BioViz Connect: Web application linking CyVerse science gateway resources to genomic visualization in the Integrated Genome Browser

Abstract

Genomics researchers do better work when they can interactively explore and visualize data. However, 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 the CyVerse science gateway to the Integrated Genome Browser (IGB), a highly interactive native application implemented in Java that runs on the users personal computer. Using BioViz Connect, users can (i) stream data from the CyVerse data store into IGB for visualization, (ii) 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 (iii) 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. Lastly, we discuss limitations of the technologies used and suggest opportunities for future work. BioViz Connect is available from https://bioviz.org.