Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web
Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web
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DOI：
10.1093/bioinformatics/bts677
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发表时间：
2013-02-01
期刊：
影响因子：
5.8
通讯作者：
Marth, Gabor
中科院分区：
文献类型：
--
作者：
Miller, Chase A.;Anthony, Jon;Marth, Gabor
动机：高通量生物学研究需要同时可视化和分析基因组数据，例如。G.读段比对、变异识别和基因组注释。传统上，这种综合分析需要桌面应用程序对本地存储的数据进行操作。然而，目前许多由大型公共财团项目生成的TB级数据集只能存储在专业的基因组分析中心。由于即使是小型实验室也能负担得起非常大的数据集，因此本地存储和分析变得越来越有限，并且很可能大多数此类数据集将很快被远程存储。G.在云端这些发展将需要基于网络的工具，使用户能够访问、分析和查看大量远程存储的数据，其复杂程度和交互性接近桌面应用程序。由于成本的迅速下降使研究人员能够收集旨在回答非常专业背景下的问题的数据，开发人员还必须提供软件库，使用户能够为他们的特定应用程序实现定制的数据分析和数据视图。这种专门的，但轻量级的，应用程序将使科学家更好地回答特定的生物学问题比可能与通用的基因组browsers.Results：使用核心网络技术（HTML5）的最新进展，我们开发了Scribl，一个灵活的基因组可视化库，专门针对基于坐标的数据，如基因组特征，DNA序列和遗传变异。Scribl简化了复杂的基于Web的图形工具的开发，这些工具接近桌面应用程序的动态性和交互性。
Motivation: High-throughput biological research requires simultaneous visualization as well as analysis of genomic data, e. g. read alignments, variant calls and genomic annotations. Traditionally, such integrative analysis required desktop applications operating on locally stored data. Many current terabyte-size datasets generated by large public consortia projects, however, are already only feasibly stored at specialist genome analysis centers. As even small laboratories can afford very large datasets, local storage and analysis are becoming increasingly limiting, and it is likely that most such datasets will soon be stored remotely, e. g. in the cloud. These developments will require web-based tools that enable users to access, analyze and view vast remotely stored data with a level of sophistication and interactivity that approximates desktop applications. As rapidly dropping cost enables researchers to collect data intended to answer questions in very specialized contexts, developers must also provide software libraries that empower users to implement customized data analyses and data views for their particular application. Such specialized, yet lightweight, applications would empower scientists to better answer specific biological questions than possible with general-purpose genome browsers currently available.Results: Using recent advances in core web technologies (HTML5), we developed Scribl, a flexible genomic visualization library specifically targeting coordinate-based data such as genomic features, DNA sequence and genetic variants. Scribl simplifies the development of sophisticated web-based graphical tools that approach the dynamism and interactivity of desktop applications.