CC* Integration-Small: Harnessing FABRIC for Scalable Human Genome Sequence Analysis

CC* Integration-Small:利用 FABRIC 进行可扩展的人类基因组序列分析

基本信息

  • 批准号:
    2201583
  • 负责人:
  • 金额:
    $ 50万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
    Standard Grant
  • 财政年份:
    2022
  • 资助国家:
    美国
  • 起止时间:
    2022-05-01 至 2024-07-31
  • 项目状态:
    已结题

项目摘要

Human genomes contain valuable information that can enable new ways of treating life-threatening diseases and improving health outcomes. However, human genomes are very large in size and require substantial computing, networking, and storage resources for processing and analysis. The goal of this project is to leverage FABRIC (https://fabric-testbed.net, an NSF-funded national research infrastructure) for efficient and secure processing and analysis of human genome sequences. Students will be involved in the research and outreach activities of the project. Software will be developed for broader use by the education and research community.This project will lead to a suite of new algorithms and techniques for efficient and secure processing and analysis of human genomes at scale using cluster computing technologies and cutting-edge, programmable hardware available on FABRIC. The research thrusts include (a) acceleration of variant calling pipelines using hardware accelerators and Big Data tools, (b) secure and efficient processing of genomes using advanced networking capabilities, and (c) a workload distribution scheme for combining the resources of FABRIC with CloudLab (https://cloudlab.us/, another NSF-funded testbed) for genome processing. Measurement data on FABRIC and CloudLab will be collected for further analysis.This project will advance the state of the art in scalable human genome sequence analysis, which is essential for the prevention and treatment of complex diseases like cancer as well as drug discovery. It will lead to an open source software for large-scale, cost-effective human genome sequence analysis using cutting-edge, everywhere programmable testbeds. The findings will be disseminated in the form of publications, software, datasets, and training materials. New coursework will be developed for computer science and informatics students. A summer camp will be conducted for high school students.The project website is hosted at https://github.com/MU-Data-Science/GAF. This repository will be maintained for 5 years after the completion of the project.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
人类基因组包含有价值的信息,可以使治疗危及生命的疾病和改善健康结果的新方法成为可能。然而,人类基因组的大小非常大,需要大量的计算、网络和存储资源来进行处理和分析。该项目的目标是利用FABRIC(https:fabric-testbed.net,NSF资助的国家研究基础设施)对人类基因组序列进行有效和安全的处理和分析。学生将参与该项目的研究和推广活动。将开发软件供教育和研究界更广泛使用,该项目将产生一套新的算法和技术,利用集群计算技术和FABRIC上现有的尖端可编程硬件,大规模地对人类基因组进行有效和安全的处理和分析。研究重点包括(a)使用硬件加速器和大数据工具加速变异调用管道,(B)使用先进的网络功能安全有效地处理基因组,以及(c)将FABRIC的资源与CloudLab(https://cloudlab.us/,另一个NSF资助的测试平台)结合起来进行基因组处理的工作负载分配方案。FABRIC和CloudLab的测量数据将被收集用于进一步分析。该项目将推进可扩展的人类基因组序列分析的最新技术,这对于预防和治疗癌症等复杂疾病以及药物发现至关重要。它将导致一个开源软件,用于大规模,具有成本效益的人类基因组序列分析,使用尖端的,无处不在的可编程测试平台。调查结果将以出版物、软件、数据集和培训材料的形式传播。将为计算机科学和信息学学生开发新的课程。将为高中生举办一个夏令营,该项目的网站设在https://github.com/MU-Data-Science/GAF。这个储存库将在项目完成后维持5年。这个奖项反映了NSF的法定使命,并通过使用基金会的知识价值和更广泛的影响审查标准进行评估,被认为值得支持。

