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.
Background:To make use of large-scale data sets from genomics, biologists need computational systems to store, process, analyze, annotate, and visualize their data. Cloud-based science gateways such as CyVerse provide storage and analysis tools but offer limited visualization capability. In parallel, desktop programs such as the Integrated Genome Browser (IGB) support interactive, dynamic data visualization using local computing resources. However, CyVerse and IGB exist separate from each other, with no easy way for users to transfer data between the two. Results:We present BioViz Connect, a new web application that connects CyVerse and IGB using the CyVerse Terrain API. Using BioViz Connect, researchers can stream their data to IGB for visualization and run analyses to create new visualizations. BioViz Connect also functions as a dashboard-style application that lets users specify genome version and visual appearance for data files, thus controlling how data will look once loaded into IGB. To demonstrate BioViz Connect, we present an example RNA-Seq data set from Arabidopsis thaliana that compares gene expression between heat-treated plants and non-heat-treated controls. Using CyVerse and BioViz Connect, we create scaled coverage graphs and visualize them in Integrated Genome Browser, showing how the blend of cloud and desktop resources give researchers greater power to explore and understand their data. Visit https://bioviz.org/connect.html to use BioViz Connect. Conclusions:BioViz Connect shows how applications that integrate remote cloud resources with interactive, desktop applications boost researchers' ability to explore and understand their data.
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