BioVizConnect: Web application linking CyVerse cloud resources to genomic visualization in the Integrated Genome Browser

Abstract

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.