Bioconductor: An Open-Source, Open-Development Computing Resource for Genomics

Bioconductor：基因组学的开源、开放开发计算资源

• 批准号: 10371030
• 负责人: VINCENT JAMES CAREY
• 金额: $ 132.4万
• 依托单位: DANA-FARBER CANCER INST
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-09-28 至 2026-02-28
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10371030
• 关键词: Address; Adoption; Advanced Development; Age; Algorithms; Archives; Area; Atlases; Bioconductor; Bioinformatics; Biological; Biological Assay; Biology; Cells; Code; Communities; Community Health Education; Comprehension; Computer software; Computing Methodologies; Data; Data Element; Data Science; Data Scientist; Data Set; Dependence; Development; Discipline; Documentation; Education; Environment; FAIR principles; Flow Cytometry; Fostering; Funding; Genome; Genomic medicine; Genomics; Goals; Grant; Growth; Health; Human; Image; Individual; Informatics; Infrastructure; Ingestion; Instruction; International; Knowledge; Linux; Maintenance; Methodology; Methods; Modernization; National Human Genome Research Institute; Performance; Population Genetics; Principal Investigator; Process; Programming Languages; Proteomics; Reproducibility; Research; Research Personnel; Resources; Services; Software Engineering; Structure; System; Systematic Bias; Technology; Testing; Training; Visualization; Work; analytical method; base; cloud based; community engagement; computing resources; data ecosystem; data quality; design; genome analysis; genome sciences; genome-wide; genomic data; genomic platform; genomic tools; improved; interoperability; member; new technology; open source; pedagogy; personalized genomic medicine; portability; research and development; software development; symposium; tool; usability

PROJECT SUMMARY Bioconductor is a project dedicated to the analysis and interpretation of high throughput genomic data, includ- ing sequencing, microarray, flow cytometry, proteomics, and imaging data. Bioconductor is based on the R sta- tistical programming language. It consists of software, annotation, and data packages developed and contributed by individuals funded by this grant, and by the national and international scientific community. Bioconductor is highly respected, widely used in the global bioinformatics community, highly cited, and has formal collaborative alignments with the Human Cell Atlas and NHGRI's Genomic Analysis, Visualization, and Informatics Lab Space (AnVIL). Work proposed in this renewal application reflects the commitment of the project to open-source/open- development creation and distribution of portable tools for genomic data science, high-quality documentation and support for users and developers, adaptation of computational methods to new technologies for cloud-scale data science, and effective training of the workforce for genome biology and personalized genomic medicine. The spe- cific aims are (1) maintenance and enhancement of the system at bioconductor.org for organizing and distributing analytic software, reference data, and curated experimental data, (2) hardening of core infrastructural software packages to increase reliability and throughput of analyses based on the system, (3) conduct research and devel- opment of best practices for taking advantage of scalable computing strategies for integrative cloud-scale genomic analysis, and (4) enhance community engagement and education practices that have been intrinsic to the project since its inception. By pursuing these aims, project investigators and contributors add to the usability, relevance, and robustness of a system and community that is unique and is uniquely situated to accelerate progress in many areas of genomic data science, ultimately contributing to biological knowledge and improvement of human health.

项目摘要 Bioconductor是一个致力于分析和解释高通量基因组数据的项目，包括 - 测序，微阵列，流动细胞仪，保护性和成像数据。生物导体基于r sta- 潮流编程语言。它由开发和贡献的软件，注释和数据包组成 由这笔赠款以及由国家和国际科学界资助的个人。生物导体是 高度尊重，广泛用于全球生物信息学界，高度引用，并具有正式的合作 与人类细胞地图集和NHGRI的基因组分析，可视化和信息实验室实验室空间的对齐 （砧）。在此续签申请中提出的工作反映了该项目开放源/开放的承诺 用于基因组数据科学的便携式工具的开发创建和分配，高质量文档和 支持用户和开发人员，将计算方法改编为新技术的云规模数据 科学，以及对基因组生物学和个性化基因组医学的劳动力的有效培训。 Spe- CIFIS的目的是（1）在BioConductor.org上维护和增强系统用于组织和分发 分析软件，参考数据和策划的实验数据，（2）核心基础设施软件的硬化 包装以提高基于系统的分析的可靠性和吞吐量，（3）进行研究和开发 利用可扩展计算策略的最佳实践的选项 分析，以及（4）增强该项目内在的社区参与和教育实践 自成立以来。通过追求这些目标，项目调查人员和贡献者增加了可用性，相关性， 独特的系统和社区的稳健性 基因组数据科学领域，最终有助于生物学知识和改善人类健康。