Supercomputing equipment to advance the frontiers of computational biology

December 07, 2006

Troy, N.Y. -- Researchers at Rensselaer Polytechnic Institute will continue to advance the frontiers of computational science with the help of IBM's Blue Gene supercomputer. Awarded under IBM's Shared University Research (SUR) program, this Blue Gene will complement the $100 million partnership between Rensselaer, IBM, and New York state to create one of the world's most powerful university-based supercomputing centers.

The equipment will provide a resource for scientists to gain experience with the Blue Gene computing environment, while also supporting a project to develop new simulation technologies for understanding biological systems. The work will help researchers develop algorithms and software that run efficiently on Blue Gene technology, which is a key part of the new Computational Center for Nanotechnology Innovations (CCNI).

This $2.23 million gift of IBM equipment counts toward the $1.4 billion Renaissance at Rensselaer campaign.

"This award further advances the strong partnership between IBM and Rensselaer to develop a leading-edge, high-performance computational capability," said Rensselaer President Shirley Ann Jackson. "It will allow our faculty and students to take the lead in research that will enable key nanotechnology innovations in the fields of energy, biotechnology, arts, and medicine."

As biology becomes a more quantitative field, researchers need new simulation technologies to understand how proteins, DNA, and other biological systems behave at the molecular level, according to the Rensselaer research team. The new SUR award is designed to help develop simulations for prototyping medical devices in "virtual patients," with potential applications in targeted drug delivery systems such as drug eluting stents, transdermal patches, and inhalers.

To be successful, these simulations must run efficiently and effectively on the latest generation of high-performance computing equipment. The project will help researchers develop critical computational biology tools that operate on the Blue Gene system, with the goal of making these available to a broad community of users.

The project's principal investigators at Rensselaer are Angel Garcia, senior constellation chaired professor in biocomputation and bioinformatics; Mark Shephard, the Samuel A. and Elisabeth C. Johnson Jr. Professor of Engineering and director of the Scientific Computation Research Center; Shekhar Garde, the Elaine and Jack S. Parker Career Development Professor of Chemical and Biological Engineering; and Kenneth Jansen, associate professor of mechanical, aerospace, and nuclear engineering.

The new Blue Gene system consists of a single rack with 1,024 dual processor compute nodes, 32 I/O nodes, a service node, a front-end node, and multiple terabytes of SAN-based disk storage.

Announced in May 2006, the Computational Center for Nanotechnology Innovations (CCNI) is a $100 million partnership between Rensselaer, IBM, and New York state to create one of the world's most powerful university-based supercomputing centers, and a top supercomputing center of any kind in the world. The center is designed to help continue the impressive advances in shrinking device dimensions seen by electronics manufacturers, and to enable key nanotechnology innovations in the fields of energy, biotechnology, arts, and medicine. Learn more at the CCNI Web site: http://rpi.edu/research/ccni/index.html.
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About the Campaign
The $1.4 billion Renaissance at Rensselaer: The Campaign for Rensselaer Polytechnic Institute, launched in 2004, fuels the Institute's strategic Rensselaer Plan, and supports groundbreaking interdisciplinary programs which have at their core the technologies driving innovations in the 21st century: biotechnology, nanotechnology, computational information technology, energy and the environment and experimental media and the arts. The campaign aims to build the Institute unrestricted endowment, and also seeks funds for endowed scholarships and fellowships, faculty positions, curriculum support, student life programs, and athletic programs and facilities. To date, the effort has raised more than $1.2 billion.

About Rensselaer
Rensselaer Polytechnic Institute, founded in 1824, is the nation's oldest technological university. The university offers bachelor's, master's, and doctoral degrees in engineering, the sciences, information technology, architecture, management, and the humanities and social sciences. Institute programs serve undergraduates, graduate students, and working professionals around the world. Rensselaer faculty are known for pre-eminence in research conducted in a wide range of fields, with particular emphasis in biotechnology, nanotechnology, information technology, and the media arts and technology. The Institute is well known for its success in the transfer of technology from the laboratory to the marketplace so that new discoveries and inventions benefit human life, protect the environment, and strengthen economic development.

Rensselaer Polytechnic Institute

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