www.openbiomed.info

Accelerating access to biomedical evidence

Need a policy model for an academic open access repository? U. of Ottawa’s got it.

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I saw the announcement on resourceshelf.com about The University of Ottawa Press decision to launch a new open access collection of 36 UOP books will be available free to the online community in the University of Ottawa’s institutional repository, uO Research,  including both French and English-language in-print titles in the arts, humanities and social sciences.  Curious about the representation of biomedicine in uO Research, I took a look at the repository.

Developed in collaboration with the University of Ottawa Library, this open access collection uses customizable DSpace opensource software, leveraging a mature product with over 900 implementation sites around the world.  One of the standard attributes of a DSpace repository is the ability to define “communities” with tagging to encourage the displaying and browsing of similar items under a department or theme.  It was easy to see that uO Research has been initially organized around academic division faculty, the Library, the University of Ottawa Press, and their electronic thesis repository collection.

I found the Faculté de médecine // Faculty of Medicine community collection to be a small but promising collection of institutional productivity, combining classic search and discovery:  full text searching,  specialized collection links, and new deposits labeled as news:

There is no limitation to the variety of potential communities, but the management of potential growth depends on articulating and adhering to policy.

I was particularly impressed by the description of  library and  academic partnership  with an emphasis that all stateholders understand and agree to the policies and procedures, available  in this clear and unambiguous format and with a clear contact person (throughout the site).

This statement is an excellent policy model for academic institutions in their own planning phase for the green variety of open access.

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Sun, August 8 2010 » Uncategorized » 1 Comment

We hold these truths self-evident: the polarity of expanding access to funded scientific research

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On July 29thAllan Adler, Vice President of government and legal affairs at the Association of American Publishers (AAP), told the House Committee on Oversight and Government Reform’s Information Policy, Census, and National Archives Subcommittee that FRPAA would seriously threaten the scholarly publishing industry:

“Publishers strongly believe that American taxpayers are entitled to the research they’ve paid for. As taxpayers ourselves collectively and individually, everyone in this room has paid for government‐fundedresearch, and the data and summary reports that result from this research. But taxpayers have not paid for the private sector, peer‐reviewed journal articles reporting on that research.”   Ouch! I will address this in a different blog post.

He added, “For over a century, non-profit and commercial publishers have served as the government’s partner in fueling scientific discovery and innovation. The presumption now that taxpayers should have free access to peer-reviewed journal articles seriously discounts the considerable contributions of our industry and highly skilled workforce of some 50,000, who are driving the US knowledge economy and supporting our leadership in science.”

On August 2nd, In Discovery, rediscovery, and open access: Part 1Peter Suber, Berkman Fellow at Harvard UniversitySenior Researcher at SPARC, the Open Access Project Director at Public Knowledge, and Research Professor of Philosophy at Earlham College. has another perspective:

“The NIH research budget is more than the GDP of 140 nations.  When taxpayers devote that kind of money to research, they can maximize the return on their investment by ensuring that the results are available to all who can build on them.  In addition, the cost of an NIH-funded research project can be hundreds or even thousands of times greater than the cost of publication.  To allow its results to be held hostage by publishers is the same mistake on a different scale as spending billions on a Large Hadron Collider and locking up the results in toll-access publications.”

He also said, “Leaving access barriers any higher than necessary means slowing the process of inquiry and wasting more effort and resources than necessary.”

So there are the opposite ends.  Some librarians and publishers are looking for a middle way to expand access, like the American Physical Society that I blogged about earlier this week, which is at least offering to put free access to their scholarly journals into public libraries in a nod to taxpayers.

