c02-visualization-applying visual analytics

Trackster(The Galaxy Track Browser)

Jeremy Goecks, Kanwei Li, The Galaxy Team, and James Taylor

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Why another Genome Browser?

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Genome Browser✦ physical depiction of data✦ visually identify correlations✦ find interesting regions, features

Galaxy (http://usegalaxy.org)

✦ Web-based, uses open standards✦ tool integration framework✦ sharing, publication framework✦ HTS/NGS focused

Trackster

What is Galaxy?

Web-based GUI for genomics that requires only a Web browser for everything: analysis, workflows, sharing, publication, and visualization

A public web service (http://usegalaxy.org) integrating a wealth of tools, compute resources, terabytes of reference data and permanent storage

Open source software that makes integrating your own tools and data and customizing for your own site simple

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Trackster

Simple, dynamic Web-based visualization for your HTS/NGS data

Supports visual analytics

Can share & publish working visualizations

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HTS Datasets on the Web

HTS datasets are often GBs, so cannot load them all at once

Multiple indices needed to load data on demand at different levels of detail

✦ IGV and Savant on the desktop......and now Trackster on the Web

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Supporting Visual Analytics

Visual analytics: using interactive visualization to reason about and solve problems

Increasingly complex genomic tools require parameter experimentation

✦ visual feedback aids exploration

Galaxy provides abstract interfaces to tools

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Dynamic filtering on element properties here, FPKM for putative transcripts

Modifying Cufflinks parameters and locally reassembling

Compatible Tools

Filtering tools

Genomic interval tools

Modified Cufflinks

Key requirement: ✦ local model or✦ access to global model

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Your Tools with Trackster

Integrate tools with Galaxy using simple, XML definition

Local model✦ just add <trackster_conf/> to tool definition

Global model✦ store and retrieve global model✦ support filtering -- decorate data with attributes

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Sharing Visualizations

Communication paramount✦ biomedical/genomics research is collaborative✦ majority of publications use visualization

“A picture is worth a 1000 words.”

A fully-interactive visualization is worth many more words

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Sharing Trackster Visualizations

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Implementation

Client: OO JavaScript, HTML5 canvas✦ Web standards✦ dynamic, customizable, tools, filters, ...

Server: uses existing Galaxy functionality✦ tool integration✦ data indexing and aggregation✦ sharing and publication

Custom Builds!

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Modular and Extensible

Data exchange uses JSON, not tied to Galaxy datatypes

Client UI (browser) components not tied to Galaxy UI✦ rendering components are CommonJS modules that

can be reused in any JS environment

Everything is extensible: displays, track types, element rendering, data providers...

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Trackster Summary

Dynamic, configurable Web-based visualization for your HTS/NGS data

Supports visual analytics

Can share & publish working visualizations

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Supported by the NHGRI (HG005542, HG004909, HG005133), NSF (DBI-0850103), Penn State University, Emory University, and the Pennsylvania Department of Public Health

Dan Blankenberg Nate Coraor

Kelly Vincent

Greg von Kuster

Enis Afgan Dannon Baker

Kanwei Li

Jeremy Goecks

Anton NekrutenkoJames Taylor

Dave Clements Jennifer Jackson

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Thanks! Questions?http://usegalaxy.org/visualization/list_published

✦ http://usegalaxy.org/u/jeremy/v/trackster-demo-1-viewing-and-navigating✦ http://usegalaxy.org/u/jeremy/v/trackster-demo-2-dynamic-filtering✦ (Running tools demo very slow on main due to high NGS tools usage; faster

demo coming soon.)

Galaxy✦ public server: http://usegalaxy.org✦ download and run: http://getgalaxy.org

BOSC BOF Session: Galaxy-Taverna integration

jeremy.goecks@emory.edu

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