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 {http://www.ploscompbiol.org}, published in partnership by the Public Library of Science {http://www.plos.org} (PLoS) and the International Society for Computational Biology {http://www.iscb.org} (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 http://www.ploscompbiol.org/papers.html, such as:

Patterns of Intron Gain and Loss in Fungi {http://dx.doi.org/10.1371/journal.pbio.0020422}

In Silico Reconstitution of Listeria Propulsion Exhibits Nano-Saltation {http://dx.doi.org/10.1371/journal.pbio.0020412}

The Roles of APC and Axin Derived from Experimental and Theoretical Analysis of the Wnt Pathway {http://dx.doi.org/10.1371/journal.pbio.0000010}

Design and Diversity in Bacterial Chemotaxis: A Comparative Study in Escherichia coli and Bacillus subtilis {http://dx.doi.org/10.1371/journal.pbio.0020049}

Semi-Supervised Methods to Predict Patient Survival from Gene Expression Data {http://dx.doi.org/10.1371/journal.pbio.0020108}

Ecology Drives the Worldwide Distribution of Human Diseases {http://dx.doi.org/10.1371/journal.pbio.0020141}

Topology and Robustness in the Drosophila Segment Polarity Network {http://dx.doi.org/10.1371/journal.pbio.0020123}

Noise Minimization in Eukaryotic Gene Expression {http://dx.doi.org/10.1371/journal.pbio.0020137}

Motifs in Brain Networks {http://dx.doi.org/10.1371/journal.pbio.0020369}

Textpresso: An Ontology-Based Information Retrieval and Extraction System
for Biological Literature {http://dx.doi.org/10.1371/journal.pbio.0020309}

The most important aspect of PLoS Computational Biology is that the quality, content, and ultimate responsibility for these journals rests with us, the scientific community. Leading researchers orchestrate the peer review of the best science with editorial support from PLoS staff. Concurrently, computational and information scientists are poised to make the most of the digital medium. Join us in creating the next generation of scholarly journals by submitting your papers. For ongoing information about this journal and research publication alerts, sign up at: http://www.ploscompbiol.org. If you would like to send a presubmission inquiry to find out whether your paper might be appropriate for PLoS Computational Biology, now is a great time to get in touch. Send us an e-mail at ploscompbiol@plos.org.

Best regards,

Philip E. Bourne


Steven Brenner (for ISCB)
Michael Eisen (for PLoS)

Associate Editors:

Sebastian Bonhoeffer
Peer Bork
Chris Burge
Richard Durbin
Jonathan Eisen
David Eisenberg
Mark Gerstein
David Haussler
Steve Henikoff
David Hillis
Eddie Holmes
Peter Hunter
Simon Levin
Wen-Hsiung Li
John Mattick
Diana Murray
Andrej Sali
Chris Sander
Arend Sidow
Janet Thornton

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 e-mail:mailto:l.estelle@jisc.ac.uk
Fred Friend (JISC) on 01494 563168, or 07747 627738, or e-mail: mailto:f.friend@ucl.ac.uk

Peter Strickland, Managing Editor, IUCr Journals - 01244 342878 or mailto:ps@iucr.org

Mary Traynor, Managing Editor, Journal of Experimental Biology - 01524
594587 or mailto:m.traynor@lancaster.ac.uk

Tim Smith, Publisher, New Journal of Physics mailto:tim.smith@iop.org

Andrea Horgan, Managing Editor, BMJ Publishing Group Ltd - 020 7383 6263 or mailto:ahorgan@bmjgroup.com

Rachel Goode, Communications Manager, Oxford Journals, OUP - +44 (0)1865 353388 or mailto:rachel.goode@oupjournals.org

Posted by Kevin Messner at 12:24 AM

Entrez Genome Project Resource for Microbial Genomes

Entrez Genome now provides the Entrez Genome Project Resource for microbial genomes offering three tabular displays for complete microbial genomes as well as those for which sequencing is in progress. New features available from the Organism Info tab include data sorting based on genomic properties, such as %GC and genome size, or biological characteristics, such viable temperature range, oxygen requirements, or the habitat of the organisms listed. There is also a breakdown of the sequencing progress for each organism record.

URL: http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi

Posted by Kevin Messner at 12:13 AM