Enhancing the GMOD Suite of Genome Annotation and Visualization Tools

描述(申请人提供)：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”使网络出版和交流民主化一样。实现这一点的主要工具将是JBrowse，这是一款功能最丰富的基于JavaScript/HTML5的基因组浏览器。这一更新建立在先前开发的jBrowse事件驱动插件框架(例如最近用于协作管理基因组注释的WebApollo应用程序)的基础上，将生成一系列用于与生物信息学、系统发生学和种群遗传学的常用工具和可视化范例以及后端工作流管理器(例如Galaxy、Maker)、分析包(BioConductor)、通用排队引擎(SGE)和分布式计算系统(Hadoop MapReducte)进行接口的“分析插件”。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，它提供了某些基因组关系(基因组共性、癌症基因组重排和细菌基因组)的方便密集的表示，并具有到其他视图的动画转换。我们将继续我们的支持和推广工作，主动提供GMOD集团(GBrowse)以前的官方Genome浏览器(GBrowse)的约3000个当前安装的升级，并确保约400个当前安装的jBrowse(以及成千上万的jBrowse用户)使用jBrowse工具箱中的最新可视化分析工具保持最新。

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.