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enabling transparent, reproducible research

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enabling transparent, reproducible research

  1. 1. | brian m. bot| senior scientist | community manager | Synapse enabling transparent, reproducible research | michael kellen | director, technology platform and services |
  2. 2. a tool to improve transparency and reproducibility of data intensive science by recording analyses in real-time Synapse
  3. 3. a collection of living research projects enabling researchers to contribute to large-scale collaborative science pre- and post-publication Synapse
  4. 4. Attractor Metagenes Columbia Professor Dimitris Anastassiou MPEG-2 compression of digital audio and video signals Modules of co-expressed genes shared across cancers Belief that these ‘attractors’ represent underlying biological mechanisms (bioinformatic ‘hallmarks of cancer’1) 1D. Hanahan, R. A. Weinberg. Hallmarks of cancer: The next generation. Cell 144, 646–674 (2011)
  5. 5. 21 february 2013 17 april 2013
  6. 6. 21 february 2013 17 april 2013 ???
  7. 7. ...
  8. 8. ...
  9. 9. TCGA Pan-Cancer Consortium Attractor Metagenes openly evolving research projects collaboration around common data
  10. 10. Omberg,  et  al.  Nature  Gene*cs •Analysis of: 12 Tumor types, 6 molecular profiling platforms •Focus series of: 4 papers in Nature Genetics, with 14 more to follow in other NPG journals TCGA Pan-Cancer Consortium
  11. 11. 18papers in press
  12. 12. 68core projects
  13. 13. 248researchers
  14. 14. 28institutions
  15. 15. 1070datasets
  16. 16. 1723results
  17. 17. versioned data, analysis freezes
  18. 18. data versioning versus data provenance
  19. 19. TCGA Pan-Cancer Consortium collaboration around common data CRC Subtyping Consortium collaboration around common question
  20. 20. CRC Subtyping Consortium
  21. 21. A B C D E F 1 2 3 4 5 6 datasets subtypes analysis groups
  22. 22. A B C D E F 1 2 3 4 5 6 datasets analysis groups G ... subtypes
  23. 23. A B C D E F 1 2 3 4 5 6 datasets analysis groups G ... subtypes
  24. 24. analysis groups G
  25. 25. A B C D E F 1 2 3 4 5 6 datasets analysis groups G ... subtypes
  26. 26. CRC Subtyping Consortium Phase I: per-group subtyping ‣ subtyping calls on common data ‣ assess agreement between methods ‣ assess associations with phenotypic traits Phase II: meta-analysis and de novo subtyping ‣ consensus subytping ‣ assess associations with clinical outcomes ‣ strategy for adoption from clinicians
  27. 27. enables transparency and reproducibility facilitates large scale collaboration encourages communication pre- and post-publication summary
  28. 28. commenting / peer review mechanisms recognition metrics for individuals and teams deeper integration with cloud compute services project snapshots linked to publications future directions
  29. 29. Acknowledgements Sage Bionetworks Synapse Development Team Alfred P. Sloan Foundation Nature Publishing Group AAAS-Science PLoS

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