Apollo: An extensible genome annotation editor

描述（由申请人提供）：DMA序列的注释是理解任何生物体中基因和基因产物生物学的必要先决条件。注释是可以绑定到基因组序列的任何特征，例如外显子、转录本、启动子或转座元件。通过将自动化序列分析结果与生物学家的专业知识相结合，获得最高质量的注释。Apollo是一个跨平台的注释编辑工具，它通过提供交互式图形显示简化了这个过程，允许生物学家查看基因组区域的许多不同的计算分析，并使用它们，以及他们对直接实验结果的了解，来创建和完善详细的注释。Apollo是一个开源Java应用程序，易于在任何平台上安装和运行。自2002年首次发布以来，Apollo已经成为使用最广泛的注释编辑器之一。促成其成功的因素包括其直观的交互式用户界面；可配置性;安装过程简单；丰富的文档;响应迅速的邮件列表；可扩展性;以及开放源代码库。它已经被下载了数千次，各种各样的学术和商业研究团体都修改或扩展了它，以满足他们的个人需求（见附录1），从而节省了无数小时的开发时间。我们正在申请资金，以继续支持和改进这一宝贵的软件资源。我们的目标包括使阿波罗完全了解序列本体，以更好地支持社区范围内对不同生物体的注释；设计新的配置界面，以简化从不同来源加载数据和设置显示偏好的过程；并增加了两个新的专业编辑器：多比对转录查看器和编辑器，允许直接参考比对数据修改基因模型；和一个重复元素编辑器。我们还计划提供更多的支持和扩展，包括研讨会和现场访问，培训生物学家使用Apollo，并向软件开发人员展示如何将他们现有的工具集成到Apollo的可扩展框架中。本提案中的工作将由劳伦斯伯克利国家实验室（LBNL）和卡内基研究所的拟南芥信息资源（TAIR）合作完成，LBNL提供大部分软件开发，卡内基提供目标软件开发资源和注释专业知识。

DESCRIPTION (provided by applicant): Annotation of DMA sequences is an essential prerequisite for understanding the biology of genes and gene products in any organism. An annotation is any feature that can be tied to genomic sequence, such as an exon, transcript, promoter, or transposable element. The highest-quality annotation is obtained by combining automated sequence analysis results with the expert knowledge of biologists. Apollo is a cross-platform annotation editing tool that streamlines this process by providing an interactive graphical display that allows biologists to view many different computational analyses of a genomic region and use them, together with their knowledge of direct experimental results, to create and refine detailed annotations. Apollo is an Open Source Java application that is easy to install and run on any platform. Since its initial release in 2002, Apollo has become one of the most widely used annotation editors. Factors contributing to its success include its intuitive, interactive user interface; configurability; simple installation process; extensive documentation; highly responsive mailing list; extensibility; and an Open Source code-base. It has been downloaded thousands of times, and a wide variety of both academic and commercial research groups have modified or extended it to suit their individual needs (see Appendix 1), thereby saving countless hours of development time We are requesting funding for continued support and improvement of this valuable software resource Our goals include making Apollo fully aware of the Sequence Ontology, to better support community-wide annotation of diverse organisms; designing new configuration interfaces to simplify the process of loading data from different sources and setting display preferences; and adding two new specialized editors: a multiple alignment transcript viewer and editor, to allow gene models to be modified in direct reference to alignment data; and a repetitive element editor. We also plan to offer more support and outreach, including workshops and on-site visits to train biologists to use Apollo and show software developers how to integrate their existing tools into Apollo's extensible framework. The work in this proposal will be performed as a collaboration between Lawrence Berkeley National Laboratory (LBNL) and The Arabidopsis Information Resource (TAIR) at the Carnegie Institution, with LBNL supplying the bulk of the software development and Carnegie providing targeted software development resources and annotation expertise.