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clearScience
The document discusses the challenges of scientific communication in the context of cancer research, particularly focusing on triple negative breast cancer and its treatment options. It emphasizes the need for improved data accessibility and reproducibility in scientific findings, advocating for a more open approach to sharing research data and methodologies. The author presents a vision for 'clear science' that involves re-imagining the communication of scientific knowledge to make it more accessible and interactive.
clearScience
- 1. clear Science dragging scientificcommunication into the information age erich s. huang, md/phd director, cancer research sage bionetworks erich.huang@sagebase.org @erichhuang
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- 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 growthsignals become independent of receptors
- 11. “triple negative” breastcancer breast cancer cell growth signals become independent of receptors
- 12. “triple negative” breastcancer the receptors are no longer present on the cell surface... breast cancer cell growth signals become independent of receptors
- 13. “triple negative” breastcancer 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” breastcancer 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
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- 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
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- 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)
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- 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
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- 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 toleratespoor 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’snot one and done... define a question
- 67. THE SCIENTIFIC PROCESS: it’snot one and done... define a question gather information
- 68. THE SCIENTIFIC PROCESS: it’snot one and done... define a question form a hypothesis gather information
- 69. THE SCIENTIFIC PROCESS: it’snot one and done... define a question form a hypothesis gather information experimentally test your hypothesis
- 70. THE SCIENTIFIC PROCESS: it’snot one and done... analyze define a question form a hypothesis experimental data gather information experimentally test your hypothesis
- 71. THE SCIENTIFIC PROCESS: it’snot 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’snot 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’snot 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 @ thebench or from a clinical cohort
- 76. generate data @ thebench or from a clinical cohort
- 77. store on local generatedata server @ the bench or from a clinical cohort
- 78. store on local generatedata server @ the bench or from a clinical cohort
- 79. store on local generatedata server @ the bench or from a clinical cohort analyze on local machine
- 80. store on local generatedata server @ the bench or from a clinical cohort analyze on local machine
- 81. store on local generatedata server @ the bench or from a clinical cohort analyze on local machine write a document
- 82. store on local generatedata server @ the bench or from a clinical cohort analyze on local machine write a document al to journ su bmit
- 83. store on local generatedata 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 generatedata 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 generatedata 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
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- 98. clear Science 1. re-imaginescientific communication
- 99. clear Science 1. re-imaginescientific communication 2. make every component of a data-intensive project (e.g. genomic analysis) web accessible
- 100. clear Science 1. re-imaginescientific 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
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- 102. leverage open, RESTfulAPIs to let users reconstitute an entire analytical environment
- 103. leverage open, RESTfulAPIs to let users reconstitute an entire analytical environment hardware
- 104. leverage open, RESTfulAPIs to let users reconstitute an entire analytical environment software hardware
- 105. leverage open, RESTfulAPIs to let users reconstitute an entire analytical environment data software hardware
- 106. leverage open, RESTfulAPIs to let users reconstitute an entire analytical environment code data software hardware
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- 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’sthe cloud, let me hand it to you ”
- 113. “ If Ihave 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.