Enhancing gnomAD Sustainability: Implementing Site Reliability Engineering Principles for Genomic Data Infrastructure

增强 gnomAD 可持续性：实施基因组数据基础设施站点可靠性工程原则

• 批准号: 10838180
• 负责人: Mark Joseph Daly
• 金额: $ 23.5万
• 依托单位: BROAD INSTITUTE, INC.
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-06-01 至 2024-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10838180
• 关键词: Academia; Administrative Supplement; Adoption; Award; Biomedical Research; Breathing; Code; Communities; Complex; Computational Biology; Data; Data Science; Data Set; Databases; Development; Diagnosis; Discipline; Disease; Documentation; Engineering; Ensure; Environment; Failure; Funding; Future; General Population; Genetic; Genetic Diseases; Genetic Variation; Genetic study; Genome; Genomics; Health; Human; Human Genetics; Human Genome; Industry; Infrastructure; Longevity; Parents; Performance; Personnel Turnover; Population; Positioning Attribute; Process; Production; Provider; Publishing; Quality of life; Reaction Time; Registries; Research; Research Personnel; Resources; Scientist; Secure; Site; Software Engineering; Structure; System; Technology; Testing; Thinking; Variant; Work; accurate diagnosis; aggregation database; base; cloud based; computer infrastructure; cost; data infrastructure; design; diverse data; empowerment; exome sequencing; expectation; experience; genome resource; genome sequencing; genomic data; improved; insight; interest; invention; large datasets; multidisciplinary; novel diagnostics; novel therapeutics; open source; operation; personalized medicine; resilience; software development; success; tool; web app

Project Summary The gnomAD (Genome Aggregation Database) project is a large-scale effort to aggregate and harmonize exome and genome sequencing data from diverse human populations, aiming to provide a comprehensive resource to identify and interpret genetic variation in the human genome. gnomAD has become a critical resource for scientists worldwide, enabling them to study the impact of genetic variation on human health and disease. The parent U24 award supports the gnomAD project by providing funding to (1) aggregate and produce increasingly large datasets, (2) integrate gnomAD with other datasets, resources, and statistical tools, and (3) disseminate the results to the wider research community. The parent award ensures the continued development of a high-quality, variant database for researchers, empowering them to advance our understanding of human genetics and contribute to the development of novel diagnostics and therapeutics. This administrative supplement proposes to strengthen the gnomAD project's longevity by incorporating Site Reliability Engineering (SRE) principles and practices. SRE is a new engineering discipline that was invented at large technology companies to streamline management of computational infrastructure, but has not yet seen widespread adoption in academia. The proposal's specific aims are twofold: the first aim involves developing SRE practices within the gnomAD project by refactoring the existing codebase. This will improve the project’s ability to meet unique challenges related to increasing data scale, manage computational environments for the production/research teams, and meet users' expectations for a highly performant browser resource. The second aim relates to creating high quality public documentation for our solutions and publishing these in tool registries for other genomics projects to use, copy, and repurpose.

项目摘要 gnomAD（基因组聚合数据库）项目是一项大规模的努力， 来自不同人群的外显子组和基因组测序数据，旨在提供一个全面的 识别和解释人类基因组遗传变异的资源。gnomAD已经成为一个关键的 为世界各地的科学家提供资源，使他们能够研究遗传变异对人类健康的影响， 疾病 母U24奖通过提供资金支持gnomAD项目，以（1）聚合和生产 越来越大的数据集，（2）将gnomAD与其他数据集、资源和统计工具集成，以及（3） 向更广泛的研究界传播成果。母公司奖确保了 为研究人员开发一个高质量的变异数据库，使他们能够推进我们的研究。 了解人类遗传学，并有助于开发新的诊断和治疗方法。 这份行政补充建议通过合并 现场可靠性工程（SRE）原则和实践。SRE是一门新的工程学科， 在大型技术公司发明，以简化计算基础设施的管理，但没有 但在学术界被广泛采用。该提案的具体目标有两个：第一个目标涉及 通过重构现有的代码库，在gnomAD项目中开发SRE实践。这将改善 该项目应对与不断增加的数据规模、管理计算能力、 为生产/研究团队提供更好的环境，并满足用户对高性能浏览器的期望 resource.第二个目标是为我们的解决方案和出版物创建高质量的公共文档 这些工具登记处供其他基因组学项目使用，复制和重新使用。