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

Beagle：用于计算生物学、模拟和数据分析的超级计算机

基本信息

批准号：
7840313
负责人：
Ian Foster
金额：
$ 696.74万
依托单位：
UNIVERSITY OF CHICAGO
依托单位国家：
美国
项目类别：
财政年份：
2010
资助国家：
美国
起止时间：
2010-09-14 至 2011-09-13
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7840313
关键词：
Agreement Behavior Binding Biological Markers Biological Process Biomedical Research Brain Mapping Breast Chicago Clinical Clinical Management Clinical Research Colon Communities Complex Computational Biology Computing Methodologies Data Analyses Development Disease Employment Funding Genetic Health Benefit Heart Diseases Human Image Inborn Genetic Diseases Injury Institution Ion Channel Knowledge Lung Malignant neoplasm of prostate Methods Neurology Organism Property Proteins Public Health Recovery Research Research Personnel Resolution Ribonucleoproteins Specificity Structure Students Study models Supercomputing System Training Trauma Universities base cancer therapy design experience frontier heat injury innovation insight millimeter novel operation programs public health relevance simulation src-Family Kinases supercomputer text searching

项目摘要

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.

描述（由申请人提供）：我们建议购买并运行一台 82 Teraflop/sec Cray XT5 超级计算机，以及相关的 1800 TB 存储系统，供芝加哥大学和其他地方的研究人员应用于解决一系列具有挑战性的研究问题。生物医学研究的前沿。与 Cray, Inc. 签订的积极合作协议、芝加哥大学对运营和应用支持的大力支持以及经验丰富的技术人员，使我们能够提出一个在学术生物医学领域具有前所未有能力的系统。一组著名的生物医学研究小组将将该系统应用于：阐明离子通道和 Src 酪氨酸激酶的生物功能和结合特异性；对RNA-蛋白质相互作用组的大规模探索，寻求对细胞网络和核糖核蛋白复合物功能的新见解；用于研究电损伤和热损伤的毫米分辨率全身模型，以获得对重大电损伤最有效的临床管理的新见解；病原生物转录调控网络的表征；离子通道功能的定量预测模拟，以及具有新性能的通道的设计；用于识别癌症治疗的新型 microRNA 相关靶标的高通量方法；大脑结构与人类行为的多对多映射，以获得有关神经损伤恢复和治疗选择的新假设；开发针对各种疾病状态的基于图像的生物标志物，包括乳腺癌、肺癌、结肠癌、前列腺癌以及心脏病；鉴定多种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界知识创建和传播的表征。除了为其主要用户的 NIH 资助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研究人员、博士后和学生使用这些方法用于基础、转化和临床研究。 Cray 系统采用创新的冷却技术，可显着降低电力需求。该系统的收购和应用将为克雷、芝加哥大学和其他机构提供就业机会，并将激发新的生物医学超级计算应用。公共健康相关性：我们建议购买并运行一台每秒 82 Teraflop 的 Cray XT5 超级计算机，以及一个相关的 1800 TB 存储系统，芝加哥大学和其他地方的研究人员将其应用于解决一系列具有挑战性的前沿研究问题。生物医学研究和具有前景的公共健康益处。与 Cray, Inc. 签订的积极合作协议、芝加哥大学对运营和应用支持的大力支持以及经验丰富的技术人员，使我们能够提出一个在学术生物医学领域具有前所未有能力的系统。

项目成果

期刊论文数量（11）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Dynamic mechanisms of cell rigidity sensing: insights from a computational model of actomyosin networks.

DOI：
10.1371/journal.pone.0049174
发表时间：
2012
期刊：
PloS one
影响因子：
3.7
作者：
Borau C;Kim T;Bidone T;García-Aznar JM;Kamm RD
通讯作者：
Kamm RD

Laboratory evidence of dynamo amplification of magnetic fields in a turbulent plasma.

DOI：
10.1038/s41467-018-02953-2
发表时间：
2018-02-09
期刊：
Nature communications
影响因子：
16.6
作者：
Tzeferacos P;Rigby A;Bott AFA;Bell AR;Bingham R;Casner A;Cattaneo F;Churazov EM;Emig J;Fiuza F;Forest CB;Foster J;Graziani C;Katz J;Koenig M;Li CK;Meinecke J;Petrasso R;Park HS;Remington BA;Ross JS;Ryu D;Ryutov D;White TG;Reville B;Miniati F;Schekochihin AA;Lamb DQ;Froula DH;Gregori G
通讯作者：
Gregori G

Efficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression.