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 ToolCostComputationalVisualization Read Alignment e.g. Bowtie, BWA FreeYN File Format Conversion e.g. Galaxy, SAMTools FreeYN Other Comand-line Tools e.g. Genetic Variation Discovery, Comparitive Genomics, etc. FreeYN UCSC Genome BrowserFreeNY Integrative Genomics ViewerFreeNY GBrowseFreeNY CLC Genomics Workbench$$$YY Savant Genome Browser - http://compbio.cs.toronto.edu/savant/ substantial disconnect between the processes of computational analysis and visualization

4. Tools for Genomic Data Analysis ToolCostComputationVisualization Read Alignment e.g. Bowtie, BWA FreeYN File Format Conversion e.g. Galaxy, SAMTools FreeYN Other Comand-line Tools e.g. Genetic Variation Discovery, Comparitive Genomics, etc. FreeYN UCSC Genome BrowserFreeNY Integrative Genomics ViewerFreeNY GBrowseFreeNY CLC Genomics Workbench$$$YY Savant Genome BrowserFreeYY Savant Genome Browser - http://compbio.cs.toronto.edu/savant/ substantial disconnect between the processes of computational analysis and visualization

5. Savant Genome Browser platform for integrated visual 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 FASTA, BAM (local and remote), BED, WIG, GFF, tab-delimited Data Format Support very fast data access (<1s); small memory footprint (<250 MB) Speed and Interactivity pack, squish for BED and GFF tracks; mismatch, SNP, matepair modes for BAM tracks Visualization Modes enables powerful analytic extensions to the browser Plugin Framework sessions, bookmarking of interesting regions, track locking, data selection Extras works on all major operating systems System Requirements Savant Genome Browser - http://compbio.cs.toronto.edu/savant/

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

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 beneficial for 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 and example 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, Misko Dzamba, Nilgun Donmez, Daniel Lister, Andy Pang, Elango Cheran http://compbio.cs.toronto.edu/savant Savant Genome Browser - http://compbio.cs.toronto.edu/savant/