Beagle: A Supercomputer for Computational Biology, Simulation, and Data Analysis

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DESCRIPTION (provided by applicant): We propose to acquire and operate an 82 Teraflop/sec Cray XT5 supercomputer, plus associated 1800 terabyte storage system, to be applied by researchers at the University of Chicago and elsewhere to a set of challenging research questions at the frontiers of biomedical research. An aggressive partnership agreement with Cray, Inc., substantial support from the University of Chicago for operations and application support, and an extremely experienced technical staff allows us to propose a system with capabilities unprecedented in academic biomedicine. A set of prominent biomedical research groups will apply the system to: elucidation of the biological function and binding specificity for ion channels and Src tyrosine kinases; large-scale explorations of RNA-protein interactomes, seeking new insights into cellular networks and the function of ribonucleoprotein complexes; millimeter-resolution, whole-body model for studies of electrical and thermal injury, to derive new insights into the most effective clinical management of major electrical trauma; characterization of transcriptional regulatory networks of pathogenic organisms; quantitatively predictive simulation of ion channel function, and the design of channels with new properties; high-throughput methods for identifying novel microRNA-related targets for cancer therapy; many-to-many mappings of brain structure to human behaviors, to obtain new hypotheses about recovery from neurology injury, and treatment options; development of image-based biomarkers for various disease states including breast, lung, colon, and prostate cancers, and cardiac disease; the identification of genetic signatures for a wide array of inherited disorders; and large-scale text mining for both clinical discovery and characterization of knowledge creation and propagation in scientific communities. In addition to providing direct support for the NIH-funded research programs of its primary users, the Cray supercomputer will also spur development and dissemination of new computational methods, and help train and inspire young investigators, postdocs, and students in the use of those methods for basic, translational, and clinical research. The Cray system uses innovative cooling and reduces power needs significantly. The acquisition and application of this system will provide employment at Cray, the University of Chicago, and other institutions, and will spark new biomedical supercomputing applications. PUBLIC HEALTH RELEVANCE: We propose to acquire and operate a 82 Teraflop/sec Cray XT5 supercomputer, plus an associated 1800 terabyte storage system, to be applied by researchers at the University of Chicago and elsewhere to a set of challenging research questions at the frontiers of biomedical research and with promising public health benefits. An aggressive partnership agreement with Cray, Inc., substantial support from the University of Chicago for operations and application support, and an extremely experienced technical staff allows us to propose a system with capabilities unprecedented in academic biomedicine.