Saving the World: Open Source and Open Science

Transcript

1. Saving the World Open Source and Open Science! Dr. Marcus D. Hanwell @mhanwell +MarcusHanwell All Things Open 22 October, 2014
2. “Standing on the Shoulders of Giants”
3. Nullius in verba Motto of the Royal Society, founded in 1660 “Take nobody’s word for it”
5. Trust, but verify
6. Trust, but verify
7. Trust, but verify
8. Trust, but verify
9. Publications measure a scientist’s value – citations!
13. “Piled Higher and Deeper” by Jorge Cham www.phdcomics.com
14. Reproducibility
15. CC-BY-SA 3.0 http://en.wikipedia.org/wiki/File:Kempelen_chess1.jpg
16. Showing What’s Inside the Box! •  Need everything to reproduce results o  Raw data collected §  How it was collected, conditions, versions o  Steps to run calculations/analysis §  Often source code o  Analyzed results SHOW YOUR WORK!
17. “Scientific research has changed the world. Now it needs to change itself.” Economist, http://www.economist.com/news/leaders/21588069-scientific-research-has-changed- world-now-it-needs-change-itself-how-science-goes-wrong
18. “Publishing Research Without Data is Simply Advertising, Not Science” Graham Steel, http://blog.okfn.org/2013/09/03/publishing-research-without-data-is-simply-advertising-not-science/
19. Reproducibility!
20. “Is the evidence for austerity based on an Excel spreadsheet error?” Washington Post, April 2013 http://www.washingtonpost.com/blogs/wonkblog/wp/2013/04/16/is-the-best-evidence-for-austerity- based-on-an-excel-spreadsheet-error/
21. What is Open??? •  What does open mean, how open is open? o  Everyone has the same access o  No commercial, no derivatives is NOT OPEN •  Certain basic rights are granted to ALL o  Share o  Modify o  Use
22. Only 6 out of 53 “landmark” cancer studies could be reproduced http://www.nature.com/nature/journal/v483/n7391/full/483531a.html
23. Reproducibility Initiative Receives $1.3M Grant to Validate 50 Landmark Cancer Studies http://blog.scienceexchange.com/2013/10/reproducibility-initiative-receives-1-3m-grant-to- validate-50-landmark-cancer-studies/
24. How OpenStack Powers the Research at CERN http://opensource.com/business/14/10/interview-tim-bell-cern-it-operating-systems
25. An Analogy: Making Beer •  I make great home brew! o  Using 5 gallon bioreactors to make “sweet nectar” •  I discovered a technique to make it better! o  I sing to my beer each evening as it ferments! o  My assertion is: §  It energizes the yeast, and makes sweeter beer... o  I have graphs showing 9/10 people prefer it o  Even did chemical analysis showing less esters!
26. CC-BY-SA, http://en.wikipedia.org/wiki/File:Brewing-textless.png
27. Do I Really Need to Share More? •  The beer I sang to was next to my stool o  It was in a colder part of my basement §  I didn’t want to sit for hours in the hot part! o  Yeast produce more esters when they are too hot §  They needed to be in a control group §  It didn’t matter if it got a little hotter over there •  Do I want to sell beer, or do science? REPRODUCIBILITY!
29. CC-BY-SA: http://en.wikipedia.org/wiki/File:PiratesVsTemp%28en%29.svg
30. Correlation does not equal causation
31. Computer code is quickly replacing mathematics as the language of science
33. GTO = ce−αr2 φi = c µi φ µ µ ∑ ρ r ( )= P µν φ µ φ ν ν ∑ µ ∑
34. GTO = ce−αr2 φi = c µi φ µ µ ∑ ρ r ( )= P µν φ µ φ ν ν ∑ µ ∑ Data Equations Source Code
36. Do you see the mistake in the code?
37. How about now?
38. Code is an expression of mathematics
39. Open Data
40. Open Source
41. Open Standards
42. Open Access
43. Scholarly Poor
44. Always Pushing the Boundaries •  Science is about learning new things •  Understanding the universe •  Communicating that understanding •  Adding to the sum of human knowledge •  It is not about o  “selling ideas” or “promoting your work”
45. Show your work
46. Show your work all
47. Going beyond impact factors and the h-index
48. Reward academics for publishing code, data, …?
49. Producing degrees with skills relevant to industry!
50. Should scientists learn to code and collaborate?
51. Publicly funded science: default to open
52. Let’s make science open again!
53. We Need Your Help! •  So many people to thank, so little space •  Opensource.com, Kitware •  The Open Science movement, open source, … •  Find me on the web marcus.hanwell@kitware.com @mhanwell +MarcusHanwell cryos.net github.com/cryos