Fast. Integrated Genome Browser & DAS. Easy. Flexible. Free. bioviz.org/igb

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1 bioviz.org/igb Integrated Genome Browser & DAS Free tools for visualizing, sharing, and publishing genomes and genome-scale data. Easy Flexible Fast Free

2 Funding: National Science Foundation Arabidopsis 2010 Program "Visualization software and data server for Arabidopsis" Visualization University of North Carolina, Charlotte Tools Research Institute - Loraine Lab startup Previously: NIH BISTI R01 "DAS2: A distributed genome annotation service" Databases Developed at Affymetrix, now open source, free software - since 2004.

3 Open source means: public development process Users request features, report bugs, ask for help via SourceForge site. Developers can view any revision since the project began - and retrieve older versions as needed! genoviz.sourceforge.net This matters ALOT in research, where you need to be able to reproduce results.

4 John Nicol UNC-Charlotte Steven Blanchard UNC-Charlotte Hiral Vora UNC-Charlotte Ehsan Tabari UNC-Charlotte David Nix Toni DiSera Huntsman Cancer Institute (Utah) Ido Tamir Institute of Molecular Pathology, Vienna Austria Interns Roshonda Barner Francesca Weaks NC A&T Ed Erwin Affymetrix Adam English UNC-Charlotte Gregg Helt Affymetrix Archana Raja UNC-Charlotte Kristen Sagliani UNCC Who we are - developers, students, scientists

5 On-going genomics revolution IGB species of interest Visualization (500 x 106 bases) 50 x coverage 8 lanes, PE 75 cycle Illumina $15,000 sequence Data Delivery assemble $15,000 (Illumina or 454) ESTs annotation DAS Quickload Indexed Flat Files

6 Integrated Genome Browser General purpose genome viewer designed for BIG data sets Runs on your desktop, not in your Web browser.

7 bioviz.org/igb How is it different from Gbrowse or Ensembl? They are Web-based. That means: Most of the drawing happens on the server. If you want to zoom in or zoom out, you click and then wait for the server to rebuild the image. And, navigation tightly wedded to data requests.

8 How Server-based systems work: Database Web Server CGI scripts load the database convert to GFF files gene models sequence EST alignments your genome project

9 How IGB, DAS, and Quickload work files Web Quick Server Load DAS2 Database servlet load the database convert to GFF files gene models sequence EST alignments your genome project bioviz.org/igb

10 How IGB, DAS, and Quickload work files Web Server DAS2 servlet Quick Load files gene models sequence EST alignments your genome project bioviz.org/igb

11 How IGB, DAS, and Quickload work files Web Server DAS2 servlet Quick Load files gene models sequence EST alignments your genome project bioviz.org/igb

12 How IGB, DAS, and Quickload work files Quick Load files gene models sequence EST alignments your genome project bioviz.org/igb

13 Who uses IGB? Over 3,500 users worldwide Plant biologists, biomedical researchers, bioinformatics scientists, software developers HCI ENcyclopedia of DNA Elements Affymetrix

14 Literature search: 90 articles used IGB techniques: ChIP-chip Morohashi K, Grotewold E: A systems approach reveals regulatory circuitry forarabidopsis trichome initiation by the GL3 and GL1 selectors. PLoS Genetics 2009, 5(2): ChIP-seq RNA-seq applications: mapping DNA binding sites, expression profiling, epigenomics Bisulfite methylation profiling results... visualized at the chromosomal level..each tier represents a graph of the hybridization profile corresponding to each dataset..

15 Demo

16 click to download and launch

17 DAS2 and Quickload Data Sources expression data from AtTile1R tiling array, probes mapped onto TAIR9 genome

18 Genome graph settings

19 What's next for 6.3 Visualizing EST and short-read sequences for SNP detection and analysis Bookmarking improvements And... your suggestions?

20 Illumina reads - low zoom

21 Illumina reads - middle zoom

22 Illumina reads - high zoom