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

基本信息

批准号：
1759874
负责人：
Matthew Sullivan
金额：
$ 121.35万
依托单位：
Ohio State University
依托单位国家：
美国
项目类别：
Continuing Grant
财政年份：
2018
资助国家：
美国
起止时间：
2018-08-15 至 2023-01-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1759874&HistoricalAwards=false
关键词：
Next generation informatics elucidate viral

项目摘要

Microbes are now appreciated for their roles in human health and disease, in promoting plant growth, and cycling nutrients in the oceans and soils. More recently, it has been recognized that the viruses that infect these microbes influence both the microbes and their communities through selective killing, moving genes between them, and reprogramming their host's metabolism during infection. Because viruses are so tiny, and most cannot be currently grown in laboratories, we are reliant upon decoding their biology through "reading" their stories via molecular sequencing techniques. This project seeks to augment iVirus, a collection of software tools (apps) and databases that leverages the NSF-funded CyVerse CyberInfrastructure (CI) to help researchers store, read and interpret these viral stories. Through development of new apps and curation of existing databases, the project will establish new analyses and features for researchers, directly train several undergraduate students, graduate students, and postdocs, and will provide two international training workshops to better "see" the viruses in their research.The microbiome is increasingly recognized to drive the nutrient and energy cycles that fuel Earth's diverse ecosystems, with their viruses modulating these impacts through killing, horizontal gene transfer, and metabolic reprogramming during infection. With the recent emergence of quantitative, sequence-based methods to comprehensively explore virus diversity in nature, the precise roles that viruses play can be increasingly elucidated. To perform these analyses, the iVirus platform was established in 2017 as part of the NSF-funded CyVerse CyberInfrastructure. iVirus currently includes apps, databases, and live documentation designed to enable researchers to better identify and analyze virus sequences by integrating and enhancing access to (meta)genomic sequence datasets and functions in the context of the NSF-funded CyVerse CyberInfrastructure. This project seeks to significantly augment iVirus in three ways: (i) aggregate and upgrade current viral ecogenomic capabilities, (ii) develop an integrated viral ecogenomic analytical pipeline, and (iii) establish direct connections and inter-operability across key databases and independent cyberinfrastructure environments. Beyond augmenting iVirus capabilities at CyVerse, we will actively seek to maximize its impact and utility for researchers through key partnerships with other existing tools (e.g., DOE Joint Genome Institute IMG/VR database). We will also continue to collect and be responsive to feedback provided through the CyVerse and the protocols.io reporting platforms, as well as collaborator and general user beta-testing and subsequent feedback on releases. Finally, we'll provide training at all levels through peer-reviewed publications, talks, and dedicated international workshops to enable the broader research community. The results of this project can be found at the iVirus website, http://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.

现在，微生物在人类健康和疾病，促进植物生长以及海洋和土壤中循环养分中的作用而受到赞赏。最近，人们已经认识到，感染这些微生物的病毒通过选择性杀戮，在它们之间移动基因并在感染过程中重新编程宿主的代谢。由于病毒是如此小，并且大多数病毒目前无法在实验室中生长，因此我们依靠通过分子测序技术“读取”其故事来解码其生物学。该项目旨在增强ivirus，这是一系列软件工具（应用程序）和数据库，这些软件工具（应用程序）利用了NSF资助的Cyberse Cyberinfradstructure（CI）来帮助研究人员存储，阅读和解释这些病毒式故事。通过开发新应用程序和现有数据库的策划，该项目将为研究人员建立新的分析和功能，直接培训几个本科生，研究生和博士后，并将提供两个国际培训研讨会，以更好地“查看”他们的研究中的病毒。越来越多地认识到微生物组，以促进千兆以来的营养和能量，以驱动艾滋病的造成侵害，并促进了ecosss的促进，并促进了ecosss的范围，并且可以使ecossss逐渐融合，并促进eCosse的依据，并以多种多样的态度来促进ecosse，并以多种多样的态度来促进eCosys的范围。水平基因转移和感染过程中的代谢重编程。随着最近基于定量的，基于序列的方法全面探索自然界的病毒多样性，病毒发挥作用的确切作用可以越来越多地阐明。为了执行这些分析，ivirus平台成立于2017年，是NSF资助的Cyberse Cyberinfradstructure的一部分。 Ivirus当前包括应用程序，数据库和实时文档，旨在通过集成和增强对NSF资助的Cyverse Cyberinfrstructure的上下文中对（META）基因组序列数据集和功能的访问来更好地识别和分析病毒序列的实时文档。该项目旨在通过三种方式显着增强艾滋病毒疗法：（i）总体和升级当前的病毒生态组能力，（ii）开发一种集成的病毒性生态分析管道，（iii）建立直接连接和跨关键数据跨关键数据和独立的cyberinfrstructure环境的连接。除了增强Cyverse的Ivirus功能外，我们还将通过与其他现有工具（例如DOE联合基因组IMG/VR数据库）的关键合作伙伴关系来积极寻求最大程度地对研究人员的影响和实用性。我们还将继续收集并响应通过cyverse和“协议”提供的反馈。io报告平台，以及合作者和一般用户beta测试以及随后对发行版的反馈。最后，我们将通过同行评审的出版物，演讲和专门的国际研讨会来提供各个层次的培训，以使更广泛的研究社区能够。该项目的结果可以在ivirus网站http://ivirus.us/..us/.this奖上反映NSF的法定任务，并被认为是值得通过基金会的知识分子优点和更广泛的影响评估审查标准来评估的。