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.

1. WOUD: Bioinformatics: tools in research
September 28th 2011
Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent
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2. Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent
Sequencing cost decreases exponentially
Genome wide analysis becomes affordable for daily research
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3. Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent
Bottleneck becomes bioinformatics
Sequence data / Run
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4. 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=0.01
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5. Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent
or gene-cluster...
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6. 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 i
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7. 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 genes
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8. Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent
H2G2: Hitchhiker’s Guide to the Genome
Genome Browser
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9. 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 types
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10. Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent
Users & Collaborators
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11. Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent
DNA methylation and expression
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12. Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent
MethylCap-Seq: Genome wide epigenetic
sequencing
#samples sequenced @ biobix
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Aug 2010 Sept 2011
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13. Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent Primary Data
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14. Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent Data
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15. Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent Aggregate Data
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16. Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent Different Data types
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17. Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent Correlation Track
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18. Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent Pinpointing the target regions
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19. Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent
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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.
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PROFFESIONAL ACTIVITIES