Abstract Background Visualization of genomic data is a key step in validating methods and results. Web-based science gateways such as CyVerse provide storage and analysis tools for genomic data but often lack visualization capability. Native, desktop visualization tools like Integrated Genome Browser enable highly interactive data visualization but are difficult to deploy in science gateways due to technical constraints. Developing ways for gateways to interoperate with independently developed, native visualization applications will enhance their value to users. Results We developed BioViz Connect, a new web application that connects the CyVerse science gateway system with native, visualization application Integrated Genome Browser (IGB) using the CyVerse Terrain Application Programming Interface (API) and a local endpoint within IGB. 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 to create new data files for visualization in IGB or other applications. To demonstrate these three core functionalities of BioViz Connect, we describe an example use case in which RNA-Seq data from Arabidopsis thaliana plants undergoing heat and desiccation stresses are interactively and visually analyzed. The example use case shows how interactive visualization helps researchers detect artifacts and sanitycheck results from statistical analysis using a visual analytics function too computationally intensive to run on the user’s local computer. BioViz Connect helps users analyze and visualize their CyVerse data in IGB without needing to download or upload their data into new systems. Instead, the data exit the CyVerse platform in small, genome-region-based portions when users request them via the IGB user interface itself. BioViz Connect is accessible from https://bioviz.org. Conclusions BioViz Connect enhances the CyVerse gateway by adding visualization capability. BioViz Connect demonstrates a new way to integrate science gateways with native, desktop applications using APIs. Competing Interest Statement The authors have declared no competing interest. Footnotes * ↵nfreese{at}uncc.edu, kraveend{at}uncc.edu, ckin...

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

10.1101/2020.05.15.098533