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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. High Throughput Sequencing • HTS machines can read billions of nucleotide bases per run • interpretation and analysis challenge • many separate tools for computational and visualization Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  3. Tools for Genomic Data Analysis • 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. FEATURE demonstration • INTERFACE • HTS READ ALIGNMENTS • EXAMPLE PLUGIN: SNP FINDER Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  7. Plugin Framework • provides ability to extend Savant beyond its core functionalities • for programmers: platform for simple development and deployment of various programs • for users: allows one mix and match modules to perform customized visual analysis Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  8. Plugin API • rich collection of functions to get data, perform computations, and create custom visualizations Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  9. On-the-fly SNP Finder user input : range change listen for range change get track data in range DETECT SNPs add bookmark draw custom graphics Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  10. Savant Plugins • SNP Finder • Bookmark Intersection • Continuous Track Statistics • Bookmark Player • Table View • we encourage plugin submissions, which can be done through the Savant website Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

  11. Conclusions & future work 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 • standard features: e.g. file formats, navigation • novel features: e.g. table view, matepair mode, 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. Future work • external datasources • e.g. SQL database, 1000 Genomes Project Online DB • improve and increase data format support • grow user and developer community Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

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

  15. Try out Savant for yourself • Poster Main conference #J17 • Live demo on Sunday, 12:40 – 2:30 • Website http://compbio.cs.toronto.edu/savant • Email savant@cs.toronto.edu Savant Genome Browser - http://compbio.cs.toronto.edu/savant/