项目成果

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Praveen Rao其他文献

Carvajal Syndrome - A Variant Of Arrhythmogenic Right Ventricular Cardiomyopathy
卡瓦哈尔综合征 - 致心律失常右室心肌病的一种变体
  • DOI:
    10.1016/j.cardfail.2022.03.314
  • 发表时间:
    2022-04-01
  • 期刊:
  • 影响因子:
    8.200
  • 作者:
    Justin Arunthamakun;Praveen Rao;Amit Alam
  • 通讯作者:
    Amit Alam
Claims data analysis of provider-to-provider tele-mentoring program impact on opioid prescribing in Missouri.
密苏里州提供者对提供者远程指导计划对阿片类药物处方影响的索赔数据分析。
  • DOI:
  • 发表时间:
    2024
  • 期刊:
  • 影响因子:
    0
  • 作者:
    Olabode Ogundele;Xing Song;Praveen Rao;Tracy Greever;Suzanne A Boren;Karen Edison;Douglas Burgess;Mirna Becevic
  • 通讯作者:
    Mirna Becevic
The Case for Designing Data-Intensive Cloud-Based Healthcare Applications
设计数据密集型基于云的医疗保健应用程序的案例
  • DOI:
  • 发表时间:
    2018
  • 期刊:
  • 影响因子:
    0
  • 作者:
    S. Bhagavan;K. Alsultan;Praveen Rao
  • 通讯作者:
    Praveen Rao
When The “Genes” No Longer Fit: An Unusual Presentation of LMNA-related Cardiomyopathy
  • DOI:
    10.1016/j.cardfail.2020.09.307
  • 发表时间:
    2020-10-01
  • 期刊:
  • 影响因子:
  • 作者:
    Justin Arunthamakun;Timothy Gong;Joshua Rutland;Matthew Wainwright;Dan Meyer;William C. Roberts;Praveen Rao;Amit Alam;Shelley Hall
  • 通讯作者:
    Shelley Hall
020 - Ventricular Arrhythmias before LVAD Do Not Increase Risk of Mortality or Rehospitalization
  • DOI:
    10.1016/j.cardfail.2016.06.037
  • 发表时间:
    2016-08-01
  • 期刊:
  • 影响因子:
  • 作者:
    Praveen Rao;David Raymer;Christopher Sparrow;Michael Nassif;Eric Novak;Daniel Cooper;Shane LaRue;Gregory Ewald;Justin Vader
  • 通讯作者:
    Justin Vader

Praveen Rao的其他文献

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{{ truncateString('Praveen Rao', 18)}}的其他基金

I-Corps: Scalable Storage of Whole Slide Images and Fast Retrieval of Tiles for Next-Generation Image Analytics
I-Corps:整个幻灯片图像的可扩展存储和用于下一代图像分析的图块的快速检索
  • 批准号:
    2024429
  • 财政年份:
    2020
  • 资助金额:
    $ 50万
  • 项目类别:
    Standard Grant
RAPID: Democratizing Genome Sequence Analysis for COVID-19 Using CloudLab
RAPID:使用 CloudLab 实现 COVID-19 基因组序列分析的大众化
  • 批准号:
    2034247
  • 财政年份:
    2020
  • 资助金额:
    $ 50万
  • 项目类别:
    Standard Grant
I-Corps: Scalable Storage of Whole Slide Images and Fast Retrieval of Tiles for Next-Generation Image Analytics
I-Corps:整个幻灯片图像的可扩展存储和用于下一代图像分析的图块的快速检索
  • 批准号:
    1841752
  • 财政年份:
    2018
  • 资助金额:
    $ 50万
  • 项目类别:
    Standard Grant
I-Corps: Scalable Knowledge Management for Risk Analysis in Finance
I-Corps:用于金融风险分析的可扩展知识管理
  • 批准号:
    1620023
  • 财政年份:
    2016
  • 资助金额:
    $ 50万
  • 项目类别:
    Standard Grant
III: Small: Scalable RDF Query Processing Using a Cloud Infrastructure
III:小型:使用云基础设施进行可扩展的 RDF 查询处理
  • 批准号:
    1115871
  • 财政年份:
    2011
  • 资助金额:
    $ 50万
  • 项目类别:
    Continuing Grant

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