Bot Strata UK 2012-10-02
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Bot Strata UK 2012-10-02



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

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



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Bot Strata UK 2012-10-02 Bot Strata UK 2012-10-02 Presentation Transcript

  • clearScience dragging scientific communication into the information ageBrian M. Bot | Senior Scientist | Sage Bionetworks
  • 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 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
  • 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
  • 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 4. test hypothesis experimentally 5. analyze experimental data 6. draw conclusions based on data 7. publish results 8. retest (frequently done by other scientists)
  • 7. publish results
  • infinite ... ∞
  • 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
  • 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 and abstraction leverage (open) RESTful APIs
  • 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 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