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SUPERCOMPUTING

New Equipment Advances Frontiers of Computational Biology

Blue Gene supercomputer from IBM
Rensselaer researchers have received a powerful new Blue Gene supercomputer from IBM. Awarded under the company’s Shared University Research (SUR) program, 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 Rensselaer’s new Computational Center for Nanotechnology Innovations.

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. Johnson ’37 and Elisabeth C. Johnson 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. This $2.23 million gift complements the $100 million partnership between Rensselaer, IBM, and New York state to create one of the world’s most powerful university-based supercomputing centers.

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