clearScienceStrataRx2012

clear Sciencedragging scientific communication intothe information ageerich s. huang, md/phddirector, cancer researchsage bionetworkserich.huang@sagebase.org@erichhuang

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Betty Jones “I have a lump near my mastectomy scar”

Betty Jones menopause ~50 years “high risk” breast cancer “normal risk” breast cancer

Betty Jones menopause 36 years ~50 years “high risk” breast cancer “normal risk” breast cancer

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

her2 receptor progesterone receptorestrogenreceptor breast cancer cell depends on receptor-driven growth signals

her2 receptor progesterone receptor LSestrogen NAreceptor S IG T H OW G R breast cancer cell depends on receptor-driven growth signals

breast cancer cellgrowth signals becomeindependent of receptors

“triple negative” breast cancer breast cancer cell growth signals become independent of receptors

“triple negative” breast cancerthe receptors are no longer present on thecell surface... breast cancer cell growth signals become independent of receptors

“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

“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

http://www.cancer.gov/images/cdr/live/CDR415523-750.jpg

Betty Jones minus plus lymph node young negative african-american triple negative multifocal cancer

Betty Jones minus plus lymph node young negative african-american = Aggressive therapeutic strategy triple negative multifocal cancer

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radiotherapy 3d planning http://radonc.ucsf.edu/patient_information/breast/images/Radiation_Oncology_breast_img_2.jpg

Betty Jones Triple negative breast cancer. What are the options?

Betty Jones Triple negative breast cancer. What are the options? Standard Stuff (Old Fashioned Targets) Anthracyclines Taxanes Anti-Metabolites

Betty Jones Triple negative breast cancer. What are the options? Standard Stuff (Old Fashioned Targets) Anthracyclines Taxanes Anti-Metabolites Platinum Agents

Betty Jones Triple negative breast cancer. What are the options? { Standard Stuff (Old Fashioned Targets) Anthracyclines conventional Taxanes chemotherapy Anti-Metabolites Platinum Agents

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)

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)

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)

Betty Jones

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molecularly-customized~4 million datapoints cancer treatment plan

E S TIM 4 6 3 EDC IT

E S TIM 6 3 4 CS- ED MI LS ITC EN O RIA G ED T 3 ID GU

molecularly-customized~4 million datapoints cancer treatment plan

Magic molecularly-customized~4 million datapoints cancer treatment plan

Open Source

Open Data

Open Access

Access

Access = Accessible?

OpenSourceOpenDataOpenAccess } Clear ?

Nature 483, 509 (29 March 2012) | doi:10.1038/483509a

the status quotolerates poorcommunicationof ﬁndings

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

so what’s inprinciplereproducible, is notpracticallyreproducible

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

THE SCIENTIFIC PROCESS:it’s not one and done... deﬁne a question

THE SCIENTIFIC PROCESS:it’s not one and done... deﬁne a question gather information

THE SCIENTIFIC PROCESS:it’s not one and done... deﬁne a question form a hypothesis gather information

THE SCIENTIFIC PROCESS:it’s not one and done... deﬁne a question form a hypothesis gather information experimentally test your hypothesis

THE SCIENTIFIC PROCESS:it’s not one and done... analyze deﬁne a question form a hypothesis experimental data gather information experimentally test your hypothesis

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

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

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

generate data@ the bench orfrom a clinical cohort

store on localgenerate data server@ the bench orfrom a clinical cohort

store on localgenerate data server@ the bench orfrom a clinical cohort analyze on local machine

store on localgenerate data server@ the bench orfrom a clinical cohort analyze on local machine write a document

store on localgenerate data server@ the bench orfrom a clinical cohort analyze on local machine write a document al to journ su bmit

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

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

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

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

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

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

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

store on local generate data server @ the bench or from a clinical cohortTHE ACTUAL SCIENCE analyze on local machine

clear Science

clear Science1. re-imagine scientiﬁc communication

clear Science1. re-imagine scientiﬁc communication2. make every component of a data-intensive project (e.g. genomic analysis) web accessible

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

leverage open, RESTful APIs

leverage open, RESTful APIs to let users reconstitute an entire analytical environment

leverage open, RESTful APIs to let users reconstitute an entire analytical environment hardware

leverage open, RESTful APIs to let users reconstitute an entire analytical environment software hardware

leverage open, RESTful APIs to let users reconstitute an entire analytical environment data software hardware

leverage open, RESTful APIs to let users reconstitute an entire analytical environment code data software hardware

code datasoftwarehardware

code data software hardwareclear Science

code data software hardwareclear Science a narrative that coherently interweaves scientiﬁc assertions with the executable data, code, software & hardware that support them

“ my computer’s the cloud, let me hand it to you ”

“ If I have seen further it is by standing on the shoulders of giants. ”

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.

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.

clearScienceStrataRx2012

by OReillyStrata on Oct 17, 2012

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