A NEW SPECIALIZED SYSTEM FOR
BIOMOLECULAR RESEARCH

A $2.7M grant from the NIH will allow the National Resource for Biomedical Supercomputing at PSC to provide U.S. biomedical researchers with access to a novel special-purpose supercomputer for biomolecular simulation, made available without cost by D. E. Shaw Research.

The National Institute of General Medical Sciences (NIGMS), part of the National Institutes of Health, has awarded a two-year, $2.7 million grant to the National Resource for Biomedical Supercomputing (NRBSC) at PSC (see p. 14) to host a specialized supercomputer for biomolecular simulation designed by D. E. Shaw Research (DESRES). The machine, called Anton, will be made available without cost by DESRES for non-commercial research by universities and other not-for-profit institutions.

PHOTO: Anton

Anton was designed to dramatically increase the speed of “molecular dynamics” (MD) simulations compared with the previous state-of-the-art, allowing biomedical researchers to understand the motions and interactions of proteins and other biologically important molecules over much longer time periods than have previously been accessible to computational study. The machine and the novel algorithms it employs were designed by a team of researchers led by David E. Shaw, chief scientist of DESRES.

“This is an incredibly exciting project in many ways,” said Joel Stiles, the director of NRBSC. “With this very generous gift from D. E. Shaw Research and the funding provided by NIH, we’ll be deploying a tool of unprecedented power for the benefit of biomedical researchers nationally. We hope and 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.” In addition, Stiles, a faculty member in Biological Sciences and the Lane Center for Computational Biology at CMU, will collaborate with Christopher Langmead in the CMU School of Computer Science to develop specialized software for analysis of data as it streams off the machine.

The award is one of 14 made by NIGMS using funding from the American Recovery and Reinvestment Act of 2009 for projects the NIH views as “Grand Opportunities” for major scientific progress. “The Grand Opportunities grants fund projects that promise to have a significant impact on a field of biomedical science,” said NIGMS Director Jeremy M. Berg. “By closing specific knowledge gaps, creating new technologies, or building community-wide resources, these awards will dramatically propel progress in key scientific fields.”

Several Anton machines are currently operational within the DESRES research lab, but the one to be installed at NRBSC will be the first outside of DESRES. Time allocations on NRBSC’s Anton machine will be made through a process of peer review. Although the NIH has supported MD-related research by individual scientists for many years, it has never before provided funds to make a supercomputing system available as a national resource.

While experimental methods such as X-ray crystallography can determine rigid molecular structures at near atomic resolution, MD simulations track atomic positions over the course of time. Changes in the shape of a biomolecule are often intimately related to its function, suggesting that atomic-level molecular dynamics simulations may ultimately play an important role in the design of therapeutic drugs. Because atomic-level MD simulations of proteins require an enormous number of calculations to simulate even a very short period of biological time, however, many of the most important biological phenomena have historically fallen outside the reach of even the most powerful general-purpose scientific supercomputers. Anton, however, has now run simulations extending for more than a millisecond of biological time — about 100 times longer than the longest previously published MD simulation.

CREATING NATIONAL CYBERINFRASTRUCTURE

The TeraGrid is the world's most comprehensive distributed cyberinfrastructure for open scientific research. As a major partner in this National Science Foundation program, PSC helps to shape the vision and progress of the TeraGrid.

PHOTO: TG

PSC staff whose work contributes to the TeraGrid include (l to r, seated) David Moses, PSC executive director; Laura McGinnis, PSC manager of education, outreach and training; Sergiu Sanielevici, PSC director of scientific applications and user support; J.Ray Scott, PSC director of systems & operations. (l to r) Matt Mathis, Chris Rapier, Shandra Williams, Brian Gill, Anjana Kar, Jenda Domaracki, Michael Lambert, Kathy Benninger, Phillip Blood, Chad Vizino, Rich Raymond, James Marsteller, Rob Light, Pallavi Ishwad, Tom Maiden, Ken Hackworth, Nathan Stone, Bryan Webb, Mahin Mahmoodi, Greg Foss, Ed Hanna, Elizabeth Albert, Brian Johanson, Robin Flaus-Scibeck, Kevin Sullivan, Jason Sommerfield, Dustin Sorge, Derek Simmel, Adam Fest, Ed Berger. (top rear: l to r) Ed Wozniak, John Urbanic, Andrew Adams, Robert Budden, Shawn Brown.

PSC and TeraGrid

PSC is actively involved in TeraGrid leadership. Scientific director Ralph Roskies oversees PSC contributions to the integrating efforts of the national Grid Infrastructure Group that guides TeraGrid. Co-scientific director Michael Levine is PSC’s representative to the TeraGrid Forum — TeraGrid’s principal decision-making group.

Other PSC staff with TeraGrid leadership roles include Sergiu Sanielevici, Area Director for User Support and Jim Marsteller, head of PSC’s security, who chairs the TeraGrid Security Working Group. Laura McGinnis plays a lead role in TeraGrid education, outreach and training (EOT) activities. PSC director of systems and operations, J. Ray Scott, leads the TeraGrid effort in Data Movement, and PSC director of strategic applications, Nick Nystrom, leads the TeraGrid Extreme Scalability Working Group, which fosters planning to meet the challenges of deploying extreme-scale resources into the TeraGrid.

PSC staff members serve on all of TeraGrid’s working groups.

© Pittsburgh Supercomputing Center, Carnegie Mellon University, University of Pittsburgh
300 S. Craig Street, Pittsburgh, PA 15213 Phone: 412.268.4960 Fax: 412.268.5832

This page last updated: May 18, 2012