clearScienceStrataRx2012

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The impetus behind Sage Bionetworks' clearScience project and how it effaces the boundary between doing science and communicating science.

The impetus behind Sage Bionetworks' clearScience project and how it effaces the boundary between doing science and communicating science.

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  • 1. clear Sciencedragging scientific communication intothe information ageerich s. huang, md/phddirector, cancer researchsage bionetworkserich.huang@sagebase.org@erichhuang
  • 2. http://www.viahealthcaredesign.com/LMCH%20Universal%20Exam%20Rm.jpg
  • 3. Betty Jones “I have a lump near my mastectomy scar”
  • 4. Betty Jones menopause ~50 years “high risk” breast cancer “normal risk” breast cancer
  • 5. Betty Jones menopause 36 years ~50 years “high risk” breast cancer “normal risk” breast cancer
  • 6. Betty Jones African American Population Non-African American Population 16% 39% 61% 84% Triple Negative Breast Cancer Triple Negative Breast Cancer All Other Types All Other Types http://jama.jamanetwork.com/article.aspx?articleid=202952
  • 7. her2 receptor progesterone receptorestrogenreceptor breast cancer cell depends on receptor-driven growth signals
  • 8. her2 receptor progesterone receptorestrogenreceptor breast cancer cell depends on receptor-driven growth signals
  • 9. her2 receptor progesterone receptor LSestrogen NAreceptor S IG T H OW G R breast cancer cell depends on receptor-driven growth signals
  • 10. breast cancer cellgrowth signals becomeindependent of receptors
  • 11. “triple negative” breast cancer breast cancer cell growth signals become independent of receptors
  • 12. “triple negative” breast cancerthe receptors are no longer present on thecell surface... breast cancer cell growth signals become independent of receptors
  • 13. “triple negative” breast cancerthe receptors are no longer present on thecell surface...but the intracellular signals persist breast cancer cell growth signals become independent of receptors
  • 14. “triple negative” breast cancerthe receptors are no longer present on thecell surface...but the intracellular signals persist T N S E L D A N N E IG EP S D H IN T OW G R breast cancer cell growth signals become independent of receptors
  • 15. http://www.cancer.gov/images/cdr/live/CDR415523-750.jpg
  • 16. http://www.cancer.gov/images/cdr/live/CDR415523-750.jpg
  • 17. http://www.cancer.gov/images/cdr/live/CDR415523-750.jpg
  • 18. Betty Jones minus plus lymph node young negative african-american triple negative multifocal cancer
  • 19. Betty Jones minus plus lymph node young negative african-american = Aggressive therapeutic strategy triple negative multifocal cancer
  • 20. http://www.flickr.com/photos/kbrookes/7497906298/sizes/h/in/photostream/
  • 21. radiotherapy 3d planning http://radonc.ucsf.edu/patient_information/breast/images/Radiation_Oncology_breast_img_2.jpg
  • 22. Betty Jones “I have a lump near my mastectomy scar”
  • 23. Betty Jones Triple negative breast cancer. What are the options?
