INCLUDING CHIMERA IN THE NRAMM AUTOMATED ELECTRON MICROSCOPY PIPELINE

将 Chimera 纳入 NRAMM 自动电子显微镜管道中

• 批准号: 7723541
• 负责人: THOMAS GODDARD
• 金额: $ 1.54万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-07-01 至 2009-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7723541
• 关键词: 3-Dimensional; Biomedical Technology; Cells; Chimera organism; Code; Color; Computer Retrieval of Information on Scientific Projects Database; Data; Data Set; Databases; Electron Microscope; Electron Microscopy; Funding; Goals; Grant; Imagery; Institution; Maps; Methods; Microscopy; Molecular; Process; Research; Research Personnel; Resources; Ribosomes; Slice; Source; Specimen; Standards of Weights and Measures; Structure; Techniques; United States National Institutes of Health; Virus; density; molecular assembly/self assembly; multicatalytic endopeptidase complex; particle; reconstruction; software development

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. This collaborative project develops the software to use Chimera visualization capabilities within the NRAMM Automated Processing Pipeline (Appion) for electron microscope single particle reconstructions. The Appion pipeline produces 3-dimensional density maps of large molecular assemblies such as viruses, ribosomes, proteasomes and other molecular machinery in the cell which has sufficiently uniform structure to allow averaging many specimens. The pipeline aims to bring this experimental technique to researchers who are not experts in this experimental methods. This is the central goal of the National Resource for Automated Molecular Microscopy, a Biomedical Technology Research Resource directed by Bridget Carragher. The visualization component of the pipeline is handled by the Chimera package developed by the RBVI. The effort to incorporated Chimera in the pipeline involves code that automatically produces standard views of pipeline generated data sets residing in a database. A more advanced capability to include Chimera sessions within the pipeline database that allow users to quickly open their data in Chimera in useful standard views (coloring, slicing, thresholding, filtering, ...) as a starting point for more specialized analysis is also planned.

该副本是利用众多研究子项目之一 由NIH/NCRR资助的中心赠款提供的资源。子弹和 调查员（PI）可能已经从其他NIH来源获得了主要资金， 因此可以在其他清晰的条目中代表。列出的机构是 对于中心，这不一定是调查员的机构。 这个协作项目开发了该软件，用于使用电子显微镜单粒子重建的NRAMM自动化处理管道（APPION）内的嵌合体可视化功能。 APPION管道产生了大分子组件的3维密度图，例如病毒，核糖体，蛋白酶体和细胞中其他分子机械，这些机械具有足够均匀的结构，可以平均许多标本。 该管道旨在将这种实验技术带给那些不是这种实验方法专家的研究人员。 这是全国自动分子显微镜资源的核心目标，这是Bridget Carragher指导的生物医学技术研究资源。 管道的可视化组件由RBVI开发的嵌合封装处理。 将嵌合在管道中的融合的努力涉及代码，该代码会自动产生位于数据库中的管道生成的数据集的标准视图。 在管道数据库中包含嵌合体会话的更高级功能，该会话允许用户以有用的标准视图（着色，切片，阈值，过滤等）在嵌合体中快速打开其数据作为更专业分析的起点。