XPS: FULL: DSD: Collaborative Research: Parallelizing and Accelerating Metagenomic Applications

XPS:完整:DSD:协作研究:并行化和加速宏基因组应用

基本信息

  • 批准号:
    1533933
  • 负责人:
  • 金额:
    $ 54.8万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
    Standard Grant
  • 财政年份:
    2015
  • 资助国家:
    美国
  • 起止时间:
    2015-09-01 至 2020-08-31
  • 项目状态:
    已结题

项目摘要

The importance of metagenomics arises from the fact that over 99% ofthe species yet to be discovered are resistant to cultivation. Unlikesingle genome sequencing, assembly of a metagenome is intractable andis in large part, an unsolved mystery. Moreover, the advent of highthroughput sequencing is fueling rapid generation of enormousmetagenomic datasets. There is no available sequenced genome for amajority of the species. There is a need to determine the number of species ina metagenomic dataset as well as the abundance of each of thesespecies. The key steps (Assembly and Clustering) in the metagenomicsanalysis algorithms are compute-intensive, while the sheer amount ofdata the algorithms operate on is staggering. The most promising wayto tackle the computational challenges is to build special purposehardware, dedicated solely to suitable algorithms.The main objective of this project is to develop a range of flexible,affordable, parallel, fast hardware-accelerated bioinformaticssolutions, using GPGPU, FPGA, and ASIC, for metagenomic analytics to provide an alternative toexpensive computer clusters. Specifically, hardware solutions formetagenomic clustering and assembly will be developed. Severalacceleration methodologies, including parallel software mapping andspecial hardware design, are proposed to explore the parallelisminside the applications and to improve the data access bandwidth inthe hardware running bioinformatics applications. The ideas proposedin this work will be evaluated in a multi-pronged manner using acombination of simulation, emulation and prototyping efforts. Further,the PIs will use a combination of commercial tools, collaboratorresources and existing internal tools. The research will be conducted in collaboration with industrial partners. Through closecollaboration with several industry partners, direct transfer of manyideas to industry is enabled. The outcome of this research will,therefore, have a direct impact on future bioinformatics applicationsolutions. This project will involve graduate and undergraduatestudents in all aspects of the research. The PIs will activelyintegrate the research results from this project into the graduate andundergraduate curricula, and develop new interdisciplinary courses onbioinformatics and computer architecture to train the next generationwork-force. Finally, the tools and techniques developed in thisresearch will be made available through web-sites for use by othereducators, researchers, and industry practitioners.
元基因组学的重要性源于这样一个事实,即超过99%的尚未被发现的物种对栽培具有抗性。与单一的基因组测序不同,元基因组的组装是棘手的,在很大程度上是一个未解的谜。此外,高通量测序的出现正在推动巨大的元基因组数据集的快速生成。该物种的大多数还没有可用的测序基因组。有必要确定元基因组数据集中的物种数量以及每个物种的丰度。元名词分析算法中的关键步骤(组装和聚类)是计算密集型的,而算法处理的数据量是惊人的。解决计算挑战的最有前途的方法是构建专门用于合适算法的专用硬件。该项目的主要目标是开发一系列灵活的、负担得起的、并行的、快速硬件加速的生物信息学解决方案,使用GPGPU、FPGA和ASIC,用于元基因组分析,提供昂贵的计算机集群的替代方案。具体地说,将开发经济集群和组装的硬件解决方案。提出了几种加速方法,包括并行软件映射和特殊硬件设计,以探索应用程序的并行性,并提高运行生物信息学应用程序的硬件的数据访问带宽。这项工作中提出的想法将采用模拟、仿真和原型工作相结合的多管齐下的方式进行评估。此外,绩效指标将综合使用商业工具、协作人资源和现有的内部工具。这项研究将与行业合作伙伴合作进行。通过与几个行业合作伙伴的密切合作,许多想法能够直接转移到行业中。因此,这项研究的结果将对未来的生物信息学应用解决方案产生直接影响。这个项目将让研究生和本科生参与研究的各个方面。专业人员将积极将这一项目的研究成果纳入研究生和本科生课程,并开发新的生物信息学和计算机体系结构跨学科课程,以培训下一代劳动力。最后,这项研究中开发的工具和技术将通过网站提供,供其他研究人员、研究人员和行业从业者使用。

