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Presentation at BOSC2012 by J Goecks - The Galaxy Visual Analysis Framework
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The Galaxy Visual Analysis Framework
Jeremy Goecks, The Galaxy Team, Anton Nekrutenko, and James Taylor
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What is Galaxy?
Web-based GUI for genomics✦ for complete analyses: obtain and integrate data, analyze,
visualize, share, publish
A tool integration framework that makes it simple to chain tool usage together step-by-step or create complex workflows
Open source software that makes it simple to ✦ integrate your own tools and data✦ customize and run on your own resources
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http://usegalaxy.org http://galaxyproject.org
Goal
An open, Web-‐based approach for
making highly interactive visual analysis
tools for NGS datasets
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Goal
An open, Web-‐based approach for
making highly interactive visual analysis
tools for NGS datasets
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distributed, extendable, sharable, fast
Goal
An open, Web-‐based approach for
making highly interactive visual analysis
tools for NGS datasets
5
distributed, extendable, sharable, fast
flexible, customizable
Goal
An open, Web-‐based approach for
making highly interactive visual analysis
tools for NGS datasets
6
distributed, extendable, sharable, fast
flexible, customizable visualization + tools
Goal
An open, Web-‐based approach for
making highly interactive visual analysis
tools for NGS datasets
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distributed, extendable, sharable, fast
flexible, customizable visualization + tools
needs to scale to huge datasets
Demo
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Trackster
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Paramamonster
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Circster
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Trackster
Completely Web-‐based✦ no downloads, no add-‐ons, no Flash
Supports arbitrarily large NGS datasets✦ SAM/BAM, BED, GFF/GTF, VCF, WIG
Highly flexible✦ e.g. custom rainbow tracks
Integrated with Galaxy tool framework✦ dynamic filtering✦ re-‐running tools
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Paramamonster
Visualization for✦ tool parameter space✦ outputs from different settings
Can easily find good settings by visual inspection✦ for many settings, across multiple regions
Can explore parameter space systematically or ad-‐hoc
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Circster
Circos-‐like visualization that provides genome-‐wide views
Complements Trackster
Very much a work in progress
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Architecture
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Datasets
...
Tools
...
Galaxy
Web browser
Galaxy HTML UI
Architecture
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Datasets
...
Tools
... Dat
a Pr
ovid
ers
Galaxy
Web browser
Galaxy HTML UI
Architecture
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Datasets
...
Tools
... Dat
a Pr
ovid
ers
Galaxy
...
Web browser
Data Managers
Visualizationsd3.js (SVG)HTML5: Canvas, CSS
Galaxy HTML UI
Future Directions
Non-‐genomic visualizations✦ phylogenetic trees✦ scatterplots
Integration of multiple visualizations✦ multiple views in same visualization✦ views in different visualizations
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Supported by the NHGRI (HG005542, HG004909, HG005133, HG006620), NSF (DBI-0850103), Penn State University, Emory University, and the Pennsylvania Department of Public Health
Dan Blankenberg Nate Coraor
Greg von Kuster
Enis Afgan Dannon Baker
Jeremy Goecks
Anton NekrutenkoJames Taylor
Dave Clements Jennifer Jackson
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http://galaxyproject.org
Galaxy publications: http://galaxyproject.org/wiki/Citing
Tech Track Talk (TT08): Sunday, 2:30p
Thanks! Questions?