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BioViz Connect: Web Application Linking CyVerse Cloud Resources to Genomic Visualization in the Integrated Genome
Karthik Raveendran1, Nowlan H Freese1, Chaitanya Kintali1
1Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States.
Frontiers in Bioinformatics
|October 28, 2022
Summary
BioViz Connect enhances genomics research by linking cloud-based CyVerse resources to the Integrated Genome Browser (IGB). This enables interactive visualization of large datasets, improving data exploration for researchers.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Genomics research generates vast datasets requiring powerful cloud-based systems (science gateways) for processing and analysis.
- Existing science gateways often lack interactive visualization capabilities crucial for data exploration.
- Interactive visualization of genomic data aids researchers in understanding complex biological information.
Purpose of the Study:
- To introduce BioViz Connect, a middleware application bridging CyVerse science gateway resources with the Integrated Genome Browser (IGB).
- To enable interactive visualization of large-scale genomics data stored on cloud platforms.
- To enhance the user experience for genomics data analysis and visualization.
Main Methods:
- Developed BioViz Connect as a web application linking CyVerse and IGB.
- Implemented data streaming from CyVerse to IGB for visualization.
- Enabled metadata addition to CyVerse data files for improved IGB usability.
- Integrated compute-intensive visual analytics functions on CyVerse infrastructure.
Main Results:
- Users can stream data from CyVerse into IGB for interactive visualization.
- BioViz Connect facilitates the addition of IGB-specific metadata to enhance data interpretation.
- Visual analytics functions can be executed on CyVerse to generate new datasets for visualization.
- Demonstrated utility with an RNA-Seq analysis of plant stress responses in Arabidopsis thaliana.
Conclusions:
- BioViz Connect successfully integrates cloud-based data processing with interactive desktop visualization.
- The application improves the workflow for genomics researchers by enabling efficient data exploration.
- Future work may involve expanding functionalities and addressing current technological limitations.
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