1. o p e n c o n
My pledge to be open (Yeah, how’s that going?)
Erin C. McKiernan

2. o p e n c o n
Why are we here?...
Calvin and Hobbes, c. Bill Watterson
(...at OpenCon)
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3. o p e n c o n
We’re here...because textbooks cost too much
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4. o p e n c o n
...because researchers can’t get the data they need
Source: www.nature.com/news/sluggish-data-sharing-hampers-reproducibility-effort-1.17694
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5. o p e n c o n
...because many students and researchers don’t have access
Students in Puerto Rico
Photos: Erin C. McKiernan
Students and researchers in Mexico
Photos: Tina Godoy
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6. o p e n c o n
So, what are we going to do about it?
Image: Newtown grafitti via Flickr, CC BY 2.0
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7. o p e n c o n
Start by changing your own actions
My original pledge to be open (2014):
• I will not edit, review, or work for closed access journals.
• I will blog my work and post preprints, when possible.
• I will publish only in open access journals.
• I will not publish in Cell, Nature, or Science.
• I will pull my name off a paper if coauthors refuse to be open.
If I am going to ’make it’ in science, it has to be on terms I can live with.
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8. o p e n c o n
My new pledge to be open
• I will not edit, review, or work for closed access journals.
• I will blog my work and post preprints, when possible.
• I will publish only in open access journals.
• I will not publish in Cell, Nature, or Science.
• I will pull my name off a paper if coauthors refuse to be open.
• I will share my code, when possible.
• I will share my raw and processed data, when possible.
• I will practice open notebook science, when possible.
• I will ask my professional society to support open access.
• I will speak out about my choices.
So...how’s all that going?
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9. o p e n c o n
Have you turned down invitations?
Yes. Here’s what I tell publishers.
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10. o p e n c o n
Have you accepted invitations?
Yes. Here’s one journal I think we should support.
riojournal.com
• all content is open access
• low pricing; options to pay
only for services you need
• open pre- and post-publication
peer review
• publishes all parts of the
research cycle
• uses online collaborative
publishing platform (ARPHA)
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11. o p e n c o n
Have you shared your preprints?
But why would you share your work before ‘publication’?
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12. o p e n c o n
Well...I’d like more citations, please!
Source: Gentil-Beccot, Mele, Brooks (2009), arXiv:0906.5418
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13. o p e n c o n
But mostly...I didn’t want this to happen
The Upturned Microscope by Nik Papageorgiou theupturnedmicroscope.com/comic/negative-data/
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14. o p e n c o n
I decided to share not just the paper but the data
McKiernan EC.(2015) PeerJ PrePrints 3:e143. DOI: 10.7287/peerj.preprints.469v3
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15. o p e n c o n
How do I make my data reusable?
• What do abbreviations mean?
• Are units clearly indicated?
• Is missing data explained?
• What are the best file formats?
• What license should I use?
Where do I start?
Image: c. Gahan Wilson
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16. o p e n c o n
Step one: I reminded myself what ’open’ means
opendefinition.org
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17. o p e n c o n
Step two: I asked for help
TL:DR
Me: What do you think of this?
Ross: This is kind of a mess. Here’s
how you can make it better.
Thank you, Ross!
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18. o p e n c o n
Step three: I read more on data sharing recommendations
• Make explicit and robust statement of your wishes re: reuse
• Use recognized waiver or license appropriate for data.
• Make data truly open (no restrictive clauses).
• If possible, place data in the public domain.
