Integrating the BioExtract Server with the iPlant Collaborative

主要研究者：Carol Lushbough（南达科他州大学）合作者：Stephen Goff（亚利桑那大学），丹尼尔Stanzione（德克萨斯大学-奥斯汀分校），Volker Brendel（爱荷华州州立大学）和Molly Nepokroeff（南达科他州大学）BioExtract Server是一个开放的，基于Web的系统，旨在通过提供一个平台来帮助研究人员分析基因组数据，以促进生物信息学工作流程的创建。通过记录用户执行的任务，在系统内创建科学工作流程。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提取，以及执行本地和Web可访问的分析工具。然后，可以将一系列记录的任务保存为可再现的、可共享的工作流，可用于随后使用原始或修改的输入和参数设置执行。iPlant Collaborative（www.iplantcollaborative.org）是由美国国家科学基金会赞助的一个项目，旨在为植物科学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，分析工具和工作流程可访问，可互操作，易于使用，并适用于研究和教育。 通过与iPlant Collaborative的合作，该项目将使研究人员能够在BioExtract Server中执行iPlant分析工具，通过BioExtract Server创建iPlant工作流程，并跨两个平台管理分析和来源数据。 此类管理的示例包括执行BioExtract服务器工具和工作流程，并使用从iPlant提取的输入创建数据提取，将BioExtract服务器工具结果存储在iPlant，以及通过BioExtract服务器注释iPlant数据。该项目的主要总体目标是使数据，分析工具和工作流程可访问，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.iplantcollaborative.org）平台提供，它将通过研讨会、演讲、出版物和教育介绍给研究和教育界。生物提取服务器集成功能将被添加到iPlant的免费的，为期2天的“iPlant基因组教育研讨会”的内容，指导研究人员和教师在使用iPlant资源。iPlant每年举办10多场校园培训课程，此外还在一些主要会议上举办研讨会（包括ASPB年会和植物社区的植物动物基因组会议，以及计算社区的SC会议系列）。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。工作人员将与各个研究人员合作，帮助确定如何利用集成功能来执行特定分析。除了创建和提供研讨会内容外，该项目还将创建演示iPlant/BioExtract服务器功能的视频。这些视频将通过iPlant网站以及BioExtract Server网站提供。最后，项目功能将被纳入年度BioExtract服务器研讨会，研讨会面向来自南达科他州NIH NCRR的IDEA生物医学研究卓越网络（INBRE）合作机构的本科研究员，PI担任生物信息学核心主任。 最后，BioExtract服务器将是一个独立的系统，可以通过开源许可证安装在单独的服务器上。 单个安装将是可配置的，并允许包含最适合单个项目需求的资源。

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.