Bioinformatics Career Day24 May 2012Felix Klein
Background    • physics diploma, University of Heidelberg    • diploma thesis in radiation dosimetry      at DKFZ    • mea...
Why bioinformatics?    • interdisciplinary    • programmed in R    • worked on data analysis3      24.05.2012         Feli...
Progress in science is driven by technology4     24.05.2012   Felix Klein
Chromatin loops5     24.05.2012   Felix Klein
Investigation of chromatin 3D structure    • role of chromatin 3D structure in gene regulation    • 4C to investigate deta...
Investigation of chromatin 3D structure7     24.05.2012   Felix Klein
Automated analysis of microscopy based     RNAi screens                                                                   ...
What was important for me?    • bioinformatics group with      members of diverse      backgrounds    • PI who successfull...
What might be interesting for you     • turn data into biology     • interaction with people from biology groups     • com...
AcknowledgementsWolfgang HuberSimon AndersJoseph BarryBernd FischerJulian GehringAleksandra PekowskaPaul Theodor PylAlejan...
Data production ratesLHC: 1.8 GB / s at peak capacity (i.e. actively conducting aprimary aspect of the LHC’s four main exp...
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P3 training and_life_as_a_postdoc_(felix_klein)

  1. 1. Bioinformatics Career Day24 May 2012Felix Klein
  2. 2. Background • physics diploma, University of Heidelberg • diploma thesis in radiation dosimetry at DKFZ • measurements at HIT2 24.05.2012 Felix Klein
  3. 3. Why bioinformatics? • interdisciplinary • programmed in R • worked on data analysis3 24.05.2012 Felix Klein
  4. 4. Progress in science is driven by technology4 24.05.2012 Felix Klein
  5. 5. Chromatin loops5 24.05.2012 Felix Klein
  6. 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 HiC6 24.05.2012 Felix Klein
  7. 7. Investigation of chromatin 3D structure7 24.05.2012 Felix Klein
  8. 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 31.577270Phenotypic profile Objects labels Object features 8
  9. 9. What was important for me? • bioinformatics group with members of diverse backgrounds • PI who successfully trained bioinformaticians • well established group in bioinformatics9 24.05.2012 Felix Klein
  10. 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, email10 24.05.2012 Felix Klein
  11. 11. AcknowledgementsWolfgang HuberSimon AndersJoseph BarryBernd FischerJulian GehringAleksandra PekowskaPaul Theodor PylAlejandro ReyesMaria SecrierCollaborators:Michael BoutrosChristian VolzEileen FurlongYad Ghavi Helm11 24.05.2012 Felix Klein
  12. 12. Data production ratesLHC: 1.8 GB / s at peak capacity (i.e. actively conducting aprimary aspect of the LHC’s four main experiments: ATLAS,ALICE, CMS, and LHCb).These experiments will take roughly a decade to complete, andeach of them is expected to produce over a 1 PB per year ofdata.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
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