Slide 1

Slide 1 text

Brianna Marshall, Digital Curation Coordinator Open Research + Reproducibility

Slide 2

Slide 2 text

About these workshops Funder Public Access Requirements Wed, Oct. 12, 2:00-3:30 at Steenbock Thurs, Oct. 13, 9:30-11:00 at Memorial Research Data Management & Sharing Wed, Nov. 16, 2:00-3:30 at Steenbock Thurs, Nov. 17, 9:30-11:00 at Memorial Open Access Publishing Wed, Dec. 14, 2:00-3:30 at Steenbock Thurs, Dec. 15, 9:30-11:00 at Memorial Open Research & Reproducibility Wed, Feb. 15, 2:00-3:30 at Steenbock Thurs, Feb 16, 9:30-11:00 at Memorial Authors’ Rights Management Wed, Mar. 15, 2:00-3:30 at Steenbock Thurs, Mar. 16, 9:30-11:00 at Memorial TBD Wed, Apr. 12, 2:00-3:30 at Steenbock Thurs, Apr. 13, 9:30-11:00 at Memorial Library administration effort to support staff work and development around these topics

Slide 3

Slide 3 text

Scope •  What is open research? •  The why and how of open research •  Open research techniques and tools •  Openness examples

Slide 4

Slide 4 text

what’s up with researchers? Ample technology to generate data but few skills to manage it effectively Movement toward openness, impacted by OSTP and spurred by early career researcher expectations Disciplinary culture shifts toward data reuse + reproducibility Need for multi-purpose online spaces to collaborate, share, store, and archive research outputs (including data)

Slide 5

Slide 5 text

research is increasingly digital. •  Multi-institutional •  Grant-funded •  Shared infrastructure •  Computationally driven Image courtesy of #wocintechchat

Slide 6

Slide 6 text

open research vs. open access

Slide 7

Slide 7 text

Image courtesy of John McKiernan, whyopenresearch.org (CC BY)

Slide 8

Slide 8 text

Image courtesy of Flickr user usoceangov (CC BY)

Slide 9

Slide 9 text

open workflows h4ps://innoscholcomm.silk.co/page/Open-Science

Slide 10

Slide 10 text

open peer review

Slide 11

Slide 11 text

http://www.shawnaross.com/2017/02/02/cfp-hacking-the-scholarly-workflow-mla-2018/

Slide 12

Slide 12 text

https://twitter.com/ctitusbrown/status/821784837149184001

Slide 13

Slide 13 text

[ retraction watch.com ]

Slide 14

Slide 14 text

Aspects of Open Research •  Project management •  Data management •  Workflows •  Tracking myriad outputs •  Collaboration

Slide 15

Slide 15 text

open research + reproducibility

Slide 16

Slide 16 text

Munafo et al. (2017) A manifesto for reproducible science. Nature. Why is reproducibility a problem?

Slide 17

Slide 17 text

https://osf.io/ezcuj/

Slide 18

Slide 18 text

Reproducibility project insights •  Original teams shared materials, methods, and data •  Replications preregistered protocols openly •  Data, materials, and code shared by replication teams From Erin McKiernan, “Sharing in Science.” (CC BY)

Slide 19

Slide 19 text

•  Version control •  Dynamic documents •  Building from source From Pierce Edmiston: github.com/pedmiston/reproducible-research

Slide 20

Slide 20 text

perks for researchers interested in making their work open

Slide 21

Slide 21 text

http://whyopenresearch.org/

Slide 22

Slide 22 text

find collaborators!

Slide 23

Slide 23 text

describing openness “For me, openness means an honesty about the messiness of research and transparency in methods and process that helps both the researcher and the audience. It helps the researcher by allowing others to comment and get involved in the research earlier if they spot flaws in the methodology or process, and the audience by showing (especially junior or first-time researchers) that research is rarely a clean progression from simply-defined goals to a final research output, and instead involves reworking and change as certain aspects of the originally-scoped research may become untenable or new areas prove to be more interesting or researchable.” –Thomas King, Open Research course participant https://courses.p2pu.org/he/courses/2377/content/4682/

Slide 24

Slide 24 text

six laws of open research 1.  All data are open and all ideas are shared. 2.  Anyone can take part at any level. 3.  There will be no patents. 4.  Suggestions are the best form of criticism. 5.  Public discussion is much more valuable than private email. 6.  An open project is bigger than, and is not owned by, any given lab. opensourcemalaria.org

Slide 25

Slide 25 text

how to be open •  Share your process – Documentation – Notes, drafts, etc. – Preregister your project •  Share your outputs – Publications – Data

