Enhancing the GMOD Suite of Genome Annotation and Visualization Tools

该项目的长期目标是使基因组的协作注释、分析和共享民主化，就像“社交网络”使网络出版和通信民主化一样。这方面的主要工具将是JBrowse，它是功能最丰富的基于JavaScript/HTML5的基因组浏览器。这种更新是建立在以前为JBrowse开发的事件驱动插件框架之上的（例如最近的WebApollo应用程序，用于基因组注释的协作管理），将生成一系列“分析插件”，用于与来自生物信息学、遗传学和群体遗传学的常用工具和可视化范例以及后端工作流程管理器进行交互。（例如Galaxy、Maker）、分析包（Bioconductor）和通用排队引擎（SGE）以及分布式计算系统（Hadoop MapReduce）。一个平行的交付是一个新的和完全集成的2D圆形几何视图在JBrowse，它提供了一个方便的密集表示某些基因组关系（基因组同线性，癌症基因组重排，和细菌基因组）与动画过渡到其他视图。我们将继续我们的支持和推广工作，积极提供升级到约3000个当前安装的GMOD组（GBrowse）以前的官方基因组浏览器，并确保约400个当前安装的JBrowse（和成千上万的JBrowse用户）保持最新的JBrowse工具箱中的最新可视化分析工具。

DESCRIPTION (provided by applicant): The long-term objective of this project is to democratize the collaborative annotation, analysis, and sharing of genomes, much as the "social web" has democratized web publishing and communication. The main vehicle for this will be JBrowse, the most feature-rich JavaScript/HTML5-based genome browser. This renewal, building on the previously-developed event-driven plugin framework for JBrowse (an example of which is the recent WebApollo app for collaborative curation of genome annotations), will generate a range of "analysis plugins" for interfacing with common tools and visualization paradigms from bioinformatics, phylogenetics, and population genetics, as well as back-end workflow managers (e.g. Galaxy, Maker), analysis packages (Bioconductor), and general queuing engines (SGE) and distributed computation systems (Hadoop MapReduce). A parallel deliverable is a new and completely integrated 2D circular-geometry view within JBrowse, which offers a conveniently dense representation of certain genome relationships (genomic synteny, cancer genome rearrangements, and bacterial genomes) with animated transitions to other views. We will continue in our support and outreach efforts, proactively offering upgrades to the ~3000 current installations of the previous official Genome Browser from the GMOD group (GBrowse), and ensuring that the ~400 current JBrowse installations (and many thousands of JBrowse users) remain up to date with the latest visual analysis tools in the JBrowse toolbox.