Enhancements to the GMOD Suite of Genome Annotation and Visualization Tools

可用性仍然是广泛采用尖端生物信息学的一个重大障碍 工具，由于缺乏用户友好的网络界面。通用模式生物 数据库（GMOD）提供基于标准的软件组件， 可以快速组装面向网络的基因组数据库。JBrowse，基因组 GMOD的浏览器，旨在使基因组信息学“民主化”， 注释和序列分析工具，更广泛的社区， 生物学家，使用JavaScript和动态网络。JBrowse现在由以下公司积极使用： 成千上万的网站和成千上万的用户。在项目的这个阶段，我们 我计划在JBrowse中构建一个synteny浏览器，这样用户就可以快速浏览 在相关基因组之间，观察进化上保守的基因结构及其 关联比对，并在其系统发育背景下可视化基因组注释。 这个synteny浏览器将具有与JBrowse相同的响应性和交互性， 平滑平移、缩放、过滤、排序和搜索， 从Web浏览器中进行拖放操作。我们还将大大 大规模提高JBrowse性能：许多JBrowse实例有数百个或 成千上万的轨道，要求效率优化，更紧凑的可视化， 和用户界面增强，以促进数据的“可兼容性”。我们将开发一个 用于定制JBrowse的图形界面，配置其外观和行为， 并安装插件，以WordPress博客平台的风格。我们将继续努力， 新开发的JBrowse分析服务器，可进行标准读取参考 对齐工具（BWA和BowTie）可从浏览器内提供给用户，我们 将为RNA-Seq，群体基因组学，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， 重点研讨会、培训材料和文件，以最大限度地利用 GMOD/JBrowse到更广泛的社区。

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.