Rachael Kuintzle
OpenCon: Advancing...
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PLoS (plos.org)
[CC BY-SA 3.0],
Open Access
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The “free, immediate, online availability of research articles, coupled with the rights to use
these articles fully in the digital environment.” -- SPARC (Scholarly Publishing and Academic
Resources Coalition)
OpenCon: Advancing...
●
PLoS (plos.org)
[CC BY-SA 3.0],
Open Access
○
The “free, immediate, online availability of research articles, coupled with the rights to use
these articles fully in the digital environment.” -- SPARC (Scholarly Publishing and Academic
Resources Coalition)
●
Open Data
○
Can be used and shared by anyone, according to the particular creative commons license.
○
Is necessary to enable replication of scientific results.
OpenCon: Advancing...
●
PLoS (plos.org)
[CC BY-SA 3.0],
Open Access
○
The “free, immediate, online availability of research articles, coupled with the rights to use
these articles fully in the digital environment.” -- SPARC (Scholarly Publishing and Academic
Resources Coalition)
●
●
Open Data
○
Can be used and shared by anyone, according to the particular creative commons license.
○
Is necessary to enable replication of scientific results.
Open Education
My OpenCon takeaways
1.
I will strive to facilitate reproducibility, and will not only share raw data
but also processed data.
My OpenCon takeaways
1.
I will strive to facilitate reproducibility, and will not only share raw data
but also processed data.
2.
I will use open educational resources or create my own when possible,
and always license my material under creative commons.
My OpenCon takeaways
1.
I will strive to facilitate reproducibility, and will not only share raw data
but also processed data.
2.
I will use open educational resources or create my own when possible,
and always license my material under creative commons.
3.
I will make an effort to share my small scripts used for data analysis,
not only the more substantial programs that I create.
My OpenCon takeaways
1.
I will strive to facilitate reproducibility, and will not only share raw data
but also processed data.
2.
I will use open educational resources or create my own when possible,
and always license my material under creative commons.
3.
I will make an effort to share my small scripts used for data
analysis, not only the more substantial programs that I create.
4.
I will deposit some images from my publications to Wikimedia.
Wikimedia Foundation
[CC BY-SA 3.0 ]
My OpenCon takeaways
1.
I will strive to facilitate reproducibility, and will not only share raw data
but also processed data.
2.
I will use open educational resources or create my own when possible,
and always license my material under creative commons.
3.
I will make an effort to share my small scripts used for data analysis,
not only the more substantial programs that I create.
4.
I will deposit some images from my publications to Wikimedia Commons.
5.
I will be proud and vocal about publishing in open access journals.
Some history
The NIH “E-Biomed” proposal, 1999
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Free, online availability of clinical studies and basic scientific research.
Some history
The NIH “E-Biomed” proposal, 1999
●
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Free, online availability of clinical studies and basic scientific research.
Two publishing pathways:
a.
b.
Standard peer review preceding publication.
Submission of work directly to E-biomed with panel approval.
Some history
The NIH “E-biomed” proposal, 1999
●
●
Free, online availability of clinical studies and basic scientific research.
Two publishing pathways:
a.
b.
Standard peer review preceding publication.
Submission of work directly to E-biomed with panel approval.
Some history
The NIH “E-Biomed” proposal, 1999
●
●
Free, online availability of clinical studies and basic scientific research.
Two publishing pathways:
a.
b.
Standard peer review preceding publication.
Submission of work directly to E-biomed with panel approval.
The compromise: PubMed Central (PMC), Feb. 2000.
SPARC’s OA Spectrum Evaluation Tool
Open Educational
Resources (OERs)
College and AP textbooks
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Free
Open-source
Peer-reviewed (unlike
many closed textbooks)
The case for sharing code
"Software that is custom-developed as part of novel methods is as
important for the method's implementation as reagents and protocols.
Such software, or the underlying algorithms, must be made available to
readers upon publication."
--Nature Methods
“Talk is cheap. Show me the code.”
-- Linus Torvalds
Kampmann, M., Bassik, M. C., & Weissman, J. S. (2014). Functional genomics platform for pooled screening and generation of mammalian
genetic interaction maps. Nature protocols, 9(8), 1825-1847.
How to share your code
iPython Notebook
(Overleaf for Python)
The Notebook app automatically stores the
current state of the computation in the
web browser to the corresponding
notebook file.
