20130319 AMIA conference

1. infrastructure for communicating
data-intensive science
brian m. bot | senior scientist | community manager | sage bionetworks
clearScience

2. a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research “commons”
why?
Sage Bionetworks

3. “We Must Guard Against
the acquisition of unwarranted influence,
whether sought or unsought, by the
Military Industrial Complex”
- Dwight D. Eisenhower 1961Medical

4. not conducive for a ‘commons’

5. institutional incrementalism
individual tenure
proprietary shortsighted solutions
not conducive for a ‘commons’

6. commonsenabling a
open data
accessible platform
clear communication

7. “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

8. open data
accessible platform
clear communication
commonsenabling a

9. accessible platform
a collaborative compute space that
allows scientists to share and analyze
data together

10. open data
accessible platform
clear communication
commonsenabling a

11. clear communication

12. Deception at Duke

13. research scandals represent
merely the extreme of a
continuum in the culture of
academic research

14. 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

15. 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

16. how are we to move science forward
if we cannot understand what was done previously?

17. let’s go back to basics

18. 4. test hypothesis experimentally
5. analyze experimental data
7. publish results
6. draw conclusions based on data
scientific method
1. 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

19. 7. publish results

20. finitein
∞
...

21. submit to journal
analyze on local
machine
write a document
sent to
reviewers
as pdf
printed
on paper
static html
representation
experimentally
generate data
accepted &
digitally
typeset
static pdf
representation
store on local
server

22. are being artificially uncoupled from
scientific claims
science itself

23. clearScience
re-imagining scientific communication
allow consumption of content at a
variety of levels of complexity
and abstraction
leverage Synapse RESTful APIs

24. clearScience
allow consumption of content at a
variety of levels of complexity
and abstraction
“hand the keys over” to the reviewers

26. scientific communication
needs to evolve

27. along with science
needs to evolve

28. “Scientists often study the past as
obsessively as historians because few
other professions depend so acutely on it.
Every experiment is a conversation with
a prior experiment,
every new theory a refutation of the old”
-Siddhartha Mukherjee, The Emperor of All Maladies

29. Acknowledgements
Sage Bionetworks
David Burdick - Senior Software Engineer
Stephen Friend - President and CEO
Erich S. Huang - Director of Cancer Research
Michael 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