Indiana Genomics initiative to benefit from new IBM supercomputer at Indiana University

Bloomington 17 October 2001Indiana University (IU) has acquired the largest university-owned supercomputer in the United States. The IBM SP supercomputer, which has been expanded to triple the university's previous computing capacity, will support IU researchers in a broad range of areas, such as life sciences. It will also serve as the backbone for a planned genomics research collaboration with IBM. The IU Teraflop SP will be used to search for Single Nucleotide Polymorphisms (SNPs) and to analyse clinical data en route to unravelling the relationships between genes and cancer.

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The Indiana University Teraflop SP can perform a trillion mathematical operations per second. It will be tightly connected to IU's massive data storage system that is capable of holding hundreds of trillions of bytes of data. This processing capability is meaningful only when harnessed to do important work. The Teraflop SP will enhance existing research programmes and make possible new research in many disciplines, including the medical sciences. As the human genome becomes increasingly well understood, one of the critical issues will be identifying what are called SNPs, places in the genome where different people display different genetic information. Here scientists expect to find some of the keys to understanding human genetic diseases.

The supercomputer is part of the information technology (IT) infrastructure needed to support the Indiana Genomics (INGEN) initiative. This initiative was funded by a major grant from the Lilly Endowment. "Indiana University's teraflop system lays the groundwork for IU to become a leading institution for genomic research", commented Irving Wladawsky-Berger, IBM vice president, Technology and Strategy, IBM Server Group. IU President Myles Brand added: "Our faculty and staff will participate in developing state-of-the-art IT tools and applications for life sciences research, including genomics, which will help us discover new ways of preventing and treating human disease."

IU is uniquely positioned to advance life sciences research through INGEN, a collaboration of scientists and physicians who will study the information that makes up the human genome and its function in human health. INGEN combines the strength of the IU School of Medicine, research programmes in biology and chemistry, and IU's leadership in high performance computing. IBM is the primary provider of supercomputing technology for INGEN. "The sequencing of the human genome launched a new era of research in the life sciences", stated Michael McRobbie, IU vice president for information technology and chief information officer. "The unprecedented amounts of genomic data require advanced computational resources. The teraflop supercomputer is a key first component of INGEN's IT infrastructure and will provide a major boost to scientific progress at IU in this area."

The expanded IBM SP supercomputer will provide the computational and data management power required to make advances in many important areas of genomic science. Biomedical and biological sciences present a tremendous wealth of data. Supercomputers are required to analyse these massive data stores and to create the linkages among different types of data, for example, clinical records and genetic information, that will enable new breakthroughs in health care. Many important questions in science and medicine involve answering the question: What are the evolutionary relationships among a group of organisms? It is now possible to infer the evolutionary relationships among organisms based on DNA sequences.

However, this process takes tremendous amounts of computation. For example, analysing the evolutionary relationships of 100 animals on one microcomputer might take as long as five years. Indiana University is collaborating with researchers at other institutions to create a parallel supercomputer version of fastDNAml, a popular package for inferring evolutionary relationships. fastDNAml has been used at Indiana University to better understand the evolutionary origins of the Microsporidia, an economically and medically important group of parasites. Better understanding of evolutionary origins of these disease-causing organisms will shed light on better methods for treating the diseases which Microsporidia cause.

Indiana University has acquired one of IBM's newest, advanced digital displays, which is the IBM T220, a 22.2-inch diagonal with 9.2-million pixels, yielding a resolution of 204 dots per inch (DPI). This resolution is so fine that certain details are visible only with a magnifying glass. Two types of images are demonstrated: satellite images and medical images. Biomedical images show the utility these advanced displays offer to biomedical researchers and clinicians. IU's extensive information technology environment has advanced visualisation laboratories that enable scientists to visualise, analyse and store vast amounts of data and information. Indiana University's two main departments of Computer Science include internationally recognised experts in high performance computing and visualisation.

"The transformation of life sciences research has brought numerous challenges to the scientific community", stated George Strawn, acting assistant director for computer and information science and engineering at the National Science Foundation (NSF). "NSF recognises that the data- and compute-intensive nature of the research requires instruments that US scientists working nationally and internationally can share. IU, in collaboration with IBM, is working to meet these challenges and to make advanced computational resources remotely accessible to the broader research community."


Leslie Versweyveld

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