Research Notes & Highlights

The National Resource for Biomedical Supercomputing

National Leadership in High-Performance Computing for Biomedical Research

Established in 1987, PSC’s National Resource for Biomedical Supercomputing (NRBSC) was the first external biomedical supercomputing program funded by the National Institutes of Health (NIH). Along with core research at the interface of supercomputing and the life sciences, NRBSC scientists develop collaborations with biomedical researchers around the country, fostering exchange among experts in computational science and biomedicine and providing computational resources, outreach and training.

The NRBSC team: (left to right) Jenda Domaracki, Jun Ma, Christal Banks, Markus Dittrich, Nikolay Simakov, Boris Kaminsky, Hugh Nicholas, Pallavi Ishwad, Art Wetzel, Greg Hood, Troy Wymore, Jack Chang, Gary Blumenthal (inset) Joel Stiles, director of NRBSC (Not pictured: Jacob Czech, James Keener, Alex Ropelewski)

“Over the past decade, computing has become essential to almost all aspects of biomedicine,” says PSC’s Joel Stiles, director of NRBSC. “Here at the NRBSC, we&38217;re developing and distributing computational tools in simulation, visualization, and education that are helping to transform our understanding of life and disease.”

Anton Comes to PSC

In September 2009, the National Institute of General Medical Sciences, part of NIH, awarded $2.7 million to NRBSC to support a partnership with D. E. Shaw Research to make an innovative new computing system, called Anton, available to U.S. biomedical scientists. This system, with hardware and software specialized to run molecular dynamics (MD) for the study of biomolecular systems such as proteins and nucleic acids, runs MD up to 100 times faster than conventional supercomputers, making it possible for the first time to extend MD simulations into the millisecond range of biological time.

While there are several Anton systems used internally at D. E. Shaw Research, NRBSC will host the first and thus far only one available to the general scientific community. A review committee convened by the National Research Council at the National Academies of Science reviewed and approved 47 proposals from scientists around the country to use Anton, and production research commenced in October 2010.

“This is an incredibly exciting project in many ways,” says NRBSC director Joel Stiles. “With this very generous gift from D. E. Shaw Research and the funding provided by NIH, we are deploying a tool of unprecedented power for the benefit of biomedical researchers nationally. We expect that this project will help to significantly advance our understanding of biomolecular structure and function, and to spur ongoing scientific and technological development in MD research and in other areas of computational biology.”

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NRBSC research focuses on three areas of biomedicine that span many scales of space and time: spatially realistic cell modeling, large-scale volumetric visualization and analysis, and computational structural biology.

Spatially realistic cell modeling centers on realistic 3-D simulations of movements and reactions of molecules within and between cells, to better understand physiological function and disease. MCell, DReAMM and PSC_DX software is developed at the NRBSC and used to model and visualize events such as (shown in this image) neurotransmission between a nerve and muscle cell.

Volumetric visualization using the NRBSC's PSC_VB software enables multiple users to share, view and analyze extremely large datasets and time series obtained from light and electron microscopes, CAT and MRI scanners, etc. This reconstructed section of a mouse brain (119,600 x 88,400 pixels) includes a full resolution inset showing alignment at a frame boundary (indicated by artificial contrast).

NRBSC structural biology focuses on computational tools used to determine the structure of proteins from their amino acid sequence and development of quantum-mechanical simulation methods for biomolecules such as enzymes. This image shows conserved residues in the “active site” of an enzyme, 5-epi-artistolocholene synthase, which is involved in the production of compounds called terpenes. PSC-developed software enables researchers to simulate enzyme reactions, to reproduce experimental reaction rates and gain new insight into enzyme function, which facilitates design of new therapeutic drugs.

Computational Service & Training

Since NRBSC's inception, PSC and NRBSC together have provided access to computing resources for more than 1,500 biomedical research projects involving more than 4,600 researchers at 285 research institutions in 46 states and two territories. Among these are several projects featured in this booklet (pp. 20 & 24).

NRBSC training activities reach hundreds of scientists each year. More than 4,600 researchers have participated in NRBSC workshops in such areas as spatially realistic cell modeling, volumetric data visualization and analysis, protein and DNA structure, genome sequence analysis and biological fluid dynamics.

NRBSC participates in a range of undergraduate and graduate training programs.These include:

  • a joint Carnegie Mellon and University of Pittsburgh Ph.D. program in computational biology (,
  • the Ray and Stephanie Lane Center for Computational Biology at Carnegie Mellon (,
  • the University of Pittsburgh Department of Computational Biology (, and

The NRBSC and PSC have developed educational programs, CMIST and BEST (see pp. 9-11), that have provided training to high-school and undergrad students and educators in the Pittsburgh region and nationally.

