Linking Integrated Genome Browser and CyVerse

连接集成基因组浏览器和 CyVerse

• 批准号: 9219976
• 负责人: Ann E Loraine
• 金额: $ 22.46万
• 依托单位: UNIVERSITY OF NORTH CAROLINA CHARLOTTE
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-14 至 2020-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9219976
• 关键词: Agave; Architecture; Back; Biological Sciences; Client; Communities; Computers; Data; Data Analyses; Data Files; Data Science; Data Set; Data Storage and Retrieval; Disease susceptibility; Environment; Foundations; Funding; Genome; Genomics; Genotype; Goals; Health; Health Professional; High Performance Computing; Human; Human Genome; Imagery; Java; Knowledge; Lead; Link; Metadata; Methods; Occupations; Online Systems; Outcome; Phase; Play; Problem Solving; Protocols documentation; Public Health; Publications; Research Infrastructure; Resources; Role; Running; Savings; Science; Scientist; Services; Surveys; System; Time; Visual; Work; base; cloud based; computing resources; cyber infrastructure; data sharing; design; genome browser; genome-wide; improved; innovation; operation; tool; user-friendly; web services; web site

Project Summary Integrated Genome Browser (IGB) is a popular desktop genome browser used by thousands of scientists worldwide to visualize, explore, and analyze large-scale data sets from genomics. Implemented in Java, IGB can run on any computer platform and provides state-of-the-art, fast zooming and visual analytics functions. Since its inception, IGB has supported a data sharing and publication system called IGB Quickload, in which users deploy metadata and data files on Web sites and then share their data by publicizing the Quickload URL. However, many users lack access to hosting services or lack technical knowledge required to set and configure a Web site. To solve this problem and give users access to advanced computational power, we propose to integrate IGB and Quickload with CyVerse, a National Science Foundation-funded cyberinfrastructure project formerly called iPlant that launched in 2008. CyVerse contains a suite of user- friendly, Web-based data analysis and data storage tools accessible via a computational interface called the Agave API Web services. We will use the Agave Web services to connect IGB with CyVerse, enabling users to share data and collaborate using CyVerse infrastructure. We propose to perform this CyVerse-to-IGB integration in four phases, with each phase building on the next. First, we will add the ability for IGB users to log into their CyVerse accounts, browse data sets within IGB, and load data directly as new IGB tracks. In Phase 2, we will use the Agave metadata API to link data curation with visualization, thus facilitating data sharing, collaborating, and publication. In Phase 3, we will create tools for users to share and publicize their results with the larger scientific community, re-using metadata they created while viewing and interacting with their data. In Phase 4, we will empower users to perform more sophisticated visual analytics functions than are currently possible within IGB (or any desktop browser) by harnessing CyVerse computational resources. This will pave the way for our team and others to develop all-new visualizations that leverage advanced computing resources available from CyVerse. More generally, this project will build new understanding of how rich client, desktop applications like IGB can interact with and leverage cloud-based resources to benefit users and advance science.

项目摘要 集成基因组浏览器（IGB）是一个流行的桌面基因组浏览器， 全球数千名科学家可视化、探索和分析大规模数据 从基因组学中获得的数据。IGB用Java实现，可以在任何计算机平台上运行， 提供最先进的快速缩放和可视化分析功能。自成立以来， IGB支持一个名为IGB Quickload的数据共享和发布系统， 用户在网站上部署元数据和数据文件，然后通过以下方式共享数据： 快速加载URL。然而，许多用户无法访问托管服务， 缺乏设置和配置网站所需技术知识。解决这个问题 为用户提供先进的计算能力，我们建议将IGB 并使用CyVerse（国家科学基金会资助的网络基础设施）进行快速加载 项目前身为iPlant，于2008年启动。CyVerse包含一套用户- 友好的，基于Web的数据分析和数据存储工具，可通过计算 接口称为Agave API Web服务。我们将使用龙舌兰网络服务， 将IGB与CyVerse连接，使用户能够使用CyVerse共享数据和协作 基础设施演进我们建议分四个阶段执行CyVerse到IGB的集成， 每一阶段都建立在下一阶段之上。首先，我们将为IGB用户添加日志记录功能 进入他们的CyVerse帐户，浏览IGB中的数据集，并直接将数据作为新的 IGB轨道。在第2阶段，我们将使用Agave元数据API将数据策展与 可视化，从而促进数据共享，协作和发布。在第三阶段，我们 将为用户创建工具，以便与更大的科学机构分享和宣传他们的结果。 社区，重用他们在查看和与数据交互时创建的元数据。 在第4阶段，我们将使用户能够执行更复杂的可视化分析 功能比目前可能在IGB（或任何桌面浏览器），利用 CyVerse计算资源。这将为我们的团队和其他人铺平道路， 开发全新的可视化效果，充分利用现有的高级计算资源 来自CyVerse更普遍地说，这个项目将建立一个新的理解， 客户端，像IGB这样的桌面应用程序可以与基于云的 资源，以造福用户和推进科学。