clearScienceStrataRx2012
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The impetus behind Sage Bionetworks' clearScience project and how it effaces the boundary between doing science and communicating science.
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clearScienceStrataRx2012
- 1. clear Science dragging scientific communication into the information age erich s. huang, md/phd director, cancer research sage bionetworks erich.huang@sagebase.org @erichhuang
- 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 receptor estrogen receptor breast cancer cell depends on receptor-driven growth signals
- 8. her2 receptor progesterone receptor estrogen receptor breast cancer cell depends on receptor-driven growth signals
- 9. her2 receptor progesterone receptor LS estrogen NA receptor S IG T H OW G R breast cancer cell depends on receptor-driven growth signals
- 10. breast cancer cell growth signals become independent of receptors
- 11. “triple negative” breast cancer breast cancer cell growth signals become independent of receptors
- 12. “triple negative” breast cancer the receptors are no longer present on the cell surface... breast cancer cell growth signals become independent of receptors
- 13. “triple negative” breast cancer the receptors are no longer present on the cell surface... but the intracellular signals persist breast cancer cell growth signals become independent of receptors
- 14. “triple negative” breast cancer the receptors are no longer present on the cell 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
- 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
- 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
- 35. molecularly-customized ~4 million datapoints cancer treatment plan
- 37. E S TIM 4 6 3 ED C IT
- 38. E S TIM 6 3 4 CS- ED MI LS IT C EN O RIA G ED T 3 ID GU
- 39. E S TIM 6 3 4 CS- ED MI LS IT C EN O RIA G ED T 3 ID GU
- 42. molecularly-customized ~4 million datapoints cancer treatment plan
- 43. molecularly-customized ~4 million datapoints cancer treatment plan
- 44. Magic molecularly-customized ~4 million datapoints cancer treatment plan
- 45. Open
- 46. Open
- 47. Open
- 48. Open Source
- 49. Open
- 50. Open Data
- 51. Open
- 52. Open Access
- 53. Access
- 55. OpenSource OpenData OpenAccess } Clear ?
- 60. Nature 483, 509 (29 March 2012) | doi:10.1038/483509a
- 61. Nature 483, 509 (29 March 2012) | doi:10.1038/483509a
- 62. the status quo tolerates poor communication of findings
- 63. the status quo can reproduce tolerates poor partially communication of findings 6% can reproduce from processed data w/ 21% discrepancies 54% can reproduce w/ 8% cannot discrepancies reproduce 11% can reproduce in principle
- 64. so what’s in principle reproducible, is not practically reproducible
- 65. 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
- 66. THE SCIENTIFIC PROCESS: it’s not one and done... define a question
- 67. THE SCIENTIFIC PROCESS: it’s not one and done... define a question gather information
- 68. THE SCIENTIFIC PROCESS: it’s not one and done... define a question form a hypothesis gather information
- 69. THE SCIENTIFIC PROCESS: it’s not one and done... define a question form a hypothesis gather information experimentally test your hypothesis
- 70. THE SCIENTIFIC PROCESS: it’s not one and done... analyze define a question form a hypothesis experimental data gather information experimentally test your hypothesis
- 71. 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
- 72. 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
- 73. 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
- 75. generate data @ the bench or from a clinical cohort
- 76. generate data @ the bench or from a clinical cohort
- 77. store on local generate data server @ the bench or from a clinical cohort
- 78. store on local generate data server @ the bench or from a clinical cohort
- 79. store on local generate data server @ the bench or from a clinical cohort analyze on local machine
- 80. store on local generate data server @ the bench or from a clinical cohort analyze on local machine
- 81. store on local generate data server @ the bench or from a clinical cohort analyze on local machine write a document
- 82. store on local generate data server @ the bench or from a clinical cohort analyze on local machine write a document al to journ su bmit
- 83. store on local generate data server @ the bench or from a clinical cohort analyze on local machine sent to write a reviewers document as pdf al to journ su bmit
- 84. store on local generate data server @ the bench or from a clinical cohort analyze on local machine sent to write a reviewers document as pdf al to journ su bmit
- 85. store on local generate data server @ the bench or from a clinical cohort accepted & digitally typeset analyze on local machine sent to write a reviewers document as pdf al to journ su bmit
- 86. printed on paper store on local generate data server @ the bench or from a clinical cohort accepted & digitally typeset analyze on local machine sent to write a reviewers document as pdf al to journ su bmit
- 87. printed on paper store on local generate data server @ the bench or from 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
- 88. printed on paper store on local generate data server @ the bench or from 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
- 89. printed on paper store on local generate data server @ the bench or from 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
- 90. printed on paper store on local generate data server @ the bench or from a clinical cohort static html representation THE 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
- 91. printed on paper store on local generate data server @ the bench or from a clinical cohort static html representation THE 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
- 92. store on local generate data server @ the bench or from a clinical cohort THE ACTUAL SCIENCE analyze on local machine
- 93. store on local generate data server @ the bench or from a clinical cohort THE ACTUAL SCIENCE analyze on local machine
- 95. clear Science
- 96. clear Science
- 97. clear Science
- 98. clear Science 1. re-imagine scientific communication
- 99. clear Science 1. re-imagine scientific communication 2. make every component of a data-intensive project (e.g. genomic analysis) web accessible
- 100. clear Science 1. re-imagine scientific communication 2. make every component of a data-intensive project (e.g. genomic analysis) web accessible 3. allow consumption of content at a variety of levels of complexity and abstraction 4. leverage open, RESTful APIs
- 101. leverage open, RESTful APIs
- 102. leverage open, RESTful APIs to let users reconstitute an entire analytical environment
- 103. leverage open, RESTful APIs to let users reconstitute an entire analytical environment hardware
- 104. leverage open, RESTful APIs to let users reconstitute an entire analytical environment software hardware
- 105. leverage open, RESTful APIs to let users reconstitute an entire analytical environment data software hardware
- 106. leverage open, RESTful APIs to let users reconstitute an entire analytical environment code data software hardware
- 108. code data software hardware clear Science
- 109. code data software hardware clear Science a narrative that coherently interweaves scientific assertions with the executable data, code, software & hardware that support them
- 110. “ my computer’s the cloud, let me hand it to you ”
- 113. “ If I have seen further it is by standing on the shoulders of giants. ”
- 114. Betty Jones “I have a lump near my mastectomy scar”
- 116. brian bot stephen friend josh greenberg david burdick mike kellen external partners myles axton ian mulvaney kelly lamarco editor head of technology senior editor nature genetics • science trans. medicine mark patterson managing exec. editor phil bourne eLife sciences eric schadt founding editor-in-chief dir. inst. for genomics & plos comp. biology multiscale biology mt. sinai school of med.
- 117. brian bot stephen friend josh greenberg david burdick mike kellen our patients external partners myles axton ian mulvaney kelly lamarco editor head of technology senior editor nature genetics • science trans. medicine mark patterson managing exec. editor phil bourne eLife sciences eric schadt founding editor-in-chief dir. inst. for genomics & plos comp. biology multiscale biology mt. sinai school of med.