“This file can be easily put under version
control and shared with colleagues.”
What’s in it for you?
(Besides the good feels)
● Researcher:
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Get your grants funded.
Get more citations.
Enable others to use or build on your code.
Ensure that your work is reproducible and avoid retractions.
What’s in it for you?
(Besides the good feels)
● Professor:
○ Reach a broader audience, outside the scope of your
enrolled students.
○ Attract more students to your course.
○ More students will have access to the textbook.
What’s in it for you?
(Besides the good feels)
● Professor:
○
○
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Reach a broader audience, outside the scope of your enrolled students.
Attract more students to your online course.
More students will have access to the textbook.
But what about impact factor...
PLOS. “Article-Level Metrics are a comprehensive set of impact indicators that enable numerous ways to
assess and navigate research most relevant to the field itself, including:”
Who am I
OSU Materials Science (MIME)
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4th Year PhD
2 Publications
4 Conference Presentations
Thin Film Electronic Ceramics
OpenCon2014
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First ever Conference for ECR’s
on Open
Corvallis Bike Collective
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Licensed CC-BY 4.0
www.openafox.com
Facilitator for the Board
OpenCon 2014 Family Photo
(Photo Credit: Aloysius Wilfred Raj CC-BY 2.0)
Open Research Impact!!!
Making your publication Open Access
Makes
You
More
Visible!!
OA Citation advantage
Licensed CC-BY 4.0
www.openafox.com
Data: Brody & Harnad (2004);
Hajjem et al. (2005)
Adopted from: Erin C. McKiernan OpenCon2014 - D2 S1 Keynote 2
Open Data
“Without data your publication is
non-sense”
Not talking sensitive data
(i.e. Personal, bio weapons, etc.)
.
Ross Mounce, Ph.D OpenCon2014 - Panel1
Licensed CC-BY 4.0
www.openafox.com
Iryna Kuchma OpenCon2014 - Panel1
Why should I Share Data?
Adapted from Piwowar & Vision (2013), PeerJ 1:e175 https://peerj.com/articles/175
Wicherts JM, Borsboom D, Kats J, Molenaar D (2006) The poor availability of psychological research
data for reanalysis. American Psychologist 61: 726–728 http://wicherts.socsci.uva.nl/datasharing.pdf
Licensed CC-BY 4.0
www.openafox.com
Wicherts, J. M., Bakker, M. & Molenaar, D. (2011) Willingness to share research data is related
to the strength of the evidence and the quality of reporting of statistical results. PLoS ONE 6,
e26828+ http://dx.doi.org/10.1371/journal.pone.0026828
Adopted from: Ross Mounce, Ph.D. OpenCon2014 - S1 Panel1
and Erin C. McKiernan OpenCon2014 - D2 S1 Keynote 2
Open Career Success!!!
Be An Early Adopter
Grant Funding Requirements
Licensed CC-BY 4.0
www.openafox.com
Merton’s Scientific Norms (1942)
Communalism: scientific results are the common property of the community
Universalism: all scientists can contribute to science regardless of race, nationality, culture, or gender
Disinterestedness: act for the benefit of a common scientific enterprise, rather than for personal gain
Originality: scientific claims contribute something new
Skepticism: scientific claims must be exposed to critical scrutiny before being accepted
Licensed CC-BY 4.0
www.openafox.com
Adopted from: Victoria Stodden OpenCon2014 - S2 Key Note
Victoria Stodden
OpenCon2014 - S2 Key Note
Licensed CC-BY 4.0
www.openafox.com
Victoria Stodden OpenCon2014 - S2 Key Note
THERE IS NO LEGITIMATE AUTHORITY IN SCIENCE
We’re all amateurs
THERE IS NO LEGITIMATE AUTHORITY IN SCIENCE
You don’t need permission to fix a broken institution
Licensed CC-BY 4.0
www.openafox.com
Adopted from: Pat Brown OpenCon2014 - S1 Keynote
Open Social Justice!!!
Licensed CC-BY 4.0
www.openafox.com
Peter Murray-Rust OpenCon2014 - S5 Panel 3
The need for “Open”
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Young researchers
Reproducible Science
The Mixed Message to Kids
The World Wide Web
(Photo courtesy Jane Andraka)
Licensed CC-BY 4.0
www.openafox.com
“Only the 0.008%
have access to
knowledge talk
about aristocracy”
Peter Murray-Rust, Jack Andraka OpenCon2014 - S5 Panel 3
Open is about values!!
