Supplement: Enhancing Community Contributions to Bioconductor With Build System Containerization and a GPU for Testing

补充：通过构建系统容器化和用于测试的 GPU 增强社区对 Bioconductor 的贡献

• 批准号: 10838736
• 负责人: VINCENT JAMES CAREY
• 金额: $ 22.75万
• 依托单位: DANA-FARBER CANCER INST
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-06 至 2026-02-28
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10838736
• 关键词: Academia; Acceleration; Achievement; Address; Adverse event; Applications Grants; Archives; Behavior; Benchmarking; Bioconductor; Biology; Cells; Clustered Regularly Interspaced Short Palindromic Repeats; Code; Communities; Comprehension; Computer software; Consumption; Data; Data Analyses; Data Science; Data Scientist; Dependence; Development; Discipline; Ecosystem; Elements; Engineering; Ensure; Environment; Event; Failure; Flow Cytometry; Funding; Genes; Genome; Genomic medicine; Genomics; Growth; Hour; Image; Industrialization; Industry; Infrastructure; Language; Linux; Methods; Modeling; National Human Genome Research Institute; Neural Network Simulation; Process; Proteins; Quality Control; Recovery; Reporting; Resources; Schedule; Site; Software Tools; Structure; System; Telemetry; TensorFlow; Testing; Update; Variant; Work; computing resources; cost; design; experimental study; genome resource; genome-wide; genomic data; improved; innovation; interest; interoperability; longitudinal database; model organism; open source; operation; parent grant; portability; response; sequencing platform; statistical learning; tool; transcriptomics

PROJECT SUMMARY/ABSTRACT "Bioconductor: An Open-Source, Open-Development Computing Resource for Genomics" is the parent grant of this application for supplemental funds. Bioconductor is an open source, open development ecosystem of software and data for the analysis and comprehension of genome- scale experiments. The system is primarily rooted in the R language but has extensive interoperability capabilities and incorporates tools developed in numerous other languages. Bioconductor resources are requested at scientific and industrial sites throughout the world, with an outflow from Bioonductor's cloud distribution systems of approximately 1TB of software and data per day. The system provides infrastructure for genome representation and representation of variants, genomic sequences and gene models for numerous model organisms, analytical software for many array and sequencing platforms, and annotation and experiment archives, all checked for consistency and portability on a daily basis. This request for supplemental funds addresses engineering requirements of the build and distribution system, which has had its present structure for over ten years, and adds support for graphical processing units in the build and test system. Our plan includes work on containerization and upscaling of the build and check system, and enhancement of the methods of recording resource use and adverse events in ecosystem build processes. In essence, the proposed work will allow the Bioconductor project to more fully embrace an "Infrastructure as Code" discipline to simplify redeployment and rescaling in response to throughput requirements, and to improve automatic discovery and reporting of system problems. Because the requirements of the genomic data science community are continually diversifying in terms of complexity and volume of data being generated, and the number of hardware platforms in use is likewise growing, the work proposed cannot be accomplished under the initial funding plan.

项目概要/摘要 “Bioconductor：基因组学的开源、开放开发计算资源”是 家长补助本申请的补充资金。 Bioconductor 是一个开源、开放的 用于分析和理解基因组的软件和数据的开发生态系统 规模实验。该系统主要植根于 R 语言，但具有广泛的 互操作能力并结合了许多其他领域开发的工具 语言。整个科学和工业场所都需要生物导体资源 全球，Bioonductor 云分发系统流出约 1TB 每天的软件和数据。该系统提供了基因组表示和 多种模型的变体、基因组序列和基因模型的表示 生物体、用于许多阵列和测序平台的分析软件以及注释和 实验档案，每天都会检查一致性和可移植性。这个要求 补充资金满足构建和分发的工程要求 系统的现有结构已经有十多年了，并增加了对图形化的支持 构建和测试系统中的处理单元。我们的计划包括容器化工作和 升级构建和检查系统，并增强记录方法 生态系统构建过程中的资源使用和不良事件。本质上，所提议的 这项工作将使 Bioconductor 项目更全面地拥抱“基础设施即代码” 简化重新部署和重新扩展以响应吞吐量要求的纪律，并 改进系统问题的自动发现和报告。因为要求 基因组数据科学界在复杂性和有效性方面不断多样化 生成的数据量以及使用的硬件平台的数量也同样如此 随着规模的不断扩大，提议的工作无法在最初的供资计划下完成。

项目成果

Tackling the widespread and critical impact of batch effects in high-throughput data.

解决高通量数据中批次效应的广泛且关键的影响。

• 发表时间: 2010
• 作者: Leek, Jeffrey T;Scharpf, Robert B;Bravo, Héctor Corrada;Simcha, David;Langmead, Benjamin;Johnson, W Evan;Geman, Donald;Baggerly, Keith;Irizarry, Rafael A
• 通讯作者: Irizarry, Rafael A

Robust decomposition of cell type mixtures in spatial transcriptomics.

空间转录组学中细胞类型混合物的稳健分解。

• 发表时间: 2022-04
• 影响因子: 46.9
• 作者: Cable, Dylan M;Murray, Evan;Zou, Luli S;Goeva, Aleksandrina;Macosko, Evan Z;Chen, Fei;Irizarry, Rafael A
• 通讯作者: Irizarry, Rafael A