Computation Core

计算核心

• 批准号: 10413893
• 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/10413893
• 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.

摘要 - 计算组件 基因表达数据库（GXD）项目的计算组件支持GXD 维护并扩展其复杂的信息基础架构。 GXD是鼠标的丰富资源 发展基因表达数据通过这些数据，研究人员可以发现表达模式至关重要 了解基因的功能以及人类发展，健康，健康的分子机制 和疾病。计算组件维护的GXD基础架构包含关系 数据库，数据加载和QC软件组件，交互式策展接口，现代网络 界面和多个批量数据传播组件。我们将发展系统以实现新的 策展和技术开发组件中描述的功能。这将包括：确保 通过常规维护，GXD信息基础架构的鲁棒性；提高性能 升级我们的索引技术堆栈和并行索引分布；将我们的策展接口升级到 现代基于网络的平台；精炼/重新培训我们的相关分类器对SCRNA-SEQ更敏感 研究；增强小鼠解剖结构的表示，以包含发育分化；和 扩展元数据捕获以在特定细胞类型中包括表达。在实现这些目标时，我们将申请 行业最佳实践，例如敏捷开发方法，自动回归测试，定期维护 时间表和全面的质量控制措施。