Networking the Future

One of the leading resources in the world for network know-how

PSC’s Advanced Networking group is one of the leading resources in the world for knowledge about networking. Through 3ROX (Three Rivers Optical Exchange), a high-speed network hub, they operate and manage network infrastructure that connects many universities and schools in Pennsylvania and West Virginia to research and education networks, such as Internet2 and National LambdaRail, that link to universities, corporations and research agencies nationally. Their research on network performance and analysis — in previous projects such as Web100 and the NPAD diagnostic server — has created valuable tools for improving network performance.

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LOGO: Wendy Huntoon

Wendy Huntoon, PSC director of networking. In September, the board of National LambdaRail (NLR) appointed Huntoon, NLR’s chief technical officer, as acting CEO.

Two grants from the National Science Foundation this year — one from the Software Development for Cyberinfrastructure (SDCI) program and another from the Academic Research Infrastructure (ARI) program — support, respectively, 3ROX research to build on Web100 and a major upgrade to the 3ROX network environment.

A $980,000 SDCI award supports a three-year project called Web10Gig. As a follow-up to Web100, Web10Gig will develop software to enable non-expert users to effectively exploit the bandwidth availability of advanced networks. Web100 ended in 2003 and produced prototype software still heavily used. PSC partnered on Web100 with the National Center for Atmospheric Research (in Colorado) and with the National Center for Supercomputing Applications (NCSA) at the University of Illinois, Urbana-Champaign, and on Web10Gig is again partnering with NCSA. “The potential broader impact of Web10Gig is huge,” says PSC director of networking Wendy Huntoon. “It can make it easy for users from the broadest range of fields and technical abilities to use the network to its full capacity. Eliminating many common network problems will have a transformative effect for researchers in many disciplines.”

An ARI award of $1.5 million for four years will enable 3ROX to renovate its network infrastructure, including upgrading its fiber-based optical capability to increase high-end transmission rates tenfold, from 10 to 100 gigabits per second. The upgrade will also include a pool of circuits (called transponders) that will enable researchers to experiment with bandwidth without having to include cost of the equipment in their grants, allowing them to be less encumbered by limitations that affect data-intensive research.

“We’re happy about these new and faster technologies,” says Huntoon, “as well as the institution of a pool of transponders for the 3ROX research community. We expect this to make bandwidth more accessible.”


Last year 3ROX joined with a coalition of Pennsylvania colleges and universities, heathcare and economic development organizations to form the Pennsylvania Research and Education Network (PennREN). In February, PennREN received $100 million in federal stimulus money through the American Recovery and Revitalization Act and $29 million in private funds to build and maintain a broadband network for expanded educational opportunity and healthcare services across the Commonwealth of Pennsylvania. This network will reach the most rural areas of Pennsylvania, providing access to more than two million households and 200,000 businesses.

At a news conference (at Carnegie Mellon University) announcing the award, Pennsylvania governor Ed Rendell estimated that the project could generate 1,000 new jobs over the next two years. Building the network will be managed by the Keystone Initiative for Network Based Education and Research (KINBER). When complete, the PennREN network will allow teleconferencing between regional hospitals and urban hubs, necessitating fewer patient transfers. The project calls for an initial bandwidth of 40 gigabits per second by January 2012.

“This system will rival any in the United States,” says PSC network director Huntoon, “and will provide the capability to connect regional networks across the Commonwealth.”

ILLUSTRATION: schematic of 3ROX network ILLUSTRATION: schematic of 3ROX network
Pittsburgh Supercomputing Center Workshops (2009-2010)

Hands-On Workshop on Computational Biophysics Using NAMD and VMD

Molecular Dynamics with Desmond

Summer Institute In Bioinformatics (For Minority-Serving Institutions)

Bioinformatics Internship Program

Methods And Applications Of Hybrid QC/MM Simulations To Biomolecular Systems

Parallel Programming and Cluster Computing

TeraGrid New User Training

A workshop underway in the PSC Computer Training Center, the David W. Deerfield II Training Center, equipped with 30 “dual-boot” workstations and a projector for overhead display of the instructor’s desktop.

Wendy Huntoon, director of networking; David Moses, executive director; David Kapcin, director of financial affairs; Sergiu Sanielevici, director, scientific applications & user support; Bob Stock, PSC associate director; Cheryl Begandy, director, education, outreach & training. Not pictured: Janet Brown, manager of networking; John Kochmar, manager of high-performance computing facilities; Nick Nystrom, director of strategic applications; J. Ray Scott, director of systems & operations; Richard Raymond, manager of user support; Joel Stiles, director of NRBSC.