I really encourage my readership to read the testimony from the FRPAA hearing.  In a democracy, the will of the majority becomes more important than the personalities.  I applaud the House subcommittee for putting the prepared testimony on the web for public digestion, as well as archive the webcast:

Opening Statement of Subcommittee Chairman Wm. Lacy Clay (available from the webcast)

Prepared Testimony of Mr. Allan Adler

Prepared Testimony of Dr. Steven Breckler

Prepared Testimony of Professor Ralph Oman

Prepared Testimony of Dr. Richard Roberts

Prepared Testimony of Ms. Sharon Terry

Prepared Testimony of Mr. Elliott Maxwell

Prepared Testimony of Dr. Sophia Colamarino

Prepared Testimony of Dr. David Shulenburger

Prepared Testimony of Ms. Catherine Nancarrow

Additional Document 1 Submitted by Ms. Nancarrow

Additional Document 2 Submitted by Ms. Nancarrow

Additional Document 3 Submitted by Ms. Nancarrow

Prepared Testimony of Dr. David Lipman

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Fri, August 6 2010 » Uncategorized » No Comments

Evidence2010-debate on the future of medical publishing in healthcare (early-bird reg. ends Aug. 6th)

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Evidence 2010 will bring together international experts from the areas of education, EBM resource development, implementation, health economics and commissioning. Register now at the Early Bird rate and make savings. August 6th is the early-bird deadline.

This 2 day conference will be aimed at:

  • Commissioners of evidence-based services
  • Those involved in assessing the cost effectiveness of clinical interventions and services
  • Developers of evidence-based resources
  • Teachers and methodologists
  • Those involved in implementation of evidence including front-line healthcare professionals

On the first day of Evidence 2010, there will be a debate of interest to fans of the open future:

Debate: The future of medical publishing in healthcare

Fiona Godlee  Editor in Chief, British Medical Journal

Bill Summerskill  Executive Editor, The Lancet

David Tovey Editor in Chief, The Cochrane Library

Tom Jefferson Scientific Editor PLOs ONE

Register now at the Early Bird rate and make savings.

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Wed, August 4 2010 » Uncategorized » No Comments

APS public access v. arXiv open access- We live in interesting times…

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The following  press release was forwarded to me by a colleague:

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

APS ONLINE JOURNALS AVAILABLE FREE IN U.S. PUBLIC LIBRARIES

Ridge, NY, 28 July 2010: The American Physical Society (APS)
announces a new public access initiative that will give readers
and researchers in public libraries in the United States full use
of all online APS journals, from the most recent articles back to
the first issue in 1893, a collection including over 400,000
scientific research papers.  APS will provide this access at no
cost to participating public libraries, as a contribution to
public engagement with the ongoing development of scientific
understanding.

APS Publisher Joseph Serene observed that “public libraries have
long played a central role in our country’s intellectual life,
and we hope that through this initiative they will become an
important avenue for the general public to reach our research
journals, which until now have been available only through the
subscriptions at research institutions that currently cover the
significant costs of peer review and online publication.”

Librarians can obtain access by accepting a simple online site
license and providing valid IP addresses of public-use computers
in their libraries
(
http://librarians.aps.org/account/public_access_new). The
license requires that public library users must be in the library
when they read the APS journals or download articles. Initially
the program will be offered to U.S. public libraries, but it may
include additional countries in the future.

“The Public Library program is entirely consistent with the APS
objective to advance and diffuse the knowledge of physics,” said
Gene Sprouse, APS Editor in Chief. “Our goal is to provide access
to everyone who wants and needs our journals and this shift in
policy represents the first of several steps the APS is taking
towards that goal.”

–Contact: Amy Halsted,
Special Assistant to the Editor in Chief,
halsted@aps.org,
631-591-4232

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

It is quite interesting to note the the field of Physics has a long-standing inclination to bypass the scholarly journal as a method of scholarly communication.

arXiv is one of the most visible and well-regarded open access repositories for Physics, Mathematics, Computer Science, Quantitative Biology, Quantitative Finance and Statistics. Its history actually pre-dates the electronic journal.  Since 1991 researchers in these disciplines can post pre-print, pre-peer review versions of research openly, allowing colleagues and the international public to see and, for scientists, incorporate or test the results in their own labs.  Just as the objects of devotion in particle physics move faster than the speed of light, research on particle physics just wants to be open, available, and shared as rapidly as possible.

