Collaborative Research: Updating iVirus - the CyVerse-powered analytical toolkit for viruses of microbes

协作研究:更新 iVirus - CyVerse 支持的微生物病毒分析工具包

基本信息

  • 批准号:
    2149505
  • 负责人:
  • 金额:
    $ 99.96万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
    Continuing Grant
  • 财政年份:
    2022
  • 资助国家:
    美国
  • 起止时间:
    2022-09-15 至 2025-08-31
  • 项目状态:
    未结题

项目摘要

Microbes are now recognized as fundamental to diverse ecosystem processes, including oceanic biogeochemical cycling, the seeding and maintenance of soil fertility and function, and modulating animal and plant microbiota between healthy and dysbiotic states. However, viruses that infect these microbes are increasingly recognized for strong ecosystem relevance through killing, gene flow, and metabolic reprogramming. Thus, more and more researchers ask ‘how are viruses affecting my system?’. This has led to diversity catalogs exploding and the study of virus-infected cells, or virocells, as another window into ecosystem impacts. At the root of these ecosystem- to planetary-scale advances are big data (i.e., Next Generation Sequencing) and our ability to make sense of it through scalable storage, searching, sharing, and analytical capabilities. These capabilities are enabled by cyberinfrastructures that empower biologists to handle data without expert programmatic knowledge and hardware maintenance concerns. Over the last decade, the number and complexity of microbial analysis platforms have steadily increased alongside sequencing data accumulating in public data repositories. While such platforms are broadly empowering biologists to make the most of big data, virus-focused tools are virtually non-existent across these platforms, which greatly limits virome and microbiome science. iVirus is an NSF-funded ecosystem of apps and resources that represent the go-to virus-focused analytical platform and it has been democratized through training workshops and webinars, publications, and public presentations to establish a large, active, and growing user-base. Through these venues, new capabilities needs have been identified. This award seeks to fill these needs by organizing virus sequence space to create reference genome and taxonomic resources; augmenting the predominantly double-stranded DNA virus toolkit with new tools for studying single-stranded DNA and all RNA viruses; improving analyses for studying virus-infected cells (virocells); and developing new long-read viromics analytics. The iVirus user-base will be broadened through extensive training, outreach, and iVirus web portal improvements that include feedback via a 25-person faculty advisory committee of collaborators, as well as from iVirus ‘live protocols’ via protocols.io, VERVE-NET community pages, dedicated twitter and email accounts, and a web-based comments form; training opportunities for diverse trainees directly involved in the project (6 data analytics undergraduates, 1 graduate student, 2 postdocs 4 research scientists) and the broader research community through viromics modules / webinars and a local hands-on course; and passive engagement opportunities from a new early career researcher World Viromics Webinar Series, and (ii) 2 web portals specific for technical support (the MAVERIC portal) and awareness and location for iVirus’ resources, datasets, tools/apps, and protocols (the iVirus portal). Together these efforts are expected to grow the iVirus user base to tens of thousands of researchers in virome and microbiome science, and related fields. To find iVirus online go to https://www.ivirus.us/.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.
微生物现在被认为是各种生态系统过程的基础,包括海洋生物地球化学循环,土壤肥力和功能的播种和维持,以及在健康和生态失调状态之间调节动物和植物微生物群。然而,感染这些微生物的病毒越来越多地被认为通过杀死,基因流动和代谢重编程与生态系统有很强的相关性。因此,越来越多的研究人员问:“病毒是如何影响我的系统的?”这导致了多样性目录的爆炸和病毒感染细胞的研究,或病毒细胞,作为另一个窗口,生态系统的影响。这些生态系统到行星规模的进步的根源是大数据(即,下一代测序)以及我们通过可扩展的存储、搜索、共享和分析功能来理解它的能力。这些能力是由网络基础设施实现的,这些网络基础设施使生物学家能够在没有专业编程知识和硬件维护问题的情况下处理数据。在过去的十年中,微生物分析平台的数量和复杂性随着公共数据库中积累的测序数据而稳步增加。虽然这些平台广泛地使生物学家能够充分利用大数据,但在这些平台上几乎不存在以病毒为中心的工具,这极大地限制了病毒组和微生物组科学。iVirus是一个由NSF资助的应用程序和资源生态系统,代表了以病毒为重点的分析平台,它已经通过培训研讨会和网络研讨会,出版物和公开演示实现了民主化,以建立一个庞大,活跃和不断增长的用户群。通过这些场所,确定了新的能力需求。该奖项旨在通过组织病毒序列空间来创建参考基因组和分类资源来满足这些需求;用研究单链DNA和所有RNA病毒的新工具来增强以双链DNA为主的病毒工具包;改进研究病毒感染细胞的分析(病毒细胞);并开发新的长读病毒组学分析。iVirus用户基础将通过广泛的培训、外联和iVirus门户网站的改进得到扩大,包括通过一个由25人组成的合作者教员咨询委员会提供反馈,以及通过www.example.com、VERVE-NET社区网页、专门的推特和电子邮件账户以及网上评论表提供iVirus "现场协议";protocols.io(6名数据分析本科生,1名研究生,2名博士后4名研究科学家)和更广泛的研究社区,通过病毒组学模块/网络研讨会和当地实践课程;和被动参与的机会,从一个新的早期职业研究员世界病毒组学网络研讨会系列,和(ii)2个门户网站的具体技术支持(MAVERIC门户)以及iVirus的资源、数据集、工具/应用程序和协议的认知和位置(iVirus门户)。这些努力预计将使iVirus的用户群扩大到病毒组和微生物组科学及相关领域的数万名研究人员。要在网上找到iVirus,请访问www.example.com奖项反映了NSF的法定使命,并被认为值得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来支持。

