September 25, 2006

BioMed Central Changes

The Health Sciences Libraries has supported open access publisher BioMed Central (BMC) through a membership fee which, until 2006, permitted unlimited waivers of the submission fee for University of Minnesota authors. Many of our faculty have taken advantage of this venue to share their research results with a world-wide audience.

This past year, BMC changed its membership accounting which is now based on the number of published articles. They assess us the entire submission fee, which averages $1350 per article in most categories (some types of non-research articles don’t assess author fees). Our membership for 2006 was for $10,000, which has now been exhausted. Going forward, our membership subscription will not accommodate payment of the submission fee, but rather a 15% discount on the fee; the remainder is the responsibility of the author, similar to page charges of other types of journals. Most of our colleagues around the country have taken a similar step, or did not renew at all, believing that the reporting of results through journal publication is an integral part of research that should be supported by funding sources as just one part of the cost of doing research.

We regret the late notice of this change, and that the transition wasn’t smoother. If you have any questions, please contact Katherine Chew at

Posted by Kevin Messner at 9:14 PM

February 7, 2006

BioMed Central launches Biology Direct

From BioMed Central: BioMed Central is pleased to announce the launch of Biology Direct, a new online open access journal with a novel system of peer review. Biology Direct launches with publications in the fields of Systems Biology, Computational Biology, and Evolutionary Biology, with an Immunology section to follow soon. The journal considers original research articles, hypotheses, and reviews and will eventually cover the full spectrum of biology.

Biology Direct is led by Editors-in-Chief David J Lipman, Director of the National Center Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM) at NIH, USA; Eugene V Koonin, Senior Investigator at NCBI; and Laura Landweber, Associate Professor at Princeton University, Princeton, NJ, USA.

The journal will operate completely open peer review, with named peer reviewers' reports published alongside each article. The journal also takes the innovative step of requiring that the author approach Biology Direct Editorial Board members directly to obtain their agreement to review the manuscript or to nominate alternative reviewers.

For more information about the launch of Biology Direct, read the press release. For more information about the journal or about how to submit a manuscript to the journal, visit the Biology Direct website.

Posted by Kevin Messner at 8:46 AM

January 26, 2006

Why We Don't Have Access to (Part of) Genome Biology

BioMedCentral ("The Open Access Publisher") is probably familiar to most of you, as they have established several promising "open access" journals in the biosciences over the last couple years. Genome Biology is emerging as one of BMC's more prominent open access titles.

Except that this journal isn't open access. At least, not all of it.

While marketing itself as an open access publisher, BMC chose to considerably muddy the publishing-model waters in its creation of several titles like Genome Biology, publishing these partly under an "author pays, open access" model, and partly under a subscription-based model. In particular, review articles are only available by subscription to the journal.

In past years, this was not a completely unworkable issue, because the print version of the journal was available by subscription for a few hundred dollars. We could readily justify paying a few hundred dollars to get this access to the review articles. Unfortunately, as of 2006, Genome Biology is no longer being published in print, and an online subscription for an institution our size is approximately $2800.

Genome Biology published 6 review articles and 28 minireviews in 2005. At $2800, a subscription would cost us $82 per article. (There is other "subscription-only" material in Genome Biology -- meeting reports and the like -- but it is not the kind of literature that many researchers are primarily interested in, or that we would pay a premium for.)

Compare $82/article to four top (by impact factor) genetics review journals: Nature Reviews Genetics is listed at approximately $40/article, Trends in Genetics at $14/article, Current Opinion in Genetics and Development at $13/article, and Annual Review of Genetics $8, for an average of $19/article.

The pricing of Genome Biology is clearly out of step. Frankly, $2800 wouldn't be so out of line, if we were purchasing the whole journal (primary research as well as review articles) by subscription. But the primary research articles in Genome Biology are published in the open access model, and the U of M Libraries already support BioMedCentral's open access publishing to the tune of $10,000. Beyond the financial consideration though, there just seems something disingenuous about a heavily marketing a journal under the idealized "open access" model, when the journal is only partly open. It seems that Genome Biology is trying to have its cake and eat it too.

We will certainly keep looking at the status and track record of this journal. If Genome Biology decreases its price, or markedly increases the amount of review content for the current price, such that it is in line with other review journals, we'll certainly look at subscribing again. Otherwise, unless it becomes apparent that Genome Biology is an indispensible research tool even at its hyperinflated price point, we will unfortunately be unable to deliver this title.

1. Cost/article figures taken from the Journal Cost-Effectiveness Search website:

Posted by Kevin Messner at 12:57 PM

January 17, 2006

Directory of Open Access Journals Reaches an Important Milestone: Now there are 2000 Journals in the DOAJ

Lund, Sweden: As of today the Directory of Open Access Journals (DOAJ, contains 2000 open access journals, i.e. quality controlled scientific and scholarly electronic journals that are freely available on the web.

