Enhancements to the GMOD Suite of Genome Annotation and Visualization Tools

基因组注释和可视化工具 GMOD 套件的增强

• 批准号: 9920732
• 负责人: Ian H Holmes
• 金额: $ 68.05万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-09-01 至 2023-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9920732
• 关键词: Adoption; Appearance; Authorization documentation; Behavior; Biological; Client; Communities; Community Developments; Computer software; Custom; Data; Data Set; Documentation; Drops; Educational workshop; Elements; Galaxy; Genes; Genome; Genomics; Grain; Informatics; Internet; Link; Linkage Disequilibrium; Manuals; Metadata; Mission; Modernization; Names; Performance; Phase; Phylogenetic Analysis; Polishes; Population; Registries; Running; Scientist; Sequence Analysis; Series; Sorting - Cell Movement; Speed; Structure; Synteny; Text; Training; Visualization; Visualization software; annotation system; base; bioinformatics tool; epigenomics; genome annotation; genome browser; genome database; genomic data; genomic tools; graphical user interface; hackathon; improved; large datasets; model organisms databases; navigation aid; operation; outreach; tool; transcriptome sequencing; usability; user-friendly; web interface; web site; web-accessible

Usability remains a significant barrier to broader adoption of cutting-edge bioinformatics tools, due to a lack of user-friendly web interfaces. The Generic Model Organism Database (GMOD) provides standards-based software components from which web-facing genome databases can be quickly assembled. JBrowse, the genome browser of GMOD, aims to "democratize" genome informatics by making genome annotations and sequence analysis tools more accessible to the broader community of biologists, using JavaScript and the dynamic web. JBrowse is now in active use by thousands of websites and tens of thousands of users. In this phase of the project, we plan to build a synteny browser into JBrowse, so that users can rapidly navigate between related genomes, view evolutionarily conserved gene structures and their associated alignments, and visualize genome annotations in their phylogenetic context. This synteny browser will have the same responsiveness and interactivity as JBrowse, with smooth panning, zooming, filtering, sorting, and searching available as drag-and-drop operations from within the web browser. We will also significantly improve JBrowse's performance at scale: many JBrowse instances have hundreds or thousands of tracks, demanding efficiency optimizations, more compact visualization, and user interface enhancements to promote data "discoverability". We will develop a graphical interface for customizing JBrowse, configuring its appearance and behavior, and installing plugins, in the style of the Wordpress blog platform. We will build on the newly-developed JBrowse analysis server to make standard read-to-reference alignment tools (BWA and BowTie) available to users from within the browser, and we will make new visualizations available for RNA-Seq, population genomics, epigenomics, and other data types. Finally, we will continue GMOD's outreach/helpdesk efforts with focused workshops, training materials, and documentation to maximize the utility of GMOD/JBrowse to the broader community.

可用性仍然是更广泛采用尖端生物信息学的重大障碍 工具，由于缺乏用户友好的网络界面。类属模式生物 数据库(GMOD)提供基于标准的软件组件 面向网络的基因组数据库可以快速组装。基因组--JBrowse GMOD的浏览器，旨在通过制作基因组来实现基因组信息学的民主化 更广泛的社区更容易访问批注和序列分析工具 生物学家，使用脚本和动态网络。JBROWSE现正由以下人员使用 数以千计的网站和数万用户。在该项目的这一阶段，我们 计划在JBROWSE中构建一个同步浏览器，以便用户可以快速导航 在相关基因组之间，查看进化上保守的基因结构及其 相关的比对，并在其系统发育背景下可视化基因组注释。 该同步浏览器将具有与JBROWSE相同的响应性和互动性， 提供流畅的平移、缩放、过滤、排序和搜索功能 从Web浏览器中进行拖放操作。我们还将显著地 大规模提高JBrowser的性能：许多JBrowser实例有数百个或 数以千计的曲目，要求效率优化，更紧凑的可视化， 以及用户界面的增强，以促进数据的“可发现性”。我们将开发一种 用于定制JBrowser、配置其外观和行为的图形界面 和安装插件，以WordPress博客平台的风格。我们将在 新开发的JBROWSE分析服务器可进行标准的阅读参考 用户可从浏览器中使用对齐工具(BWA和蝴蝶结)，并且我们 将为RNA-Seq、种群基因组、表观基因组学、 和其他数据类型。最后，我们将继续GMOD的外展/服务台工作 有重点的研讨会、培训材料和文档，以最大限度地利用 Gmod/j浏览到更广泛的社区。