keynote: erin mckiernan, my pledge to be open (yeah, how’s that going?)

opencon

My pledge to be open (Yeah, how’s that going?)

Erin C. McKiernan

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Why are we here?...

Calvin and Hobbes, c. Bill Watterson

(...at OpenCon)

Slide 2/44 — Erin C. McKiernan @emckiernan13

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We’re here...because textbooks cost too much


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...because researchers can’t get the data they need

Source: www.nature.com/news/sluggish-data-sharing-hampers-reproducibility-effort-1.17694


http://www.nature.com/news/sluggish-data-sharing-hampers-reproducibility-effort-1.17694

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...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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So, what are we going to do about it?

Image: Newtown grafitti via Flickr, CC BY 2.0


https://www.flickr.com/photos/newtown_grafitti/9932746336

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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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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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Have you turned down invitations?

Yes. Here’s what I tell publishers.


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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)


riojournal.com

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Have you shared your preprints?

But why would you share your work before ‘publication’?


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Well...I’d like more citations, please!

Source: Gentil-Beccot, Mele, Brooks (2009), arXiv:0906.5418


http://arxiv.org/abs/0906.5418

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But mostly...I didn’t want this to happen

The Upturned Microscope by Nik Papageorgiou theupturnedmicroscope.com/comic/negative-data/


http://theupturnedmicroscope.com/comic/negative-data/

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I decided to share not just the paper but the data

McKiernan EC.(2015) PeerJ PrePrints 3:e143. DOI: 10.7287/peerj.preprints.469v3


https://peerj.com/preprints/469/

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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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Step one: I reminded myself what ’open’ means

opendefinition.org


http://opendefinition.org/

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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!


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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


http://pantonprinciples.org/

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Step four: I learned more about licenses

Source: choosealicense.com


http://choosealicense.com

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Step five: I researched different repositories


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Providing all code and data via GitHub

github.com/emckiernan/eki-study


https://github.com/emckiernan/eki-study

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iPython notebook as a sharing tool

“...provides a platform to support reproducible research”

Source: ipython.org/notebook.html


http://ipython.org/notebook.html

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My notebook: accessing the raw data




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My notebook: analyzing the data




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My notebook: Visualizing the data




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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


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A valid question and the perfect response


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“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


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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


https://github.com/ContentMine/neuro

http://www.slideshare.net/petermurrayrust/contentmining-in-neuroscience

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A model project using open notebook science

opensourcemalaria.org


http://opensourcemalaria.org/

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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


http://openwetware.org/wiki/Open_Source_Research

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Momentum is building...


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Perceptions of open access are changing

(NPG), Nature Publishing Group (2015): Author Insights 2015 survey. figshare. dx.doi.org/10.6084/m9.figshare.1425362


http://dx.doi.org/10.6084/m9.figshare.1425362

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Studies finding open citation advantage keep coming

Source: sparceurope.org/oaca/


http://sparceurope.org/oaca/

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New study on the open data citation advantage

Source: S. B. F. Dorch, T. M. Drachen, O. Ellegaard. November 2015. arxiv.1511.02512


http://arxiv.org/abs/1511.02512

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Universities are adding open access to P&T guidelines

Source:academicaffairs.iupui.edu/PromotionTenure/IUPUI-Guidelines


http://academicaffairs.iupui.edu/PromotionTenure/IUPUI-Guidelines

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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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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


http://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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Academics share their open scholarship success stories

ARCS & The Winnower collaboration, thewinnower.com/keywords/arcs2015


https://thewinnower.com/keywords/arcs2015

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Oh yeah, and did I mention...


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I GOT A JOB!!

Assistant ProfessorDepartment of Physics (Biomedical Physics Program)Faculty of ScienceNational Autonomous University of Mexico


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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


https://www.flickr.com/photos/lofink/4344960203

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Maybe this will help...


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Project launch: Why Open Research?

whyopenresearch.org


whyopenresearch.org

keynote: erin mckiernan, my pledge to be open (yeah, how’s that going?)

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