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公园被授予赠款，以扩展现有的软件系统Galaxy（http://galaxyproject.org），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。要增强的分析功能包括一组工具，允许基准科学家通过全基因组多个对齐方式进行大规模分析，而无需离开其网络浏览器；一种交互式统计遗传学工具套件，用于全面分析高通量基因分型实验产生的数据；用于检测选择，重组和其他关键进化参数的进化分析工具集，可以直接应用于现有序列和对齐数据集；以及通过实施可以通过示例和明确构建的简单而强大的分析工作流程来改善生命科学研究可重复性的新颖方法。该项目是与埃默里大学（Emory University）和加利福尼亚大学圣地亚哥分校的一项合作努力。Galaxy桥接计算工具和用户之间的急需差距，通过使现有工具的界面变得琐碎，使新工具的界面变得现代化，从而使新工具的开发人员从刮擦工具中开发了互动，并通过划分的工具进行了整体互动，并进行了复杂的互动，并进行了复杂的互动和辅助分析。 Galaxy拥有两个蓬勃发展的用户社区：那些使用公共星系实例的人可以访问具有网络浏览器的各种工具和数据库，以及那些利用Galaxy Framework的便携性和最小的安装要求的人，以创建自己的银河系实例，并为本地开发的工具和私人数据提供便捷的访问。