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Durable Common Fund Data Interfaces and Tutorials with Bioconductor

持久的共同基金数据接口和 Bioconductor 教程

基本信息

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
项目类别：
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

项目摘要

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.

项目总结