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KEYNOTE: Erin McKiernan, My pledge to be open (Yeah, how’s that going?)

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KEYNOTE: Erin McKiernan, My pledge to be open (Yeah, how’s that going?)

As given at OpenCon 2015 Brussels. Marking the official launch of http://whyopenresearch.org/

Published in: Career

KEYNOTE: Erin McKiernan, My pledge to be open (Yeah, how’s that going?)

  1. 1. o p e n c o n My pledge to be open (Yeah, how’s that going?) Erin C. McKiernan
  2. 2. o p e n c o n Why are we here?... Calvin and Hobbes, c. Bill Watterson (...at OpenCon) Slide 2/44 — Erin C. McKiernan @emckiernan13
  3. 3. o p e n c o n We’re here...because textbooks cost too much Slide 3/44 — Erin C. McKiernan @emckiernan13
  4. 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 Slide 4/44 — Erin C. McKiernan @emckiernan13
  5. 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 Slide 5/44 — Erin C. McKiernan @emckiernan13
  6. 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 Slide 6/44 — Erin C. McKiernan @emckiernan13
  7. 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. Slide 7/44 — Erin C. McKiernan @emckiernan13
  8. 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? Slide 8/44 — Erin C. McKiernan @emckiernan13
  9. 9. o p e n c o n Have you turned down invitations? Yes. Here’s what I tell publishers. Slide 9/44 — Erin C. McKiernan @emckiernan13
  10. 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) Slide 10/44 — Erin C. McKiernan @emckiernan13
  11. 11. o p e n c o n Have you shared your preprints? But why would you share your work before ‘publication’? Slide 11/44 — Erin C. McKiernan @emckiernan13
  12. 12. o p e n c o n Well...I’d like more citations, please! Source: Gentil-Beccot, Mele, Brooks (2009), arXiv:0906.5418 Slide 12/44 — Erin C. McKiernan @emckiernan13
  13. 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/ Slide 13/44 — Erin C. McKiernan @emckiernan13
  14. 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 Slide 14/44 — Erin C. McKiernan @emckiernan13
  15. 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 Slide 15/44 — Erin C. McKiernan @emckiernan13
  16. 16. o p e n c o n Step one: I reminded myself what ’open’ means opendefinition.org Slide 16/44 — Erin C. McKiernan @emckiernan13
  17. 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! Slide 17/44 — Erin C. McKiernan @emckiernan13
  18. 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 Slide 18/44 — Erin C. McKiernan @emckiernan13
  19. 19. o p e n c o n Step four: I learned more about licenses Source: choosealicense.com Slide 19/44 — Erin C. McKiernan @emckiernan13
  20. 20. o p e n c o n Step five: I researched different repositories Slide 20/44 — Erin C. McKiernan @emckiernan13
  21. 21. o p e n c o n Providing all code and data via GitHub github.com/emckiernan/eki-study Slide 21/44 — Erin C. McKiernan @emckiernan13
  22. 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 Slide 22/44 — Erin C. McKiernan @emckiernan13
  23. 23. o p e n c o n My notebook: accessing the raw data github.com/emckiernan/eki-study Slide 23/44 — Erin C. McKiernan @emckiernan13
  24. 24. o p e n c o n My notebook: analyzing the data github.com/emckiernan/eki-study Slide 24/44 — Erin C. McKiernan @emckiernan13
  25. 25. o p e n c o n My notebook: Visualizing the data github.com/emckiernan/eki-study Slide 25/44 — Erin C. McKiernan @emckiernan13
  26. 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 Slide 26/44 — Erin C. McKiernan @emckiernan13
  27. 27. o p e n c o n A valid question and the perfect response Slide 27/44 — Erin C. McKiernan @emckiernan13
  28. 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 Slide 28/44 — Erin C. McKiernan @emckiernan13
  29. 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 Slide 29/44 — Erin C. McKiernan @emckiernan13
  30. 30. o p e n c o n A model project using open notebook science opensourcemalaria.org Slide 30/44 — Erin C. McKiernan @emckiernan13
  31. 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 Slide 31/44 — Erin C. McKiernan @emckiernan13
  32. 32. o p e n c o n Momentum is building... Slide 32/44 — Erin C. McKiernan @emckiernan13
  33. 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 Slide 33/44 — Erin C. McKiernan @emckiernan13
  34. 34. o p e n c o n Studies finding open citation advantage keep coming Source: sparceurope.org/oaca/ Slide 34/44 — Erin C. McKiernan @emckiernan13
  35. 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 Slide 35/44 — Erin C. McKiernan @emckiernan13
  36. 36. o p e n c o n Universities are adding open access to P&T guidelines Source:academicaffairs.iupui.edu/PromotionTenure/IUPUI-Guidelines Slide 36/44 — Erin C. McKiernan @emckiernan13
  37. 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 Slide 37/44 — Erin C. McKiernan @emckiernan13
  38. 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 Slide 38/44 — Erin C. McKiernan @emckiernan13
  39. 39. o p e n c o n Academics share their open scholarship success stories ARCS & The Winnower collaboration, thewinnower.com/keywords/arcs2015 Slide 39/44 — Erin C. McKiernan @emckiernan13
  40. 40. o p e n c o n Oh yeah, and did I mention... Slide 40/44 — Erin C. McKiernan @emckiernan13
  41. 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 Slide 41/44 — Erin C. McKiernan @emckiernan13
  42. 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 Slide 42/44 — Erin C. McKiernan @emckiernan13
  43. 43. o p e n c o n Maybe this will help... Slide 43/44 — Erin C. McKiernan @emckiernan13
  44. 44. o p e n c o n Project launch: Why Open Research? whyopenresearch.org Slide 44/44 — Erin C. McKiernan @emckiernan13

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