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

描述(由申请人提供)：我们建议获得并操作一台82teraflop/秒的Cray XT5超级计算机，以及相关的1800万亿字节存储系统，供芝加哥大学和其他地方的研究人员应用于生物医学研究前沿的一系列具有挑战性的研究问题。与Cray，Inc.的积极合作协议、芝加哥大学对运营和应用程序支持的大量支持以及经验丰富的技术人员使我们能够提出一个具有学术生物医学领域前所未有的能力的系统。一组著名的生物医学研究小组将应用该系统：阐明离子通道和Src酪氨酸激酶的生物学功能和结合特异性；大规模探索RNA-蛋白质相互作用，寻求对细胞网络和核糖核蛋白复合体功能的新见解；用于研究电和热损伤的毫米分辨率全身模型，以得出对主要电创伤的最有效临床治疗的新见解；病原体转录调控网络的特征；离子通道功能的定量预测模拟，以及具有新特性的通道的设计；高通量方法，确定癌症治疗的新的microRNA相关靶点；多对多的大脑结构与人类行为的映射，以获得关于从神经损伤中恢复的新假设和治疗选择；为包括乳腺癌、肺癌、结肠癌、前列腺癌和心脏病在内的各种疾病状态开发基于图像的生物标记物；识别广泛的遗传性疾病的遗传特征；以及大规模文本挖掘，用于临床发现以及科学社区中知识创造和传播的表征。除了为NIH资助的主要用户的研究项目提供直接支持外，Cray超级计算机还将促进新计算方法的开发和传播，并帮助培训和激励年轻的研究人员、博士后和学生使用这些方法进行基础、翻译和临床研究。Cray系统使用创新的冷却技术，显著降低了电力需求。该系统的收购和应用将为克雷大学、芝加哥大学和其他机构提供就业机会，并将引发新的生物医学超级计算应用。 与公共健康相关：我们提议购买并运营一台82万亿次/秒的Cray XT5超级计算机，外加一个相关的1800万亿字节存储系统，芝加哥大学和其他地方的研究人员将应用于生物医学研究前沿的一系列具有挑战性的研究问题，并有望为公众健康带来好处。与Cray，Inc.的积极合作协议、芝加哥大学对运营和应用程序支持的大量支持以及经验丰富的技术人员使我们能够提出一个具有学术生物医学领域前所未有的能力的系统。

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.