The goal of the Directory of Open Access Journals is still to increase the visibility and accessibility of open access scholarly journals, and thereby promote their increased usage and impact. The directory aims to comprehensively cover all open access scholarly journals that use an appropriate quality control system. Journals in all languages and subject areas will be included in the DOAJ. The selection criteria have been updated based on feedback from users to be more understandable (

The database records are freely available for reuse in library catalogues and other services and can be harvested by using the OAI-PMH (, and thereby increase the visibility of the open access journals.

We are very happy to see that the usage of the DOAJ is constantly increasing on all parameters. Every month visitors from more than 150 countries are using the service, hundreds of libraries all over the world have included the DOAJ titles in their catalogues and other services, and commercial aggregators are as well benefiting of the service.

New titles are added frequently and to ensure that the holding information is correct you have to update your records regularly. We also have to remove titles from DOAJ if they no longer lives up to the selection criteria e.g. during the last 6 months of 2005 50 titles where removed.

We are working with publishers of hybrid journals (subscription based journals where authors /institutions for a publication charge can publish articles in open access) in order to include even these articles in the DOAJ. It is our intention to be able to inform about this in the near future.

Feedback form the community tells us that the DOAJ is an important service. In order to be able to maintain and further develop the service we have decided to launch a Donation Programme that makes it possible for all users/institutions to contribute to the continued maintenance and development of DOAJ. If you/your institution would consider contributing please go to for further information.

DOAJ is or has been supported by the Information Program of the Open Society Institute (, along with SPARC (The Scholarly Publishing and Academic Resources Coalition), ( SPARC Europe, (, BIBSAM, the Royal Library of Sweden ( and Axiell (

If you know of a journal that should be included in the directory, use this form to report it to the directory:
Information about how to obtain DOAJ records for use in a library catalogue or other service you will find at:

Thank you for your interest and support!

Lotte Jorgensen
Lars Björnshauge

Lotte Jorgensen
Lund University Libraries, Head Office
P.O.Box 134, SE-221 00 LUND, Sweden
Visiting address Tornavägen 9B, Lund
Tel: 046-222 34 31
Fax: 046-222 36 82

Posted by Kevin Messner at 11:08 AM

May 2, 2005

NIH Public Access Policy comes into effect

The National Institutes of Health (NIH) Policy on Enhancing Public Access to Archived Publications Resulting from NIH-Funded Research came into effect this week.

The policy applies to any "research supported, in whole or in part, with direct costs from NIH". From May 2, 2005, NIH-funded investigators are requested to submit an electronic version of the author's final manuscript, upon acceptance for publication, to PubMed Central.

Peter Suber has a worthwhile commentary on this event and where it puts us:

Posted by Kevin Messner at 4:27 PM

April 29, 2005

Editorial from NEJM on NIH open access

Here's an editorial of possible interest in this week's New England Journal of Medicine on the imminent (May 2) implementation of NIH's open access policy: Public Access to NIH-Funded Research. New England Journal of Medicine [0028-4793] Steinbrook, R. 2005 352(17) 1739

Discusses some of the possible short-term implications for authors and for PubMed Central.

Posted by Kevin Messner at 3:03 PM

March 5, 2005

Evolutionary Bioinformatics Online: Call for papers

Evolutionary Bioinformatics Online is an international peer-reviewed Open Access journal focusing on evolutionary bioinformatics. There is growing awareness that to understand organismal form and function, through the use of molecular, genetic, genomic, and proteomic data, due consideration must be given to an organism's evolutionary context - history constrains the path an organism is obliged to take, and leaves an indelible mark on its component parts. Being an Open Access journal means that the papers published are freely available to everyone via the Internet. Further, our authors retain copyright of their work. We do not charge our readers any form of subscription, but we normally ask our authors to make an article-processing payment when papers are accepted for publication. However for our launch issue we are waiving all article processing payments. Fees will apply for subsequent issues. Institutions can also support Evolutionary Bioinformatics Online and the other Libertas Academica Open Access journals by becoming a member institution. An unlimited number of authors from member institutions can publish papers without paying the article-processing fee. Details are available at our website. For detailed author instructions, go to Author Instructions. Please do not hesitate to contact me if you have any comments or questions. Yours sincerely Tim Hill Publisher Libertas Academica Ltd * This is a new title and is the official journal of THE BIOINFORMATICS INSTITUTE.
Posted by Kevin Messner at 2:01 AM

February 18, 2005

NIH Grant Recipients Are 'Asked' to Post Data: New Policy on 'Public Access' Draws Criticism

By Rick Weiss
Washington Post Staff Writer
Friday, February 4, 2005; Page A15

Researchers who receive grant money from the National Institutes of Health will be "asked" to submit their results to a public Web site within a year after they are published in a scientific journal, under a new and controversial NIH policy announced yesterday.