  • 24. Betty Jones Triple negative breast cancer. What are the options? Standard Stuff (Old Fashioned Targets) Anthracyclines Taxanes Anti-Metabolites
  • 25. Betty Jones Triple negative breast cancer. What are the options? Standard Stuff (Old Fashioned Targets) Anthracyclines Taxanes Anti-Metabolites Platinum Agents
  • 26. Betty Jones Triple negative breast cancer. What are the options? { Standard Stuff (Old Fashioned Targets) Anthracyclines conventional Taxanes chemotherapy Anti-Metabolites Platinum Agents
  • 27. Betty Jones Triple negative breast cancer. What are the options? { Standard Stuff (Old Fashioned Targets) Anthracyclines conventional Taxanes chemotherapy Anti-Metabolites Platinum Agents Targeted Agents Cetuximab + Platinum (BALI-1) Bevacizumab (GeparQuinto) PARP Inhibitors SRC Inhibitors HDAC Inhibitors (ER-alpha)
  • 28. Betty Jones Triple negative breast cancer. What are the options? { Standard Stuff (Old Fashioned Targets) Anthracyclines conventional Taxanes chemotherapy Anti-Metabolites Platinum Agents { Targeted Agents Cetuximab + Platinum (BALI-1) Bevacizumab (GeparQuinto) new therapies PARP Inhibitors SRC Inhibitors HDAC Inhibitors (ER-alpha)
  • 29. Betty Jones Triple negative breast cancer. What are the options? { Standard Stuff (Old Fashioned Targets) Anthracyclines conventional Taxanes chemotherapy Anti-Metabolites CURRENT KNOWLEDGE: Platinum Agents ALL THESE THERAPIES { Targeted Agents ARE A Platinum (BALI-1) Cetuximab + WASH Bevacizumab (GeparQuinto) new therapies PARP Inhibitors SRC Inhibitors HDAC Inhibitors (ER-alpha)
  • 30. Betty Jones
  • 31. Betty Jones
  • 32. http://www.viahealthcaredesign.com/LMCH%20Universal%20Exam%20Rm.jpg
  • 33. molecularly-customized~4 million datapoints cancer treatment plan
  • 34. E S TIM 4 6 3 EDC IT
  • 35. E S TIM 6 3 4 CS- ED MI LS ITC EN O RIA G ED T 3 ID GU
  • 36. E S TIM 6 3 4 CS- ED MI LS ITC EN O RIA G ED T 3 ID GU
  • 37. molecularly-customized~4 million datapoints cancer treatment plan
  • 38. molecularly-customized~4 million datapoints cancer treatment plan
  • 39. Magic molecularly-customized~4 million datapoints cancer treatment plan
  • 40. Open
  • 41. Open
  • 42. Open
  • 43. Open Source
  • 44. Open
  • 45. Open Data
  • 46. Open
  • 47. Open Access
  • 48. Access
  • 49. Access = Accessible?
  • 50. OpenSourceOpenDataOpenAccess } Clear ?
  • 51. Nature 483, 509 (29 March 2012) | doi:10.1038/483509a
  • 52. Nature 483, 509 (29 March 2012) | doi:10.1038/483509a
  • 53. the status quotolerates poorcommunicationof findings
  • 54. the status quo can reproducetolerates poor partiallycommunicationof findings 6% can reproduce from processed data w/ 21% discrepancies 54% can reproduce w/ 8% cannot discrepancies reproduce 11% can reproduce in principle
  • 55. so what’s inprinciplereproducible, is notpracticallyreproducible
  • 56. so what’s in principle 208,294,724 reproducible, is not datapoints practically reproducible 124 pages supplemental material ? lines unobtainable source code ? version or architecture of R? R packages key R package “ClaNC” no longer available 442 citations
  • 57. THE SCIENTIFIC PROCESS:it’s not one and done... define a question
  • 58. THE SCIENTIFIC PROCESS:it’s not one and done... define a question gather information
  • 59. THE SCIENTIFIC PROCESS:it’s not one and done... define a question form a hypothesis gather information
  • 60. THE SCIENTIFIC PROCESS:it’s not one and done... define a question form a hypothesis gather information experimentally test your hypothesis
  • 61. THE SCIENTIFIC PROCESS:it’s not one and done... analyze define a question form a hypothesis experimental data gather information experimentally test your hypothesis
  • 62. THE SCIENTIFIC PROCESS:it’s not one and done... analyze define a question form a hypothesis experimental data gather information experimentally test draw conclusions your hypothesis
  • 63. THE SCIENTIFIC PROCESS:it’s not one and done... analyze define a question form a hypothesis experimental data report, i.e. “publish” gather information experimentally test draw conclusions your hypothesis
  • 64. THE SCIENTIFIC PROCESS:it’s not one and done... analyze define a question form a hypothesis experimental data report, i.e. “publish” gather information experimentally test draw conclusions your hypothesis validation by the scientific community validation by clinical trials
  • 65. generate data@ the bench orfrom a clinical cohort
  • 66. generate data@ the bench orfrom a clinical cohort
  • 67. store on localgenerate data server@ the bench orfrom a clinical cohort
  • 68. store on localgenerate data server@ the bench orfrom a clinical cohort
  • 69. store on localgenerate data server@ the bench orfrom a clinical cohort analyze on local machine
  • 70. store on localgenerate data server@ the bench orfrom a clinical cohort analyze on local machine
  • 71. store on localgenerate data server@ the bench orfrom a clinical cohort analyze on local machine write a document