Mario Savio stands on top of police car in front of UC Berkeley’s Sproul Hall on Oct 1. 1964. The protest is
considered the birth of the Free Speech Movement. (Courtesy of UC Berkeley, The Bancroft Library).
Why Reform Educational Materials?
Textbooks greatly
exceed normal
inflation!
Licensed CC-BY 4.0
www.openafox.com
Adopted from: Daniel DeMarte, Ph.D. OpenCon2014 - Panel4
Impact Factor of OA?
Image: John R. McKiernan
For more info: occamstypewriter.org/scurry/2012/08/13/sick-of-impactfactors/
Licensed
CC-BY 4.0
www.openafox.com
Adopted from: Erin C. McKiernan OpenCon2014 - D2 S1 Keynote 2
Peer review in OA vs. Traditional
● Retraction rate is highest in high IF subscription journals
● There is No controlled study comparing peer review in
subscription vs. OA journals
● Peer review is often
transparent in OA
journals
Licensed CC-BY 4.0
www.openafox.com
Adopted from: Erin C. McKiernan OpenCon2014 - D2 S1 Keynote 2
But OA cost too much… (Nope)
● Self-archiving costs nothing!!
● Many OA journals do not charge
● Or it is a one-time Fee (PeerJ)
● Or have Waivers
● Funding is available (ex. Wellcome Trust)
● Many institutions/funders have funds for APCs
Licensed CC-BY 4.0
www.openafox.com
Adopted from: Erin C. McKiernan OpenCon2014 - D2 S1 Keynote 2
Open Access
Current Models, Policies, and Options
Michaela Willi Hooper
Scholarly Communication Librarian
michaela.willihooper@oregonstate.edu
Image: “Unlocked” by samstockton. Used under CC BY-NC 2.0
Image: “Japanese Tea Flavoured Ice Cream” by Timothy Takemoto. Used under CC BY-NC 2.0.
Gold OA
Pro
Version of record immediately,
freely available to everyone!
Con
Article processing charges
Gold OA: Finding & Vetting
Green OA
Subscription
Journal
Repository
Pros
Publish in (most) journals and
still make your research freely
accessible
APCs less likely
Value-added services, long-term
preservation in a repository
Cons
Extra step of putting in one or
more repositories
Publisher embargoes
(Usually) can’t archive version
of record
Article Versions
PrePrint
PostPrint
Version of Record
(Publisher’s Version)
Green OA: checking publisher policies
Federal Agency Mandate
Feb. 22, 2013: OSTP Memo: “Increasing Access to the Results of Federally
Funded Scientific Research”
Image: “whitehouse.jpg” by Michael Pierce. Used under CC BY 2.0.
Federal Agency Mandate: Agency Responses
Currently have policies: AHQR, ASPR, CDC, DOD, DOE, FDA, NASA, NIH, NIST,
NOAA, NSF, Smithsonian, USAID, USDA, USGS, VA
Still waiting: DHS, DOI, ED, EPA, DOC, ODNI
Federal Agency Mandates: Learn More
http://guides.library.oregonstate.edu/publicaccess
Beyond Federal Agencies
Other organizations with public access policies for grantees:
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Gates Foundation
Howard Hughes Medical Foundation
MacArthur Foundation
WorldBank
Learn more:
Image: “Furman Forsythia” by Oregon State University. Used under CC BY-SA 2.0.
Oregon State Open Access Policy
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June 13, 2013: Unanimously approved by OSU Faculty Senate.
Applies to all articles published after approval.
“Opt-out” waiver.
Library charged with moving the policy forward.
Image: “facultysenateaddress” by Oregon State
University. Used under CC BY-SA 2.0.
Oregon State Open Access Policy
“Each Faculty member grants to Oregon State University permission to make
available his or her scholarly articles and to reproduce and distribute those articles
for the purpose of open dissemination.”
http://cdss.library.oregonstate.edu/open-access
Services from ScholarsArchive@OSU
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Preservation and access of articles, data, supplementary materials
Easy deposit form
Usage statistics / altmetrics
One-step integration with NIH (PubMed Central) & Dept. of Energy (PAGES)
systems for grantees
Image: “sorry for the inconvenience…” by Ben Terrett. Used under CC BY-NC-ND 2.0.