Enhancing the GMOD Suite of Genome Annotation and Visualization Tools

描述(由申请人提供)：通用模式生物数据库项目是一个开源社区的努力，为基因组信息学的软件工具带来标准化和互操作性。GMOD软件套件包括许多用于分析、管理、可视化和整合生物数据的程序。这些工具中最显眼和最受欢迎的是GBrowse基因组浏览器(它使基因组序列和注释数据可以在万维网上访问)和它的后续jBrowse(它显著升级了GBrowse用户界面，使其可与较新的网络应用程序，如Gmail或Google Maps相媲美)。其他GMOD工具包括Chado(用于管理基因组注释的关系数据库模式和软件层)、Apollo(生物计算学家可以用来编辑注释的程序)、Maker(用于计算生成注释的工作流自动化程序)和Galaxy(用于交互比较基因组学的工具套件)。在本提案最初的资助期内，我们开发了初始版本的jBrowse，增强了GBrowse以显示人口多样性数据，并设立了GMOD服务台职位，以增加GMOD工具，特别是基础设施组件的渗透率。在这一更新期间，我们将继续致力于JBROWSE方面的工作，重点是针对大型问题的可扩展性(包括显示大量短读测序数据)；可扩展性(以便允许单独的GMOD开发人员定制他们的浏览器)；可移植性问题(包括在移动设备上的实现)；以及社区注释功能(以便科学家可以在Web上上传、分享、审查、标记和讨论注释，以及查看数据库中已有的注释)。我们还将致力于开发工具，以帮助当前的GBrowse用户迁移到JBrowse，同时继续对GBrowse的传统支持。最后，我们将继续支持GMOD服务台，重点是转录学和下一代测序数据、种群基因组和多样性数据、工作流程和管道工具、软件互操作性问题，以及对GBrowse和jBrowse的支持。

DESCRIPTION (provided by applicant): The Generic Model Organism Database Project is an open-source community effort to bring standardization and interoperability to software tools for genome informatics. The GMOD software suite includes many programs for the analysis, management, visualization and integration of biological data. Amongst the most visible and popular of these tools are the GBrowse genome browser (which makes genome sequence and annotation data accessible over the world-wide web) and its successor JBrowse (which significantly upgrades the GBrowse user interface to make it comparable to newer web applications, such as GMail or Google Maps). Other GMOD tools include Chado (a relational database schema and software layer for managing genome annotations), Apollo (a program with which biocurators can edit annotations), Maker (a workflow automator for generating annotations computationally) and Galaxy (a suite of tools for interactive comparative genomics). During the initial funding period of this proposal, we developed the initial release of JBrowse, enhanced GBrowse to display population diversity data, and established the GMOD Help Desk position to increase penetration of the GMOD tools, especially infrastructural components. In this renewal period, we will continue work on JBrowse, concentrating on scalability to large problems (including display of high-volume short-read sequencing data); extensibility (so as to permit individual GMOD developers to customize their browsers); portability issues (including implementations on mobile devices); and community annotation features (so that scientists can upload, share, review, mark-up and discuss annotations over the web, as well as viewing annotations already in the database). We will also work on developing tools to assist current GBrowse users in migrating to JBrowse, while continuing legacy support for GBrowse. Finally we will continue to support the GMOD Help Desk, with emphasis on transcriptomics and next-generation sequencing data, population genomic and diversity data, workflow and pipeline tools, software interoperability issues, and support of GBrowse and JBrowse.