April 13, 2006

Bioinformatics: Building Bridges Tutorial Webcasts and Slides

Webcasts of several of the tutorial sessions offered in the Bioinformatics: Building Bridges Symposium are available to U of M and Mayo Clinic personnel on the Minnesota Supercomputing Institute site: http://www.msi.umn.edu/webcast/. Additionally, slides from my tutorial on "Literature Resources on Bioinformatics" are available at: http://magrath.lib.umn.edu/bioinfsymptutorial

Posted by Kevin Messner at 3:33 PM

March 16, 2006

Register Now for Bioinformatics: Building Bridges Symposium!

The Fifth Annual Bioinformatics: Building Bridges Symposium, to be held on Friday, April 14, 2006 in the Digital Technology Center, 402 Walter Library is an event with world-renown speakers, posters, exhibits, tutorials, demonstrations, and a lunch hosted by the Bioinformatics Graduate Faculty.

It is free, but, since space is limited, advance registration is required. Advance registration will close on Friday, March 24.

Advance registration and more information is available at: http://www.binf.umn.edu/bisymp06/

We have room for a few more posters. You can submit a poster when you register. If you have already registered but would like to add a poster, or have put your name done for a poster but have not completed it, please email poster information to me. Do this by March 24, so we have time to duplicate it for the symposium handout.

Thursday, April 13 tutorial registration will NOT close. More information on tutorials is available at: http://www.binf.umn.edu/bisymp06/tutorials.html

Posted by Kevin Messner at 9:56 AM

April 5, 2005

"Publication, the Public University, and Public Interest” Presidential Conference

Scholarship means little without publication. But the definitions of ‘publication’ are undergoing major changes.

We would like to invite you to take part in the University Libraries’ upcoming conference: "Publication, the Public University, and Public Interest.” (http://www.lib.umn.edu/ppp) Part of the President’s 21st Century Interdisciplinary Conference Series, the conference (scheduled for Tuesday, April 19) promises to tackle topics of significance to students, researchers and scholars across the University.

The digital age has brought unprecedented opportunities to share research discoveries with a global audience, prompting a revolution some have compared to post-Gutenberg times. Yet as the Internet and World Wide Web have unleashed new resources and capabilities, they have also challenged the conventions of how research is published and shared.

Traditional modes of publishing–print journals and monographs–have served scholars for decades. Today, though, scholars in some disciplines advocate making research results available through open archives (e.g., institutionally-sponsored or other non-profit venues), and some are even suggesting that universities and funding agencies require open access.

“Publication, the Public University and the Public Interest” will feature three notable speakers in the morning plenary session (the provost from Michigan, a dean from Virginia, and a faculty member from NYU). They will speak to institutional policy, faculty reward structures, and the changing landscape of intellectual property law. The afternoon will provide a venue for small discussion groups (facilitated by University of Minnesota faculty) to surface issues for further analysis and dialogue on campus.

We hope that you can attend for the entire day, but you may register for the morning session or the afternoon session individually. We also hope you’ll encourage your graduate students to attend. The conference is free, but pre-registration is required. Visit http://www.lib.umn.edu/ppp for more information and to register.

This may be one of the few conferences where all constituents, all disciplines…all of us have something at stake. We hope you and your students will join us.

Posted by Kevin Messner at 2:49 AM

March 14, 2005

FEMS journals to be published by Blackwell beginning in 2006

The Federation of European Microbiological Societies (FEMS) and Blackwell Publishing have announced a new publishing partnership. The Federation selected Blackwell Publishing to publish its five journals: FEMS Microbiology Letters, FEMS Microbiology Reviews, FEMS Microbiology Ecology, FEMS Immunology and Medical Microbiology, and FEMS Yeast Research. Blackwell will take over publication of the journals from Elsevier in January 2006.

Posted by Kevin Messner at 2:31 AM

March 11, 2005

European Journal of Biochemistry changes name to FEBS Journal

EJB. European Journal of Biochemistry has changed its title to:

FEBS Journal. ISSN: 1742-464X. Full text from 2005 volume 272 issue 1.

http://www.blackwellsynergy.com/openurl?genre=journal&issn=0014-2956

Posted by Kevin Messner at 2:17 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: www.nih.gov/about/publicaccess/publicaccess_imp.pdf

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 http://www.plos.org/news/announce_nihpapolicy.html

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 article’s 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 NIH’s 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 www.taxpayeraccess.org.