项目成果

期刊论文数量(1)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
MEDAL: Scalable DIMM based Near Data Processing Accelerator for DNA Seeding Algorithm
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Yuan Xie其他文献

GENOMIC CHARACTERISTICS OF ADHESION MOLECULES IN PATIENTS WITH SYMPTOMATIC PULMONARY EMBOLISM
有症状肺栓塞患者粘附分子的基因组特征
  • DOI:
    10.1136/heartjnl-2012-302920y.8
  • 发表时间:
    2012
  • 期刊:
  • 影响因子:
    5.7
  • 作者:
    Yuan Xie;Zhu Gong;Qianglin Duan;Qiang Wang;Haoming Song;A. Liang;Hao Wang;Wen;Lemin Wang
  • 通讯作者:
    Lemin Wang
The Value of Big N Target Auditors in Corporate Takeovers
Big N Target 审计师在公司收购中的价值
  • DOI:
    10.2139/ssrn.1465151
  • 发表时间:
    2013
  • 期刊:
  • 影响因子:
    0
  • 作者:
    Yuan Xie;Han Yi;Yinqi Zhang
  • 通讯作者:
    Yinqi Zhang
Curcumin restrains hepatic glucose production by blocking cAMP/PKA signaling and reducing acetyl CoA accumulation in high-fat diet (HFD)-fed mice
姜黄素通过阻断 cAMP/PKA 信号传导并减少高脂饮食 (HFD) 喂养的小鼠中乙酰辅酶 A 的积累来抑制肝葡萄糖的产生
  • DOI:
    10.1016/j.mce.2018.02.018
  • 发表时间:
    2018-10
  • 期刊:
  • 影响因子:
    4.1
  • 作者:
    Zixia Wang;Dan Xu;Linlin She;Yirui Zhang;Qingli Wei;Jiye Aa;Guangji Wang;Baolin Liu;Yuan Xie
  • 通讯作者:
    Yuan Xie
Association Between Arterial Blood Gas Variation and Intraocular Pressure in Healthy Subjects Exposed to Acute Short-Term Hypobaric Hypoxia
暴露于急性短期低压缺氧的健康受试者的动脉血气变化与眼压之间的关联
  • DOI:
    10.1167/tvst.8.6.22
  • 发表时间:
    2019
  • 期刊:
  • 影响因子:
    3
  • 作者:
    Yuan Xie;Yiquan Yang;Ying Han;Di;Yunxiao Sun;Xin;Anh Nguyen;Yihan Chen;Jiaxin Tian;Qing Zhang;C. Xin;K. Cao;Huai;Xiaofang Liu;Guozhong Wang;Ningli Wang
  • 通讯作者:
    Ningli Wang
Heterogeneous spheroids with tunable interior morphologies by dropletbased microfluidics
通过基于液滴的微流体技术制备具有可调内部形态的异质球体
  • DOI:
    10.1088/1758-5090/ac5e12
  • 发表时间:
    2022
  • 期刊:
  • 影响因子:
    9
  • 作者:
    Zhen Zhan;Zeyang Liu;Haochen Nan;Jianjie Li;Yuan Xie;Chengzhi Hu
  • 通讯作者:
    Chengzhi Hu

Yuan Xie的其他文献

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{{ truncateString('Yuan Xie', 18)}}的其他基金