The highly anticipated "public access" policy -- which aims to make it easier for Americans to see the results of research they paid for with their tax dollars -- represents a compromise between competing forces that had lobbied the agency intensely during the past year.

On one side were the publishers of highly profitable scientific journals who feared that free access -- even months after paper publication -- would undermine their subscription base. They were joined by some not-for-profit scientific societies that count on revenue from their print journals to support their research and training programs.

On the other side were patient advocacy groups and others who argued that taxpayers should not have to pay subscription or per-article fees to see the results of federally supported medical research.

They argue that journals would not be significantly harmed because the policy applies to only the 10 percent or so of published biomedical articles that result from NIH-funded research. Individuals and libraries would still subscribe, they say, to read the other 90 percent of the contents.

Both sides expressed irritation with the decision, which NIH Director Elias A. Zerhouni said at a news briefing yesterday would take effect May 2.

Proponents of quick access complained that the policy marks a retreat from an earlier version, floated by NIH in September, which had called for public access within six months. Even the 12-month deadline is voluntary, they noted.

The policy "falls short of the bright light of transparency that Dr. Zerhouni promised," said Rick Johnson, director of the Scholarly Publishing and Academic Resources Coalition and a member of the Alliance for Taxpayer Access, a coalition of groups that support changes in scientific publishing.

Former NIH director Harold Varmus, now president of Memorial Sloan-Kettering Cancer Center in New York and a longtime proponent of public access, called the new policy "a significant move" but echoed others' disappointment that it does not use stronger language. Instead of requesting that scientists submit their results, the policy could have said scientists are "expected" to do so, he said.

But the publishing industry's campaign to oppose NIH's efforts -- spearheaded by former House member Patricia Schroeder (D-Colo.), who is now president of the Association of American Publishers -- also fell short of its goals. The AAP yesterday said it is "concerned" about the outcome. Not-for-profits also complained.

"It's wasteful and duplicative of what we're already doing," said Martin Frank, chairman of the DC Principles Coalition for Free Access to Science and executive director of the American Physiological Society, one of several not-for-profit science organizations that Frank said already make their articles available to the public relatively quickly after publication. "The $2.5 million to $4 million that the NIH is going to spend on this could be better spent on biomedical research," he said.

Zerhouni has said there are advantages to having the articles all in one federally managed database, including easier cross-comparisons of data among different articles.

Both sides had at least one complaint in common: The policy leaves it up to scientists to decide when to make their articles public. That puts scientists in an awkward position of wanting to release them quickly to please the NIH -- their funding source -- and slowly to please their paper publishers -- upon whom they are equally dependent for professional prestige.

"For many authors, the dilemma will be painful and career-jeopardizing," said Johnson, noting that life would have been much easier for scientists had the NIH simply demanded public access as a condition of receiving grant money.

Details of the new policy can be seen at:

Posted by Kevin Messner at 1:32 AM

February 14, 2005

The Public Library of Science Urges Researchers to Comply With the National Institutes of Health's New Public Access Policy

February 3, 2005: San Francisco, CA - The Public Library of Science [PLoS] applauds the US National Institutes of Health [NIH] for today's announcement that it expects all of its grantees to make articles arising from their NIH-funded research freely available online in the National Library of Medicine's PubMed Central.

While NIH's Public Access Policy could, and PLoS believes should, have been stronger in several respects, it sets an important precedent for all sponsors of scientific research. "The US government has now endorsed the principle that the results of federally funded research should be freely available to the public," said Michael B. Eisen, Ph.D., co-founder of PLoS. "Scientists and the scientific community now have an historic opportunity to make this principle a reality."

Read the full statement at

Posted by Kevin Messner at 1:52 AM

Public Interest Advocates Question NIH Enhanced Access Policy, Emphasizing NIH Must Be Held Accountable For Bringing Taxpayer-Funded Science to the American Public

Thursday, February 3, 2005 (Washington, DC) Public interest supporters of the NIH Enhanced Public Access Plan today declared the just-announced policy falls short of their expectations and long-standing recommendations. In a letter addressed to Health and Human Services (HHS) Secretary Michael Leavitt, the Alliance for Taxpayer Access outlined its key concerns with the NIH plan:

The policy is entirely voluntary. Although NIH research in question is funded by taxpayer dollars, the agency is leaving the decision up to each author whether to make their research results available.

The policy lacks any definitive time frame or deadline by which NIH-funded research must be available for public use.

