Brian Bot, Oct 2, 2012. Strata Conference, London, UK

1. clearScience
dragging scientific communication
into the information age
Brian M. Bot | Senior Scientist | Sage Bionetworks

2. Deception at Duke

3. “I will help you. Trust me.”
- Anil Potti to Juliet Jacobs (pictured above)

5. open

6. open source

7. open data

8. open access

9. access2research

10. accessible

11. clear

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

13. the status quo tolerates
poor communication
of findings can
reproduce
partially
can reproduce from 6%
processed data w/
discrepancies
21%
54%
cannot
can reproduce 8% reproduce
w/discrepancies
11%
can
reproduce in
principle
Ioannidis A. et al. Repeatability of published microarray gene expression analyses. Nature Genetics 41, 149-155 (2009) | doi:10.1038/ng.295

14. often what is in principle
reproducible, is not
practically reproducible
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
unidentified publication
‣ from journal with 5 year impact factor of 28
‣ article freely available for download
‣ data freely available for download

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

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

17. let’s go back to basics

18. scientific method
1. define a question
2. gather information and resources (background research)
3. form a hypothesis
4. test hypothesis experimentally
5. analyze experimental data
6. draw conclusions based on data
7. publish results
8. retest (frequently done by other scientists)

19. 7. publish results

20. infinite
...
∞

21. printed
on paper
store on local
server
experimentally generate
data @ the bench or static html
from a clinical cohort representation
accepted &
digitally
typeset
static pdf
representation
analyze on local
machine
sent to
write a document reviewers
as pdf
rn al
t to jou
s ubmi

22. scientific claims
are being artificially uncoupled from
science itself

23. science is hard

24. communication is hard
(especially for scientists)

25. getting harder in an era of
‘BIG DATA’

26. clearScience
re-imagining scientific communication
allow consumption of content at a
variety of levels of complexity
and abstraction
leverage (open) RESTful APIs

27. clearScience
RESTful APIs
allow users to reassemble an entire
analysis environment

28. clearScience
analysis environment
‣ hardware
‣ software
‣ data
‣ code

30. scientific communication
needs to evolve

31. needs to evolve
along with science

32. make it easy to do
good science

33. make it easy to do
clearScience

34. Acknowledgements
Sage Bionetworks External Partners
David Burdick - Rockstar Engineer Myles Axton - Nature Genetics
Stephen Friend - President and CEO Phil Bourne - PLoS Computational Biology
Erich S. Huang - Director of Cancer Research Josh Greenberg - Alfred P. Sloan Foundation
Mike Kellen - Director of Technology Kelly LaMarco - Science Translational Medicine
Ian Mulvaney - eLife Sciences
Eric Schadt - Open Network Biology