Continued Development of Stanford Microarray Database

描述(由申请人提供)：斯坦福微阵列数据库(SMD)是一个开源的DNA微阵列研究数据库，它可以支持单个实验室、合作小组的研究需求，一直到成为机构规模的数据库，为许多地点的数千用户服务。作为一个研究数据库系统，SMD不仅提供数据存储和访问控制，还提供当前的生物注释和各种数据检索、质量评估和分析工具，支持微阵列数据发表前和发表后的使用。SMD既支持双色数据(包括GenePix、ScanAlyze和Agilent特征提取软件的输出)，也支持来自Affymetrix GeneChips和NimbleGen阵列的单通道数据。斯坦福大学的设施为斯坦福大学的数百名研究人员和他们在世界各地100多个机构的合作者提供服务，并向公众提供约12,000个微阵列的数据。SMD的软件在过去三年中定期发布，并在其他几个机构安装在各种操作系统和数据库平台上，为这些网站的许多研究人员提供服务。这一拟议项目的主要目标是扩大和改进SMD的工具，以进一步促进生物医学研究，并为生物学家和数据分析人员提供更好的控制和分析的一致性。在这笔赠款的第一个资助期，我们特别专注于数据库基础设施的开发，以稳健和定期发布SMD的代码和模式。在这次续订申请中，我们正在扩大我们的重点，以提供更多工具，使SMD安装的用户受益。具体地说，我们建议(1)继续维护、发布和支持SMD软件包，(2)通过将GenePattern软件集成到SMD软件包中，显著增加分析工具的数量和采用它们的速度，这也将允许用户创建数据检索管道，(3)创建工具，使SMD用户能够轻松地从ArrayExpress和GEO公共微阵列数据库导入数据，以及(4)提供数据结构和软件，以在SMD中为更高密度的平台提供支持，例如平铺和SNP阵列。总之，完成这些目标将为生物医学研究人员和临床医生提供强大的工具，使他们能够更全面地分析自己的微阵列数据，并从已经公布的微阵列数据中获得更多好处，从而增加两者的价值。生物医学研究正在迅速发展，这在很大程度上是由于高通量技术的应用，如微阵列。许多临床医生和研究人员正在以创新的方式使用微阵列来研究从癌症到传染病再到心脏病的各种人类疾病，以及基础生物学的基本方面，这经常为人类生物学提供新的见解。这项建议为这些研究人员提供了一个数据库和工具，他们可以用来组织和分析他们的数据，并确保他们的研究对人类健康产生最大可能的影响。

DESCRIPTION (provided by applicant): The Stanford Microarray Database (SMD) is an open source, DNA microarray research database, which can support the research needs of single laboratories, collaborating groups, all the way up to being an institutional- scale database, serving thousands of users at many locations. As a research database system, SMD provides not only data storage and access control, but current biological annotation and a variety of tools for data retrieval, quality assessment and analysis, which support pre- and post-publication uses of microarray data. SMD supports both two-color data (including the output of the GenePix, ScanAlyze, and Agilent feature extraction software) and single-channel data from Affymetrix GeneChips and Nimblegen Arrays. The Stanford installation serves hundreds of researchers at Stanford and their collaborators at over one hundred institutions worldwide, and provides public access to data from approximately 12,000 microarrays. SMD's software has had regular releases over the last three years, and been installed at several other institutions on a variety of operating systems and database platforms, serving many researchers at those sites. The major goals of this proposed project are to expand and improve the tools in SMD to further enable biomedical research, and to provide biologists and data analysts with greater control and consistency in their analyses. In the first funding period of this grant, we specifically focused on development of the database infrastructure to make robust and regular releases of SMD's code and schema. In this renewal application, we are expanding our focus to provide additional tools that will benefit users of SMD installations. Specifically, we propose to (1) provide continued maintenance, release and support of the SMD software package, (2) significantly increase the number of analysis tools and speed with which they can be adopted by integrating the GenePattern software into the SMD software package, which will also allow users to create data retrieval pipelines, (3) create tools that enable SMD users to easily import data from the ArrayExpress and GEO public microarray data repositories and (4) provide data structures and software to provide support in SMD for higher density platforms, such as tiling and SNP arrays. In sum, completion of these aims will provide biomedical researchers and clinicians with powerful tools that will allow them to more completely analyze their own microarray data, as well as derive more benefit from already published microarray data, thereby increasing the value of both. Biomedical research is rapidly evolving, largely due to the application of high-throughput technologies, such as microarrays. Many clinicians and researchers are using microarrays in innovative ways to investigate a diversity of human diseases, from cancer to infectious diseases to heart disease, as well as fundamental aspects of basic biology, which frequently provide new insights into human biology. This proposal provides these researchers with a database and tools with which they can organize and analyze their data, and ensure that their research has the greatest possible impact on human health.