clearsciencestratarx2012
DESCRIPTION
The impetus behind Sage Bionetworks' clearScience project and how it effaces the boundary between doing science and communicating science.TRANSCRIPT
clearSciencedragging scientific communication into the information age
erich s. huang, md/phddirector, cancer researchsage bionetworks
[email protected]@erichhuang
http://www.viahealthcaredesign.com/LMCH%20Universal%20Exam%20Rm.jpg
Betty Jones
“I have a lump near my mastectomy scar”
Betty Jones
menopause~50 years
“high risk” breast cancer “normal risk” breast cancer
36 years
Betty Jones
menopause~50 years
“high risk” breast cancer “normal risk” breast cancer
61%
39%
Triple Negative Breast CancerAll Other Types
84%
16%
Triple Negative Breast CancerAll Other Types
Betty Jones
African American Population Non-African American Population
http://jama.jamanetwork.com/article.aspx?articleid=202952
breast cancer celldepends on receptor-driven growth signals
estrogenreceptor
progesteronereceptor
her2receptor
breast cancer celldepends on receptor-driven growth signals
estrogenreceptor
progesteronereceptor
her2receptor
breast cancer celldepends on receptor-driven growth signals
estrogenreceptor
progesteronereceptor
her2receptor
GROWTH SIGNALS
breast cancer cellgrowth signals becomeindependent of receptors
“triple negative” breast cancer
breast cancer cellgrowth signals becomeindependent of receptors
“triple negative” breast cancerthe receptors are no longer present on the cell surface...
breast cancer cellgrowth signals becomeindependent of receptors
“triple negative” breast cancerthe receptors are no longer present on the cell surface...but the intracellular signals persist
breast cancer cellgrowth signals becomeindependent of receptors
“triple negative” breast cancerthe receptors are no longer present on the cell surface...but the intracellular signals persist
breast cancer cellgrowth signals becomeindependent of receptors
INDEPENDENT
GROWTH SIGNALS
http://www.cancer.gov/images/cdr/live/CDR415523-750.jpg
http://www.cancer.gov/images/cdr/live/CDR415523-750.jpg
http://www.cancer.gov/images/cdr/live/CDR415523-750.jpg
Betty Jones
minus plus
young lymph node negative
african-american
triple negative
multifocal cancer
Betty Jones
minus plus
young lymph node negative
african-american
triple negative
multifocal cancer
= Aggressive therapeutic strategy
http://www.flickr.com/photos/kbrookes/7497906298/sizes/h/in/photostream/
http://radonc.ucsf.edu/patient_information/breast/images/Radiation_Oncology_breast_img_2.jpg
radiotherapy 3d planning
Betty Jones
“I have a lump near my mastectomy scar”
Betty JonesTriple negative breast cancer.What are the options?
Betty JonesTriple negative breast cancer.What are the options?
Standard Stuff (Old Fashioned Targets)
AnthracyclinesTaxanesAnti-Metabolites
Betty JonesTriple negative breast cancer.What are the options?
Standard Stuff (Old Fashioned Targets)
AnthracyclinesTaxanesAnti-Metabolites
Platinum Agents
Betty JonesTriple negative breast cancer.What are the options?
Standard Stuff (Old Fashioned Targets)
AnthracyclinesTaxanesAnti-Metabolites
Platinum Agents{conventional
chemotherapy
Betty JonesTriple negative breast cancer.What are the options?
Standard Stuff (Old Fashioned Targets)
AnthracyclinesTaxanesAnti-Metabolites
Platinum Agents
Targeted AgentsCetuximab + Platinum (BALI-1)Bevacizumab (GeparQuinto)PARP InhibitorsSRC InhibitorsHDAC Inhibitors (ER-alpha)
{conventional chemotherapy
Betty JonesTriple negative breast cancer.What are the options?
Standard Stuff (Old Fashioned Targets)
AnthracyclinesTaxanesAnti-Metabolites
Platinum Agents
Targeted AgentsCetuximab + Platinum (BALI-1)Bevacizumab (GeparQuinto)PARP InhibitorsSRC InhibitorsHDAC Inhibitors (ER-alpha)
{conventional chemotherapy
{new therapies
Betty JonesTriple negative breast cancer.What are the options?
Standard Stuff (Old Fashioned Targets)
AnthracyclinesTaxanesAnti-Metabolites
Platinum Agents
Targeted AgentsCetuximab + Platinum (BALI-1)Bevacizumab (GeparQuinto)PARP InhibitorsSRC InhibitorsHDAC Inhibitors (ER-alpha)
{conventional chemotherapy
{new therapies
CURRENT KNOWLEDGE:ALL THESE THERAPIESARE A WASH
Betty Jones
Betty Jones
http://www.viahealthcaredesign.com/LMCH%20Universal%20Exam%20Rm.jpg
~4 million datapoints molecularly-customizedcancer treatment plan
CITED 463 TIMES
CITED 463 TIMES
3 GENOMICS-
GUIDED TRIALS
CITED 463 TIMES
3 GENOMICS-
GUIDED TRIALS
~4 million datapoints molecularly-customizedcancer treatment plan
~4 million datapoints molecularly-customizedcancer treatment plan
~4 million datapoints molecularly-customizedcancer treatment planMagic
Open
Open
Open
SourceOpen
Open
DataOpen
Open
AccessOpen
Access
Access = Accessible?
OpenSourceOpenDataOpenAccess
}Clear ?
