Web-based visual analysis for high-throughput genomics

• Type of Material: Article
• Authors: Jeremy Goecks, Emory University; Carl Eberhard, Emory University; Tomithy Too, National University of Singapore; The Galaxy Team, Emory University; Anton Nekrutenko, Penn State University; James Taylor, Emory University
• Language: English
• Date: 2013-06-13
• Publisher: BioMed Central
• Publication Version: Final Published Version
• Copyright Statement: © 2013 Goecks et al.; licensee BioMed Central Ltd.
• License: Creative Commons Attribution 2.0 Generic
• Final Published Version (URL): http://www.biomedcentral.com/1471-2164/14/397
• Title of Journal or Parent Work: BMC Genomics
• ISSN: 1471-2164
• Volume: 14
• Issue: 397
• Start Page: 1
• End Page: 11
• Grant/Funding Information: This project was supported by American Recovery and Reinvestment Act (ARRA) funds through grant number HG005542 from the National Human Genome Research Institute, National Institutes of Health, as well as grants HG005133, HG004909 and HG006620 and National Science Foundation grant DBI 0543285. Additional funding is provided, in part, under a grant from the Pennsylvania Department of Health using Tobacco Settlement Funds.
• Keywords: Galaxy; Phylogenetic tree; Genome browser; Circos; Visualization; Visual analysis
• Research Categories: Biology, Bioinformatics; Biology, Genetics

Abstract

Background Visualization plays an essential role in genomics research by making it possible to observe correlations and trends in large datasets as well as communicate findings to others. Visual analysis, which combines visualization with analysis tools to enable seamless use of both approaches for scientific investigation, offers a powerful method for performing complex genomic analyses. However, there are numerous challenges that arise when creating rich, interactive Web-based visualizations/visual analysis applications for high-throughput genomics. These challenges include managing data flow from Web server to Web browser, integrating analysis tools and visualizations, and sharing visualizations with colleagues. Results We have created a platform that simplifies the creation of Web-based visualization/visual analysis applications for high-throughput genomics. This platform provides components that make it simple to efficiently query very large datasets, draw common representations of genomic data, integrate with analysis tools, and share or publish fully interactive visualizations. Using this platform, we have created a Circos-style genome-wide viewer, a generic scatter plot for correlation analysis, an interactive phylogenetic tree, a scalable genome browser for next-generation sequencing data, and an application for systematically exploring tool parameter spaces to find good parameter values. All visualizations are interactive and fully customizable. The platform is integrated with the Galaxy (http://galaxyproject.org) genomics workbench, making it easy to integrate new visual applications into Galaxy. Conclusions Visualization and visual analysis play an important role in high-throughput genomics experiments, and approaches are needed to make it easier to create applications for these activities. Our framework provides a foundation for creating Web-based visualizations and integrating them into Galaxy. Finally, the visualizations we have created using the framework are useful tools for high-throughput genomics experiments.