Helt G A, Lewis S, Loraine A E, Rubin G M
Berkeley Drosophila Genome Project (BDGP), Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720-3200, USA.
Genome Res. 1998 Mar;8(3):291-305. doi: 10.1101/gr.8.3.291.
Visualization tools for bioinformatics ideally should provide universal access to the most current data in an interactive and intuitive graphical user interface. Since the introduction of Java, a language designed for distributed programming over the Web, the technology now exists to build a genomic data visualization tool that meets these requirements. Using Java we have developed a prototype genome browser applet (BioViews) that incorporates a three-level graphical view of genomic data: a physical map, an annotated sequence map, and a DNA sequence display. Annotated biological features are displayed on the physical and sequence-based maps, and the different views are interconnected. The applet is linked to several databases and can retrieve features and display hyperlinked textual data on selected features. In addition to browsing genomic data, different types of analyses can be performed interactively and the results of these analyses visualized alongside prior annotations. Our genome browser is built on top of extensible, reusable graphic components specifically designed for bioinformatics. Other groups can (and do) reuse this work in various ways. Genome centers can reuse large parts of the genome browser with minor modifications, bioinformatics groups working on sequence analysis can reuse components to build front ends for analysis programs, and biology laboratories can reuse components to publish results as dynamic Web documents.
理想情况下，生物信息学的可视化工具应能通过交互式且直观的图形用户界面，让用户普遍获取最新数据。自用于基于网络的分布式编程的Java语言问世以来，如今已有技术可构建满足这些要求的基因组数据可视化工具。我们使用Java开发了一个基因组浏览器小程序原型（BioViews），它包含基因组数据的三级图形视图：物理图谱、注释序列图谱和DNA序列显示。带注释的生物学特征显示在物理图谱和基于序列的图谱上，并且不同视图相互关联。该小程序链接到多个数据库，能够检索特征并在选定特征上显示超链接文本数据。除了浏览基因组数据外，还可以交互式地执行不同类型的分析，并将这些分析结果与先前的注释一起可视化显示。我们的基因组浏览器基于专门为生物信息学设计的可扩展、可重用图形组件构建。其他团队可以（并且确实）以各种方式重用这项工作。基因组中心可以对基因组浏览器的大部分内容稍作修改后进行重用，从事序列分析的生物信息学团队可以重用组件来构建分析程序的前端，而生物实验室可以重用组件将结果作为动态网页文档发布。
