BioViz Connect: Web Application Linking CyVerse Cloud Resources to Genomic Visualization in the Integrated Genome Browser.
BioViz Connect: Web Application Linking CyVerse Cloud Resources to Genomic Visualization in the Integrated Genome Browser.
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DOI：
10.3389/fbinf.2022.764619
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发表时间：
2022
期刊：
影响因子：
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通讯作者：
Loraine, Ann E
中科院分区：
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作者：
Raveendran, Karthik;Freese, Nowlan H;Kintali, Chaitanya;Tiwari, Srishti;Bole, Pawan;Dias, Chester;Loraine, Ann E
当基因组学研究人员能够交互式地探索和可视化数据时，他们的工作会更好。由于实验数据集的庞大规模，研究人员越来越多地使用强大的基于云的系统来处理和分析数据。这些远程系统被称为科学网关，提供了对高性能计算和存储资源的用户友好的基于Web的访问，但通常缺乏交互式可视化功能。在本文中，我们提出了BioViz连接，一个中间件Web应用程序，链接CyVerse科学网关资源的集成基因组浏览器（IGB），一个高度交互式的本地应用程序，在Java中实现，运行在用户的个人计算机上。使用BioViz Connect，用户可以1）将CyVerse数据存储中的数据流式传输到IGB中进行可视化，2）通过将IGB特定元数据添加到CyVerse数据文件（包括基因组版本和跟踪外观）来改善自己和他人的IGB用户体验，以及3）在CyVerse基础设施上运行计算密集型可视化分析功能，以创建新的数据集，用于在IGB或其他应用程序中进行可视化。为了展示BioViz Connect如何促进交互式数据可视化，我们描述了一个示例RNA-Seq数据分析，研究热和干燥胁迫如何影响模式植物拟南芥中的基因表达。RNA-Seq用例说明了IGB的交互式可视化如何帮助用户识别有问题的实验样本，使用阳性对照检查结果，并使用通过Terrain API部署到CyVerse的Docker映像在IGB（或其他工具）中创建新的数据文件以进行交互式可视化。最后，我们讨论了所使用的技术的局限性，并提出了未来工作的机会。BioViz Connect可从https://bioviz.org获得。
Genomics researchers do better work when they can interactively explore and visualize data. Due to the vast size of experimental datasets, researchers are increasingly using powerful, cloud-based systems to process and analyze data. These remote systems, called science gateways, offer user-friendly, Web-based access to high performance computing and storage resources, but typically lack interactive visualization capability. In this paper, we present BioViz Connect, a middleware Web application that links CyVerse science gateway resources to the Integrated Genome Browser (IGB), a highly interactive native application implemented in Java that runs on the user’s personal computer. Using BioViz Connect, users can 1) stream data from the CyVerse data store into IGB for visualization, 2) improve the IGB user experience for themselves and others by adding IGB specific metadata to CyVerse data files, including genome version and track appearance, and 3) run compute-intensive visual analytics functions on CyVerse infrastructure to create new datasets for visualization in IGB or other applications. To demonstrate how BioViz Connect facilitates interactive data visualization, we describe an example RNA-Seq data analysis investigating how heat and desiccation stresses affect gene expression in the model plant Arabidopsis thaliana. The RNA-Seq use case illustrates how interactive visualization with IGB can help a user identify problematic experimental samples, sanity-check results using a positive control, and create new data files for interactive visualization in IGB (or other tools) using a Docker image deployed to CyVerse via the Terrain API. Lastly, we discuss limitations of the technologies used and suggest opportunities for future work. BioViz Connect is available from https://bioviz.org.