APS and other publishers in these specialized research fields have been known to offer authors the convenience of manuscript submission that just involves downloading the arXiv pre-print, along with the step of asking authors to re-assign their copyright in the traditional copyright transfer procedure, through the directions for authors of APS journal articles.  Still if you look at the copyright transfer agreement, authors retain the ability to post and use their articles in other ways, provided either the author asks for permission to use the APS-formatted version or simply uses their own pre-print version and notes a link to the APS-copyrighted version.  In effect, arXiv continues to hold the attention of anyone in these data-driven research fields, and APS is fortunate to attract submissions.  Then again, the global research community continues to desire the status of faculty tenure and appointments, and the journal article is more valuable for advancement than a non-peer reviewed arXiv submission, at least for those seeking academic status and prosperity.

arXiv has encountered its own survival moments over nearly two decades, as its growth overwhelmed the original support provided by Los Alamos National Laboratory.  Cornell University took over hosting with support provided by the National Sciences Foundation.  Recently, Cornell instituted a voluntary subscription model based on institutional usage by other universities, a 3-year plan going forward to find sustainability.  The success of this joint-funding appeal is evidence of one model for institutional support of open access repositories in narrowly defined research fields.

Now we have a very different model of open access at public libraries promoted by APS.  Any public library large enough to have a science librarian will probably immediately let their local school district(s) and colleges know that students have a new place to do physics research.  Not that any public library could take this approach, but public library service demands are constant competition for even keeping web sites up to date, let alone obtaining  access by filing  a simple online site license and providing valid IP addresses of public-use computers in their libraries.

With this initial burst of publicity for APS public library access,  it will be interesting to see how many public libraries register for this offer.  Certainly the peer-reviewing improvements and editorial enhancements by APS will enhance the usability of articles online, compared to arXiv.

But arXiv offers immediate uninhibited access to the pulse of science, not limited to a library building.  On any internet-enabled device. It is so 21st century.

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Sun, August 1 2010 » Uncategorized » 1 Comment

Cancer patients are taxpayers, and JCO could afford an open access experiment

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The Journal of Clinical Oncology (JCO), published by the American Society of Clinical Oncology(ASCO), is considered a top shelf medical journal, ranked 4th for impact in oncology by the current Journal Citation Reports.  JCO follows the historical standard of requiring assignment of author’s copyright to the publisher upon article acceptance.  Authors submit manuscripts with the understanding that, if accepted, the copyright of the article, including the right to reproduce the article in all forms and media, shall be assigned exclusively to ASCO. Posting articles on institutional repositories is prohibited.

The leadership of JCO certainly believe in their mission and want their journal to remain respected and useful to the clinical oncology research community. Here’s how they tell it, in very nice suits.

From the medical library viewpoint, the 2010 cost for a JCO institutional subscription is somewhere in the middle, neither cheap nor expensive, though some hospital libraries would be hard pressed to pay:

What if you are at a hospital that cannot afford a subscription to JCO?  To view a full-text article without a subscription, you can purchase access to the article for 24 hours at a cost of $19.00 per article.

By the way, ASCO had an extremely good year in 2009, ending up with a $7,800,000 surplus and net assets of nearly $50,000,000:

Excerpt from ASCO 2009 Annual Report

Yes, cancer care and research is big business. Now, before you start to think that those ASCO assets are going into ASCO-sponsored scholarships and research funding, you should be reminded that  there is an independently-operated ASCO Cancer Foundation which raises research funds and distributes grants and scholarships.

So what does the ASCO do with a $7,800,000 surplus and net assets of nearly $50,000,000?

According to the video you might have just watched above, their flagship journal JCO wants to be “the one journal that every hematologist/oncologist has to read.” So what if the cost of that journal’s subscription prevented some hematologist/oncologists in certain hospitals from reading it?  I bet there are plenty of oncologists that understand the critical nature of their research findings and would be willing to use a portion of their grant funding to publish in author-fee based open access journal, the more prestigious and noticed by colleagues, the better. PLoS gold open access has made this point.

My modest proposal is that ASCO use some of its prosperity to fund an experiment in gold open access and test the waters for those that are willing to pay for universal access to their results.  Perhaps even price this gold experiment with the additional waiver of copyright assignment and permission to place the paper on an institutional repository.

