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leveraging the web to make science more collaborative

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leveraging the web to make science more collaborative

  1. 1. Synapse leveraging the web to make science more collaborative brian m. bot | sage bionetworks | @BrianMBot
  2. 2. sage bionetworks 35 FTEs - hiring 5 additional 1/2 research - 1/3 platform - 1/6 leadership & support
  3. 3. sage bionetworks a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons focused on a world where biomedical research will fundamentally change to be more open and collaborative supports communities of researchers working collaboratively across disciplines
  4. 4. sage bionetworks focused on a world where biomedical research will fundamentally change to be more open and collaborative
  5. 5. open sage bionetworks focused on a world where biomedical research will fundamentally change to be more open and collaborative
  6. 6. open sage bionetworks access focused on a world where biomedical research will fundamentally change to be more open and collaborative
  7. 7. sage bionetworks accessibility focused on a world where biomedical research will fundamentally change to be more open and collaborative
  8. 8. open sage bionetworks access focused on a world where biomedical research will fundamentally change to be more open and collaborative
  9. 9. open sage bionetworks focused on a world where biomedical research will fundamentally change to be more open and collaborative
  10. 10. open sage bionetworks data focused on a world where biomedical research will fundamentally change to be more open and collaborative
  11. 11. open sage bionetworks science focused on a world where biomedical research will fundamentally change to be more open and collaborative
  12. 12. sage bionetworks science focused on a world where biomedical research will fundamentally change to be more open and collaborative
  13. 13. sage bionetworks a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons focused on a world where biomedical research will fundamentally change to be more open and collaborative supports communities of researchers working collaboratively across disciplines
  14. 14. sage bionetworks tool for collaborative science re-imagined informed consent patients as partners a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons
  15. 15. sage bionetworks enables sharing of all resources (data, code, results) and their relationships to one another multi-channel communication instead of uni-directional broadcasting aides in reproducibility by enabling communication throughout the research process not only at time of publication a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons
  16. 16. sage bionetworks distributed & versioned file system rich annotations (metadata) customizable schemas for structured data agnostic to storage solution (cloud, local server, etc.) wiki authoring access controls (share whatever with whomever) a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons
  17. 17. sage bionetworks a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons open RESTful APIs www.synapse.org programmatic clients
  18. 18. sage bionetworks a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons User  registra*on/cer*fica*on      User  agreement  to     Terms  and  Condi*ons  of  Use   Data  Use  Procedure   Data  privacy  Policy          Removal  of  direct  iden*fiers    Tier  access      Login  requirement,  encryp*on  in  and  out,  firewalls    IT  policy    Training-­‐  Audi*ng-­‐  Monitoring    Consequences  for  viola*on  (inten*onal  or  not) Synapse Governance a complete process
  19. 19. sage bionetworks a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons focused on a world where biomedical research will fundamentally change to be more open and collaborative supports communities of researchers working collaboratively across disciplines
  20. 20. sage bionetworks supports communities of researchers working collaboratively across disciplines
  21. 21. CRC Subtyping Consortium DREAM Challenges Progenitor Cell Biology Consortium TCGA Pan-Cancer Consortium CommonMind Consortium PsychENCODE Accelerating Medicines Partnership Resilience Project Influenza Vaccinations Dengue Fever Psychosis Spectrum Disorder Oncology Molecular Classifiers Next Gen Scientific Publishing Mozilla Science Labs sage bionetworks
  22. 22. DREAM Challenges
  23. 23. DREAM Challenges 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)
  24. 24. DREAM Challenges 17 April 2013
  25. 25. DREAM Challenges
  26. 26. CRC Subtyping Consortium DREAM Challenges Progenitor Cell Biology Consortium TCGA Pan-Cancer Consortium CommonMind Consortium PsychENCODE Accelerating Medicines Partnership Resilience Project Influenza Vaccinations Dengue Fever Psychosis Spectrum Disorder Oncology Molecular Classifiers Next Gen Scientific Publishing Mozilla Science Labs sage bionetworks
  27. 27. Accelerating Medicines Partnership public / private partnership between NIH, 10 biopharmaceutical companies and several non-profit organizations
  28. 28. Accelerating Medicines Partnership biopharma AbbVie Biogen Idec Bristol-Myers Squibb GlaxoSmithKline Johnson & Johnson Lilly Merck Pfizer Sanofi Takeda non-profit Alzheimer’s Association Alzheimer’s Drug Discovery Foundation American Diabetes Association Arthritis Foundation Foundation for the NIH Geoffrey Beene Foundation Juvenile Diabetes Research Foundation Lupus Foundation of America Lupus Research Institute/Alliance for Lupus Research PhRMA Rheumatology Research Foundation USAgainstAlzheimer’s
  29. 29. Accelerating Medicines Partnership ($ Millions) Total Project Total NIH Total Industry Alzheimer’s Disease 129.5 67.6 61.9 Type 2 Diabetes 58.4 30.4 28 Rheumatoid Arthritis 41.6 20.9 20.7 TOTAL 229.5 118.9 110.6
  30. 30. Accelerating Medicines Partnership cross-project data generation shRNA compounds RNAi human mouse drosophila iPSC RNA-seq Whole exome WGS methylation miRNA proteomics phenotypic measurements modificationssystems data generation X X
  31. 31. Accelerating Medicines Partnership Target Discovery Target Discovery Target Discovery Target Discovery Target Validation Target Validation Target Validation Target Validation Shared Information for Target Identification coordinate sharing of early-phase target identification insights
  32. 32. Accelerating Medicines Partnership
  33. 33. Accelerating Medicines Partnership
  34. 34. CRC Subtyping Consortium DREAM Challenges Progenitor Cell Biology Consortium TCGA Pan-Cancer Consortium CommonMind Consortium PsychENCODE Accelerating Medicines Partnership Resilience Project Influenza Vaccinations Dengue Fever Psychosis Spectrum Disorder Oncology Molecular Classifiers Next Gen Scientific Publishing Mozilla Science Labs sage bionetworks
  35. 35. TCGA Pan-Cancer Consortium 18NPG papers 68core projects 248researchers 28institutions 1070datasets 1723results
  36. 36. TCGA Pan-Cancer Consortium
  37. 37. TCGA Pan-Cancer Consortium Cyriac Kandoth
  38. 38. TCGA Pan-Cancer Consortium doi:10.7303/syn1710680.4
  39. 39. CRC Subtyping Consortium DREAM Challenges Progenitor Cell Biology Consortium TCGA Pan-Cancer Consortium CommonMind Consortium PsychENCODE Accelerating Medicines Partnership Resilience Project Influenza Vaccinations Dengue Fever Psychosis Spectrum Disorder Oncology Molecular Classifiers Next Gen Scientific Publishing Mozilla Science Labs sage bionetworks
  40. 40. CRC Subtyping Consortium
  41. 41. CRC Subtyping Consortium A B C D E F 1 2 3 4 5 6 groups datasets subtypes
  42. 42. CRC Subtyping Consortium A B C D E F 1 2 3 4 5 6 groups datasets subtypes …
  43. 43. collaborative analyses cloud-based file storage CRC Subtyping Consortium
  44. 44. code associated with results CRC Subtyping Consortium
  45. 45. CRC Subtyping Consortium
  46. 46. Synapse leveraging the web to make science more collaborative brian m. bot m1-a111 brian.bot@sagebase.org @BrianMBot Synapse engineering team Michael Kellen, Director Christopher Bare Marcel Blonk John Hill Jay Hodgson Bruce Hoff Xavier Schildwachter

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