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

* * *


LETTER

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 NIH’s 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 author’s 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 NIH’s 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.

Sincerely,
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

My NCBI Replaces the Cubby: Includes Automatic E-mailing of Search Updates and Filters

he PubMed® Cubby will soon be replaced by My NCBI. My NCBI works similarly to the Cubby in that it retains user information in order to provide additional services. To use My NCBI you must be signed in. You can sign in using an existing Cubby account, or if you do not have an account, you can register for a My NCBI account.

[Editor's Note: This feature was implemented in PubMed on February 1, 2005.]

Read the full NLM Technical Bulletin article at http://www.nlm.nih.gov/pubs/techbull/jf05/jf05_myncbi.html

Posted by Kevin Messner at 1:06 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 (http://www.pubmedcentral.nih.gov), 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: http://www.nih.gov/about/publicaccess/index.htm.

CONTACT:
Don Ralbovsky
OD Office of Communications and Public Liaison
301-496-5787

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 {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
Editor-in-Chief

Advisors:

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

Publishers
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

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

October 19, 2004

Health Informatics Seminar on Medical Language Processing Research October 21

On Thursday, October 21, The University Libraries will co-sponsor a presentation in the Health Informatics Seminar Series. Dr. Alexa McCray, Director of the National Center for Biomedical Communication, a division of the National Library of Medicine, will be speaking on "Mapping the Gene Ontology into the Unified Medical Language System." The seminar will be held in room 2-101 Basic Sciences and Biomedical Engineering at 3:15.

Dr. McCray's research interests include medical language interpretation and processing, digital libraries, and consumer health informatics. The Unified Medical Language System is an automated language processing system for health sciences topics. Its applications include forming part of the query processing system for the PubMed bibliographic information search service. The Gene Ontology is another controlled vocabulary system being developed for the biomolecular sciences, an attempt to bring order to wide variations in terminology which may be applied by scientists to very similar genes, gene products, and functions.

Some of Dr. McCray's work on the topic was recently reported in: Lomax, J. and McCray, A. Mapping the Gene Ontology into the Unified Medical Language System. Comparative and Functional Genomics 5(4): 354-361 (2004). Dr. McCray's presentation is a part of the University Libraries' celebration of National Medical Libraries Month.

Posted by Kevin Messner at 12:42 AM

NIH Asserts that Open Access be Provided to Research Manuscripts it Funds

nihlogo.gifFollowing a summer of pressure from Congress on the subject, and a series of meetings of NIH officials, publishers, advocacy groups, researchers, and librarians, the National Institutes of Health have issued a Notice on Enhanced Public Access to NIH Research Information, marking out an important new position in providing access to research literature funded by the government agency.

The notice states, "NIH intends to request that its grantees and supported Principal Investigators provide the NIH with electronic copies of all final version manuscripts upon acceptance for publication if the research was supported in whole or in part by NIH funding." The manuscripts will be housed in the National Library of Medicine's PubMed Central journal archive service. Open access journals such as those published by BioMedCentral, Public Library of Science, and many other titles already comply with the proposed NIH policy.

NIH currently funds over a quarter of the medical research performed worldwide. The agency's move is a response to the growing unavailability of the research literature to the scientific community, due in large part to rapid inflation over the past decade in the sci-tech publishing sector. The "Open Access" movement has emerged in response to the crisis, seeking publishing models that will provide more consistent access to the research literature to both researchers who produce and read the literature, and to the general public which funds much of the research through NIH, NSF, and other government agencies.

NIH has prepared a web site explaining its stance on public access to the literature: http://www.nih.gov/about/publicaccess/index.htm. The agency seeks comments on its policy proposal. Comments should be submitted by November 16, 2004.

Posted by Kevin Messner at 12:41 AM

PLoS Medicine Inaugural Issue to Release October 19

pmed_cover_200.gifThe Public Library of Science (PLoS), a non-profit publisher dedicated to an open access model of scientific journal publication, will unveil its new journal, PLoS Medicine, on October 19.

PLoS launched its first journal, PLoS Biology, in October 2003. PLoS Medicine PLoS seeks to publish high-profile research articles in these two flagship journals, to compete in the top tier of publications in their respective fields. PLoS Medicine "aims to publish outstanding human studies that substantially enhance the understanding of human health and disease." After less than one year of publication, PLoS Biology recently increased its online publication schedule to a weekly release, one indication of a welcome reception with the biology research community.

