Enhancement of the GBrowse Genome Annotation Browser

GBrowse 基因组注释浏览器的增强

• 批准号: 8151702
• 负责人: Ian H Holmes
• 金额: $ 28.87万
• 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 2011-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8151702
• 关键词: Adoption; Biological; Biology; Communities; Computer software; Data; Databases; Documentation; Education and Outreach; Educational workshop; Feedback; Generic Drugs; Genome; Genomics; Imagery; Individual; Modeling; Penetration; Personal Computers; Population; Protocols documentation; Published Comment; Reporting; Running; Services; Software Tools; System; Time; Training Support; Visual; base; biological research; data management; data mining; data modeling; genetic association; genome database; improved; meetings; model organisms databases; tool; web site

DESCRIPTION (provided by applicant): The Generic Model Organism Database (GMOD) software tools comprises a set of biological data management and visualization components suited for creating integrated online databases of genomic data. This proposal seeks to significantly enhance the functionality of one of the most popular of the GMOD tools, the GBrowse genome annotation browser, by giving it smooth scrolling and zooming abilities, as well as a facility for commenting on existing annotations that encourages democratic genome annotation. In recognition of the shift of biology away from the analysis of a single individual and towards the study of whole populations, we also propose to add features that make GBrowse suitable for visualizing genetic association and diversity data. These enhancements will be implemented without destroying the aspects of GBrowse that made it popular in the first place: the ability to install and run it on personal computers and other modest hardware. This proposal further seeks to encourage the take up by the community of the integrated GMOD suite. While individual components of GMOD have been taken up enthusiastically by the community and are widely used, the full suite of tools, which includes a database schema, a workflow management system, a data mining system and a template-based web site, have not achieved the same penetration due to the lack of comprehensive documentation, packaging and examples. We wish to rectify this situation by establishing a full-time support center responsible for GMOD packaging, documentation, end-user education and outreach.

描述（由申请人提供）：通用模式生物数据库（GMOD）软件工具包括一组生物数据管理和可视化组件，适用于创建基因组数据的集成在线数据库。该提案旨在显著增强GMOD工具中最受欢迎的工具之一GBrowse基因组注释浏览器的功能，使其具有流畅的滚动和缩放能力，以及对鼓励民主基因组注释的现有注释进行评论的功能。在认识到生物学从单个个体的分析转向对整个种群的研究的转变，我们还建议添加功能，使GBrowse适合可视化遗传关联和多样性数据。这些增强将在不破坏GBrowse最初使其流行的方面的情况下实现：在个人计算机和其他普通硬件上安装和运行它的能力。这项建议进一步鼓励社区采用综合GMOD套件。虽然GMOD的个别组成部分受到社区的热烈欢迎并得到广泛使用，但整套工具，包括数据库模式、工作流程管理系统、数据挖掘系统和基于模板的网站，由于缺乏全面的文件、包装和实例，没有达到同样的渗透率。我们希望通过建立一个全职的支持中心来纠正这种情况，该中心负责GMOD包装、文档、最终用户教育和推广。