  • 72. store on localgenerate data server@ the bench orfrom a clinical cohort analyze on local machine write a document al to journ su bmit
  • 73. store on localgenerate data server@ the bench orfrom a clinical cohort analyze on local machine sent to write a reviewers document as pdf al to journ su bmit
  • 74. store on localgenerate data server@ the bench orfrom a clinical cohort analyze on local machine sent to write a reviewers document as pdf al to journ su bmit
  • 75. store on localgenerate data server@ the bench orfrom a clinical cohort accepted & digitally typeset analyze on local machine sent to write a reviewers document as pdf al to journ su bmit
  • 76. printed on paper store on localgenerate data server@ the bench orfrom a clinical cohort accepted & digitally typeset analyze on local machine sent to write a reviewers document as pdf al to journ su bmit
  • 77. printed on paper store on localgenerate data server@ the bench orfrom a clinical cohort static html representation accepted & digitally typeset analyze on local machine sent to write a reviewers document as pdf al to journ su bmit
  • 78. printed on paper store on localgenerate data server@ the bench orfrom a clinical cohort static html representation accepted & digitally typeset static pdf representation analyze on local machine sent to write a reviewers document as pdf al to journ su bmit
  • 79. printed on paper store on localgenerate data server@ the bench orfrom a clinical cohort static html representation accepted & digitally typeset static pdf representation analyze on local machine sent to write a reviewers document as pdf al to journ su bmit
  • 80. printed on paper store on local generate data server @ the bench or from a clinical cohort static html representationTHE ACTUAL SCIENCE accepted & digitally typeset static pdf representation analyze on local machine sent to write a reviewers document as pdf al to journ su bmit
  • 81. printed on paper store on local generate data server @ the bench or from a clinical cohort static html representationTHE ACTUAL SCIENCE accepted & digitally typeset static pdf representation analyze on local machine SCIENTIFIC CLAIMS sent to write a reviewers document as pdf al to journ su bmit
  • 82. store on local generate data server @ the bench or from a clinical cohortTHE ACTUAL SCIENCE analyze on local machine
  • 83. store on local generate data server @ the bench or from a clinical cohortTHE ACTUAL SCIENCE analyze on local machine
  • 84. clear Science
  • 85. clear Science
  • 86. clear Science
  • 87. clear Science1. re-imagine scientific communication
  • 88. clear Science1. re-imagine scientific communication2. make every component of a data-intensive project (e.g. genomic analysis) web accessible
  • 89. clear Science1. re-imagine scientific communication2. make every component of a data-intensive project (e.g. genomic analysis) web accessible3. allow consumption of content at a variety of levels of complexity and abstraction4. leverage open, RESTful APIs
  • 90. leverage open, RESTful APIs
  • 91. leverage open, RESTful APIs to let users reconstitute an entire analytical environment
  • 92. leverage open, RESTful APIs to let users reconstitute an entire analytical environment hardware
  • 93. leverage open, RESTful APIs to let users reconstitute an entire analytical environment software hardware
  • 94. leverage open, RESTful APIs to let users reconstitute an entire analytical environment data software hardware
  • 95. leverage open, RESTful APIs to let users reconstitute an entire analytical environment code data software hardware
  • 96. code datasoftwarehardware
  • 97. code data software hardwareclear Science
  • 98. code data software hardwareclear Science a narrative that coherently interweaves scientific assertions with the executable data, code, software & hardware that support them
  • 99. “ my computer’s the cloud, let me hand it to you ”
  • 100. “ If I have seen further it is by standing on the shoulders of giants. ”
  • 101. Betty Jones “I have a lump near my mastectomy scar”
  • 102. brian bot stephen friend josh greenberg david burdick mike kellen external partnersmyles axton ian mulvaney kelly lamarcoeditor head of technology senior editornature genetics • science trans. medicine mark patterson managing exec. editorphil bourne eLife sciences eric schadtfounding editor-in-chief dir. inst. for genomics &plos comp. biology multiscale biology mt. sinai school of med.
  • 103. brian bot stephen friend josh greenberg david burdick mike kellenour patients external partnersmyles axton ian mulvaney kelly lamarcoeditor head of technology senior editornature genetics • science trans. medicine mark patterson managing exec. editorphil bourne eLife sciences eric schadtfounding editor-in-chief dir. inst. for genomics &plos comp. biology multiscale biology mt. sinai school of med.