The policy puts grant recipients in the untenable position of trying to meet the contradictory expectations of their funding agency and their publisher.

Addressing Leavitt as well as NIH indirectly, members of the Alliance for Taxpayer Access emphasized the need to hold NIH accountable for achieving the stated goals of sharing taxpayer-funded research with the American people and fulfilling the intentions behind the original Congressional mandate. They called on HHS to report to Congress and the public in the near term on progress toward full taxpayer access using two practical metrics:

1. The proportion of eligible research articles that have been deposited in PubMed Central, and

2. The lag time between an articles publication in a journal and its availability in PubMed Central.

Rick Johnson, Director of the Scholarly Publishing and Academic Resources Coalition (SPARC), said, Frankly, this just-announced policy is neither what we hoped for nor proposed and it falls far short of the bright light of transparency that Dr. Zerhouni promised earlier this week in his ethics reforms.

Johnson continued, However, we are eager for it to succeed. The proof is in the pudding. The coming months will tell whether NIH inspires and leads the community of researchers and scholars to accept the public trust invested in them. Today we urge them to do so.

What will we consider success? asked Sharon Terry, president and CEO of the Genetic Alliance. Plainly put, today a patient with cancer does not have immediate or even timely access to the published results of NIH research. The question we all must ask: A year from now, will the world have changed? Will this same patient have free access to all NIH-funded studies on cancer soon after publication?

This is a big if for all of us, Terry added. If six months after enactment, we see a flood of NIH-funded research posted on PubMed Central, then we will be among the first to celebrate. However if the vast majority of taxpayer-funded NIH research produced during this timeframe is not yet available to be used by scientists, patients, physicians and all engaged in promoting public health, then NIH will have failed. It will have failed not only Congress and the President, but more importantly, it will have failed science and the American people. Until the outcome is clear, we can only state emphatically that NIHs foremost responsibility is to the taxpayer who paid for the research.

AIDS Vaccine Advocacy Coalition Board Member, Robert Reinhard, expressed concern for the lack of incentive for researchers to provide prompt access: The potential 12 month delay does not improve much, if any, upon the status quo. NIH guidance also should encourage pursuit of alternative publication venues that commit to free dissemination of knowledge to those who need it.

If NIH is going to delegate its responsibility and rely on the good faith of the research community, Reinhard added, then NIH should lead by example. What better step could they take than by strongly encouraging NIH intramural researchers to ensure that any paper which bears the name of an NIH employee is posted immediately in PubMed Central.

Johnson and other members of the Alliance for Taxpayer Access have long argued that there is no legitimate reason for NIH funded research to be withheld from taxpayers for any longer than is absolutely necessary, and that ultimately, it must be available immediately.


The Alliance for Taxpayer Access is an informal coalition of stakeholders who support reforms that will make publicly funded biomedical research accessible to the public. The Alliance was formed in 2004 specifically to urge that peer-reviewed articles on taxpayer-funded research at NIH become fully accessible and available online and at no extra cost to the American public. Details and FAQ's on the Alliance may be found at

Press Contact: Bob Witeck
202-887-0500 ext. 19
202-997-4055 mobile
Witeck-Combs Communications on behalf of the Alliance for Taxpayer Access

* * *


February 3, 2005

The Honorable Michael Leavitt
Secretary of Health and Human Services
Hubert H. Humphrey Building
200 Independence Avenue SW
Room 615F
Washington, DC 20201

Dear Secretary Leavitt:

The Alliance for Taxpayer Access is a coalition of taxpayers, patients, physicians, researchers, and institutions that have played a leading role in the national debate regarding timely and unfettered public access to federally funded biomedical research. We are writing today to share our views on the just-released National Institutes of Health (NIH) Enhanced Public Access Policy.

First, however, we wish to express our appreciation for your responses to questions posed during your recent confirmation hearings in which you stated your support for a public access policy that makes NIH research results available in a timely and accessible manner. These responses exhibited your understanding of the essential issue at stake and the opportunities presented by today's information and communication technologies to accelerate innovation and discovery for the benefit of taxpayers.

Despite our delight with this recognition of the taxpayers interests, we are deeply troubled by key aspects of the final policy announced by NIH. We believe an opportunity to demonstrate NIHs concern with public transparency in its operation has been neglected. Our concerns, which focus on issues that we fear will impair successful achievement of the goals we share with NIH, are these:

The voluntary nature of the policy. NIH has handed over an essential NIH responsibility and trust to ensure the advancement of scientific knowledge to individual investigators. Before the Internet, there were historical and economic reasons that NIH relied solely on a system that surrenders public research to private interests via the authors transfer of exclusive ownership of an article to his/her publisher. But today NIH is able to, and should, capture copies of NIH funded research results not just the research that public-spirited authors wish to contribute, but all NIH-funded research. It is able to, and should, track the outputs of its grant portfolio, archive this public treasure, and make it publicly available. The cost is tiny and the benefit great.

