NMRbox information management: CONNJUR and BMRB integration

NMRbox 信息管理：CONNJUR 和 BMRB 集成

• 批准号: 10652470
• 负责人: JEFFREY C HOCH
• 金额: $ 38.03万
• 依托单位: UNIVERSITY OF CONNECTICUT SCH OF MED/DNT
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-09-01 至 2025-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10652470
• 关键词: Biomolecular Nuclear Magnetic Resonance; Chemicals; Collection; Communities; Complex; Computer software; Consumption; Custom; Data; Data Analyses; Data Set; Deposition; Development; Ensure; Environment; Extensible Markup Language; Fostering; Glean; Goals; Harvest; Individual; Information Management; Investigation; Knowledge; Libraries; Manuals; Metadata; Occupations; Operating System; Pathway interactions; Process; Productivity; Pythons; Recording of previous events; Reporting; Reproducibility; Research; Research Personnel; Resources; Sampling; Services; Software Tools; System; Time; Translations; Validation; Work; analytical tool; cluster computing; computerized data processing; data dictionary; data modeling; data repository; data submission; data visualization; design; experimental study; file format; improved; interoperability; metabolomics; open source; preservation; prototype; public database; reconstruction; repository; small molecule; tool

TRD2 Summary Biomolecular NMR data computation is complex, requiring both semi-automated and manual processing steps. The NMRbox platform provides easy access to the myriad software tools used during an individual investigation. The efforts of TRD1 ensure that all of this software functions within the same operating system environment. The goals of TRD2 are to provide information management solutions to promote software interoperability across the NMRbox platform (TRD1) and with the analytics of TRD3; to foster reproducibility through the active curation of scientific datasets and workflows; to facilitate the integration of experimental and derived data with information from public databases to generate new knowledge, and to help aggregate this diverse panoply of experimental data and metadata to create and facilitate richer depositions to the appropriate public data repositories. A key component to enriching repository depositions is the collection of provenance metadata which reports on the history or lineage of how computations were orchestrated and intermediate and final results obtained. Knowing the pathway of how results were obtained is a critical component to reproducing and building upon scientific claims. The aims of this project period are fourfold. The CONNJUR data model and CONNJUR software integration environments (integral components of NMRbox) will be extended to capture more metadata to support the tracking of provenance (or data lineage), to foster reproducibility, to promote software interoperability both within and without NMRbox, and to support a richer metadata set for depositions to the public data repositories. In addition, the workflow management system will be extended to support high-throughput computational workflows by connecting to powerful job management systems such as HTCondor and DAGMan. The data and process logging capabilities of NMRbox will be used for automatic harvesting of whatever metadata can be gleaned by these mechanisms. Finally, more direct access to BMRB resources will be provided through direct machine-to- machine services.

TRD2摘要 生物分子NMR数据计算很复杂，需要半自动和手动处理步骤。 NMRBox平台可轻松访问个人调查过程中使用的众多软件工具。 TRD1的努力确保所有这些软件都在同一操作系统环境中发挥作用。 TRD2的目标是提供信息管理解决方案，以促进跨越软件的互操作性 NMRBox平台（TRD1）和TRD3的分析；通过主动策划促进可重复性 科学数据集和工作流；促进实验和衍生数据与信息的集成 从公共数据库生成新知识，并帮助汇总实验的这种多样性 数据和元数据以创建和促进对适当的公共数据存储库的富裕沉积。钥匙 丰富存储库沉积的组成部分是出处元数据的收集 计算方式的历史或血统，并获得了中间和最终结果。会心 如何获得结果的途径是繁殖和建立科学的关键组成部分 主张。 这个项目期间的目标是四倍。 Connjur数据模型和Connjur软件集成 环境（NMRBox的积分组件）将扩展以捕获更多的元数据以支持 跟踪出处（或数据谱系），以促进可重复性，以促进软件互操作性 并且没有NMRBox，并支持将较丰富的元数据设置为向公共数据存储库沉积。在 此外，将扩展工作流管理系统以支持高通量计算工作流程 通过连接到HTCONDOR和DAGMAN等强大的工作管理系统。数据和过程 NMRBox的记录功能将用于自动收集任何元数据 这些机制。最后，将通过直接的机器到 - 机器服务。