There are certainly many major publishers that are trying to maintain revenue while testing the waters of the rising tide of open access with a model such as this.

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Wed, July 28 2010 » Uncategorized » No Comments

July 27th hearing on FRPAA: Who opposes public access to publicly funded research?

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From the ARL SPARC press release:

Washington, DC – The U.S. House of Representatives Committee on Oversight and Government Reform Subcommittee on Information Policy, the Census and National Archives announced it will hold a hearing on the issue of public access to federally funded research on Thursday, July 29. The hearing will provide an opportunity for the Committee to hear the perspectives of a broad range of stakeholders on the potential impact of opening up access to the results of the United States’ more than $60 billion annual investment in scientific research.
The Subcommittee’s interest stems from the growing number of visible expressions of interest in the issue of public access that have surfaced in recent months, in both the Legislative and Executive branches of government. Notably, the White House Office of Science and Technology Policy earlier this year hosted a Public Access Policy Forum on mechanisms that would leverage federal investments in scientific research and increase access to information.
Additionally, H.R. 5037, the Federal Research Public Access Act (FRPAA), which was introduced into the House on April 15 by Rep. Mike Doyle (R-PA) and is supported by a growing bi-partisan host of cosponsors, was referred to the Committee. The bill, and its identical Senate counterpart (introduced by Sens. Joe Lieberman (I-CT) and John Cornyn (R-TX)), proposes to require those eleven federal agencies with extramural research budgets of $100 million or more to implement policies that deliver timely, free, online public access to the published results of the research they fund.

========= END SPARC PRESS RELEASE==============

Want to see the arguments that the commercial sector will take? They are going to try to kill the House bill H.R. 5037 with this kind of argument:

  • the government to become a competitor of independent publishers operating within the private sector in a well-established marketplace.
  • Duplicates existing mechanisms that enable the public to access research in the sciences, social sciences and humanities published in scholarly journals.
  • It would require the affected federal agencies to develop and maintain costly electronic repositories.
  • Agencies will need to divert millions of dollars away from federal research grants and towards database costs.

The letter that the opposition published in the DCPrinciples web site, signed by:

Acoustical Society of America
American Academy of Pediatrics
American Association of Anatomists
American Association for Cancer Research
American Association for Clinical Chemistry
American Association for Dental Research
American Association of Immunologists
American Association of Physics Teachers
American Astronomical Society
American Chemical Society
American College of Clinical Pharmacology
American College of Radiology
American Dairy Science Association
American Dental Association
American Geophysical Union
American Institute of Aeronautics and Astronautics
American Institute of Biological Sciences
American Institute of Physics
American Medical Association
American Psychiatric Publishing, Inc.
American Psychological Association
American Physiological Society
American Registry of Professional Animal Scientists
American Roentgen Ray Society
American Society of Animal Science
American Society of Agronomy
American Society for Biochemistry and Molecular Biology
American Society for Investigative Pathology
American Society for Pharmacology & Experimental Therapeutics
American Society of Plant Biologists
Association for Research in Vision and Ophthalmology
AVS–Science &Technology of Materials, Interfaces and Processing
Cambridge University Press
Crop Science Society of America
Elsevier
The Endocrine Society
Entomological Society of America
European Association for Cardiothoracic Surgery
Federation of American Societies for Experimental Biology (FASEB)
Genetics Society of America
Human Factors and Ergonomics Society
International Association for Dental Research
International Union of Biochemistry and Molecular Biology (IUBMB)
John Wiley and Sons
Lynne Rienner Publishers, Inc.
The McGraw-Hill Companies
Mycological Society of America
The Optical Society
Oxford University Press
The Physiological Society
Poultry Science Association

So it has come down to special interests promising to honor and protect the public interest, even as libraries continue to drop subscriptions from many of these publishers (some public libraries do not have a single journal from any of these publishers).  Does the current system work?   Will we be better off with more open access or with the status quo?

Time for you to contact congress or plan to be in DC on July 27th.

