CSC News

March 01, 2007

Heber Receives Funding to Develop Bioinformatics Computing Cluster

Dr. Steffen Heber has been awarded $227,029 by the NC Biotechnology Center to fund his research proposal titled “A Bioinformatics Computing Cluster for NC State University.” 
The award will run from February 1, 2007 through January 31, 2008.
Research Abstract – The Bioinformatics Research Center (BRC) at NC State University is one of the world's premier centers for education and research in bioinformatics.  Established by the Board of Governors of the University of North Carolina System in 2000, the BRC is located on NC State University's Centennial Campus in Raleigh. BRC research focuses on the development of new computational and statistical tools for the analysis and interpretation of genomic data. More than 40 faculty in the mathematical, biological, and computer sciences are affiliated with the bioinformatics program. The BRC is also dedicated to providing outstanding educational and training opportunities for graduate students and genomic scientists. The BRC offers graduate programs in bioinformatics and statistical genetics. At the moment, more than 80 students are registered in these programs.
A major impediment for the BRC is the lack of computational equipment. Microarray and protein mass spectrometry data are growing steadily, and computationally intensive techniques like Monte Carlo simulations and whole genome analyses require more and more computer power. Although the university [] and the region [] have considerable high-performance computational resources, these resources are often geared to purely academic use and are difficult or impossible to customize for the diverse requirements of our bioinformatics applications. This conflicts with the increasing and continuously changing computational needs resulting from the BRC's interdisciplinary nature and its various industry connections. The BRC's own computing resources are outdated and insufficient for the large number of affiliated researchers. The need for computation by individual researcher and individual research groups is highly variable over time. Sometimes, a researcher may need to simultaneously run many demanding jobs. At other times, the researcher might have little need for computation. This variability of computing needs over time suggests that the most sensible strategy for BRC-affiliated researchers is to share computing resources. Computing is central to bioinformatics and it is essential that the BRC has access to adequate computing. In short, additional computer resources are an absolute necessity for the BRC to remain competitive as a statewide biotechnology center.
This proposal requests funds for a 54 dual-Xeon compute node Linux cluster in order to enhance the computational resources of the BRC, and to enter into an HPC partnership with the NC State Information Technology Division (ITD). The BRC purchases HPC hardware (compute blades and/or storage) and any specialized software licenses. NC State ITD provides space, an option to combine the purchased computing power with the one available by the general HPC program, and the system administration and support. In return for services provided by ITD, when computing resources are not being used, the server(s) are available to the general NC State HPC cluster user community. This partnership will leverage the proposed cluster investment in two ways: first, while remaining in complete control of the purchased computers, BRC faculty will gain access to the HPC resources - currently more than 400 blade processors. Second, by having a shared, ITD housed and administered computing resource, BRC faculties will not have to waste space and funds to maintain their own personal systems. This is especially important since many of the BRC associated faculty are starting investigators with small to medium sized groups. If necessary in the future, the proposed cluster could be expanded easily by purchasing new nodes.
The proposed Linux cluster in conjunction with ITD's Faculty HPC Partnership Program will considerably improve our ability to advance in research, and it will increase our competitive ability to obtain federal funding, to attract new faculty, as well as to facilitate cross collaborative efforts with other triangle universities and companies by leveraging grid technology. It will strengthen the position of the BRC as a statewide Bioinformatic resource, and a center for statistical data analysis.

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