ANALYSIS OF GENETIC DATA USING BIOCONDUCTOR R

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 该项目的目的是确定BHSUS生物资源保护中心(CCBR)成员能够使用开源BioConductor R环境/包中现有设施进行的特定类型的遗传分析，学习如何在该环境中操作适当的包，以便为CCBR工作人员在其项目中提供有用的分析结果，最后培训这些工作人员使用这些计算资源。最后一步特别重要，因为理想情况下，它将培训CCBR成员对计算环境的基本利用，因为它是一个开放源码的开发环境，通过对包的上瘾不断演变，以适应新的遗传技术和技术的计算要求。 这个项目将包括三个步骤。首先，本学期我将与CCBR工作人员合作，确定在当前项目的背景下出现的少量(3或4)计算任务，特别是那些可用的专有软件不存在或不具有适当灵活性的任务，以及BioConductor目前有可用的开发人员贡献的软件包。其次，我将通过将这些程序包应用于CCBR实验室目前正在进行的项目产生的任务/数据，来开发自己使用这些程序包的工具。最后，我将为CCBR的适当工作人员提供有关BioConductor的实施和基本使用以及在他们可用的计算环境中使用专门确定的包的定向培训。

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.