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
• 负责人: Kelly Wrighton
• 金额: $ 33.07万
• 依托单位: Colorado State University
• 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
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2149506&HistoricalAwards=false
• 关键词: Collaborative; Research; Updating; iVirus; CyVerse

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.

微生物被认为是多种生态系统过程的基础，包括海洋生物地球化学的生育能力和功能，以及在健康和失调状态之间的植物和植物菌群越来越多的研究人员问：“这是如何影响TEM的，这会导致多样性的目录爆炸，并研究了感染病毒的细胞或virocells。进步是通过可扩展的存储，搜索，共享和分析能力来理解它的大数据。稳定的数据累积了dablic A存储库，而这些平台则赋予生物学家能够充分利用以病毒为中心的大数据，这在这些平台上不存在，这极大地限制了Virome和E Ivirus。在代表以病毒为重点的分析平台的应用程序和资源中，它通过培训和网络研讨会进行了民主化，以通过这些场所建立大型，活跃的活跃的ND增长。该奖项旨在通过组织病毒序列空间来填补参考基因组和分类资源，以增加双链DNA病毒工具包，并使用新的工具来研究单链DNA和所有RNA病毒；细胞（Virocells）；通过协议，verve-net社区页面，专门的Twitter和电子邮件帐户，ivirus的“实时协议”（6个数据分析地下研究生，1名研究生，2个PostDocs 4研究科学家） /网络研讨会和本地动手课程；在网上找到Ivirus的数千名研究人员和相关领域优点和更广泛的影响审查标准。