Towards the Awesome - Making Collaborative Versioned Science a Reality

My talk from 'Open Science: The Transparency Revolution' at NIAID Office of Cyber Infrastructure and Computational Biology (OCICB) annual Bioinformatics & Computational Biosciences Festival.

Transcript

1. Towards the Awesome: Making Collaborative Versioned Science a Reality Arfon Smith @arfon Creative Commons Attribution 3.0 Unported License http://is.gd/NIAID
2. http://www.flickr.com/photos/blachswan
3. http://www.flickr.com/photos/esoastronomy/
4. http://www.flickr.com/photos/esoastronomy/ http://www.flickr.com/photos/jamiegilbert
5. http://amandabauer.blogspot.com/
8. Diffraction grating Telescope Detector
14. 130 130 1 2048 189 189 258 258 480 562 378 378 493 521 390 397 851 851 247 274 319 319 304 580 493 511 610 636 188 188 228 228 > cat bad_pix_mask.txt
15. Wasteful
16. Wasteful 2 days work !
17. Wasteful 2 days work 3 observing runs/week !
18. Wasteful 2 days work 3 observing runs/week 52 weeks in year
19. Wasteful 2 days work 3 observing runs/week 52 weeks in year 15 year detector lifetime
20. Wasteful 2 days work 3 observing runs/week 52 weeks in year 15 year detector lifetime ! 2*3*52*15 = 4680 days (13 years)
21. Wasteful… but the norm 2 days work 3 observing runs/week 52 weeks in year 15 year detector lifetime ! 2*3*52*15 = 4680 days (13 years)
22. We don’t know any different
23. We’re taught to focus on research not tools
24. We don’t act any different
25. (Paper) products of research, not software valued
26. Not treating software as first class research objects
27. !
28. What is a GitHub?
33. GitHub
37. How does it work?
38. The pull request
40. Code first, permission later
49. Better at collaborating because they have to be
50. “open source is… reproducible by necessity” Fernando Perez http://blog.fperez.org/2013/11/an-ambitious-experiment-in-data-science.html
51. ‘Open Source’ way of working
52. (doesn’t have to mean this) Open Public? =
53. Open (within your team, department or institution)
54. Electronic
55. Available
56. Asynchronous, exposed process
57. Lock-free
58. Low friction collaboration
59. What’s happening today?
60. Collaboration around code
64. Collaborative authoring
67. Collaborative teaching
71. Collaborative data collection
74. Towards Collaborative Versioned Science
75. How do we make this behaviour the norm?
76. Credit
81. “publishing a paper about code is basically just advertising” David Donoho http://www.stanford.edu/~vcs/Video.html
83. How to derive meaningful metrics from open contributions?
86. Reproducibility Data intensive
90. Barriers are cultural, not technical
91. “Academic environments of today do not reward tool builders” Ed Lazowska, OSTP event http://lazowska.cs.washington.edu/MS/MS.OSTP.pdf
92. A VISION AND STRATEGY FOR SOFTWARE FOR SCIENCE, ENGINEERING, AND EDUCATION
93. Establish a virtuous cycle# •  6%working%groups,%each%with%# •  3:6%faculty%from%each%ins;tu;on# 14# http://lazowska.cs.washington.edu/MS/MS.OSTP.pdf
94. http://lazowska.cs.washington.edu/MS/MS.OSTP.pdf Software Tools, Environments, and Support# •  SoSware%environments%and%tools%are%crucial% •  Organic,#sustainable,#reusable,#extensible# •  Easy#to#translate#across#problem#domains# •  The#creaHon#and#usage#of#today’s#tools#and#sojware# environments#are#distracHng#from#the#science# •  Today's%academic%environments%do%not%reward%tool%builders# •  How#can#the#development,#hardening,#sustaining,#sharing,# and#integraHon#of#techniques#into#a#reusable#sojware# infrastructure#be#recognized#and#incenHvized?# 17# Example%approach:%Teams%of%soSware%architects,%engineers,% and%researchers%who%will%produce%data%science%tools%and%will%be% evaluated%on%the%impact%of%these%tools%
95. What can you do today?
96. http://www.flickr.com/photos/tamaleaver/
97. Why are you sharing?
98. Share more often
99. If you’re going to share it then you better put a licence on it
101. Treat documentation as a first class entity
102. Share more often (no matter how small)
103. 130 130 1 2048 189 189 258 258 480 562 378 378 493 521 390 397 851 851 247 274 319 319 304 580 493 511 610 636 188 188 228 228 > cat bad_pix_mask.txt > git clone git@github.com:arfon/aat/pixel_masks
104. Thanks. arfon@github.com @arfon "