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（基因组汇总数据库）项目是汇总和协调的大规模努力 外显子和基因组测序数据来自人类人群的数据，旨在提供全面的 资源识别和解释人类基因组中的遗传变异。 gnomad已成为关键 全球科学家资源，使他们能够研究遗传变异对人类健康的影响 疾病。 父母U24奖通过为（1）汇总和生产提供资金来支持GNOMAD项目 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在一起，以及（3） 将结果传播给更广泛的研究界。父母奖确保继续 为研究人员开发高质量的变体数据库，使他们能够促进我们 了解人类遗传学，并有助于新的诊断和治疗的发展。 这项行政补充提案通过合并来加强GNOMAD项目的寿命 站点可靠性工程（SRE）原理和实践。 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架构的管理，但没有 尚未在学术界广泛采用。提案的具体目的是双重的：第一个目的涉及 通过重构现有代码库来开发GNOMAD项目中的SRE实践。这将有所改善 该项目应对与增​​加数据量表相关的独特挑战，管理计算的能力 生产/研究团队的环境，并满足用户对高性能浏览器的期望 资源。第二个目标涉及为我们的解决方案创建高质量的公共文档和发布 这些在用于使用，复制和改革的其他基因组项目的工具注册表中。