ANALYSIS OF GENETIC DATA USING BIOCONDUCTOR R

使用 BIOCONDUCTOR R 分析遗传数据

• 批准号: 7610322
• 负责人: Richard B. Gayle
• 金额: $ 1.23万
• 依托单位: UNIVERSITY OF SOUTH DAKOTA
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-05-01 至 2008-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7610322
• 关键词: Bioconductor; Biological; Computer Retrieval of Information on Scientific Projects Database; Computer software; Data; Development; Environment; Funding; Genetic Techniques; Grant; Institution; Learning; Numbers; Output; Purpose; Research; Research Personnel; Resources; Source; Technology; Training; United States National Institutes of Health; Work; addiction; computing resources; genetic analysis; member; open source

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The purpose of the project is to identify specific types of genetic analyses performed by members of BHSUs Center for the Conservation of Biological Resources (CCBR) amenable to the use of facilities available in the open source Bioconductor R environment/package, to learn how to manipulate the appropriate packages in that environment to provide analytical output useful to CCBR staff members in their projects, and then finally to train these staff members in the use of these computing resources. This last step is particularly important because it will, ideally, train CCBR members in the basic utilization of a computing environment which, because it is an open source development environment, evolves constantly through the addiction of packages to accommodate the computing requirements of new genetic techniques and technologies. This project will involve three steps. First, I will work with members of the CCBR staff this semester to identify a small number (3 or 4) of computing tasks which arise in the context of current projects, focusing particularly on tasks for which available proprietary software is either non-existent or not suitably flexible and for which Bioconductor has a currently available developer-contributed software packages. Second, I will develop facility in using these packages myself by applying them to tasks/data arising from projects currently being undertaken in the CCBR lab. Finally, I will provide directed training to appropriate CCBR staff in the implementation and basic use of Bioconductor and in the use of the specifically identified packages in the computing environments available to them.

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 该项目的目的是确定由BHSU成员进行的特定类型的遗传分析的生物资源保护中心（CCBR）服从于在开源Bioconductor R环境/包中可用的设施的使用，学习如何在该环境中操作适当的包，以提供有用的分析输出CCBR的工作人员在他们的项目，然后最终培训这些工作人员在使用这些计算资源。 这最后一步特别重要，因为它将在理想情况下培训CCBR成员基本利用计算环境，因为它是一个开放源代码的开发环境，通过软件包的添加不断发展，以适应新的遗传技术和技术的计算要求。 该项目将包括三个步骤。 首先，本学期我将与CCBR的工作人员合作，确定当前项目中出现的少量（3或4个）计算任务，特别关注可用的专有软件不存在或不灵活的任务，以及Bioconductor目前提供的开发人员贡献的软件包。 其次，我将通过将这些软件包应用于CCBR实验室目前正在进行的项目中产生的任务/数据，来开发自己使用这些软件包的能力。 最后，我将为CCBR的相关工作人员提供有关Bioconductor的实施和基本使用以及在计算环境中使用特定软件包的直接培训。