The lack of a definitive time frame for public availability. The NIH policy delegates to investigators the decision on an access embargo period within a 12-month time frame. As a result, there is no assurance that articles reflecting NIH-funded research will be available to the public in PubMed Central on a timely basis. Clearly, 12-months is too lengthy a delay in a field as dynamic as biomedicine. NIH has impaired its effectiveness by yielding its authority to act decisively on behalf of taxpayers.

Because the policy lacks both a deadline and mandatory participation requirements, it risks becoming an unenforceable paper tiger. It places ultimate confidence in the willing participation of the research community. Few will be more pleased than the members of ATA if this confidence proves to be well placed. But the reality is that NIH has placed the grant recipient in an untenable position squarely between the contradictory expectations of the funding agency and the publisher. The policy offers no means by which to protect authors from undue pressures from publishing interests to delay making their article readily available on PubMed Central.

Recognizing that the immediate opportunity to re-shape the policy is behind us, we recommend these actions to make the best of the policy:

Lead by example. Require NIHs own intramural researchers to deposit all of their final works (which, by law, are in the public domain) into PubMed Central as soon as they are accepted for publication.

Evaluate the effectiveness of the policy soon and simply. To ensure the policy is achieving its purpose, HHS should adopt the following two evaluation metrics, to be collected on an ongoing basis: 1) the proportion of eligible research articles that have been deposited in PubMed Central; and 2) the average embargo period of deposited material. We urge your department to submit an annual report to the Congress and the public on the policy, focusing especially on these two aspects. We believe it is appropriate that the initial report be submitted by December 1, 2005. If the data do not indicate that the vast majority of NIH research is available in PubMed Central soon after publication, then we believe the policy should be adjusted to better achieve a satisfactory outcome.

In closing, ATA hopes that the NIH Public Access policy will truly provide American taxpayers with greater access to the invaluable biomedical research in which they have invested. We also hope that an effective NIH policy will serve as a role model for other HHS agencies and, eventually, for other departments and agencies throughout the government. We look forward to working closely with you and your staff to ensure achievement of our mutual goal of providing greater public access to taxpayer-funded research.

Richard K. Johnson
Director, SPARC
on behalf of the Alliance for Taxpayer Access

Richard K. Johnson, Director
SPARC (Scholarly Publishing & Academic Resources Coalition)
21 Dupont Circle NW / Washington, DC 20036 USA
Tel +202 296 2296 x157 Fax +202 872 0884
E-mail URL

Posted by Kevin Messner at 1:21 AM

February 4, 2005

NIH Calls on Scientists to Speed Public Release of Research Publications: Online Archive Will Make Articles Accessible to the Public

Thursday, February 3, 2005

The National Institutes of Health (NIH) announced today a new policy designed to accelerate the public's access to published articles resulting from NIH-funded research. The policy ? the first of its kind for NIH ? calls on scientists to release to the public manuscripts from research supported by NIH as soon as possible, and within 12 months of final publication.

These peer-reviewed, NIH-funded research publications will be available in a Web-based archive to be managed by the National Library of Medicine (NLM), a component of NIH. The online archive will increase the public's access to health-related publications at a time when demand for such information is on a steady rise.

"With the rapid growth in the public's use of the Internet, NIH must take a leadership role in making available to the public the research that we support," said NIH Director Elias A. Zerhouni, M.D. "While this new policy is voluntary, we are strongly encouraging all NIH-supported researchers to release their published manuscripts as soon as possible for the benefit of the public. Scientists have a right to see the results of their work disseminated as quickly and broadly as possible, and NIH is committed to helping our scientists exercise this right. We urge publishers to work closely with authors in implementing this policy."

"In developing this policy, we made a concerted effort to balance the importance of this archive to NIH's public health mission, with the need to provide flexibility for authors, their institutions, and publishers in those cases where immediate release is not possible," Zerhouni added. "NIH recognizes the importance of preserving quality peer review and the viability of a diversity of publishing models. Nevertheless, we expect that only in limited cases will authors deem it necessary to select the longest delay period."

The NIH policy will achieve several important goals, including:

1. creating a stable archive of peer-reviewed research publications resulting from NIH-funded studies to ensure the permanent preservation of these vital research findings;

2. securing a searchable compendium of these research publications that NIH and its awardees can use to manage more efficiently and to understand better their research portfolios, monitor scientific productivity, and, ultimately, help set research priorities; and

3. making published results of NIH-funded research more readily accessible to the public, health care providers, educators, and scientists.

