Web-based visual analysis for high-throughput genomics

BMC Genomics

Software

Anton Nekrutenko¹  Tomithy Too²  Jeremy Goecks³  Carl Eberhard³  James Taylor³ 

[1] Center for Comparative Genomics and Bioinformatics, Penn State University, 505 Wartik Lab, 16802, University Park, PA, USA;Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore;Department of Biology, Emory University, 1510 Clifton Road NE, 30322, Atlanta, GA, USA;Department of Mathematics and Computer Science, Emory University, 400 Downman Dr, 30322, Atlanta, GA, USA;

关键词: Visualization;    Visual analysis;    Galaxy;    Genome browser;    Circos;    Phylogenetic tree;   

DOI  :  10.1186/1471-2164-14-397

 received in 2013-01-21, accepted in 2013-05-31,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundVisualization 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.ResultsWe 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.ConclusionsVisualization 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.

【 授权许可】

Unknown   
© Goecks et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.