Supercomputing Equipment to Advance Computational Biology

Researchers at Rensselaer Polytechnic Institute said they 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.

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

IBM Blue Gene is a family of supercomputers optimized for bandwidth, scalability and the ability to handle large amounts of data, designed for scientific applications such as biological research, weather forecasting, simulations and modeling. The full Blue Gene/L machine was designed and built in collaboration with the Department of Energy's NNSA/Lawrence Livermore National Laboratory in California, and has a peak speed of 360 Teraflops.

The new Blue Gene system consists of a single rack with 1024 dual processor compute nodes, 32 I/O nodes, a service node, a front-end node and multiple terabytes of SAN-based disk storage. 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 at RPI.

Rensselaer President Shirley Ann Jackson said, “This award further advances the strong partnership between IBM and Rensselaer to develop a leading-edge, high-performance computational capability. 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, RPI said. 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 wide variety of users.

The project’s principal investigators at RPI are Angel Garcia, a professor in biocomputation and bioinformatics; Mark Shephard, a professor of engineering and director of the Scientific Computation Research Center; Shekhar Garde, professor of chemical and biological engineering; and Kenneth Jansen, associate professor of mechanical, aerospace and nuclear engineering.

For more information, visit: rpi.edu/research/ccni/index.html