Beginning May 2, 2005, the policy requests that NIH-funded scientists submit an electronic version of the author's final manuscript, upon acceptance for publication, resulting from research supported in whole or in part by NIH. The author's final manuscript is defined as the final version accepted for journal publication, and includes all modifications from the publishing peer review process.

The policy gives authors the flexibility to designate a specific time frame for public release -- ranging from immediate public access after final publication to a 12 month delay -- when they submit their manuscripts to NIH. Authors are strongly encouraged to exercise their right to specify that their articles will be publicly available through PubMed Central (PMC) as soon as possible.

PMC (, a part of the NIH's National Library of Medicine (NLM), is the agency's digital repository of full-text, peer-reviewed biomedical, behavioral, and clinical research journals. It is a publicly-accessible, stable, permanent, and searchable electronic archive.

The release of this policy follows months of intensive deliberations with representatives of patient and scientific organizations, researchers, and publishers. NIH posted the draft policy for public comment in September, and received and reviewed over 6,000 public comments.

As part of on-going efforts to implement this new policy, NIH plans to establish a Public Access Advisory Working Group, as a subgroup of the NLM's Board of Regents. The Working Group will include representatives of the patient advocacy, scientific, library, and publishing communities, and will provide advice on implementation issues and assess progress in meeting the new policy's stated goals.

Additional information on the new policy and related documents, including a "Questions and Answers" fact sheet, can be found at:

Don Ralbovsky
OD Office of Communications and Public Liaison

Posted by Kevin Messner at 1:13 AM

January 19, 2005

NIH Revises Plan for Quick, Free Access to Study Results

By Rick Weiss
Washington Post Staff Writer
Tuesday, January 18, 2005; Page A15

An ambitious proposal to make the results of federally funded medical research available to the public quickly and for free has been scaled back by the National Institutes of Health under pressure from scientific publishers, who argued that the plan would eat into their profits and harm the scientific enterprise they support.

The initial plan, encouraged by Congress and hailed by patient advocacy groups, called for the results of NIH-funded research to be posted on a publicly accessible Web site within six months after they are published in a scientific journal. Most research results now are available only by subscription to the journal -- at a cost that often reaches into the thousands of dollars -- or on a pay-per-article basis that can cost $100 or more for two or three articles.

In the final version of the plan, however, the recommended six-month deadline for posting results has been stretched to a year. That change has angered many advocates of public access, who have argued it isn't fair that taxpayers must either wait or ante up to see the results of research they have already paid for.

A scheduled announcement of the policy was abruptly canceled last week by the Department of Health and Human Services, of which NIH is a part. Two sources within the department, speaking on the condition of anonymity because they are not authorized to speak for the department, said the announcement was delayed in order to keep it off the federal agenda until after today's confirmation hearings for Michael Leavitt, President Bush's nominee to become HHS secretary.

Sensitivities about the relationship between NIH and private industry are especially high these days. The agency has been pilloried in the past year by Congress and others for allowing many of its scientists to collaborate with drug and biotech companies in lucrative deals that raise conflict-of-interest issues. Several NIH-watchers said one reason for canceling the rollout of the new plan might have been to avoid calling attention to what could be perceived as another instance of the agency failing to stand up to moneyed interests -- in this case scientific publishers, the largest of which have enjoyed skyrocketing profit margins of 30 percent or more in recent years.

"There's been so much embarrassment flying around about transparency and the public interest at NIH, it's just coming to a head," said Bob Witeck, a spokesman for the Alliance for Taxpayer Access, a coalition of groups favoring easier access to publicly funded scientific findings.

Several business coalitions -- including the Association of American Publishers, whose president is Patricia Schroeder, a former congresswoman from Colorado -- had lobbied strenuously against the initial proposal, which they said would jeopardize many journals' existence by undercutting their paid subscriber base.

"The publishers were crawling all over the place," said Rick Johnson, director of the Scholarly Publishing and Academic Resources Coalition, an alliance of academic and research libraries trying to change the current system. He and others have argued that few scientists or libraries would cancel their subscriptions just because NIH-funded content was available free elsewhere, because such research represents only a fraction of the content of most journals.

Johnson also noted that the revised policy of asking scientists to post their results within 12 months of publication was a minimal request, because many journals already make their content freely available on the Internet after a year. (The policy has focused on getting scientists to post their results on a centralized, government Web site rather than trying to force journals to make their pages public, which raises copyright and other issues.)

NIH Director Elias A. Zerhouni denied that the agency had buckled under industry pressure. Zerhouni said in a telephone interview that there are so many different kinds of publishers -- including many nonprofit publishers run by scientific societies, which reinvest their profits in scientific and educational endeavors -- that it did not make sense to demand a six-month release deadline for all.

