clearScience          dragging scientific communication              into the information ageBrian M. Bot | Senior Scientis...
Deception at Duke
“I will help you. Trust me.”         - Anil Potti to Juliet Jacobs (pictured above)
open
open source
open data
open access
access2research
accessible
clear
research scandals representmerely the extreme of acontinuum in the culture ofacademic research
the status quo tolerates poor communication of findings                                                                    ...
often what is in principle                                                                                         reprodu...
how are we to move science forwardif we cannot understand what was done previously ?
Nature 483, 509 (29 March 2012) | doi:10.1038/483509a
let’s go back to basics
scientific method  1. define a question   2. gather information and resources (background research)     3. form a hypothesis...
7. publish results
infinite          ... ∞
printed                                                                  on paper                                         ...
scientific claimsare being artificially uncoupled from          science itself
science is hard
communication is hard    (especially for scientists)
getting harder in an era of  ‘BIG DATA’
clearScience re-imagining scientific communication  allow consumption of content at a    variety of levels of complexity   ...
clearScience            RESTful APIs  allow users to reassemble an entire         analysis environment
clearScience     analysis environment        ‣   hardware        ‣   software        ‣   data        ‣   code
scientific communication     needs to evolve
needs to evolvealong with science
make it easy to do  good science
make it easy to do  clearScience
AcknowledgementsSage Bionetworks                               External PartnersDavid Burdick - Rockstar Engineer         ...
Bot Strata UK 2012-10-02
Bot Strata UK 2012-10-02
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Bot Strata UK 2012-10-02

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

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Bot Strata UK 2012-10-02

  1. 1. clearScience dragging scientific communication into the information ageBrian M. Bot | Senior Scientist | Sage Bionetworks
  2. 2. Deception at Duke
  3. 3. “I will help you. Trust me.” - Anil Potti to Juliet Jacobs (pictured above)
  4. 4. open
  5. 5. open source
  6. 6. open data
  7. 7. open access
  8. 8. access2research
  9. 9. accessible
  10. 10. clear
  11. 11. research scandals representmerely the extreme of acontinuum in the culture ofacademic research
  12. 12. 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 principleIoannidis A. et al. Repeatability of published microarray gene expression analyses. Nature Genetics 41, 149-155 (2009) | doi:10.1038/ng.295
  13. 13. 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 citationsunidentified publication ‣ from journal with 5 year impact factor of 28 ‣ article freely available for download ‣ data freely available for download
  14. 14. how are we to move science forwardif we cannot understand what was done previously ?
  15. 15. Nature 483, 509 (29 March 2012) | doi:10.1038/483509a
  16. 16. let’s go back to basics
  17. 17. 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)
  18. 18. 7. publish results
  19. 19. infinite ... ∞
  20. 20. printed on paper store on local serverexperimentally generatedata @ the bench or static htmlfrom 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
  21. 21. scientific claimsare being artificially uncoupled from science itself
  22. 22. science is hard
  23. 23. communication is hard (especially for scientists)
  24. 24. getting harder in an era of ‘BIG DATA’
  25. 25. clearScience re-imagining scientific communication allow consumption of content at a variety of levels of complexity and abstraction leverage (open) RESTful APIs
  26. 26. clearScience RESTful APIs allow users to reassemble an entire analysis environment
  27. 27. clearScience analysis environment ‣ hardware ‣ software ‣ data ‣ code
  28. 28. scientific communication needs to evolve
  29. 29. needs to evolvealong with science
  30. 30. make it easy to do good science
  31. 31. make it easy to do clearScience
  32. 32. AcknowledgementsSage Bionetworks External PartnersDavid Burdick - Rockstar Engineer Myles Axton - Nature GeneticsStephen Friend - President and CEO Phil Bourne - PLoS Computational BiologyErich S. Huang - Director of Cancer Research Josh Greenberg - Alfred P. Sloan FoundationMike Kellen - Director of Technology Kelly LaMarco - Science Translational Medicine Ian Mulvaney - eLife Sciences Eric Schadt - Open Network Biology
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