Computation Core

计算核心

• 批准号: 10172378
• 负责人: JOEL E. RICHARDSON
• 金额: $ 44.3万
• 依托单位: JACKSON LABORATORY
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-12-02 至 2026-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10172378
• 关键词: Address; Anatomy; Architecture; Atlases; Biological; Cells; Computer software; Data; Data Set; Development; Developmental Anatomy; Developmental Gene; Disease; Ensure; Gene Expression; Health; Human Development; Industry; Informatics; Information Systems; Infrastructure; Literature; Machine Learning; Maintenance; Measures; Metadata; Modernization; Molecular; Mus; Online Systems; Ontology; Pattern; Performance; Quality Control; Reporting; Reproducibility; Research Personnel; Resources; Schedule; Secure; Structure; System; Technology; Testing; Triage; Update; cell type; data dissemination; data management; data warehouse; disease phenotype; experimental study; gene expression database; gene function; improved; indexing; informatics infrastructure; interoperability; method development; mouse development; novel; phenotypic data; relational database; single cell technology; single-cell RNA sequencing; sound; technology development; tool; transcriptome sequencing; web interface; whole genome

Abstract - COMPUTATION COMPONENT The Computation Component of the Gene Expression Database (GXD) project supports GXD by maintaining and extending its sophisticated informatics infrastructure. GXD is a rich resource of mouse developmental gene expression data through which researchers can discover expression patterns crucial for understanding the function of genes and the molecular mechanisms that underlie human development, health, and disease. The GXD infrastructure maintained by the Computation Component contains relational databases, data loading and QC software components, an interactive curatorial interface, a modern web interface, and multiple bulk data dissemination components. We will evolve the system to enable the new functionality described in the Curation and Technology Development Components. This will include: ensuring the robustness of GXD’s information infrastructure through regular maintenance; improving performance by upgrading our indexing technology stack and parallelizing index distribution; upgrading our curation interface to a modern web-based platform; refining/retraining our relevance classifier to be more sensitive to scRNA-seq studies; enhancing the representation of mouse anatomy to encompass developmental differentiation; and extending metadata capture to include expression in specific cell types. In achieving these aims, we will apply industry best practices such as agile development methods, automatic regression testing, regular maintenance schedules, and comprehensive quality control measures.

抽象计算组件 基因表达数据库(GXD)项目的计算组件通过以下方式支持GXD 维护和扩展其复杂的信息学基础设施。GXD是一种丰富的小鼠资源 发育中的基因表达数据，研究人员可以通过这些数据发现对 了解基因的功能和构成人类发育、健康、 和疾病。由计算组件维护的GXD基础设施包含关系 数据库、数据加载和质量控制软件组件、交互式策展界面、现代网络 接口和多个批量数据分发组件。我们将发展该系统，以支持新的 培训和技术开发组件中介绍的功能。这将包括：确保 通过定期维护提高GXD信息基础设施的健壮性；通过以下方式提高性能 升级我们的索引技术堆栈和并行化索引分发；将我们的精选界面升级到 一个现代的基于网络的平台；改进/重新训练我们的相关性分类器，使其对scRNA-seq更敏感 研究；加强对小鼠解剖学的再现，以涵盖发育分化；以及 扩展元数据捕获以包括特定单元格类型中的表达式。为了实现这些目标，我们将应用 行业最佳实践，如敏捷开发方法、自动回归测试、定期维护 时间表和全面的质量控制措施。