Durable Common Fund Data Interfaces and Tutorials with Bioconductor

持久的共同基金数据接口和 Bioconductor 教程

• 批准号: 10356362
• 负责人: VINCENT JAMES CAREY
• 金额: $ 37.71万
• 依托单位: BRIGHAM AND WOMEN'S HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-22 至 2023-09-21
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10356362
• 关键词: 3-Dimensional; Adopted; Architecture; Attenuated; Awareness; Bioconductor; Bioinformatics; Biological; Biological Assay; Biology; Biotechnology; Breast Cancer Cell; Breast Cancer cell line; Cancer Biology; Client; Cloud Computing; Coculture Techniques; Collection; Communities; Computer software; Data; Data Analyses; Data Discovery; Data Science; Data Set; Data Storage and Retrieval; Diapause; Documentation; Ecosystem; Education; Educational Materials; Educational workshop; Endocrine; Environment; Epigenetic Process; Estrogen receptor positive; FAIR principles; Fostering; Funding; Gene Expression Regulation; Gene Structure; Genetic; Genome; Genomics; Genotype-Tissue Expression Project; Grain; Harvest; Ingestion; International; Investigation; Laboratories; Language; Letters; Maintenance; Metadata; Methodology; Methods; Modeling; Molecular Biology; Morphologic artifacts; Mutate; National Human Genome Research Institute; Neurosciences; Organoids; Outcome; Pharmacogenomics; Pilot Projects; Problem Solving; Productivity; Publishing; Ramp; Recording of previous events; Research; Research Personnel; Resistance; Resources; Scientist; Software Design; Structure; Structure-Activity Relationship; T47D; Testing; Training; United States National Institutes of Health; Visualization; Work; base; cancer drug resistance; cancer genomics; computational platform; cost effective; data ecosystem; data quality; data resource; data structure; design; experience; experimental study; genomic data; indexing; innovation; insight; interest; mRNA Expression; malignant breast neoplasm; molecular domain; multiple omics; neoplastic cell; open data; outreach; symposium; therapy resistant; tool; tumor

Project Summary The NIH Common Fund Data Ecosystem collects together a dozen data-rich projects producing high- throughput data with cutting-edge assays. The overall ecosystem design includes plans for cross-project data harvesting and analysis on a collaborative cloud computing platform. While a long-range plan may culminate in highly structured analytic workbenches, we propose to use approaches established in the Bioconductor project to design community-driven modular approaches to data structure and interactive analysis of selected Common Fund assets. Our first aim is to produce standard, easy to use interfaces to resources provided in the 4D Nucleome, Illuminating the Druggable Genome, and Genotype-Tissue Expression projects. These Common Fund projects provide data of considerable interest by the general research community, but data discovery and use is hampered by intrinsic complexity as well as differing access and delivery methods adopted by the various Common Fund projects. We will interface well-established data containers and query methods to allow familiar R/Bioconductor programming idioms to work smoothly with resources from the selected Common Fund projects. The two-decade history of Bioconductor's approach to modular software design, documentation, integration, and distribution will sharply increase the likelihood of durable improvement in access to and utilization of Common Fund Assets. Our second aim is to leverage the new interfaces and containers to carry out four analytical projects in the investigation of origins of treatment persistent tumor cells in organoid cultures, with the objective of identifying compounds that can attenuate and provide insights into epigenetic mechanisms of treatment persistence. The operational and substantive outcomes of this project will form the basis of a comprehensive, highly community-driven approach to building strong bridges between consortia innovating at the cutting edge of biotechnology, and scientists innovating in integrative translational inference based on genome biology.

项目摘要 NIH共同基金数据生态系统将十几个数据富含数据的项目聚集在一起，产生高 带有尖端测定的吞吐量数据。整体生态系统设计包括跨项目数据的计划 在协作云计算平台上的收获和分析。远程计划可能会达到高潮 在高度结构化的分析工作台中，我们建议使用在生物导体中建立的方法 设计社区驱动的模块化方法，以实现数据结构和互动分析。 共同的基金资产。我们的第一个目的是生产标准，易于使用的接口到提供的资源 4D核心，阐明了可毒基因组和基因型 - 组织表达项目。这些 通用基金项目提供了一般研究界的相当兴趣的数据，但是数据 发现和使用受到内在复杂性以及不同的访问和交付方法的阻碍 由各种普通基金项目通过。我们将连接完整的数据容器并查询 允许熟悉的R/Bioconductor编程成语的方法与来自 选定的共同基金项目。生物导体模块化软件方法的两个十年历史 设计，文档，集成和分销将大大提高持久改进的可能性 在获取和利用共同基金资产方面。我们的第二个目标是利用新的接口和 在研究治疗起源的持续性肿瘤细胞起源时进行四个分析项目的容器 在器官培养物中，目的是识别可以减弱并提供见解的化合物 治疗持久性的表观遗传机制。该项目的运营和实质性结果将 构成了一种全面，高度社区驱动的方法，以建造强大的桥梁 在生物技术的最前沿进行创新的联盟，以及在综合翻译中创新的科学家 基于基因组生物学的推论。