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Bringing the data back to the researchers

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Bringing the data back to the researchers
by ir. Geert Trooskens - BIOBIX, UGent

Genome wide analysis is getting bigger, better and faster.
Researchers are looking for answers in the vast amounts of different data sets that come out these analyses, conceivably leaving important information on a storage disk.
We present the Hitchhikers Guide to the Genome (H2G2): a platform that allows (epi-)genetic, genomic, and proteomic data fusion and visualization.

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    Bringing the data back to the researchers Bringing the data back to the researchers Presentation Transcript

    • WOUD: Bioinformatics: tools in researchSeptember 28th 2011 Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent BioBii 1
    • Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent Sequencing cost decreases exponentially Genome wide analysis becomes affordable for daily research $ 00 $ 0 .0 00 00 $ ??? 0. .0 0 00 $ 00 0 10 . 0 10 . 10 10 2001 2006 2011 2016BioBii 2
    • Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent Bottleneck becomes bioinformatics Sequence data / Run 10 0. 10 00 0. 0. 1. 00 00 00 10 0 0 0M M M M B B B B ?? 2001 2006 2011 2016BioBii 3
    • Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent In high throughput analysis, the final report is in a lot of cases still a genelist. 1 Gene One p=0.000001 2 Gene Two p=0.00005 3 Gene Three p=0.00008 4 Gene Four p=0.0001 5 Gene Five p=0.008 6 Gene Six p=0.009 7 Gene Seven p=0.01BioBii 4
    • Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent or gene-cluster...BioBii 5
    • Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent I spent 25k on a sequencing project and all I got back was a lousy gene list BioBi iBioBii 6
    • Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent We need a tool that allows us to get new insights in these genome-wide data sets Genome browsers are the most natural way to investigate genomic data Tracks Different samples and data types are displayed in different tracks The data has genomic coordinates Looking on a deeper level than genesBioBii 7
    • Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent H2G2: Hitchhiker’s Guide to the Genome Genome BrowserBioBii 8
    • Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent H2G2: Hitchhiker’s Guide to the Genome Web-Based flex open source framework 200K+ lines of code - 2 years of development Rich Genome browsing experience zooming,dragging,scrolling,semantic zooming Custom tracks Allows us to build custom tracks to visualize a plethora of different data 30+ different tracks with different data typesBioBii 9
    • Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent Users & CollaboratorsBioBii 10
    • Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent DNA methylation and expressionBioBii 11
    • Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent MethylCap-Seq: Genome wide epigenetic sequencing #samples sequenced @ biobix 400 300 200 100 0 Aug 2010 Sept 2011BioBii 12
    • Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent Primary DataBioBii 13
    • Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent DataBioBii 14
    • Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent Aggregate DataBioBii 15
    • Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent Different Data typesBioBii 16
    • Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent Correlation TrackBioBii 17
    • Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent Pinpointing the target regionsBioBii 18
    • Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent BioBii Curriculum vitae BOLCA Selin Selin.Bolca@UGent.be °April 8th, 1981; Belgium EDUCATION Wim Gerben Tim Mathematics, Berkenboom Instituut, St-Niklaas (1993-1997) Joachim Selin 1993-1999: Latin Science Mathematics, St-Jozef Klein Seminarie, St-Niklaas (1997-1999) 1999-2004: Engineer in Cell and Gene Biotechnology, Faculty of Bioscience Engineering, Ghent University (Belgium). Graduated with great distinction. Training: ‘Development of an RT-PCR protocol to amplify the full S-segment of hantaviruses in Belgian rodents’, Research Laboratory for Vector-Borne Diseases, Military Hospital Queen Astrid, Brussels. Promotors: Med. Maj. C. Vandenvelde and Mr. P. Heyman.Simon Master Jeroen Geert Klaas thesis: ‘Flow cytometry as a means to study the intestinal microbial ecosystem’,   Daisy Laboratory of Microbial Ecology and Technology (LabMET), Faculty of Bioscience Engineering, Ghent University. Promotors: Prof. Dr. W. Verstraete and Prof. Dr. N. Boon. 19 PROFFESIONAL ACTIVITIES