项目成果

期刊论文数量(1)
专著数量(0)
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Matthew Sullivan其他文献

The Expansion of Science Policy in the United States in Three Cases: rDNA Research, The Human Genome Project, and the National Nanotechnology Initiative
美国科学政策的扩展三个案例:rDNA 研究、人类基因组计划和国家纳米技术计划
  • DOI:
  • 发表时间:
    2018
  • 期刊:
  • 影响因子:
    0
  • 作者:
    Matthew Sullivan
  • 通讯作者:
    Matthew Sullivan
Incidence of opportunistic infections during ibrutinib treatment for B-cell malignancies
B 细胞恶性肿瘤伊布替尼治疗期间机会性感染的发生率
  • DOI:
    10.1038/s41375-019-0481-1
  • 发表时间:
    2019-05-13
  • 期刊:
  • 影响因子:
    13.400
  • 作者:
    Kerry A. Rogers;Luay Mousa;Qiuhong Zhao;Seema A. Bhat;John C. Byrd;Zeinab El Boghdadly;Tomas Guerrero;Lauren B. Levine;Fabienne Lucas;Polina Shindiapina;Audrey M. Sigmund;Matthew Sullivan;Tracy E. Wiczer;Jennifer A. Woyach;Farrukh T. Awan
  • 通讯作者:
    Farrukh T. Awan
Comparison of commercially-available metakaolins and slags in binary and ternary concrete mixtures
  • DOI:
  • 发表时间:
    2018-05
  • 期刊:
  • 影响因子:
    0
  • 作者:
    Matthew Sullivan
  • 通讯作者:
    Matthew Sullivan
Code conversion with the quantum Golay code for a universal transversal gate set
  • DOI:
    10.1103/physreva.109.042416
  • 发表时间:
    2023-07
  • 期刊:
  • 影响因子:
    2.9
  • 作者:
    Matthew Sullivan
  • 通讯作者:
    Matthew Sullivan
Planar graphs without 3-cycles and with 4-cycles far apart are 3-choosable
  • DOI:
  • 发表时间:
    2016-09
  • 期刊:
  • 影响因子:
    0
  • 作者:
    Matthew Sullivan
  • 通讯作者:
    Matthew Sullivan

Matthew Sullivan的其他文献

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{{ truncateString('Matthew Sullivan', 18)}}的其他基金

