1. Bioinformatics Career Day
24 May 2012
Felix Klein

2. Background
• physics diploma, University of Heidelberg
• diploma thesis in radiation dosimetry
at DKFZ
• measurements at HIT
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3. Why bioinformatics?
• interdisciplinary
• programmed in R
• worked on data analysis
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4. Progress in science is driven by technology
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5. Chromatin loops
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6. Investigation of chromatin 3D structure
• role of chromatin 3D structure in gene regulation
• 4C to investigate detailed interactions of
cis-regulatory modules (CRMs)
• global chromatin interactome using HiC
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7. Investigation of chromatin 3D structure
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8. Automated analysis of microscopy based
RNAi screens
Features
Imaging Segmentation extraction
Source image Calibrated image Segmentation mask
9.241719
g.pd
g.x g.y g.s g.p g.pdm
g.s g.p
194 67
[1,] 123.1391 3.288660 194 67 9.241719
[2,] 206.7460 9.442248 961 153 20.513190
[3,] 502.9589 7.616438 219 60 8.286918
[4,] 20.1919 22.358418 1568 157 22.219461
3.288660
[5,] 344.7959 45.501992 2259 233 35.158966
Summary Classification [6,] 188.2611 50.451863 2711 249 28.732680
g.y
[7,] 269.7996 46.404036 2131 180 26.419631
aft apt neg [8,] 106.6127 58.364243 1348 143 21.662879
[9,] 218.5582 77.299007 1913 215 25.724580
[10,] 19.1766 81.840147 1908 209 26.303760
123.1391
[11,] 6.3558 62.017647 340 68 10.314127
g.x
[12,] 58.9873 86.034128 2139 214 27.463158
[13,] 245.1087 94.387405 1048 123 18.280901
[14,] 411.2741 109.198678 2572 225 28.660816
int pos [15,]
[16,]
167.8151 107.966014 1942 160
281.7084 121.609892 2871 209
24.671533
31.577270
Phenotypic profile Objects labels Object features
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9. What was important for me?
• bioinformatics group with
members of diverse
backgrounds
• PI who successfully
trained bioinformaticians
• well established group in
bioinformatics
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10. What might be interesting for you
• turn data into biology
• interaction with people from biology groups
• communication skills !!!
• workload divides mainly into:
• programming (50 %)
• reports, meetings, email
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11. Acknowledgements
Wolfgang Huber
Simon Anders
Joseph Barry
Bernd Fischer
Julian Gehring
Aleksandra Pekowska
Paul Theodor Pyl
Alejandro Reyes
Maria Secrier
Collaborators:
Michael Boutros
Christian Volz
Eileen Furlong
Yad Ghavi Helm
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12. Data production rates
LHC: 1.8 GB / s at peak capacity (i.e. actively conducting a
primary aspect of the LHC’s four main experiments: ATLAS,
ALICE, CMS, and LHCb).
These experiments will take roughly a decade to complete, and
each of them is expected to produce over a 1 PB per year of
data.
One Illumina HiSeq: up to 600 Gb/run , i.e. ~600 GB/10 days =
18 TB/year (not including derived data e.g. BAM)
One Digital Embryo (2008): 3.5 TB (2048 x 2048 x 370 x 1226)
EMBL-EBI: in 9/2011, data storage capacity was 14 PB