"I could not prove that a six-month deadline would not harm a significant part of the industry," Zerhouni said. "The new policy continues to call for release of information as soon as possible after publication, but it really leaves it in the hands of the scientists to decide when. What's important is that we're creating a precedent in which the agency that funds medical research is establishing a public database containing all its scientific output. I am certain that over time people will see this as a win-win."

Some advocates for public access agreed that even a voluntary policy encouraging release within 12 months could result in more access than is available today, if the NIH makes clear to its grantees that it is serious about wanting them to participate.

"The next year will tell if it's working. If a lot of people do it, it won't matter what the language is," said Michael Eisen, co-founder of the Public Library of Science, which publishes scientific journals freely accessible to the public. "What's important is for NIH to convincingly say they're behind it."

Posted by Kevin Messner at 12:53 AM

January 14, 2005

Announcing a New Computational Biology Community Journal

It is with great pleasure that we announce the launch of PLoS Computational Biology {}, published in partnership by the Public Library of Science {} (PLoS) and the International Society for Computational Biology {} (ISCB). An open access, peer-reviewed journal publishing significant biological advances that arise through computation, PLoS Computational Biology officially commences publication in June, 2005 at ISCB's 13th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2005). *We are now accepting submissions and are writing to ask that you submit your best computational biology research to this exciting new community resource.*

PLoS Computational Biology is something different at an important time in the evolution of our field. Computational methods are playing an increasingly central role in diverse areas of biological inquiry. PLoS Computational Biology is a journal of broad scope regarding biological scales, with computation at its heart. Until now, there has been no single publication that focuses on the important contributions to the understanding of living systems afforded by computation. The Editors and the Advisory Board are committed to offering a recognized single venue for high quality works with real biological outcomes that can be appreciated by experimentalists working at different biological scales, perhaps to the point of adopting the methods presented in their own work.

Coupled with immediate free access to all content, PLoS Computational Biology provides an excellent consultative system of peer review, in which a team of leading academic editors generate constructive and efficient feedback. PLoS Computational Biology is accessible to all, and immediately searchable via PubMed. In addition, you retain the copyrights, and give the broadest possible
audience -- scientists all over the world -- the ability to read, copy and use your findings in their own setting. Submitted papers receive an initial review for suitability for the journal within 2-4 working days. If suitable, a complete review is returned within 3-4 weeks.

By being published in partnership with ISCB, PLoS Computational Biology is already primed by 2000 members as potential authors, and the credibility afforded by an active, young, international society. To review the quality and scope of the articles we publish, and the relationship PLoS already enjoys with the computational community, please have a look at the relevant papers published in PLoS Biology over the past year at, such as:

Patterns of Intron Gain and Loss in Fungi {}

In Silico Reconstitution of Listeria Propulsion Exhibits Nano-Saltation {}

The Roles of APC and Axin Derived from Experimental and Theoretical Analysis of the Wnt Pathway {}

Design and Diversity in Bacterial Chemotaxis: A Comparative Study in Escherichia coli and Bacillus subtilis {}

Semi-Supervised Methods to Predict Patient Survival from Gene Expression Data {}

Ecology Drives the Worldwide Distribution of Human Diseases {}

Topology and Robustness in the Drosophila Segment Polarity Network {}

Noise Minimization in Eukaryotic Gene Expression {}

Motifs in Brain Networks {}

Textpresso: An Ontology-Based Information Retrieval and Extraction System
for Biological Literature {}

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Posted by Kevin Messner at 12:42 AM

Successful Publishers Announced under JISC's Open Access Programme

6th January, 2005. Following a remarkable year for the spread of open access ideas and the gathering of momentum for real change, the New Year begins with an announcement by JISC of the winners of funding under the second round of its Open Access programme. Following the success of the first year of the JISC programme, the decision has been made to award five publishers funds to support open access delivery for their journals.

A total of 150,000 will be awarded to some of the key scholarly publications in their fields. These journals are: The New Journal of Physics (published by the Institute of Physics Publishing); Nucleic Acids Research (Oxford University Press); Journal of Medical Genetics (BMJ Publishing Group Ltd); the journals of the International Union of Crystallography (IUCr); and The Journal of Experimental Botany (The Society for Experimental Biology). JISC funding will ensure the waiving of all or part of the submission/publication fees for all UK HE authors. The New Journal of Physics, the IUCr and the Journal of Experimental Botany were successful bidders in the first round of funding, these further funds enabling them to consolidate the considerable gains made during the first year of the programme.