The open access academic publishing movement has emerged as a response to rapidly increasing journal subscription prices, and inconsistent support of online journal access, by many commercial and society publishers. In an open access model, published literature is made freely available to the public, not only to institutions or individuals who can pay the costs of subscription, licensing, and account maintenance. Instead, costs of publication are paid for by authors (typically from research or institutional grants).

Under PLoS’ open access model, “A complete version of the work and all supplemental materials…is deposited immediately upon initial publication in at least one online repository…that seeks to enable open access, unrestricted distribution, interoperability, and long-term archiving (for the biomedical sciences, PubMed Central is such a repository).” PLoS articles are published with the understanding that all users are free to copy, use, and distribute the article to others (so long as authorship is attributed).

The journal has prepared an FAQ with further details on their publishing model and the publication process. The University Libraries are an institutional member of Public Library of Science. As a membership benefit, authors from the U of M who publish in either PLoS journal will receive a 10% discount on publication charges.

Consistent with its open access policy, PLoS Medicine will be available online for free to the academic community and to the general public. The print form of the journal will also be available at the Bio-Medical and Veterinary Medical libraries.

Posted by Kevin Messner at 12:40 AM

Journal Cancellations for 2005

Journal cuts, particularly in the sciences, have seemingly become an annual ritual in many academic libraries, and the U of M Libraries are no exception. High annual price inflation rates for research journals in science and technology (inflation of circa 10%, per year -- meaning prices of journals double about every seven years), increased costs associated with providing online journal access, and essentially flat library budgets, mean that the Libraries are able to provide fewer journals each year.

A list of journals which are being cut for 2005 is available at http://www.lib.umn.edu/articles/jcancel2005.phtml. In a few cases where noted, a duplicate print copy of a journal is being cut, but another copy is still available at the University. In other cases, only the print form of the journal is being cut and the online version retained.

While this latter move preserves current access to the journal, it is important to note that it is a perilous management strategy, because we do not typically own access to the online journals. Rather, our annual access licenses are essentially lease agreements. Hence, if we have to cancel the online subscription -- or even if we do continue to subscribe, but the publisher changes the terms of their license agreement at some point in the future -- we can easily lose access to years we have already paid for.

In the molecular biosciences, cuts in the past several years have primarily focused on duplicate subscriptions to journals held in print at libraries on both the Minneapolis and Saint Paul parts of campus (e.g., one subscription at Bio-Med, and another at Magrath Library). Because of this strategy and the purchase of online access for most key journals, the cuts have not had a deep impact. However, there are very few duplicates and other "easy cuts" (e.g., foreign titles) left in the collections. Assuming current inflation trends continue, subscription cuts will quickly become evident and difficult for many bioscience researchers on campus.

To avoid serious deficits in access to the core bioscience literature, it is vital that faculty take initiative and insist University administration move to provide significant, lasting funding increases to the University Libraries. However the Libraries provide access to the subscription-based literature in the coming years, it is absolutely clear that access will be increasingly expensive.

Taking a long-term view, faculty should also consider journal costs when they are choosing where to publish and what journals to serve as editors. Journals from commercial publishers (e.g., Elsevier, Wiley, Springer, Blackwell, etc.) are typically most prone to high inflation, though journals from society publishers (e.g., ACS, ASM, EMBO) are by no means immune to substantial price increases -- especially when societies sell or outsource their journal operations to commercial puslishers. For example, EMBO outsourced its journals to the commercial Nature Publishing Group at the end of 2003, and NPG immediately doubled the U of M's subscription price for EMBO Journal and EMBO Reports.

Posted by Kevin Messner at 12:27 AM

ILLiad for ILL is coming soon!

What is ILLiad? It's the new interlibrary loan (ILL) management software that will be implemented in Fall Semester 2004. Interlibrary loan is the process by which the U of M Libraries, in coopoeration with other libraries across the country, can get a copy of an article or a book not owned by the University Libraries to fill particular library user needs. With ILLiad, you'll be able to:

- submit ILL requests more conveniently. With ILLiad, you enter your address and other personal information only once, when you register.
- view the status and history of all your ILL requests
- order online, any time, any place!
- view your articles electronically

Please note: your ILLiad account will be separate from your MNCAT account.

Watch for further information in the coming weeks about how you can register for and start using ILLiad to improve your ILL experience!

Posted by Kevin Messner at 12:25 AM