College of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, Peking University, Beijing, 100871, P.R. China.
BMC Bioinformatics. 2012 Jan 5;13:2. doi: 10.1186/1471-2105-13-2.
With the rapid growth of genome sequencing projects, genome browser is becoming indispensable, not only as a visualization system but also as an interactive platform to support open data access and collaborative work. Thus a customizable genome browser framework with rich functions and flexible configuration is needed to facilitate various genome research projects.
Based on next-generation web technologies, we have developed a general-purpose genome browser framework ABrowse which provides interactive browsing experience, open data access and collaborative work support. By supporting Google-map-like smooth navigation, ABrowse offers end users highly interactive browsing experience. To facilitate further data analysis, multiple data access approaches are supported for external platforms to retrieve data from ABrowse. To promote collaborative work, an online user-space is provided for end users to create, store and share comments, annotations and landmarks. For data providers, ABrowse is highly customizable and configurable. The framework provides a set of utilities to import annotation data conveniently. To build ABrowse on existing annotation databases, data providers could specify SQL statements according to database schema. And customized pages for detailed information display of annotation entries could be easily plugged in. For developers, new drawing strategies could be integrated into ABrowse for new types of annotation data. In addition, standard web service is provided for data retrieval remotely, providing underlying machine-oriented programming interface for open data access.
ABrowse framework is valuable for end users, data providers and developers by providing rich user functions and flexible customization approaches. The source code is published under GNU Lesser General Public License v3.0 and is accessible at http://www.abrowse.org/. To demonstrate all the features of ABrowse, a live demo for Arabidopsis thaliana genome has been built at http://arabidopsis.cbi.edu.cn/.
随着基因组测序项目的快速增长，基因组浏览器变得不可或缺，它不仅是一个可视化系统，还是一个支持开放数据访问和协作工作的交互平台。因此，需要一个具有丰富功能和灵活配置的可定制基因组浏览器框架，以方便各种基因组研究项目。
基于下一代网络技术，我们开发了一个通用的基因组浏览器框架 ABrowse，它提供了交互式浏览体验、开放数据访问和协作工作支持。通过支持类似谷歌地图的平滑导航，ABrowse 为最终用户提供了高度交互的浏览体验。为了方便进一步的数据分析，支持多种数据访问方法，以便外部平台从 ABrowse 检索数据。为了促进协作工作，为最终用户提供了一个在线用户空间，用于创建、存储和共享注释、标注和地标。对于数据提供者，ABrowse 具有高度的可定制性和可配置性。该框架提供了一组实用程序，方便导入注释数据。要在现有的注释数据库上构建 ABrowse，数据提供者可以根据数据库模式指定 SQL 语句。并且可以轻松地插入用于注释条目详细信息显示的定制页面。对于开发人员，可以将新的绘图策略集成到 ABrowse 中，以支持新类型的注释数据。此外，还提供了标准的 Web 服务来远程检索数据，为开放数据访问提供底层面向机器的编程接口。
ABrowse 框架通过提供丰富的用户功能和灵活的定制方法，对最终用户、数据提供者和开发人员都具有价值。源代码根据 GNU Lesser General Public License v3.0 发布，并可在 http://www.abrowse.org/ 获得。为了展示 ABrowse 的所有功能，我们在 http://arabidopsis.cbi.edu.cn/ 上构建了一个 Arabidopsis thaliana 基因组的实时演示。
