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- 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 2 24.05.2012 Felix Klein
- 3. Why bioinformatics? • interdisciplinary • programmed in R • worked on data analysis 3 24.05.2012 Felix Klein
- 4. Progress in science is driven by technology 4 24.05.2012 Felix Klein
- 5. Chromatin loops 5 24.05.2012 Felix Klein
- 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 6 24.05.2012 Felix Klein
- 7. Investigation of chromatin 3D structure 7 24.05.2012 Felix Klein
- 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 8
- 9. What was important for me? • bioinformatics group with members of diverse backgrounds • PI who successfully trained bioinformaticians • well established group in bioinformatics 9 24.05.2012 Felix Klein
- 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 10 24.05.2012 Felix Klein
- 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 11 24.05.2012 Felix Klein
- 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