Research Notes & Highlights

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. In a current project, Web10Gig, PSC network staff are helping to develop software to enable non-expert users to more fully exploit the bandwidth of advanced networks.

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LOGO: Wendy Huntoon

Wendy Huntoon, PSC director of networking, has served in several national leadership roles in research and education networks and is currently chief architect in the office of the chief technology officer for Internet2, an advanced networking consortium led by the research and education community.

In January, 3ROX contracted with the National Oceanic and Atmospheric Administration for $2.6 million to provide a high-speed optical fiber link to NOAA's Environmental Security Computing Center (ESCC) in Fairmont, West Virginia. The connection to ESCC provides 10 Gigabit per second capability, and allows ESCC access to national and international research networks such as Internet2 and National LambdaRail.

In February, 3ROX partnered with Drexel University in Philadelphia to implement a five-fold upgrade to the Internet bandwidth of both 3ROX and Drexel at essentially no cost increase. Prior to partnering, 3ROX and Drexel each had individual one-gigabit (a billion bits per second) connections to Internet2, a high-performance research and education network that connects universities, corporations and research agencies nationally. Normally, the next level of service available would be 10 gigabits, which is cost prohibitive, but the new connection makes it possible to have two connections, each with five gigabits of committed bandwidth.

The partnership consolidates Internet2 connections in Pennsylvania from the previous three — 3ROX, Drexel and MAGPI (Mid-Atlantic Gigapop in Philadelphia for Internet2) — to two: MAGPI and 3ROX/ Drexel. 3ROX serves universities, research sites and K-12 schools in western Pennsylvania and West Virginia, and Drexel connects the Drexel campus and its related research sites with the 14 Pennsylvania State System of Higher Education universities. With the new connection, both 3ROX and Drexel will be able to improve the quality and quantity of services they provide.

ILLUSTRATION: schematic of 3ROX network ILLUSTRATION: schematic of 3ROX

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: (l to r) Christal Banks, Markus Dittrich, Nikolay Simakov, Boris Kaminsky, Hugh Nicholas, Pallavi Ishwad, Art Wetzel, Greg Hood, Troy Wymore, Jack Chang, Gary Blumenthal. (Not pictured: Jacob Czech)

“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’re developing and distributing computational tools in simulation, visualization, and education that are helping to transform our understanding of life and disease.”

Anton Program Extended

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, making an innovative new computing system, called Anton, available to U.S. biomedical scientists. This system, with hardware and software specialized for molecular dynamics (MD) simulations of biomolecular systems such as proteins and nucleic acids, runs MD up to 100 times faster than conventional supercomputers, making it possible to extend MD simulations into the millisecond range of biological time. Due to a successful initial year that included 47 biomedical projects (see pp. 18-23), NRBSC and DESRES extended the program, enabling a new round of projects to begin in October 2011.

"With this generous gift from D. E. Shaw Research and the funding provided by NIH," says NRBSC scientist Markus Dittrich, who coordinates the Anton program, "we are deploying a tool of unprecedented power for the benefit of biomedical researchers nationally."

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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.

One of NRBSC's research highlights this year was a cover article in the March 10 issue of Nature, the prestigious international science journal (see pp. 24-27). As part of this project, NRBSC scientists processed and analyzed several tens of terabytes of electron microscopy image data.

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 software enables multiple users to assemble and manipulate extremely large datasets and time series obtained from light and electron microscopy or CAT and MRI scans, etc. This cropped subvolume of a C. elegans embryo in its eggshell was assembled from 700 electron-microscopy images captured by Richard Fetter in Cornelia Bargmann's laboratory and aligned by Greg Hood at NRBSC. C. elegans is a roundworm much studied as a model organism.

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 co-varying residues of class D betalactamases, with the surface colored red for OXA-1 and blue for OXA-2. 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.

PSC's NRBSC Workshops


Hands-On Workshop on Computational Biophysics using NAMD and VMD
Summer Institute in Bioinformatics (for minority-serving institutions)
Anton Training Workshop (held three times)
Bioinformatics Internship Program
Computational Modules in Science Teaching Workshop