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. Desktop visualization tools like Integrated Genome Browser (IGB) enable highly interactive data visualization but are difficult to deploy in science gateways. Developing ways for gateways to interoperate with pre-existing external tools like IGB would enhance their value to users.
Results We developed BioViz Connect, a new web application that connects CyVerse and IGB using the CyVerse Terrain Application Programming Interface (API). Using BioViz Connect, users can (i) stream their CyVerse data to IGB for visualization, (ii) add IGB specific metadata such as genome version and track appearance to CyVerse data, and (iii) run compute-intensive visual analytics functions to create new visualizations for IGB. To demonstrate BioViz Connect, we present an example visual analysis of RNA-Seq data from Arabidopsis thaliana plants undergoing heat and desiccation stresses. The example shows how researchers can seamlessly analyze and visualize their CyVerse data in IGB. BioViz Connect is accessible from https://bioviz.org.
Conclusions BioViz Connect demonstrates a new way to integrate science gateways with desktop applications using APIs.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
nfreese{at}uncc.edu
kraveend{at}uncc.edu
ckintali{at}uncc.edu
stiwari8{at}uncc.edu
pbole{at}uncc.edu
aloraine{at}uncc.edu
Abbreviations
- API
- Application Programming Interface
- CSS
- Cascading Style Sheets
- HTML
- HyperText Markup Language
- IGB
- Integrated Genome Browser
- REST
- REpresentational State Transfer