Research Notes & Highlights

The National Resource for Biomedical Supercomputing

National Leadership in High-Performance Computing for Biomedical Research

The NRBSC team: (l to r) Markus Dittrich (director), Greg Hood, Hugh Nicholas, Pat Sudac, Art Wetzel, Alex Ropelewski, Pallavi Ishwad. (Not in photo: Jacob Czech)

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) and has continued uninterrupted since then. 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.

In September 2012, NRBSC gained renewed NIH support as a participant in a newly funded Biomedical Technology Research Center (BTRC) on High-Performance Computing for Multiscale-Modeling of Biological Systems. This $8 million grant, from NIH’s National Institute of General Medical Sciences, establishes a collaboration between the University of Pittsburgh, Carnegie Mellon University and PSC. The principal investigator of the BTRC, Ivet Bahar, chairs the Department of Computational & Systems Biology at the University of Pittsburgh School of Medicine. Markus Dittrich of NRBSC leads the PSC component, and Robert F. Murphy, director of the Lane Center for Computational Biology, leads Carnegie Mellon’s participation.

“This collaboration opens many opportunities as NRBSC goes forward,” says Dittrich. “Through the new BTRC we continue our work in cellular modeling, structural biology, and large-scale volumetric image analysis, and we gain through synergy with the outstanding computational biology programs at the University of Pittsburgh and Carnegie Mellon.”

Ivet Bahar, Professor and John K. Vries Chair, Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh, leads the newly established Biomedical Technology Research Center on High-Performance Computing for Multiscale-Modeling of Biological Systems. “I’m very optimistic about the collaborative possibilities of this joint effort,” says Bahar. “Our vision is to begin to fill the gaps among modeling efforts at disparate scales of structural biology, cellular microphysiology and large-scale image analysis. We will build the framework to unify these efforts and gain insights that will help to alleviate neurobiological disorders. The experience and expertise of PSC are an essential element of this.”

Robert F. Murphy, Ray and Stephanie Lane Professor of Computational Biology and Professor of Biological Sciences, Biomedical Engineering, and Machine Learning, Carnegie Mellon University. He was a co-principal investigator on the original PSC biomedical supercomputing grant. “We have imagined this new center as a Pittsburgh center, joining the two universities, the University of Pittsburgh and Carnegie Mellon, with PSC strengths in training and in spatially realistic cellular modeling, structural biology, and large-scale volumetric image analysis. We now have an opportunity to combine that work with work in the Lane Center on image-derived modeling of cellular organization and machine learning for structural biology and to go beyond what we’ve done before.”

Anton Program Extended

A supplementary award to the newly established BTRC also provides $1.1 million to extend the Anton program for another two years. In partnership with D. E. Shaw Research (DESRES), this program makes an innovative computing system available to U.S. biomedical scientists. Having served 91 research projects by more than 70 individual research groups in two years, the Anton program commenced a new round of allocations in November 2012.

“We are thrilled about the impact that Anton has had over the last two years,” says Markus Dittrich of NRBSC, “and we are excited to be able to offer continued access to this great resource for the biomedical community.”

NRBSC research focuses on three areas of biomedicine that span many scales of space and time:

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

Biomedical image processing using NRBSC developed software enables accurate three-dimensional reconstruction of brain circuits from massive serial-section electron microscopy image sets. The example shown here spans a cortical region of mouse brain and is built from 3000 individual camera images at four nanometer resolution. After registration at the NRBSC, the large sectional reconstruction occupies 12 gigabytes. Thousands of these sections are then combined and aligned into 3D volumes for visualization and analysis of neural pathways.

NRBSC structural biology focuses on computational tools to determine the structure of proteins from their amino-acid sequence and quantum-mechanical simulation methods for biomolecules such as enzymes. This image shows structure for the oxacillinase class D beta-lactamase enzyme, with the “active site” in blue. Beta-lactamase is a bacterial enzyme that is a major mechanism of antibiotic resistance. PSC-developed software enables researchers to simulate enzyme reactions and gain new insight into enzyme function, which facilitates design of new therapeutic drugs.

PSC's NRBSC Workshops (2011-2012)

Computer Simulation of Biomolecular Dynamics and Reactions
Computational Methods for Spatially Realistic Microphysiological Simulations
Summer Institute in Bioinformatics (for minority-serving institutions)
Anton Training Workshop
Bioinformatics Internship Program

NRBSC and PSC have also developed educational programs, CMIST and BEST, 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-howOne 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 (NLR), that link to universities, corporations and research agencies nationally. Their research has created valuable tools for improving network performance. In a current project, Web10G, PSC network staff are helping to develop software to enable non-expert users to more fully exploit the bandwidth of advanced networks

More information:

Improved Connectivity in Pennsylvania and West Virginia

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 and Drexel University opened a high-performance network link, Philadelphia to Pittsburgh, via high-performance, fiber-optic network. This link, using the FrameNet service of NLR, provides bandwidth of 10 Gigabit Ethernet (10 billion bits per second), about 100 times faster than current high-end download rates for most residential Internet service. The new link augmented connectivity through the 3ROX/Drexel Internet2 hub. This partnership, formed in early 2011, provides network services to universities, research sites and K-12 schools in western Pennsylvania and West Virginia along with Drexel and its affiliated research sites and 14 Pennsylvania State System of Higher Education universities. “This link,” said Huntoon, “is the framework for a consolidated high-performance network infrastructure across Pennsylvania.”

This year 3ROX also improved network service in West Virginia, upgrading the link between PSC and West Virginia University (WVU) and adding WVNET (West Virginia Network) as a member. The new link to WVU increases bandwidth 64-fold. “This is a big step forward for research and education connectivity to WVU,” said Huntoon.

By joining as a participant in 3ROX, WVNET upgrades connectivity from West Virginia K-20 schools to research and education networks such as Internet2 to two 10 gigabit-per-second connections (one from Morgantown and another from Huntington). More important than the improved bandwidth per se, says Dan O’Hanlon, director of WVNET, is the collaboration with 3ROX. “It’s a big gain for West Virginia,” said O’Hanlon, “that we’re now able to collaborate with people who are involved in supercomputing and have world-class experience in running a research and education network.”

The catalyst for the upgrades, says Huntoon, was the 10 Gbps connection that 3ROX provided last year for the National Oceanic and Atmospheric Administration Environmental Security Computing Center in Fairmont, West Virginia. “The NOAA grant was stimulus funding,” says Huntoon, “and because we had infrastructure in place, we’ve been able to provide these expanded services very competitively from a cost perspective. These upgrades transform the West Virginia Internet landscape.”

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