Cancer Bioinformatics Services

翻译后摘要：癌症生物信息学服务（CBS） 癌症生物信息学服务（CBS）专注于为UPCI研究人员提供分析专业知识， 计算基础设施、专业数据库和研究分析，以支持癌症生物标志物 的发现这些最先进的生物信息学能力涉及癌症之间的深度合作， 生物信息学服务（CBS）和生物医学信息学系生物信息学系， 匹兹堡超级计算中心、个性化医学研究所和匹兹堡大学 模拟和建模中心。CBS在下一个更新期的目标是：1）提供 生物信息学分析支持所有微阵列和下一代测序（NGS）平台。这 包括实验设计、差异表达（DE）分析、miRNA靶点分析、拷贝数分析、 分析，查询公共数据库和先进的途径分析，使用商业（Incidity Pathway 分析，GeneGo和学术（例如Cytoscape）工具。2)执行TCGA和其他的综合分析 来自所有平台的聚生体数据，包括表达、甲基化、体细胞变体和拷贝数。第三章 根据共同数据使用协议（DUA），开发和实施匹兹堡基因组资源 存储库（PGRR），用于存储、分析和归档大PB大小基因组数据的基础设施 例如来自癌症基因组图谱（TCGA）项目。哥伦比亚广播公司还将开发PGRR信息会议 并发展生物资讯服务，方便使用。4)为程序开发专门的数据库 例如UPCI SkinSPORE，其整合了不同临床数据源，从而能够整合基因组学 使用开源信息学将生物学整合到临床表型的生物标志物数据， 床旁（i2b2）平台和相关技术。5)为癌症基因组学研究中心提供资讯科技支援 (CGF)高性能计算需求，6）准备数据以供发布，包括将数据提交给 基因表达大全（GEO），并协助手稿准备，和7）与卫生部合作 科学图书馆系统（HSLS）评估生物信息学工具的许可和教学季度 向用户社区提供生物信息学课程。CBS的目标是提供具有成本效益和效率的 为UPCI CCSG社区提供生物信息学分析服务。目前的建议侧重于扩大 这些服务对于科学发现新的癌症生物标志物和治疗方法至关重要。 目标的在本项目期间，所有10个研究项目都使用CBS服务。

Abstract: Cancer Bioinformatics Services (CBS) Cancer Bioinformatics Service (CBS) focuses on providing UPCI investigators with the analysis expertise, computational infrastructure, specialized databases and research analytics to support cancer biomarker discovery. These state-of-the-art bioinformatics capabilities involve deep collaborations between the Cancer Bioinformatics Service (CBS) and the Department of Biomedical Informatics bioinformatics faculty, the Pittsburgh Supercomputing Center, the Institute of Personalized Medicine and the University of Pittsburgh’s Simulation and Modeling Center. The aims of CBS for the next renewal period are to: 1) Provide bioinformatics analysis support for all microarray and Next Generation Sequencing (NGS) platforms. This includes experimental design, differential expression (DE) analysis, miRNA target analysis, copy number analysis, queries of public databases and advanced pathway analysis using commercial (Ingenuity Pathway analysis, GeneGo, and academic (e.g. Cytoscape) tools. 2) Perform integrative analysis of TCGA and other consortia data from all platforms including expression, methylation, somatic variants and copy number. 3) Develop and implement, under a common Data Use Agreement (DUA), the Pittsburgh Genome Resource Repository (PGRR), an infrastructure for storage, analysis and archiving of large petabyte size genomic data such as from The Cancer Genome Atlas (TCGA) project. CBS will also develop PGRR informational sessions and also develop bioinformatics services to facilitate use. 4) Develop specialized databases for programs such as UPCI Skin SPORE that integrate disparate clinical data sources, enabling integration of genomics biomarker data with clinical phenotypes using the open source Informatics for Integrating Biology to the Bedside (i2b2) platforms and related technologies. 5) Provide IT support for the Cancer Genomics Facility (CGF) high performance computing needs, 6) Prepare data for publication including submitting data to the Gene Expression Omnibus (GEO) and assist with manuscript preparation, and 7) Collaborate with the Health Sciences Library System (HSLS) to evaluate bioinformatics tools for licensing and teach quarterly bioinformatics courses to the user community. The goal of CBS is to provide cost effective and efficient bioinformatics analysis services to the UPCI CCSG community. The current proposal focuses on expanding these services as they are critical to the scientific discovery of new cancer biomarkers and therapeutic targets. During that current project period all 10 Research Programs used CBS services.