Acoustical Society of America
American Academy of Pediatrics
3
American Association of Anatomists
American Association for Cancer Research
American Association for Clinical Chemistry
American Association for Dental Research
American Association of Immunologists
American Association of Physics Teachers
American Astronomical Society
American Chemical Society
American College of Clinical Pharmacology
American College of Radiology
American Dairy Science Association
American Dental Association
American Geophysical Union
American Institute of Aeronautics and Astronautics
American Institute of Biological Sciences
American Institute of Physics
American Medical Association
American Psychiatric Publishing, Inc.
American Psychological Association
American Physiological Society
American Registry of Professional Animal Scientists
American Roentgen Ray Society
American Society of Animal Science
American Society of Agronomy
American Society for Biochemistry and Molecular Biology
American Society for Investigative Pathology
American Society for Pharmacology & Experimental Therapeutics
American Society of Plant Biologists
Association for Research in Vision and Ophthalmology
AVS–Science &Technology of Materials, Interfaces and Processing
Cambridge University Press
Crop Science Society of America
Elsevier
The Endocrine Society
Entomological Society of America
European Association for Cardiothoracic Surgery
Federation of American Societies for Experimental Biology (FASEB)
Genetics Society of America
Human Factors and Ergonomics Society
International Association for Dental Research
International Union of Biochemistry and Molecular Biology (IUBMB)
John Wiley and Sons
Lynne Rienner Publishers, Inc.
The McGraw-Hill Companies
Mycological Society of America
The Optical Society
Oxford University Press
The Physiological Society
Poultry Science Association
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Tue, July 20 2010 » Uncategorized » 4 Comments

More on predatory open access from Jeffrey Beal and the Charleston Advisor

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Back in May I highlighted Jeffrey Beal’s article in the Charleston Advisor open access archive (the OA archive  is open, unlike the rest of the journal) , an entertaining exposé about several open access publisher websites that don’t describe or respond to questions about peer review or anything else…just register as an author, insert your credit card, and hope for the best.   Yes, it was a sure sign of tarnished gold open access.

Lots of us appreciated Jeffery’s diligence and used various means to circulate his indictment.  That means that as new open access publishers appear, they get  the scrutiny they deserve from more eyeballs, and Jeffrey will get new nominations for potential predatory practices. It didn’t take long for Jeffrey to sound the warning bells again.

The July 2010 issue of the Charleston Advisor contains Jeffrey’s Update: Predatory Open-Access Scholarly Publishers. The first candidate for open access infamy include:

There are several questionable things present in the Medwell Journals website.

What did I notice?

  • The contact information page is an ingest form.  Will they get back to you?
  • Use of a gmail account for contact on the subscription ordering page.
  • No contact information linked or provided for journal editors.
  • Must register and enter the manuscript system to see information about fees.
  • A “News” page which actually prints news, not from their own journals or business, but from the Journal of Clinical Investigation( see “Genetic Link to Heart Failure.” [a subliminal appeal to legitimacy?!]

The second candidate suggested for scrutiny by Jeffrey is International Research Journals.

What did I notice?

  • This blog is about biomedical open access, so I took a closer look at one of the biomedical titles. The Journal of Medicine and Medical Sciences may certainly intend to be as general as the PLoS Medicine, but it will be hard to accomplish with only a single editor on the editorial board,  listed without email or phone number.
  • Use of a gmail account on the contact page.  Refreshingly, there are two Nigerian cell phone numbers listed. The weekend had already begun in Nigeria when I used skype to verify the numbers worked.
  • The Guide to Authors for the Journal of Medicine and Medical Sciences attempts to describe a unique submission style for paper elements and citation references, apparently in ignorance of the  International Biomedical (Vancouver) style, a well-known international standard that would really simplify the production of manuscripts with citation management tools, as well as provide guidelines for nearly every detail you might forget to think about in setting up a new biomedical journal.
  • Author processing fees for articles are published, mostly around $400US – $450US .  Since my first impression is that this at best an immature or amateur start-up,  a competitively low fee is not a bad strategy.  On the other hand, the expenses of what we see in this website are pretty minimal, so what does the money go for? There is no advisory board to lend credibility or confidence.