Slide 26

Slide 26 text

open dissemination •  Create a project identity on various tools •  Make the project blog the core part of our project identity •  Share research progress, outputs and methods on a regular basis, via our website/ blogs and other media •  Share data openly, including survey results •  Share methodology and research instruments under a CC-BY license Adapted from Open Research Course, “Examples of Open Dissemination.” https://courses.p2pu.org/he/courses/2377/content/4695/

Slide 27

Slide 27 text

tools supporting open dissemination •  Social networks – Personal – Academic •  Repositories •  Collaboration platforms •  Portfolios/personal websites

Slide 28

Slide 28 text

open access open dissemination open licensing open attitudes

Slide 29

Slide 29 text

Image courtesy of: https://courses.p2pu.org/he/courses/ 2377/open-research-2014/ openness examples

Slide 30

Slide 30 text

KARL BROMAN @kbroman Department of Biostatistics & Medical Informatics UW-Madison

Slide 31

Slide 31 text

No content

Slide 32

Slide 32 text

steps toward reproducible research –  Everything with a script –  Organize your data and code –  Automate the process –  Turn scripts into reproducible reports –  Turn repeated code into functions –  Package functions for reuse –  Use version control –  License your software Note: These steps apply primarily to computational research. http://kbroman.org/steps2rr/

Slide 33

Slide 33 text

ERIN MCKIERNAN @emckiernan13 Postdoctoral Fellow, Neuroscience Wilfrid Laurier University

Slide 34

Slide 34 text

erin’s openness pledge I pledge to: –  edit and review only for open access journals –  publish only in open access journals –  openly share my working manuscripts –  openly share my code, when possible –  openly share my data, when possible –  openly share my notebooks, when possible –  ask my professional societies to support open research –  speak out in support of open research

Slide 35

Slide 35 text

https://www.youtube.com/watch?v=h4jWAj6Ji08 learn more about erin’s pledge

Slide 36

Slide 36 text

JOHN HAWKS @johnhawks Vilas-Borghesi Distinguished Achievement Professor of Anthropology UW-Madison

Slide 37

Slide 37 text

[ http://elifesciences.org/content/4/e09560 ]

Slide 38

Slide 38 text

- Denne Reed, Homo Naledi team [ http://www.nature.com/news/crowdsourcing-digs-up-an-early-human-species-1.18305 ] “We’re more interested in openly sharing data… the advantages in collaboration far outweigh any of the risks.”

Slide 39

Slide 39 text

and from the flip side…

Slide 40

Slide 40 text

No content

Slide 41

Slide 41 text

“The investigators collected their samples, returned home and published the startling results in European medical journals. Few Liberians were then trained in laboratory or epidemiological methods. Even today, downloading one of the papers would cost a physician here $45, about half a week’s salary. …To our knowledge, no senior official now serving in Liberia’s Ministry of Health had ever heard of the antibody studies’ findings. Nor had top officials in the international organizations so valiantly supporting the Ebola response in Liberia, including United Nations agencies and foreign medical teams.” - BERNICE DAHN, VERA MUSSAH and CAMERON NUTT http://www.nytimes.com/2015/04/08/opinion/yes-we-were-warned-about-ebola.html

Slide 42

Slide 42 text

Open Research + Libraries CU Boulder – Open and Digital Scholarship Services University of Cambridge Open Research pilot

Slide 43

Slide 43 text

What We Can Do Be proactive supporters of open research beyond enforcing compliance. How? •  Immerse ourselves in the tools •  Help bridge the technical skills gap •  Create targeted programming •  Partner with existing platforms

Slide 44

Slide 44 text

What We Can Do Right Now! Immerse ourselves in the tools •  Familiarize yourself with the Open Science Framework, Authorea, Jupyter notebooks, and R. Help bridge the technical skills gap •  Library involvement and leadership in Software Carpentry and Data Carpentry. Create targeted programming •  Presentations and workshops on open research related topics. Partner with existing platforms •  OSF for Institutions! Further library commitment to LabArchives.

Slide 45

Slide 45 text

•  Open Science Framework •  Preregistering research •  Preprints •  SHARE collaboration

Slide 46

Slide 46 text

OSF for institutions

Slide 47

Slide 47 text

workflow consultations https://innoscholcomm.silk.co/page/'Follow-the-crowd'

Slide 48

Slide 48 text

Image used courtesy of Michelle Craft, Wisconsin Institute of Discovery at UW-Madison

Slide 49

Slide 49 text

Image used courtesy of Flickr user feuilllu (CC BY)

Slide 50

Slide 50 text

resources

Slide 51

Slide 51 text

whyopenresearch.org

Slide 52

Slide 52 text

open research course https://courses.p2pu.org/he/courses/2377/open-research-2014/

Slide 53

Slide 53 text

discussion points •  What do you think is the future of open research and libraries? •  What do you want to learn about open research and reproducibility? What are you most curious about? •  What are good strategies for engaging departments in discussion on these topics?