Enhancing the GMOD Suite of Genome Annotation and Visualization Tools

增强 GMOD 基因组注释和可视化工具套件

• 批准号: 8108959
• 负责人: Ian H Holmes
• 金额: $ 47.28万
• 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 2014-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8108959
• 关键词: Address; Animal Model; Arizona; Behavior; Biological; California; Collaborations; Communities; Computer software; Data; Databases; Devices; Funding; Galaxy; Generic Drugs; Genome; Genomics; Goals; Image; Imagery; Individual; Informatics; Information Technology; Institutes; Internet; Link; Maps; North Carolina; Ontario; Ontology; Penetration; Phylogeny; Population; Positioning Attribute; Reading; Recommendation; Scientist; Social Network; Software Tools; Standardization; Universities; Work; anticancer research; comparative; comparative genomics; feeding; genome sequencing; improved; insight; interoperability; meetings; migration; model organisms databases; next generation; novel; open source; outreach; portability; programs; relational database; tool; transcriptomics; wiki

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. PUBLIC HEALTH RELEVANCE: The Generic Model Organism Database software suite, especially the genome browser programs GBrowse and JBrowse, have had a transformative effect on model organism genomics. We plan numerous enhancements of these tools to meet the challenges of displaying next-generation sequencing data and community annotation of genomes, and to support migration of the many GBrowse users to the more recent JBrowse. Through continued support of the GMOD Help Desk Position, we will increase penetration and utility of the GMOD software suite.

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努力为基因组信息学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。这些工具中最引人注目和最受欢迎的是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）及其继任者JBrowse（它大大升级了GBrowse用户界面，使其与较新的网络应用程序，如Gmail或Google地图）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（生物学家可以编辑注释的程序），Maker（用于计算生成注释的工作流程自动机）和Galaxy（用于交互式比较基因组学的一套工具）。在本提案的初始资助期间，我们开发了JBrowse的初始版本，增强了GBrowse以显示人口多样性数据，并建立了GMOD帮助台职位以增加GMOD工具的渗透率，特别是基础设施组件。在此更新期间，我们将继续JBrowse的工作，重点关注大型问题的可伸缩性（包括显示高容量短读测序数据）;可扩展性（以便允许个别GMOD开发人员自定义其浏览器）;可移植性问题（包括在移动的设备上的实现）;和社区注释功能（以便科学家可以通过网络上传、共享、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帮助台，重点是转录组学和下一代测序数据，人口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GBrowse和JBrowse的支持。 公共卫生相关性：通用模式生物数据库软件套件，特别是基因组浏览器程序GBrowse和JBrowse，对模式生物基因组学产生了变革性的影响。我们计划对这些工具进行大量增强，以应对显示下一代测序数据和基因组社区注释的挑战，并支持许多GBrowse用户迁移到更新的JBrowse。通过对GMOD帮助台职位的持续支持，我们将提高GMOD软件套件的渗透率和实用性。