Anyway, you also have Jeffrey Beal’s  impressions. Thanks, Jeffrey!

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Fri, July 16 2010 » Uncategorized » No Comments

The next domino: SIU follows UC in opposing NPG subscription increases, urging open access alternatives

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On June 4th the University of California Library System issued a very public complaint about Nature Publishing Group‘s proposed triple-digit increase in institutional subscription costs, coupled with a threat of author and editorial boycott by faculty.

On June 24th, David Carlson, the Dean of Library Affairs at Southern Illinois University(SIU), Carbondale, and Associate Dean Connie Poole at the SIU School of Medicine, Springfield, issued a memo to their own faculty regarding the recent NPG controversy with California State University Libraries.

Here are the major recommendations to SIU faculty on the Carbondale and Springfield campuses, if you don’t have time to read the entire memo:

  • Be aware of the financial value of the work you contribute when you write, review, and edit articles.
  • Whenever possible, choose to publish in journals with equitable business models – open-access journals, or those with reasonably priced subscriptions.
  • Assert your rights as an author. Negotiate with publishers for better control of and broader access to your published work through an author addendum such as the Scholar’s Copyright Addendum (http://scholars.sciencecommons.org/).
  • Place a copy of your work in SIU’s digital repository, OpenSIUC, and encourage your colleagues to do the same. This will not only be a positive contribution, but will advance the visibility, impact, and reach of your research.
  • This past year, the SIU Faculty Senate and Graduate Council endorsed a resolution for faculty to support Open Access. A second resolution called for faculty to “grant SIUC permission to make his or her scholarly journal articles… openly accessible in OpenSIUC.” Support this effort and provide your permission when you are surveyed in the Fall.
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Tue, July 13 2010 » Uncategorized » No Comments

An OASIS in the turbulent open access times

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OASIS, the Open Access Scholarly Information Sourcebook, was launched in 2009 with seed funding provided by the Information Program of the Open Society Institute and the personal efforts of two open access advocates, Alma Swan and Leslie Chan.  Their efforts are supported by an international steering committee/advisory board of very recognizable open access advocates

OASIS  combines the traditional notion of pulling together useful content with the practice of community building, allowing registration  and participation among a group of pre-defined communities of interest:

If you browse around the site, it becomes quickly apparent that all the content dates from mid to late 2009, so OA bloggers and tweeters can rest assured that OASIS is not attempting to be generating its own report of  immediate news.  There is certainly usefulness in creating and distributing customizable materials that project a consistent story, as well as build an easier on-ramp to open access advocacy.  The organizers and advisors of OASIS are some of the busiest and in-demand advocates for open knowledge issues in their respective countries and in cross-pollinating advocacy organizations. 

Now that is it built, will users come?  It would be interesting to see the pattern of users registering for the site.   Just as my blog is attempting to fill a niche of need -to-know about open access and biomedicine, perhaps the simple categories of librarian or researcher are too general to lead a reader to enroll.   But for front line advocates new to their advocacy roll, there is a good set of  repurposeable material to get started, endorsed by the champions of open access and covered by a Creative Commons Attribution-Share Alike 3.0 Unported License.

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Sun, July 11 2010 » Uncategorized » No Comments

UTK’s Office of Research and the University Libraries Support OA with $$$

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When a library tweets about open access funding, I sit up and listen.  The University of Tennessee, Knoxville Office of Research and University Libraries have renewed a fund of $20,000 for FY 2009-2010 to support publishing in open access journals.  Credit must be given to the Library Scholarly Communication unit, which guides digital library initiatives, including an institutional repository and promotion of scholarly discussion on the benefits of open access.

UTK joins the unversities in the Compact for Open Access Publishing that I wrote about earlier this year that are creating funding specifically to encourage faculty to publish in peer-reviewed open access publications.  By having an institutional repository to accompany their open access funding, UTK  is supporting both gold and green open access models.

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Fri, July 9 2010 » Uncategorized » No Comments