tools for communicating in the computational sciences
Transcript of tools for communicating in the computational sciences
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tools for communicating in the computational sciences
Brian M. Bot | Senior Scientist | Sage Bionetworks
clearScience
14 December 2012
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Sage Bionetworks
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Sage Bionetworks
I love Sage notebooks!
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a non-profit organization which pilots a variety of components that are necessary to build a scientific research “commons”
why?
Sage Bionetworks
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“We Must Guard Against the acquisition of unwarranted influence,
whether sought or unsought, by the Military Industrial Complex”
- Dwight D. Eisenhower 1961 Medical
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not conducive for a ‘commons’
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institutional incrementalism
individual tenure
proprietary short term solutions
not conducive for a ‘commons’
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commonsenabling a
open data
accessible platform
clear communication
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“The problem is that right now, it’s not easy to donate your data to health research.”
“The goal of Consent to Research is to play a part in the transformation of health from
something we experience passively to something we
experience actively.”
http://weconsent.usJohn Wilbanks, Chief Commons Officer
open data
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open data
accessible platform
clear communication
commonsenabling a
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‣ compute ‣ hardware ‣ software
‣ data ‣ code
analysis environment
RESTful APIs
accessible platform
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open data
accessible platform
clear communication
commonsenabling a
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clear communication
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Deception at Duke
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research scandals represent merely the extreme of a continuum in the culture of academic research
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the status quo tolerates poor communication of findings
6%
21%
8%
11%
54%cannot reproduce
can reproduce in principle
can reproduce w/discrepancies
can reproduce from processed data w/discrepancies
can reproduce partially
Ioannidis A. et al. Repeatability of published microarray gene expression analyses. Nature Genetics 41, 149-155 (2009) | doi:10.1038/ng.295
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208,294,724 datapoints
124 pages supplemental material
?? lines unobtainable source code
?? version or architecture of statistical analysis program (R)
enumerable R packages and package dependencies
key R package “ClaNC” no longer available
442 citations
often what is in principle reproducible, is not practically reproducible
unidentified publication‣ from journal with 5 year impact factor of 28‣ article freely available for download‣ data freely available for download
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how are we to move science forward
if we cannot understand what was done previously?
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let’s go back to basics
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4. test hypothesis experimentally
5. analyze experimental data
7. publish results
6. draw conclusions based on data
scientific method1. define a question
2. gather information and resources (background research)
3. form a hypothesis
8. retest (frequently done by other scientists)
4. test hypothesis experimentally
5. analyze experimental data
7. publish results
6. draw conclusions based on data
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7. publish results
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finitein
∞...
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submit to journal
analyze on local machine
write a documentsent to reviewers as pdf
printed on paper
static html representation
experimentally generate data
accepted & digitally typeset
static pdf representation
store on local server
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are being artificially uncoupled from
scientific claims
science itself
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is hardscience
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is hardcommunication
(especially for scientists)
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clearSciencere-imagining scientific communication
allow consumption of content at a variety of levels of complexity
and abstraction
leverage Synapse RESTful APIs
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clearScienceallow consumption of content at a
variety of levels of complexity and abstraction
“hand the keys over” to the reviewers
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scientific communicationneeds to evolve
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along with scienceneeds to evolve
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make it easy to do
good science
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clearScience
make it easy to do
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AcknowledgementsSage Bionetworks
David Burdick - Rockstar Engineer
Stephen Friend - President and CEO
Erich S. Huang - Director of Cancer Research
Mike Kellen - Director of Technology
External Partners
Myles Axton - Nature Genetics
Phil Bourne - PLoS Computational Biology
Josh Greenberg - Alfred P. Sloan Foundation
Kelly LaMarco - Science Translational Medicine
Eric Schadt - Mount Sinai School of Medicine