Source: Panton Principles, Principles for open data in science. Murray-Rust, Peter; Neylon, Cameron; Pollock, Rufus; Wilbanks, John;
(19 Feb 2010). Retrieved October 2015 from pantonprinciples.org
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19. o p e n c o n
Step four: I learned more about licenses
Source: choosealicense.com
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20. o p e n c o n
Step five: I researched different repositories
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21. o p e n c o n
Providing all code and data via GitHub
github.com/emckiernan/eki-study
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22. o p e n c o n
iPython notebook as a sharing tool
“...provides a platform to support reproducible research”
Source: ipython.org/notebook.html
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23. o p e n c o n
My notebook: accessing the raw data
github.com/emckiernan/eki-study
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24. o p e n c o n
My notebook: analyzing the data
github.com/emckiernan/eki-study
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25. o p e n c o n
My notebook: Visualizing the data
github.com/emckiernan/eki-study
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26. o p e n c o n
Open science is reproducible science
Image: c. John R. McKiernan
With GitHub repo and iPython
notebook, anyone can:
• access my raw and
processed data
• reproduce my analysis
• replot the figures from
my preprint
• reanalyze my data using
different methods
• contribute new tools and
analysis to the project
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27. o p e n c o n
A valid question and the perfect response
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28. o p e n c o n
“You cannot assume how others will want to re-use your work.”
- Peter Murray-Rust, ContentMine
“The best thing to do with your data will be thought of by
someone else.”
- Rufus Pollock, Open Knowledge
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29. o p e n c o n
My new adventure: data mining and open notebooks
• can we extract digital information from published electrophysiology traces?
• what new (neuro)science can we discover?
• in collaboration with Peter Murray-Rust and ContentMine
• project is up on GitHub (github.com/ContentMine/neuro)
• project will be done as open notebook science
Image: Peter Murray-Rust www.slideshare.net/petermurrayrust/contentmining-in-neuroscience
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30. o p e n c o n
A model project using open notebook science
opensourcemalaria.org
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31. o p e n c o n
Six laws of open source research
• 1st law: All data are open and all ideas are shared.
• 2nd law: Anyone can take part at any level.
• 3rd law: There will be no patents.
• 4th law: Suggestions are the best form of criticism.
• 5th law: Public discussion is much more valuable than private email.
• 6th law: An open project is bigger than, and not owned by, any given lab.
Source: openwetware.org/wiki/Open Source Research
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32. o p e n c o n
Momentum is building...
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33. o p e n c o n
Perceptions of open access are changing
(NPG), Nature Publishing Group (2015): Author Insights 2015 survey. figshare. dx.doi.org/10.6084/m9.figshare.1425362
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34. o p e n c o n
Studies finding open citation advantage keep coming
Source: sparceurope.org/oaca/
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35. o p e n c o n
New study on the open data citation advantage
Source: S. B. F. Dorch, T. M. Drachen, O. Ellegaard. November 2015. arxiv.1511.02512
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36. o p e n c o n
Universities are adding open access to P&T guidelines
Source:academicaffairs.iupui.edu/PromotionTenure/IUPUI-Guidelines
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37. o p e n c o n
Scientific societies changing in response to feedback
Last year,we wrote a letter...
The Winnower 1:e140865.54468 (2014). DOI: 10.15200/winn.140865.54468
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38. o p e n c o n
Scientific society goes open
www.sfn.org/News-and-Calendar/News-and-Calendar/News/Spotlight/2015/SfN-Journals-Adopt-CCBY-License
http://www.jneurosci.org/site/misc/ifa policies.xhtml
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39. o p e n c o n
Academics share their open scholarship success stories
ARCS & The Winnower collaboration, thewinnower.com/keywords/arcs2015
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40. o p e n c o n
Oh yeah, and did I mention...
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41. o p e n c o n
I GOT A JOB!!
Assistant Professor
Department of Physics (Biomedical Physics Program)
Faculty of Science
National Autonomous University of Mexico
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42. o p e n c o n
We can do this!
• Momentum is building - open
is becoming the norm.
• Open advocates are seeing
success in academia and
business ventures.
• Open advocates are moving
into faculty positions.
• We’re standing up for our
beliefs and enacting change.
• ‘Open’ starts with you and
choices you make.
• Don’t be afraid to ask for help.
David Lofink via flickr, CC BY 2.0
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43. o p e n c o n
Maybe this will help...
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44. o p e n c o n
Project launch: Why Open Research?
whyopenresearch.org
Slide 44/44 — Erin C. McKiernan @emckiernan13