Integrating the BioExtract Server with the iPlant Collaborative

将 BioExtract 服务器与 iPlant Collaborative 集成

• 批准号: 1126481
• 负责人: Carol Lushbough
• 金额: $ 72.58万
• 依托单位: University of South Dakota Main Campus
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-01 至 2015-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1126481&HistoricalAwards=false
• 关键词: Integrating; BioExtract; Server; iPlant; Collaborative

PI: Carol Lushbough (University of South Dakota)Collaborators: Stephen Goff (University of Arizona), Daniel Stanzione (University of Texas - Austin), Volker Brendel (Iowa State University) and Molly Nepokroeff (University of South Dakota)The BioExtract Server is an open, Web-based system designed to aid researchers in the analysis of genomic data by providing a platform to facilitate the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and Web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. The iPlant Collaborative (www.iplantcollaborative.org) is a project sponsored by the National Science Foundation to build a computer infrastructure for research in the plant sciences. By sponsoring distributed informatics projects, iPlant extends high level computation to researchers through access to data, analytic tools, and workflows. One of the primary goals of the iPlant Collaborative is the reuse and integration of relevant technology that exists in the science community and to collaborate with other researchers when building new infrastructure. The overall goal of this project is to make data, analytic tools, and workflows accessible, interoperable, easy to use, and applicable to research and education. In collaboration with the iPlant Collaborative, this project will enable researchers to execute iPlant analytic tools within the BioExtract Server, create iPlant workflows through the BioExtract Server, and manage analysis and provenance data across both platforms. Examples of such management include executing BioExtract Server tools and workflows and creating data extracts with input drawn from iPlant, storing BioExtract Sever tool results at iPlant, and annotating iPlant data through the BioExtract Server. The primary, overall objective of this project is to make data, analytic tools, and workflows accessible, interoperable, easy to use, and applicable to research and education. As the project's functionality becomes available through the BioExtract Server (bioextract.org) / iPlant (www.iplantcollaborative.org) platforms, it will be introduced to the research and educational communities through workshops, presentations, publications, and education. BioExtract Server integrated functionality will be added to the content of iPlant's free, 2-day "iPlant Genomic Education Workshops" which instruct researchers and faculty in the use of iPlant resources. The iPlant Collaborative holds more than 10 on-campus training sessions per year, in addition to workshops at a number of major conferences (including the ASPB Annual Meeting and the Plant & Animal Genome Meeting for the plant community, and the SC conference series for the computing community). Through these workshops, project personnel will demonstrate how the integrated iPlant/BioExtract Server functionality can be applied to general research questions. Personnel will work with individual researchers to help identify ways in which the integrated functionality could be leveraged to perform specific analysis. In addition to creating and delivering workshop content, the project will create videos demonstrating the iPlant/BioExtract Server functionality. These videos will be made available through the iPlant website as well as the BioExtract Server site. Finally, project functionality will be incorporated into yearly BioExtract Server workshops for the Undergraduate Research Fellows from the partner institutions of South Dakota NIH NCRR's IDeA Networks of Biomedical Research Excellence (INBRE) for which the PI serves as the Bioinformatics Core Director. Finally, the BioExtract Server will be an independent system available through an open source license that can be installed on individual servers. Individual installations will be configurable and allow for the inclusion of resources that best fit individual project needs.

Pi：Carol Lushbough(南达科他大学)合作者：Stephen Goff(亚利桑那大学)、Daniel Stanzione(得克萨斯大学奥斯汀分校)、Volker Brendel(爱荷华州立大学)和Molly Nepokroef(南达科他大学)BioExtract服务器是一个开放的、基于网络的系统，旨在通过提供一个促进创建生物信息流的平台来帮助研究人员分析基因组数据。通过记录用户执行的任务，在系统内创建科学工作流。这些任务可能包括查询多个分布式数据源，将查询结果保存为可搜索的数据摘录，以及执行本地和Web可访问的分析工具。然后，可以将所记录的一系列任务保存为可重现、可共享的工作流，以便随后使用原始或修改的输入和参数设置来执行。IPlants Collaborative(www.iants Collaborative.org)是由国家科学基金会赞助的一个项目，旨在为植物科学的研究建立计算机基础设施。通过赞助分布式信息学项目，iPLANT通过访问数据、分析工具和工作流程，将高级计算扩展到研究人员。IPLANT Collaborative的主要目标之一是重新利用和整合科学界现有的相关技术，并在建立新的基础设施时与其他研究人员合作。该项目的总体目标是使数据、分析工具和工作流可访问、可互操作、易于使用并适用于研究和教育。该项目将与iPLANT协作组合作，使研究人员能够在BioExtract服务器内执行iPLANT分析工具，通过BioExtract服务器创建iPLANT工作流程，并跨两个平台管理分析和来源数据。这类管理的例子包括执行BioExtract服务器工具和工作流程，使用从iPlant提取的输入创建数据提取，将BioExtract服务器工具结果存储在iFactory中，以及通过BioExtract服务器对iFactory数据进行注释。该项目的主要总体目标是使数据、分析工具和工作流可访问、可互操作、易于使用并适用于研究和教育。随着该项目的功能通过BioExtract服务器(BioExtract.org)/iPLANT(www.iants Collaborative.org)平台可用，它将通过研讨会、演讲、出版物和教育向研究和教育界介绍。BioExtract服务器集成功能将被添加到为期两天的免费“iPlant基因组教育研讨会”的内容中，这些研讨会将指导研究人员和教职员工如何使用iPlant资源。除了在一些重要会议(包括为植物界举办的ASPB年会和动植物基因组会议，以及为计算界举办的SC系列会议)上的研讨会外，iPlant Collaborative每年还举办10次以上的校园培训课程。通过这些研讨会，项目人员将演示如何将集成的iPLANT/BioExtract服务器功能应用于一般研究问题。人员将与个别研究人员合作，帮助确定可以利用集成功能执行特定分析的方法。除了创建和提供研讨会内容外，该项目还将制作演示iFactory/BioExtract服务器功能的视频。这些视频将通过iPLANT网站和BioExtract服务器网站提供。最后，项目功能将被纳入每年为来自南达科他州NIH NCRR的IDEA网络生物医学研究卓越(INBRE)合作机构的本科生研究员举办的BioExtract服务器研讨会，PI担任该网络的生物信息学核心主任。最后，BioExtract服务器将是一个独立的系统，可以通过开放源码许可证安装在单独的服务器上。个别安装将是可配置的，并允许包含最适合个别项目需要的资源。