Continued Development of Stanford Microarray Database

斯坦福微阵列数据库的持续开发

• 批准号: 8327884
• 负责人: CATHERINE A BALL
• 金额: $ 29.81万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-02-25 至 2012-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8327884
• 关键词: Adopted; Architecture; Biological; Biology; Biomedical Research; Code; Collaborations; Color; Communicable Diseases; Computer software; DNA Microarray Chip; Data; Data Analyses; Data Storage and Retrieval; Databases; Development; Ensure; Film; Funding; Goals; Grant; Health; Heart Diseases; Human; Human Biology; Institution; Laboratories; Learning; Location; Mails; Maintenance; Malignant Neoplasms; Methods; Operating System; Output; Plug-in; Publications; Publishing; Research; Research Infrastructure; Research Personnel; Research Support; Side; Site; Speed; Structure; Sum; System; Testing; Vendor; Writing; base; data format; data sharing; density; file format; high throughput technology; human disease; improved; innovation; insight; open source; tool; web site

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.

描述（由申请人提供）：斯坦福大学微阵列数据库（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，一直到成为一个机构规模的数据库，为许多地点的数千名用户提供服务。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，但目前的生物注释和各种工具的数据检索，质量评估和分析，支持前和出版后使用的微阵列数据。SMD支持双色数据（包括GenePix、ScanAlyze和Agilent特征提取软件的输出）和来自Affyssoft GeneChips和Nimblegen阵列的单通道数据。斯坦福大学的装置为斯坦福大学的数百名研究人员及其在全球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，并安装在其他几个机构的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。该项目的主要目标是扩展和改进SMD中的工具，以进一步实现生物医学研究，并为生物学家和数据分析师提供更好的控制和分析一致性。在该资助的第一个资助期内，我们特别专注于数据库基础设施的开发，以便定期发布SMD的代码和模式。在此更新申请中，我们正在扩大我们的重点，以提供更多使SMD安装用户受益的工具。具体而言，我们建议（1）提供SMD软件包的持续维护、发布和支持，（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公共微阵列数据存储库导入数据，以及（4）提供数据结构和软件，以在SMD中为更高密度平台提供支持，例如平铺和SNP阵列。总之，这些目标的完成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，并从已经发表的微阵列数据中获得更多的好处，从而增加两者的价值。生物医学研究正在迅速发展，主要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人类疾病的多样性，从癌症到传染病到心脏病，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。该提案为这些研究人员提供了一个数据库和工具，使他们能够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的影响。

项目成果

Implementation of GenePattern within the Stanford Microarray Database.

• DOI: 10.1093/nar/gkn786
• 发表时间: 2009-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Hubble J;Demeter J;Jin H;Mao M;Nitzberg M;Reddy TB;Wymore F;Zachariah ZK;Sherlock G;Ball CA
• 通讯作者: Ball CA

The Stanford Microarray Database: implementation of new analysis tools and open source release of software.

斯坦福微阵列数据库：新分析工具的实现和软件的开源发布。

• DOI: 10.1093/nar/gkl1019
• 发表时间: 2007-01
• 期刊: NUCLEIC ACIDS RESEARCH
• 影响因子: 14.9
• 作者: Demeter, Janos;Beauheim, Catherine;Gollub, Jeremy;Hernandez-Boussard, Tina;Jin, Heng;Maier, Donald;Matese, John C.;Nitzberg, Michael;Wymore, Farrell;Zachariah, Zachariah K.;Brown, Patrick O.;Sherlock, Gavin;Ball, Catherine A.
• 通讯作者: Ball, Catherine A.

The Stanford Microarray Database: a user's guide.

斯坦福微阵列数据库：用户指南。

• DOI: 10.1385/1-59745-097-9:191
• 发表时间: 2006
• 期刊: Methods in molecular biology (Clifton, N.J.)
• 作者: Gollub,Jeremy;Ball,CatherineA;Sherlock,Gavin
• 通讯作者: Sherlock,Gavin

OntologyWidget - a reusable, embeddable widget for easily locating ontology terms.

OntologyWidget - 一个可重用、可嵌入的小部件，用于轻松定位本体术语。

• DOI: 10.1186/1471-2105-8-338
• 发表时间: 2007
• 期刊: BMC bioinformatics
• 影响因子: 3
• 作者: Beauheim,CatherineC;Wymore,Farrell;Nitzberg,Michael;Zachariah,ZachariahK;Jin,Heng;Skene,JHPate;Ball,CatherineA;Sherlock,Gavin
• 通讯作者: Sherlock,Gavin