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Savant Genome Browser

Savant Genome Browser

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Savant Genome Browser

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  1. Savant Genome Browser Marc Fiume Department of Computer Science University of Toronto

  2. Challenge in Genome Informatics • genomic data is generated in high volumes • interpretation and analysis challenge • many different tools have been developed for computation and visualization Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  3. HTS data analysis pipeline • substantial disconnect between the processes of computational analysis and visualization Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  4. Tools for Genomic Data Analysis • substantial disconnect between the processes of computational analysis and visualization Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  5. Savant Genome Browser • platform for integratedvisual analysis of genomic data • feature-rich genome browser • computationally extensible via plugin framework Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  6. Summary of Features Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  7. FEATURE demonstration • INTERFACE • HTS READ ALIGNMENTS • EXAMPLE PLUGIN: SNP FINDER Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  8. Power of visual analytics • task: find the correct parameter for some command line tool Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  9. Plugin Framework • unlocks the potential for performing visual analytics • platform is beneficialfor both users and tool developers • for users: perform data analyses on-the-fly within a visual environment using the latest tools • for programmers: enables simple development and deployment of various programs Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  10. Plugin Development • plugin development is easy • API contains over a hundred prebuilt functions (e.g. get track data, add bookmarks, draw custom graphics, etc.) • SDK includes API andexample plugin project on website Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  11. ConclusionS Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  12. Conclusions • Savant is a platform for integrated visualization and analysis of genomic data • stand-alone genome browser • novel features: e.g. table view, visualization modes, data selection, etc. • computationally extensible through plugin framework • makes interpretation and analysis of genomic data easier and more efficient Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  13. Acknowledgements • Savant Team • Marc Fiume, Vanessa Williams, Andrew Brook, Michael Brudno • Usability and Testing • Paul Medvedev, MiskoDzamba, NilgunDonmez, • Daniel Lister, Andy Pang, ElangoCheran • http://compbio.cs.toronto.edu/savant Savant Genome Browser - http://compbio.cs.toronto.edu/savant/