SHF:SMALL:Collaborative Research: Exploring Nonvolatility of Emerging Memory Technologies for Architecture Design
SHF:SMALL:合作研究:探索新兴内存技术的非易失性以用于架构设计
  • 批准号:
    1816833
  • 财政年份:
    2018
  • 资助金额:
    $ 54.8万
  • 项目类别:
    Standard Grant
SPX: Collaborative Research: Ula! - An Integrated Deep Neural Network (DNN) Acceleration Framework with Enhanced Unsupervised Learning Capability
SPX:合作研究:乌拉!
  • 批准号:
    1725447
  • 财政年份:
    2017
  • 资助金额:
    $ 54.8万
  • 项目类别:
    Standard Grant
II-New: RICARDO: Research Infrastructure for Circuit and Architecture Design with Emerging Technologies
II-新:RICARDO:利用新兴技术进行电路和架构设计的研究基础设施
  • 批准号:
    1730309
  • 财政年份:
    2017
  • 资助金额:
    $ 54.8万
  • 项目类别:
    Standard Grant
SHF: Medium: ASKS - Architecture Support for darK Silicon
SHF:中:ASKS - 对 darK Silicon 的架构支持
  • 批准号:
    1409798
  • 财政年份:
    2014
  • 资助金额:
    $ 54.8万
  • 项目类别:
    Standard Grant
SHF: Small: Collaborative Research: STEMS: STatistic Emerging Memory Simulator
SHF:小型:协作研究:STEMS:统计新兴内存模拟器
  • 批准号:
    1461698
  • 财政年份:
    2014
  • 资助金额:
    $ 54.8万
  • 项目类别:
    Standard Grant
SHF: Medium: ASKS - Architecture Support for darK Silicon
SHF:中:ASKS - 对 darK Silicon 的架构支持
  • 批准号:
    1500848
  • 财政年份:
    2014
  • 资助金额:
    $ 54.8万
  • 项目类别:
    Standard Grant
SHF: Small: Collaborative Research: STEMS: STatistic Emerging Memory Simulator
SHF:小型:协作研究:STEMS:统计新兴内存模拟器
  • 批准号:
    1218867
  • 财政年份:
    2012
  • 资助金额:
    $ 54.8万
  • 项目类别:
    Standard Grant
ADAMS: Architecture and Design Automation for 3D Multi-core Systems
ADAMS:3D 多核系统的架构和设计自动化
  • 批准号:
    0903432
  • 财政年份:
    2009
  • 资助金额:
    $ 54.8万
  • 项目类别:
    Standard Grant
CSR: Medium: Collaborative Research: Providing Predictable Timing for Task Migration in Embedded Multi-Core Environments (TiME-ME)
CSR:中:协作研究:为嵌入式多核环境中的任务迁移提供可预测的时序 (TiME-ME)
  • 批准号:
    0905365
  • 财政年份:
    2009
  • 资助金额:
    $ 54.8万
  • 项目类别:
    Continuing Grant
Student Travel Support for International Symposium on High-Performance Computer Architecture (HPCA) 2010
2010 年高性能计算机架构 (HPCA) 国际研讨会的学生旅行支持
  • 批准号:
    0952841
  • 财政年份:
    2009
  • 资助金额:
    $ 54.8万
  • 项目类别:
    Standard Grant

相似国自然基金

钴基Full-Heusler合金的掺杂效应和薄膜噪声特性研究
  • 批准号:
    51871067
  • 批准年份:
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  • 资助金额:
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XPS: FULL: DSD: Collaborative Research: Parallelizing and Accelerating Metagenomic Applications
XPS:完整:DSD:协作研究:并行化和加速宏基因组应用
  • 批准号:
    1720635
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XPS: FULL: DSD: Collaborative Research: Parallelizing and Accelerating Metagenomic Applications
XPS:完整:DSD:协作研究:并行化和加速宏基因组应用
  • 批准号:
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    $ 54.8万
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    1439052
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    2014
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    $ 54.8万
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XPS: FULL: DSD: Collaborative Research: Rapid Prototyping HPC Environment for Deep Learning
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