Department of Computational Genomics, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W41-6. doi: 10.1093/nar/gkt530. Epub 2013 Jun 8.
Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.
随着越来越多的基因组和相关基因组信息的可用，基因组浏览器的重要性日益增加。然而，新一代测序技术带来的信息增加，同时也导致传统基因组浏览器的效率逐渐微妙地下降。在这里，我们展示了 Genome Maps，这是一种实现了数据传输和管理创新模型的基因组浏览器。该程序使用了 HTML5 新标准中的高效技术，如可伸缩矢量图形，优化了服务器和客户端两侧的工作负载，并确保了未来的可扩展性。因此，数据管理和表示完全由浏览器执行，无需任何 Java 小程序、Flash 或其他插件技术的安装。关于基因、转录本、外显子、调控特征、单核苷酸多态性、核型等的相关生物数据从 Web 服务导入，并作为轨道提供。此外，几个 DAS 服务器已经包含在 Genome Maps 中。作为一个新颖的特点，这个基于网络的基因组浏览器允许本地上传巨大的基因组数据文件（例如 VCF 或 BAM），这些文件可以在客户端实时动态可视化，从而方便了受隐私限制影响的医疗数据的管理。最后，通过仅包含几行代码，Genome Maps 可以轻松集成到任何 Web 应用程序中。Genome Maps 是一个开源的协作倡议，可在 GitHub 存储库中获取（https://github.com/compbio-bigdata-viz/genome-maps）。Genome Maps 可在以下网址获取：http://www.genomemaps.org。