RUI: Collaborative Research: Structural and Compositional Modification of Memristive Niobium Oxide Films for Neuromorphic Computing Applications
RUI:合作研究:用于神经形态计算应用的忆阻氧化铌薄膜的结构和成分改性
  • 批准号:
    2103197
  • 财政年份:
    2021
  • 资助金额:
    $ 99.96万
  • 项目类别:
    Standard Grant
Next generation informatics to elucidate viral ecology and ecosystem impacts in nature
下一代信息学阐明自然界中的病毒生态学和生态系统影响
  • 批准号:
    1759874
  • 财政年份:
    2018
  • 资助金额:
    $ 99.96万
  • 项目类别:
    Continuing Grant
Collaborative Research: Inferring Cellular Lysis and Regeneration of Organic Matter by Marine Viruses
合作研究:推断海洋病毒对有机物的细胞裂解和再生
  • 批准号:
    1829640
  • 财政年份:
    2018
  • 资助金额:
    $ 99.96万
  • 项目类别:
    Continuing Grant
Ecology and biogeochemical impacts of DNA and RNA viruses throughout the global oceans
DNA 和 RNA 病毒对全球海洋的生态和生物地球化学影响
  • 批准号:
    1829831
  • 财政年份:
    2018
  • 资助金额:
    $ 99.96万
  • 项目类别:
    Standard Grant
Ecological impacts and drivers of double-stranded DNA viral communities in the global oceans
全球海洋中双链 DNA 病毒群落的生态影响和驱动因素
  • 批准号:
    1536989
  • 财政年份:
    2015
  • 资助金额:
    $ 99.96万
  • 项目类别:
    Standard Grant
RUI: Fluctuations and Phase Transitions in Iron Pnictide Superconductors
RUI:铁磷族超导体中的涨落和相变
  • 批准号:
    1305637
  • 财政年份:
    2013
  • 资助金额:
    $ 99.96万
  • 项目类别:
    Standard Grant
Targeted and comparative viral community genomics of the Eastern North Pacific
北太平洋东部地区的目标和比较病毒群落基因组学
  • 批准号:
    0961947
  • 财政年份:
    2010
  • 资助金额:
    $ 99.96万
  • 项目类别:
    Standard Grant
EAGER: Viral tagging: Combining flow cytometry and genomics to explore virus-host interactions
EAGER:病毒标签:结合流式细胞术和基因组学探索病毒与宿主的相互作用
  • 批准号:
    0940390
  • 财政年份:
    2009
  • 资助金额:
    $ 99.96万
  • 项目类别:
    Standard Grant
Collaborative Research: PHANTOME: Phage ANnotation TOols and MEthods
合作研究:PHANTOME:噬菌体注释工具和方法
  • 批准号:
    0850105
  • 财政年份:
    2009
  • 资助金额:
    $ 99.96万
  • 项目类别:
    Continuing Grant
RUI: Critical Dynamics of the Electron-Doped Cuprate Superconductors
RUI:电子掺杂铜酸盐超导体的临界动力学
  • 批准号:
    0706557
  • 财政年份:
    2007
  • 资助金额:
    $ 99.96万
  • 项目类别:
    Standard Grant

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相似海外基金

Collaborative Research: Updating iVirus - the CyVerse-powered analytical toolkit for viruses of microbes
协作研究:更新 iVirus - CyVerse 支持的微生物病毒分析工具包
  • 批准号:
    2149506
  • 财政年份:
    2022
  • 资助金额:
    $ 99.96万
  • 项目类别:
    Continuing Grant
Collaborative Research: A New Nonlinear Modal Updating Framework for Soft, Hydrated Materials
协作研究:用于软水合材料的新型非线性模态更新框架
  • 批准号:
    1728186
  • 财政年份:
    2017
  • 资助金额:
    $ 99.96万
  • 项目类别:
    Standard Grant
Collaborative Research: A New Nonlinear Modal Updating Framework for Soft, Hydrated Materials
协作研究:用于软水合材料的新型非线性模态更新框架
  • 批准号:
    1727761
  • 财政年份:
    2017
  • 资助金额:
    $ 99.96万
  • 项目类别:
    Standard Grant
Collaborative Research: Updating the Militarized Dispute Data Through Crowdsourcing: MID5
协作研究:通过众包更新军事化争端数据:MID5
  • 批准号:
    1528409
  • 财政年份:
    2015
  • 资助金额:
    $ 99.96万
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Collaborative Research: Updating the Militarized Dispute Data Through Crowdsourcing: MID5
协作研究:通过众包更新军事化争端数据:MID5
  • 批准号:
    1528624
  • 财政年份:
    2015
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Collaborative Research: Updating the WeBWorK National Problem Library
合作研究:更新WeBWorK国家问题库
  • 批准号:
    1226081
  • 财政年份:
    2012
  • 资助金额:
    $ 99.96万
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Collaborative Research: Updating the WeBWorK National Problem Library
合作研究:更新WeBWorK国家问题库
  • 批准号:
    1226176
  • 财政年份:
    2012
  • 资助金额:
    $ 99.96万
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Collaborative Research: Contentious Issues in World Politics: Updating the ICOW Dataset
合作研究:世界政治中有争议的问题:更新 ICOW 数据集
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    0960567
  • 财政年份:
    2010
  • 资助金额:
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Collaborative Research: Contingent Reasoning and Bayesian Updating in Games of Incomplete Information: An Experimental Analysis
协作研究:不完全信息博弈中的条件推理和贝叶斯更新:实验分析
  • 批准号:
    1031101
  • 财政年份:
    2010
  • 资助金额:
    $ 99.96万
  • 项目类别:
    Standard Grant
Collaborative Research: Contingent Reasoning and Bayesian Updating in Games of Incomplete Information: An Experimental Analysis
协作研究:不完全信息博弈中的条件推理和贝叶斯更新:实验分析
  • 批准号:
    1030467
  • 财政年份:
    2010
  • 资助金额:
    $ 99.96万
  • 项目类别:
    Standard Grant
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