BioViz Connect

BioViz Connect links CyVerse science gateway resources with the Integrated Genome Browser (IGB) to stream genomic data and enable visualization of compute-derived datasets for interactive genomic analysis.

Key Features:

• Data Streaming: Streams data from the CyVerse data store directly into the Integrated Genome Browser (IGB) for interactive visualization.
• IGB-specific Metadata Annotation: Attaches metadata such as genome version and track appearance settings to CyVerse data files for accurate visualization in IGB.
• Compute-Intensive Visual Analytics: Leverages CyVerse high-performance computing to execute compute-intensive visual analytics that produce new datasets for visualization.
• Docker Execution via Terrain API: Executes Docker images on CyVerse via the Terrain API to generate data files intended for downstream visualization in IGB or compatible tools.

Scientific Applications:

• Interactive Genomic Data Exploration: Enables researchers to explore large genomic datasets interactively within IGB using streamed CyVerse data and compute-derived results.
• RNA-Seq Analysis of Arabidopsis thaliana Stress Responses: Supported an RNA-Seq case study examining gene expression changes in Arabidopsis thaliana under heat and desiccation stresses.
• Quality Assessment and Sanity Checks: Facilitates identification of problematic experimental samples and validation using positive controls by visual inspection in IGB.
• Generation of Visualizable Derivative Data: Produces new data files via CyVerse compute (including Docker workflows) for subsequent interactive visualization and analysis.

Methodology:

Operates as middleware that streams data from CyVerse into IGB, uses CyVerse high-performance computing to run compute-intensive visual analytics (including Docker images deployed via the Terrain API), and returns generated datasets for visualization.