting in Tune with Web100 & Net100

They call it the Information Superhighway, so why drive if you're going to putter along in second gear? This question, in various forms, inspired Web100, a research program funded by Cisco Systems and the National Science Foundation to help researchers realize the network's data-transfer potential.

Most high-performance networks have bandwidth that can transfer data at 100 million bits per second (Mbps) or faster, but until recently researchers have seldom realized rates above a few Mbps. Network engineers at PSC, the National Center for Atmospheric Research (NCAR) and the National Center for Supercomputing Applications, have collaborated to improve this situation by developing software to "tune" computer operating systems to better exploit available network bandwidth.

						     Heffner and Matt Mathis.

Undergrad Excellence
In May, John Heffner (left), who worked for two years as a student intern at PSC on the Web100 project, under the direction of PSC network engineer Matt Mathis (right), received the Alan Newell Award for Excellence in Undergraduate Research from Carnegie Mellon University. Heffner received the honor for his senior thesis, "High Bandwidth TCP queueing." In September, he joined the PSC staff full-time.

The problem is that most computer operating systems come configured to transfer data at only one speed - usually slow - regardless of the underlying network. The network throttle of computer operating systems is controlled through the Transmission Control Protocol (TCP). By making adjustments to TCP settings, networking experts can tweak the operating system to move data faster.

The goal of Web100, which released its software publicly in February, is to eliminate the need for a human expert by automatically tuning the TCP settings to optimize performance. "We want to make it easier for everyone to move data across networks at 100 Mbps or higher," says Matt Mathis, PSC network research coordinator. Many research projects nationwide, including the NASA Earth Observer and the Visible Human (see p. 6), are now using Web100.

In September 2001, the U.S. Department of Energy awarded $2.5 million for a related project called Net100. In this project, which expands on Web 100, PSC's network group is collaborating with NCAR, Lawrence Berkeley National Laboratory and Oak Ridge National Laboratory. The goal is to make the operating system tune itself in response to changing conditions on the network. Net100 will develop tools to probe the state of the network and feed this information to an auto-tuning capability based on Web100.

PHOTO: Peter
						     Freeman speaking at PSC.

On June 19, 2002, Peter Freeman, new director of the National Science Foundation's Computer and Information Science and Engineering directorate, visited PSC. At an afternoon gathering with PSC staff, Freeman noted the importance of the NSF Partnerships for Advanced Computational Infrastructure program. "In case after case," he said, "the capabilities of modern high-end cyberinfrastructure provide opportunities to revolutionize the conduct of science."

Still, the challenges of solving hardware and software problems, said Freeman, pale in comparison to the difficulties of building a team of people to serve the science and engineering community and work together with them to effectively exploit the powerful technologies of cyberinfrastructure. "Machines come and go," said Freeman. "I know how important the people are to a center like this."

						     operational management team.

The PSC operational management team (l to r): J. Ray Scott, assistant director, systems and operations; David Kapcin, manager, financial affairs; Bob Stock, associate director; David Deerfield, assistant director, biomedical initiative; Sergiu Sanielevici, assistant director, scientific applications and user support; Rich Raymond, manager, user support;. Elvira Prologo, manager, administrative staff. Not in photo: Janet Brown, manager, networking.


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All of PSC

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A protein model.

An International Protein Structure Experiment

Where Nerves End

A workshop in session at PSC.
    Pittsburgh Supercomputing Center Workshops (2000-2001)
  • Developing Bioinformatics Programs
  • Scaling to New Heights
  • Statistical Analysis of Neuronal Data
  • Realistic Microphysical Simulations Using MCell
  • Parallel Programming Techniques
  • Nucleic Acid and Protein Sequence Analysis
  • Methods and Applications of Molecular Dynamics to Biopolymers

The Pittsburgh GigaPoP

Tele-Immersion: Human Interaction at a Distance