Nature 483, 509 (29 March 2012) | doi:10.1038/483509a
Nature 483, 509 (29 March 2012) | doi:10.1038/483509a
the status quo tolerates poor communication of findings
the status quo tolerates poor communication of findings
6%
21%
8%
11%
54%cannotreproduce
can reproduce in principle
can reproduce w/discrepancies
can reproduce from processed data w/discrepancies
can reproduce partially
so what’s in principle reproducible, is not practically reproducible
208,294,724datapoints
124 pagessupplemental material
? lines unobtainable source code
? version or architecture of R
? R packageskey R package “ClaNC”no longer available
442 citations
so what’s in principle reproducible, is not practically reproducible
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
gather information
form a hypothesis
THE SCIENTIFIC PROCESS:it’s not one and done...
define a question
gather information
form a hypothesis
experimentally testyour hypothesis
THE SCIENTIFIC PROCESS:it’s not one and done...
define a question
gather information
form a hypothesis
experimentally testyour hypothesis
analyze experimental data
THE SCIENTIFIC PROCESS:it’s not one and done...
define a question
gather information
form a hypothesis
experimentally testyour hypothesis
analyze experimental data
draw conclusions
THE SCIENTIFIC PROCESS:it’s not one and done...
define a question
gather information
form a hypothesis
experimentally testyour hypothesis
analyze experimental data
draw conclusions
report, i.e. “publish”
THE SCIENTIFIC PROCESS:it’s not one and done...
define a question
gather information
form a hypothesis
experimentally testyour hypothesis
analyze experimental data
draw conclusions
report, i.e. “publish”
validation by the scientific communityvalidation by clinical trials
THE SCIENTIFIC PROCESS:it’s not one and done...
generate data @ the bench orfrom a clinical cohort
generate data @ the bench orfrom a clinical cohort
generate data @ the bench orfrom a clinical cohort
store on local server
generate data @ the bench orfrom a clinical cohort
store on local server
analyze on local machine
generate data @ the bench orfrom a clinical cohort
store on local server
analyze on local machine
generate data @ the bench orfrom a clinical cohort
store on local server
analyze on local machine
write a document
generate data @ the bench orfrom a clinical cohort
store on local server
submit to journal
analyze on local machine
write a document
generate data @ the bench orfrom a clinical cohort
store on local server
submit to journal
analyze on local machine
write a document
sent to reviewers as pdf
generate data @ the bench orfrom a clinical cohort
store on local server
submit to journal
analyze on local machine
write a document
sent to reviewers as pdf
generate data @ the bench orfrom a clinical cohort
store on local server
submit to journal
analyze on local machine
write a document
sent to reviewers as pdf
generate data @ the bench orfrom a clinical cohort
accepted & digitally typeset
store on local server
submit to journal
analyze on local machine
write a document
sent to reviewers as pdf
printed on paper
generate data @ the bench orfrom a clinical cohort
accepted & digitally typeset
store on local server
submit to journal
analyze on local machine
write a document
sent to reviewers as pdf
printed on paper
static html representation
generate data @ the bench orfrom a clinical cohort
accepted & digitally typeset
store on local server
submit to journal
analyze on local machine
write a document
sent to reviewers as pdf
printed on paper
static html representation
generate data @ the bench orfrom a clinical cohort
accepted & digitally typeset
static pdf representation
store on local server
submit to journal
analyze on local machine
write a document
sent to reviewers as pdf
printed on paper
static html representation
generate data @ the bench orfrom a clinical cohort
accepted & digitally typeset
static pdf representation
store on local server
submit to journal
analyze on local machine
write a document
sent to reviewers as pdf
printed on paper
static html representation
generate data @ the bench orfrom a clinical cohort
accepted & digitally typeset
static pdf representation
store on local server
THE ACTUAL SCIENCE
submit to journal
analyze on local machine
write a document
sent to reviewers as pdf
printed on paper
static html representation
generate data @ the bench orfrom a clinical cohort
accepted & digitally typeset
static pdf representation
store on local server
THE ACTUAL SCIENCE
SCIENTIFIC CLAIMS
analyze on local machine
generate data @ the bench orfrom a clinical cohort
store on local server
THE ACTUAL SCIENCE
analyze on local machine
generate data @ the bench orfrom a clinical cohort
store on local server
THE ACTUAL SCIENCE
clearScience
clearScience
clearScience
clearScience1. re-imagine scientific communication
clearScience1. re-imagine scientific communication2. make every component of a data-intensive project
(e.g. genomic analysis) web accessible
clearScience1. 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 abstractionleverage open, RESTful APIs4.
leverage open, RESTful APIs
leverage open, RESTful APIsto let users reconstitute an entire analytical environment
leverage open, RESTful APIs
hardware
to let users reconstitute an entire analytical environment
leverage open, RESTful APIs
hardware
software
to let users reconstitute an entire analytical environment
leverage open, RESTful APIs
hardware
software
data
to let users reconstitute an entire analytical environment
leverage open, RESTful APIs
hardware
software
data
code
to let users reconstitute an entire analytical environment
hardware
software
data
code
hardware
software
data
code
clearScience
hardware
software
data
code
clearSciencea 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.
“”
Betty Jones
“I have a lump near my mastectomy scar”
josh greenbergbrian botstephen frienddavid burdickmike kellen
myles axtoneditornature genetics
phil bournefounding editor-in-chiefplos comp. biology
ian mulvaneyhead of technology
•mark pattersonmanaging exec. editoreLife sciences
external partners
kelly lamarcosenior editorscience trans. medicine
eric schadtdir. inst. for genomics & multiscale biologymt. sinai school of med.
josh greenbergbrian botstephen frienddavid burdickmike kellen
myles axtoneditornature genetics
phil bournefounding editor-in-chiefplos comp. biology
ian mulvaneyhead of technology
•mark pattersonmanaging exec. editoreLife sciences
external partners
kelly lamarcosenior editorscience trans. medicine
eric schadtdir. inst. for genomics & multiscale biologymt. sinai school of med.
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