BIOINFORMATICS SHARED RESOURCE

生物信息学共享资源

• 批准号: 7506833
• 负责人: John Greally
• 金额: $ 14.13万
• 依托单位: ALBERT EINSTEIN COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-09-25 至 2012-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7506833
• 关键词: Administrator; Affinity; Albert Einstein Cancer Center; Area; Bioinformatics; Bioinformatics Shared Resource; Biological; Biostatistics Shared Resource; Breast; Cancer Center; Clinical; Clinical Data; Clinical Investigator; Clinical Research; Collaborations; Common Data Element; Communities; Computer software; Contracts; Correlative Study; Custom; Data; Data Analyses; Data Quality; Databases; Development; Disorder by Site; Employee; Environment; Facility Construction Funding Category; Foundations; Genomics; Goals; Growth; Head and Neck Cancer; Informatics; Information Management; Laboratories; Left; Link; Malignant Neoplasms; Metadata; Microarray Analysis; Mining; Molecular Biology; Numbers; Online Systems; Output; Pathway Analysis; Patients; Phase; Process; Proteomics; Rate; Records; Recruitment Activity; Research; Research Infrastructure; Resources; Sampling; Science; Senior Scientist; Services; Source; Standards of Weights and Measures; System; Techniques; Technology; Time; Vocabulary; Work; Yin; base; cancer Biomedical Informatics Grid; data integration; data management; design; epigenomics; expectation; high throughput technology; interoperability; member; programs; repository; skills; tool; web based interface

The Bioinformatics Shared Resource (BISR) was established in 2004 with a focus on developing relational database resources for the AECC research community as the essential foundation for the management of data from high-throughput technologies (especially microarrays), and for the integration of data from different sources. Since then, the BISR has established web-based clinical study databases, and has adapted to the management of data from evolving microarray platforms and applications; in particular, the NimbleGen custom microarray system. The BISR has also been integrated into the cancer biomedical informatics grid (caBIG) project and currently has three contracts from NCI for its contributions to this program. The BISR is closely linked with the Biostatistics Shared Resource and is designed to focus on data management and mining, leaving the responsibility for data analysis with the latter facility. However, the expertise of both groups has been used to develop AECC's high-throughput analytical capabilities along with software programs to analyze microarray data that work within the database environment and generate not only the final output but also intermediate analyses that are informative about data quality. These analytical approaches are developed and supervised by AECC biostatisticians, but implemented by the BISR staff, leveraging the strengths of both groups to meet the evolving major challenge of processing and analyzing high-throughput genomic, epigenomic and proteomic data from basic and translational applications as they emerge and expand at this Center. The BISR has developed a pilot clinical study database for the AECC Head and Neck Cancer Affinity Group that allows the integration of laboratory and clinical data from multiple sources and maintains HIPAA-compliance through the use of metadata repositories that can be extrapolated to other disease sites. A second component to the bioinformatics infrastructure is being developed to support pre-existing applications such as TransFac, microarray analysis software, batched Blat and Entrez analyses, and biological pathway analysis tools such as GenMAPP and PathwayAssist. The facility is currently staffed by 5.25 FTE consisting of three bioinformaticists who provide consultative support to AECC members along with two programmers, and a part-time staff member who serves as a systems administrator and database administrator.

生物信息学共享资源（BISR）成立于2004年，重点是发展关系 AECC研究社区的数据库资源是管理的基础 来自高通量技术（尤其是微阵列）的数据，以及从不同的数据集成 来源。从那以后，BISR建立了基于Web的临床研究数据库，并适应了 从不断发展的微阵列平台和应用程序中管理数据；特别是敏捷 自定义微阵列系统。 BISR也已集成到癌症生物医学信息学网格中 （Cabig）项目，目前签订了NCI的三份合同，因为其对该计划的贡献。 BISR是 与生物统计学共享资源密切相关，旨在专注于数据管理和 采矿，使后一个设施负责数据分析。但是，两者的专业知识 组已用于开发AECC的高通量分析能力以及软件 分析在数据库环境中起作用的微阵列数据的程序，不仅生成 最终输出，但还进行了有关数据质量信息丰富的中间分析。这些分析 方法是由AECC生物统计学家开发和监督的，但由BISR员工实施， 利用两组的优势来应对不断发展的处理和分析的重大挑战 来自基本和翻译应用的高通量基因组，表观基因组和蛋白质组学数据 在这个中心出现并扩展。 BISR已为AECC开发了一个试验临床研究数据库 头部和颈部癌亲和力组，允许将实验室和临床数据整合到多个 来源并通过使用可以推断的元数据存储库来维持HIPAA符合性 到其他疾病部位。正在开发生物信息学基础设施的第二个组成部分来支持 现有的应用程序，例如TransFac，微阵列分析软件，批处理布拉特和Entrez分析， 以及生物途径分析工具，例如Genmapp和途径辅助学家。该设施目前配备人员 由5.25 FTE组成，由三位生物信息学家组成，他们向AECC成员提供协商支持 与两名程序员以及一名兼职人员一起担任系统管理员和数据库 行政人员。