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.
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.
More information: http://www.psc.edu/biomed/biomed.html
Networking the Future
ONE OF THE LEADING RESOURCES IN THE WORLD FOR NETWORK KNOW-HOW.
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.
More information: http://www.ncne.org/
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.
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.
© Pittsburgh Supercomputing Center.