CORE 1: Data Management and Bioinformatics Core

核心 1：数据管理和生物信息学核心

• 批准号: 10549998
• 负责人: ANDREJ SALI
• 金额: $ 14.41万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-08-17 至 2028-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10549998
• 关键词: Affect; Bioinformatics; Biological; Cell model; Cells; Chromosome Mapping; Computer software; Data; Data Analyses; Data Set; Databases; Development; Disease; Ecosystem; Ensure; Genetic; Human; Infrastructure; Integration Host Factors; Intuition; Journals; Link; Maps; Mission; Modeling; Molecular; Ontology; Pathway interactions; Peer Review; Performance; Proteins; Proteomics; Publications; Publishing; Reproducibility; Research; Research Personnel; Resources; Site; Software Tools; Source; Supercomputing; Tuberculosis; Visual; Visualization; bacterial genetics; candidate validation; data and analysis portal; data exchange; data integration; data management; digital object identifier; disease prognosis; genetic information; genome wide association study; network models; novel; pathogen; respiratory virus; targeted treatment; tool; transcriptomics; web portal; web site

DATA MANAGEMENT AND BIOINFORMATICS CORE SUMMARY The HPMI Data Management and Bioinformatics Core will support the Center's mission in all stages of research and publication, facilitating reproducible analysis, visualization, and access to center data and results. The Core will be composed of four major components: software and analysis workflows for data integration the Cytoscape and the Cytoscape Ecosystem; the Network Data Exchange (NDEx); and the HPMI Data and Analysis Portal. First, we will develop workflows to integrate proteomics, transcriptomics, genetics, and functional data generated by Projects 1 and 2 with existing -omics and GWAS datasets to select host factor candidates for validation. Second, Cytoscape will provide a range of tools for analyzing and visualizing molecular networks, interaction data, and hierarchical network models from both Projects. The third component, NDEx, will provide database infrastructure to support the sharing, reviewing, and disseminating of network data and models. It will also enable consolidated access to public biological network resources for use by HPMI investigators. Finally, the HPMI Data and Analysis Portal will provide a common access point for software tools and pipelines and their associated data. The above components – software and analysis workflows for data integration, visual network maps in Cytoscape, and storage of networks and models in NDEx – will all be made accessible through the HPMI’s website. Additionally, publications using HPMI products will be enhanced by the recent additions to Cytoscape for dynamically embedding network data in peer- reviewed journals. Finally, the Core will draw on an impressive array of hardware infrastructure for supercomputing, including high performance clusters at multiple sites.

数据管理和生物信息学核心 摘要 HPMI数据管理和生物信息学核心将在以下所有阶段支持中心的使命 研究和出版，促进可重现的分析、可视化和访问中心数据和结果。 核心将由四个主要组成部分组成：用于数据集成的软件和分析工作流 细胞景观和细胞景观生态系统；网络数据交换(NDX)；HPMI数据和 分析门户。首先，我们将开发工作流程，将蛋白质组学、转录组学、遗传学和 由项目1和项目2生成的功能数据与现有的组学和GWAS数据集一起选择宿主因素 需要验证的候选人。其次，Cytosscape将提供一系列分析和可视化工具 来自两个项目的分子网络、相互作用数据和分层网络模型。第三 组件NDeX将提供数据库基础设施，以支持共享、审查和传播 网络数据和模型。它还将实现对公共生物网络资源的统一访问以供使用 由HPMI调查人员提供。最后，HPMI数据和分析门户将为 软件工具和管道及其关联数据。上述组件--软件和分析 用于数据集成的工作流、Cytosscape中的可视化网络图以及中的网络和模型存储 NDX-将通过HPMI的网站访问所有内容。此外，使用HPMI产品的出版物 将通过最近添加到Cytoscape的功能得到增强，该功能用于在对等设备中动态嵌入网络数据 审阅了期刊。最后，核心将利用一系列令人印象深刻的硬件基础设施来实现 超级计算，包括多个站点的高性能集群。