Preliminary results from the first year of the open access programme show that JISC funding has enabled significant advances to be made by the successful publishers and their journals in terms of submissions, access, visibility and costs:

The New Journal of Physics has seen UK submissions increase by 300% in the last six months, while access to articles from UK users has risen 71%. The journal's impact factor has risen from 1.76 to 2.48. The Journal of Experimental Biology has seen access rise by 27%, with JISC support enabling the journal to maintain its subscription costs at the 2004 level. Access has risen by some 300% for the journals of the International Union of Crystallography, "making UK crystallographic research much more visible worldwide." Uptake of PLoS Biology, a new journal, has been "remarkably robust", and JISC support has helped PLoS's strong advocacy role, including oral testimony to the House of Commons Select Committee by Harold Varmus, founder of PLoS.

Peter Strickland, Managing Editor of the IUCr journals, welcomed the continued investment represented by the second round of the JISC programme: "I am very pleased that the IUCr has been awarded a second round of funding by JISC. This will give valuable impetus to our open-access publishing initiative, which has received very positive feedback from our authors and editors, and has significantly increased access to structural science research worldwide."

"With the rapid growth in Open Access options, the ability to fund publication charges has become an important consideration in the decision where to publish," said Ken Lillywhite, Journals Business Director at Institute of Physics Publishing, another second-time recipient of funding. "By funding publication charges for New Journal of Physics, JISC has effectively removed this barrier for every British scientist working in a HEFCE-funded institution. Since JISC's decision to offer financial support for authors publishing in our journal, we have received many more UK papers from scientists working in British universities. We look forward to further growth in 2005."

Mary Traynor, Managing Editor of the Journal of Experimental Botany said: "The Journal of Experimental Botany is the only high ranking plant science journal offering an Open Access option to all plant scientists. We have been highly encouraged by the initial success of our policy and the JISC award will support development of our initiative in addition to enabling us to waive Open Access fees for UK authors."

Professor Eamonn Maher, Editor of Journal of Medical Genetics, commented: "I think this is a very exciting development that will be followed with great interest by journal editors, authors and subscribers. The JISC support has provided a wonderful opportunity to study the possible consequences of an open-access policy for a clinical medical journal."

"We are delighted that JISC is supporting our open access initiative with Nucleic Acids Research," said Martin Richardson, Managing Director of Oxford Journals at Oxford University Press. "NAR is one of the most prestigious journals to make a complete switch to open access, and our University Press status means that we're keen to experiment with, and learn from, new distribution models that might help make research more accessible. Support from JISC will really help us and our authors test the viability of this model."

Lorraine Estelle, JISC Collections Team Manager, who announced the results of the second round, said: "The first round of this programme has been a significant success, giving us some much-needed evidence of the potential of open access to stimulate research and to make visible the outputs of researchers in the UK. We look forward to the further success of this programme."

A further round of funding will be made available to the publishing community later in 2005.

For further information, please contact:

Lorraine Estelle (JISC) on 020 7848 2563 or 07767 297171 or
Fred Friend (JISC) on 01494 563168, or 07747 627738, or e-mail:

Peter Strickland, Managing Editor, IUCr Journals - 01244 342878 or

Mary Traynor, Managing Editor, Journal of Experimental Biology - 01524
594587 or

Tim Smith, Publisher, New Journal of Physics

Andrea Horgan, Managing Editor, BMJ Publishing Group Ltd - 020 7383 6263 or

Rachel Goode, Communications Manager, Oxford Journals, OUP - +44 (0)1865 353388 or

Posted by Kevin Messner at 12:24 AM

December 29, 2004

Nucleic Acids Research to go Open Access in 2005

Nucleic Acids Research, an Oxford University Press journal in press since 1974, has announced that it will switch to a full open access publication model in 2005. Under the open access model, each online issue of the journal will be made freely available to the public upon publication. Author charges of US $1500 per article accepted for publication have been set to recoup publication costs for OUP.

NAR has provided an option for institutions to purchase an institutional membership to the journal, which will reduce the publication charge for authors to $500. The Magrath Library will purchase the US $2855 institutional membership for UMTC (which comes with a print copy of the journal). University of Minnesota authors published nine articles in NAR in 2003, and three so far in 2004.

NAR was listed in 2003 by the Institute for Scientific Information (ISI) as one of the ten "hottest" journals in biology and biochemistry in the last decade. The journal currently ranks #27 out of 261 journals in Biochemistry and Molecular Biology on the ISI Journal Citation Reports Impact Factor list (which includes review-oriented journals as well as primary literature titles). It includes the popular annual Database and Web Server issues, which highlight developments in bioinformatics and computational biology resources.

Posted by Kevin Messner at 2:47 PM

November 12, 2004

Directory of Open Access Journals

This service covers free, full text, quality controlled scientific and scholarly journals. We aim to cover all subjects and languages.


Posted by Kevin Messner at 2:39 AM