Cyberinfrastructure for Accessible and Reproducible Research in Life Sciences

用于生命科学研究可访问和可重复的网络基础设施

• 批准号: 0850103
• 负责人: Anton Nekrutenko
• 金额: $ 111.85万
• 依托单位: Pennsylvania State Univ University Park
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-01 至 2014-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0850103&HistoricalAwards=false
• 关键词: Cyberinfrastructure; Accessible; Reproducible; Research; Life

Pennsylvania State University University Park is awarded a grant to extend an existing software system, Galaxy (http://galaxyproject.org) that integrates computational biology tools for experimental biologists to access sequence, polymorphism and functional datasets. Analytic functions to be enhanced include a set of tools allowing bench scientists to perform large-scale analyses with whole-genome multiple alignments without ever leaving their web browsers; an interactive statistical genetics tool kit for comprehensive analysis of data generated from high-throughput genotyping experiments; an evolutionary analysis toolset for detection of selection, recombination and other critical evolutionary parameters, that can be applied directly to existing sequence and alignment datasets; and novel approaches for improving reproducibility of research in life sciences by implementing simple yet powerful analysis workflows that can be constructed by example and explicitly. The project is a collaborative effort with Brigham and Women's Hospital, Emory University, and University of California, San Diego.Galaxy bridges a critically important gap between computational tools and users, by making it trivial to modernize the interfaces of existing tools, freeing developers of new tools from the need to develop interfaces from scratch, and facilitating tool interoperability and complex analyses by seamlessly integrating diverse tools and databases. Galaxy has two thriving communities of users: those who use the public Galaxy instance to access a variety of tools and databases with nothing more than a web browser, and those who take advantage of Galaxy framework?s portability and minimal installation requirements to create their own Galaxy instances and provide easy access to locally developed tools and private data.

宾夕法尼亚州立大学大学公园获得一笔赠款，用于扩展现有的软件系统Galaxy（http：//www.example.com），该系统集成了计算生物学工具，供实验生物学家访问序列、多态性和功能数据集。有待加强的分析功能包括一套工具，使实验室科学家能够在不离开网络浏览器的情况下进行全基因组多重比对的大规模分析;一套交互式统计遗传学工具包，用于全面分析高通量基因分型实验产生的数据;进化分析工具集，用于检测选择、重组和其他关键进化参数，可以直接应用于现有的序列和比对数据集;以及通过实施简单而强大的分析工作流程来提高生命科学研究的再现性的新方法，这些工作流程可以通过示例和明确地构建。该项目是与布里格姆妇女医院、埃默里大学和加州大学圣地亚哥分校合作的成果。Galaxy弥合了计算工具和用户之间至关重要的鸿沟，使现有工具的界面现代化变得微不足道，使新工具的开发人员无需从头开始开发界面，并通过无缝集成各种工具和数据库来促进工具互操作性和复杂分析。Galaxy有两个蓬勃发展的用户社区：那些使用公共Galaxy实例访问各种工具和数据库的用户，而这些工具和数据库只需要一个Web浏览器，以及那些利用Galaxy框架的用户。的便携性和最低的安装要求，以创建自己的银河实例，并提供方便地访问本地开发的工具和私人数据。