opencon
Why are we here?...
Calvin and Hobbes, c. Bill Watterson
(...at OpenCon)
Slide 2/44 — Erin C. McKiernan @emckiernan13
opencon
...because researchers can’t get the data they need
Source: www.nature.com/news/sluggish-data-sharing-hampers-reproducibility-effort-1.17694
Slide 4/44 — Erin C. McKiernan @emckiernan13
opencon
...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
Slide 5/44 — Erin C. McKiernan @emckiernan13
opencon
So, what are we going to do about it?
Image: Newtown grafitti via Flickr, CC BY 2.0
Slide 6/44 — Erin C. McKiernan @emckiernan13
opencon
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.
Slide 7/44 — Erin C. McKiernan @emckiernan13
opencon
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?
Slide 8/44 — Erin C. McKiernan @emckiernan13
opencon
Have you turned down invitations?
Yes. Here’s what I tell publishers.
Slide 9/44 — Erin C. McKiernan @emckiernan13
opencon
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 payonly for services you need
• open pre- and post-publicationpeer review
• publishes all parts of theresearch cycle
• uses online collaborativepublishing platform (ARPHA)
Slide 10/44 — Erin C. McKiernan @emckiernan13
opencon
Have you shared your preprints?
But why would you share your work before ‘publication’?
Slide 11/44 — Erin C. McKiernan @emckiernan13
opencon
Well...I’d like more citations, please!
Source: Gentil-Beccot, Mele, Brooks (2009), arXiv:0906.5418
Slide 12/44 — Erin C. McKiernan @emckiernan13
opencon
But mostly...I didn’t want this to happen
The Upturned Microscope by Nik Papageorgiou theupturnedmicroscope.com/comic/negative-data/
Slide 13/44 — Erin C. McKiernan @emckiernan13
opencon
I decided to share not just the paper but the data
McKiernan EC.(2015) PeerJ PrePrints 3:e143. DOI: 10.7287/peerj.preprints.469v3
Slide 14/44 — Erin C. McKiernan @emckiernan13
opencon
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
Slide 15/44 — Erin C. McKiernan @emckiernan13
opencon
Step one: I reminded myself what ’open’ means
opendefinition.org
Slide 16/44 — Erin C. McKiernan @emckiernan13
opencon
Step two: I asked for help
TL:DR
Me: What do you think of this?
Ross: This is kind of a mess. Here’show you can make it better.
Thank you, Ross!
Slide 17/44 — Erin C. McKiernan @emckiernan13
opencon
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
Slide 18/44 — Erin C. McKiernan @emckiernan13
opencon
Step four: I learned more about licenses
Source: choosealicense.com
Slide 19/44 — Erin C. McKiernan @emckiernan13
opencon
Step five: I researched different repositories
Slide 20/44 — Erin C. McKiernan @emckiernan13
opencon
Providing all code and data via GitHub
github.com/emckiernan/eki-study
Slide 21/44 — Erin C. McKiernan @emckiernan13
opencon
iPython notebook as a sharing tool
“...provides a platform to support reproducible research”
Source: ipython.org/notebook.html
Slide 22/44 — Erin C. McKiernan @emckiernan13
opencon
My notebook: accessing the raw data
github.com/emckiernan/eki-study
Slide 23/44 — Erin C. McKiernan @emckiernan13
opencon
My notebook: analyzing the data
github.com/emckiernan/eki-study
Slide 24/44 — Erin C. McKiernan @emckiernan13
opencon
My notebook: Visualizing the data
github.com/emckiernan/eki-study
Slide 25/44 — Erin C. McKiernan @emckiernan13
opencon
Open science is reproducible science
Image: c. John R. McKiernan
With GitHub repo and iPythonnotebook, anyone can:
• access my raw andprocessed data
• reproduce my analysis
• replot the figures frommy preprint
• reanalyze my data usingdifferent methods
• contribute new tools andanalysis to the project
Slide 26/44 — Erin C. McKiernan @emckiernan13
opencon
“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 bysomeone else.”
- Rufus Pollock, Open Knowledge
Slide 28/44 — Erin C. McKiernan @emckiernan13
opencon
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
Slide 29/44 — Erin C. McKiernan @emckiernan13
opencon
A model project using open notebook science
opensourcemalaria.org
Slide 30/44 — Erin C. McKiernan @emckiernan13
opencon
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
Slide 31/44 — Erin C. McKiernan @emckiernan13
opencon
Perceptions of open access are changing
(NPG), Nature Publishing Group (2015): Author Insights 2015 survey. figshare. dx.doi.org/10.6084/m9.figshare.1425362
Slide 33/44 — Erin C. McKiernan @emckiernan13
opencon
Studies finding open citation advantage keep coming
Source: sparceurope.org/oaca/
Slide 34/44 — Erin C. McKiernan @emckiernan13
opencon
New study on the open data citation advantage
Source: S. B. F. Dorch, T. M. Drachen, O. Ellegaard. November 2015. arxiv.1511.02512
Slide 35/44 — Erin C. McKiernan @emckiernan13
opencon
Universities are adding open access to P&T guidelines
Source:academicaffairs.iupui.edu/PromotionTenure/IUPUI-Guidelines
Slide 36/44 — Erin C. McKiernan @emckiernan13
opencon
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
Slide 37/44 — Erin C. McKiernan @emckiernan13
opencon
Scientific society goes open
www.sfn.org/News-and-Calendar/News-and-Calendar/News/Spotlight/2015/SfN-Journals-Adopt-CCBY-Licensehttp://www.jneurosci.org/site/misc/ifa policies.xhtml
Slide 38/44 — Erin C. McKiernan @emckiernan13
opencon
Academics share their open scholarship success stories
ARCS & The Winnower collaboration, thewinnower.com/keywords/arcs2015
Slide 39/44 — Erin C. McKiernan @emckiernan13
opencon
I GOT A JOB!!
Assistant ProfessorDepartment of Physics (Biomedical Physics Program)Faculty of ScienceNational Autonomous University of Mexico
Slide 41/44 — Erin C. McKiernan @emckiernan13
opencon
We can do this!
• Momentum is building - openis becoming the norm.
• Open advocates are seeingsuccess in academia andbusiness ventures.
• Open advocates are movinginto faculty positions.
• We’re standing up for ourbeliefs and enacting change.
• ‘Open’ starts with you andchoices you make.
• Don’t be afraid to ask for help.
David Lofink via flickr, CC BY 2.0
Slide 42/44 — Erin C. McKiernan @emckiernan13
opencon
Project launch: Why Open Research?
whyopenresearch.org
Slide 44/44 — Erin C. McKiernan @emckiernan13