huang stratarx 2012-10-16

clearSciencedragging scientific communication into the information age

erich s. huang, md/phddirector, cancer researchsage bionetworks

[email protected]@erichhuang

mailto:[email protected]

mailto:[email protected]

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

GROWTH SIGNALS

breast cancer cellgrowth signals becomeindependent of receptors

“triple negative” breast cancer


“triple negative” breast cancerthe receptors are no longer present on the cell surface...


“triple negative” breast cancerthe receptors are no longer present on the cell surface...but the intracellular signals persist


“triple negative” breast cancerthe receptors are no longer present on the cell surface...but the intracellular signals persist


INDEPENDENT

GROWTH SIGNALS

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


Betty JonesTriple negative breast cancer.What are the options?


Standard Stuff (Old Fashioned Targets)

AnthracyclinesTaxanesAnti-Metabolites




Platinum Agents




Platinum Agents{conventional

chemotherapy




Platinum Agents

Targeted AgentsCetuximab + Platinum (BALI-1)Bevacizumab (GeparQuinto)PARP InhibitorsSRC InhibitorsHDAC Inhibitors (ER-alpha)

{conventional chemotherapy




Platinum Agents



{new therapies




Platinum Agents



{new therapies

CURRENT KNOWLEDGE:ALL THESE THERAPIESARE A WASH

Betty Jones

~4 million datapoints molecularly-customizedcancer treatment plan

CITED 463 TIMES

CITED 463 TIMES

3 GENOMICS-

GUIDED TRIALS

~4 million datapoints molecularly-customizedcancer treatment plan

~4 million datapoints molecularly-customizedcancer treatment planMagic

SourceOpen

DataOpen

AccessOpen

Access

Access = Accessible?

OpenSourceOpenDataOpenAccess

}Clear ?

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


define a question

gather information

form a hypothesis


define a question

gather information

form a hypothesis

experimentally testyour hypothesis


define a question

gather information

form a hypothesis


analyze experimental data


define a question

gather information

form a hypothesis



draw conclusions


define a question

gather information

form a hypothesis



draw conclusions

report, i.e. “publish”


define a question

gather information

form a hypothesis



draw conclusions

report, i.e. “publish”

validation by the scientific communityvalidation by clinical trials


generate data @ the bench orfrom a clinical cohort


store on local server

analyze on local machine




write a document



submit to journal


write a document



submit to journal


write a document

sent to reviewers as pdf



submit to journal


write a document



accepted & digitally typeset


submit to journal


write a document


printed on paper




submit to journal


write a document


printed on paper

static html representation




submit to journal


write a document


printed on paper




static pdf representation


submit to journal


write a document


printed on paper






THE ACTUAL SCIENCE

submit to journal


write a document


printed on paper






THE ACTUAL SCIENCE

SCIENTIFIC CLAIMS




THE ACTUAL SCIENCE

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


hardware

to let users reconstitute an entire analytical environment


hardware

software



hardware

software

data



hardware

software

data

code


hardwaresoftware

datacode

hardwaresoftware

datacode

clearScience

hardwaresoftware

datacode

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”

“

clear

Scien

ce s

cree

ncas

t

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

“”

Betty Jones


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.

our patients

huang stratarx 2012-10-16

Health & Medicine