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tools for reproducible research in an increasingly digital world

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tools for reproducible research in an increasingly digital world

  1. 1. brian m. bot | sage bionetworks | @BrianMBot mayo clinic - 2015 jan 28 tools for reproducible research in an increasingly digital world
  2. 2. sage bionetworks ~40 FTEs 1/2 research - 1/3 platform - 1/6 leadership/support
  3. 3. sage bionetworks focused on a world where biomedical research will fundamentally change to be more open and collaborative
  4. 4. production
  5. 5. distribution
  6. 6. aggregation
  7. 7. 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 the status quo tolerates poor communication of findings Ioannidis A. et al. Nature Genetics 2009
  8. 8. 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 1231 citations often what is in principle reproducible, is not practically reproducible unidentified publication ‣ from journal with 5 year impact factor of 27 ‣ article freely available for download ‣ data freely available for download
  9. 9. “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
  10. 10. 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
  11. 11. 7. publish results
  12. 12. finitein ∞ ...
  13. 13. conducting research for others to consume (even if the ‘other’ is future you) reproducible research
  14. 14. tools for reproducible research code data analysis
  15. 15. tools for reproducible research code version control
  16. 16. tools for reproducible research code version control client-server distributed
  17. 17. tools for reproducible research code version control client-server (e.g svn, cvs)
  18. 18. tools for reproducible research code version control client-server distributed
  19. 19. tools for reproducible research code version control (e.g git, mercurial) distributed
  20. 20. tools for reproducible research code version control distributed
  21. 21. tools for reproducible research code data analysis
  22. 22. tools for reproducible research data generic domain repositories results
  23. 23. tools for reproducible research data digital object identifier (doi) a unique identifier which remains fixed over the lifetime of a web-accessible object metadata, including the object’s location, is stored in association with the doi and may change over time referring to an online document by its doi provides more stable linking than simply referring to a url
  24. 24. tools for reproducible research code data analysis
  25. 25. tools for reproducible research analysis R Sweave knitr great if you know LaTeX
  26. 26. tools for reproducible research analysis R Sweave knitr great if you are lazy (like me)
  27. 27. tools for reproducible research analysis knitr # Hello World Title ### Author: Brian M. Bot This is a narrative with inline code execution to tell me that pi is equal to `r pi`. And a plot to show a simple function. ```{r} x <- 1:100 y <- log(x)/x plot(x,y) ```
  28. 28. tools for reproducible research analysis knitr # Hello World Title ### Author: Brian M. Bot This is a narrative with inline code execution to tell me that pi is equal to `r pi`. And a plot to show a simple function. ```{r} x <- 1:100 y <- log(x)/x plot(x,y) ```
  29. 29. tools for reproducible research analysis ipython notebook
  30. 30. tools for reproducible research other tools galaxy docker packrat shiny
  31. 31. tools for reproducible research other tools enables sharing of all resources (data, code, results) and their relationships to one another
  32. 32. tools for reproducible research
  33. 33. tools for reproducible research
  34. 34. tools for reproducible research
  35. 35. Go Hawks!
  36. 36. mayo clinic - 2015 jan 28 in an increasingly digital world brian m. bot —————— brian.bot@sagebase.org @BrianMBot sage bionetworks tools for reproducible research

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