Cancer Genomics: Integrative and Salable Solutions in R/Bioconductor

癌症基因组学：R/Bioconductor 中的综合且可销售的解决方案

• 批准号: 10017896
• 负责人: Martin T Morgan
• 金额: $ 70.49万
• 依托单位: ROSWELL PARK CANCER INSTITUTE CORP
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-09-01 至 2021-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10017896
• 关键词: Address; Adoption; Architecture; Archives; Area; Bioconductor; Biological; Biological Assay; Cancer Biology; Cells; Cellular Assay; Communities; Community Participation; Complex; Comprehension; Computer software; DNA Methylation; DNA Sequence; Data; Data Set; Development; Documentation; Ecosystem; Environment; Epigenetic Process; Event; Exposure to; FAIR principles; Funding; Gene Expression; Genes; Genome; Genomic DNA; Genomics; Goals; Growth; Individual; Infrastructure; Institution; Link; Maintenance; Malignant Neoplasms; Memory; Messenger RNA; Methods; Molecular; Molecular Biology; Point Mutation; Precision therapeutics; Programming Languages; Proteins; Protocols documentation; Recurrence; Regulatory Element; Reporting; Reproducibility; Research; Research Personnel; Resources; Role; Sales; Specimen; Standardization; Statistical Data Interpretation; Structure; System; Technology; The Cancer Genome Atlas; Training; Training Support; Untranslated RNA; Variant; Visualization; anticancer research; base; cancer cell; cancer genomics; clinically relevant; cloud based; computer infrastructure; cost; data resource; differential expression; experimental study; falls; genetic information; genomic data; improved; interoperability; learning materials; multiple omics; navigation aid; neoplastic cell; novel; novel strategies; open source; operation; outreach; programs; residence; response; single cell analysis; software development; software infrastructure; training opportunity; tumor heterogeneity; tumor microenvironment; tumor-immune system interactions; usability

Abstract Bioconductor is an ecosystem of more than 1,500 open-source software and data packages for the statistical analysis and comprehension of high-throughput genomic data. It is widely used by the cancer genomics research community for statistical analysis and visualization. This software ecosystem is supported by core data classes and methods, reused by both users and developers, that provide convenient representations and efficient operations for many kinds of high-throughput molecular data. Falling sequencing costs and single-cell assays enable increasingly resolved study of the molecular biology of cancer, through combined assaying of DNA sequence, epigenetics, gene expression, protein, and other aspects, even at the single-cell level, for a single specimen. These developments present new challenges in complexity, size, and interpretability of the data. The overarching goal of this project is to create and adapt core Bioconductor software infrastructure to meet these challenges, through the following aims. First, we develop infrastructure for the analysis of single-cell multi-omic experiments. Second, we implement FAIR principles for improved somatic variant prioritization, by defining performant data architecture that harmonizes and integrates the large amount of experimental and annotation data available through Bioconductor. Users of our system will be able to create provenance-rich interoperable reports on structural and functional contexts of somatic variants for use in prioritization. Third, we develop scalable infrastructure for the curation, distribution, maintenance, discoverability, and usability of cancer data resources within and externally to Bioconductor. Finally, we develop a program of user training and new outreach approaches to support adoption of advanced Bioconductor infrastructure by developers of new cancer-related packages and existing packages critical to the cancer research community.

抽象的 生物导体是1,500多个开源软件和统计数据包的生态系统 高通量基因组数据的分析和理解。它被癌症基因组学广泛使用 统计分析和可视化的研究社区。该软件生态系统由核心支持 用户和开发人员重复使用的数据类和方法，提供方便的表示形式和 许多高通量分子数据的有效操作。排序成本下降和单细胞 通过合并的测定，对癌症分子生物学的分子生物学进行了越来越解决的测定 DNA序列，表观遗传学，基因表达，蛋白质和其他方面，甚至在单细胞水平上 单个标本。这些发展提出了复杂性，规模和解释性的新挑战 数据。该项目的总体目标是创建和适应核心生物导体软件基础架构 通过以下目标应对这些挑战。首先，我们开发用于分析的基础架构 单细胞多摩变实验。其次，我们实施公平的原则以改善躯体变体 优先级，通过定义性能数据体系结构来协调和集成大量 实验和注释数据可通过生物导体获得。我们系统的用户将能够创建 富含出处的可互操作报告，内容涉及用于用于用于用于用于的体细胞变体的结构和功能上下文 优先级。第三，我们开发可扩展的基础架构，用于策展，分布，维护， 可发现性能以及癌症数据资源内部和外部对生物导体的可用性。最后，我们 制定用户培训和新的外展方法计划，以支持采用高级 新的与癌症相关套件的开发商和现有包装的生物导体基础设施至关重要 癌症研究界。