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.

Technology

WOUD: Bioinformatics: tools in research
September 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

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BioBii 2

Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent

Bottleneck becomes bioinformatics
Sequence data / Run

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BioBii 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=0.01

BioBii 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 i

BioBii 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 genes

BioBii 7

Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent

H2G2: Hitchhiker’s Guide to the Genome
Genome Browser

BioBii 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 types

BioBii 9

Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent

Users & Collaborators

BioBii 10

Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent

DNA methylation and expression

BioBii 11

Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent

MethylCap-Seq: Genome wide epigenetic
sequencing
#samples sequenced @ biobix

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0

Aug 2010 Sept 2011

BioBii 12

Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent Primary Data

BioBii 13

Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent Data

BioBii 14

Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent Aggregate Data

BioBii 15

Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent Different Data types

BioBii 16

Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent Correlation Track

BioBii 17

Bringing the Data Back to the Researchers
Geert Trooskens, BIOBIX, UGent Pinpointing the target regions

BioBii 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

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1. WOUD: Bioinformatics: tools in research September 28th 2011 Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent BioBii 1

2. 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 2016 BioBii 2

3. 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 2016 BioBii 3

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 BioBii 4

5. Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent or gene-cluster... BioBii 5

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 BioBii 6

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 BioBii 7

8. Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent H2G2: Hitchhiker’s Guide to the Genome Genome Browser BioBii 8

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 BioBii 9

10. Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent Users & Collaborators BioBii 10

11. Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent DNA methylation and expression BioBii 11

12. 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 2011 BioBii 12

13. Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent Primary Data BioBii 13

14. Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent Data BioBii 14

15. Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent Aggregate Data BioBii 15

16. Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent Different Data types BioBii 16

17. Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent Correlation Track BioBii 17

18. Bringing the Data Back to the Researchers Geert Trooskens, BIOBIX, UGent Pinpointing the target regions BioBii 18

19. 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

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