Mark Patterson's blog

A new Managing Editor for PLoS ONE

Mark Patterson — Fri, 4 Apr 2008 05:20:44 -0700

Pete Binfield joined PLoS this week as the Managing Editor for PLoS ONE.

Pete’s originally a physical scientist, and obtained a PhD in optical physics at Aberdeen University. He then embarked on a career in publishing, beginning at the Institute of Physics Publishing, followed by stints at Kluwer Academic, Springer and most recently at SAGE Publications. Pete’s 13-year career in publishing covers a wealth of experience which includes commissioning books, all aspects of running journals and business development. He said that the prospect of taking the lead editorial role on PLoS ONE was “tremendously exciting, at this important stage in the development of Open Access”, and we’re delighted that he’s joining us. Pete’s lived and worked in the UK, the Netherlands, and is currently living in Ventura, California, with his wife and toddler. For the next few months, Pete will be based in San Francisco every other week, until he and his family relocate.

Pete will build on the solid foundations that have been created by the first PLoS ONE Managing Editor, Chris Surridge, who will be staying on as a Consulting Editor for the next month. And all of us at PLoS would like to take the opportunity to thank Chris for the tremendous work he’s put into PLoS ONE, and to wish him every success in his next ventures.

Pete joins an expanding team for PLoS ONE, which reflects the steady growth in submissions (we hit 300 submissions for the first time in February), and will be sharing news about PLoS ONE, and his plans for the future in the coming months.

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Welcome the new Managing Editor of PLoS ONE

from A Blog Around The Clock on Fri, 2008-04-04 06:39

There is a change in the command center of PLoS ONE this month. The transition will be seamless. The new editor, Peter Binfield has joined us a couple of weeks ago and has assumed the Big Kahuna position on the...

PLoS Computational Biology, PLoS Genetics and PLoS Pathogens forge ahead

Mark Patterson — Tue, 26 Feb 2008 20:02:37 -0800

PLoS Computational Biology, PLoS Genetics and PLoS Pathogens were launched in the Summer of 2005, and are now entering a new phase in their development. In a few days, they will join PLoS ONE and PLoS Neglected Tropical Diseases on the Topaz publishing platform, and will benefit from more rapid publication along with tools for user interaction – commentary, notes and ratings.

Although the technical underpinnings of PLoS Computational Biology, PLoS Genetics and PLoS Pathogens have undergone a major transition (and a lot of people at PLoS have worked very hard to make this happen), the core values of the journals remain rock solid. Each journal is run by a dedicated board of academic editors (here, here and here) who oversee a highly selective peer-review process to publish great work covering their particular research field, along with an entertaining and at times provocative selection of opinion and commentary. And although the so-called PLoS “Community Journals” are just two and a half years old, they are already incredibly successful – citations, media coverage, and usage of the journals are climbing steadily, and the journals now each receive 50-100 submissions per month.

All the feedback that we receive indicates that the PLoS Community Journals have rapidly found their niches. They have developed their own ‘personalities’ and are highly rated by their respective communities, both as a venue for publication and as a valuable source of information. Building on these solid foundations, the Topaz platform will bring some valuable additional benefits. Authors of research articles, for example, will see an increase in publication speed, as a result of a streamlined publication process. Author files will be carefully checked, lightly edited and tagged (for XML production), but the body text of the article will remain largely unaltered. We are also introducing a workflow that will help authors who use Latex. Finally, we have a mechanism for highlighting any corrections that need to be made to published articles – this can take place within days, instead of the usual lag of several months between spotting an error and the publication of a formal correction. Once these new processes are bedded in, we hope to shave at least two-three weeks off the time to publication.

Readers will notice some more options when they are looking at the articles – notes can be added, a discussion can be started or joined, and the article can be rated. With respect to scholarly journals, these “web2.0” features are still in their infancy, and are yet to achieve a critical mass of activity. Nevertheless, it will be fascinating to see whether these discipline-based PLoS journals provide the nucleus for high-quality discourse. We shall make every effort to encourage that, and the editorial boards will be joined by some new faces who will take a particular interest in developing this aspect of the journals.

One final point about these changes concerns the finances of the journals. The streamlined production and web hosting via Topaz brings cost savings too, which will take the journals very close to economic self-sufficiency. If they continue to grow at their current trajectories, one or two of the community journals will be supporting themselves by the end of this year. This is important because one of our goals in launching community-run journals was to provide a financially self-sufficient model for a high-impact scholarly journal. This goal is now within reach.

The migration of PLoS Computational Biology, PLoS Genetics, and PLoS Pathogens places five of our journals on the open source publishing platform called Topaz. PLoS Biology and PLoS Medicine will follow later this year. That project has already started – no rest for the wicked…

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TOPAZ Upgrade and other Big News from PLoS

from A Blog Around The Clock on Wed, 2008-02-27 07:25

It was a heroic (and sometimes nerve-wrecking) couple of months for the IT/Web team at PLoS, but the fruits of their labor are now visible to all. PLoS Computational Biology, PLoS Genetics and PLoS Pathogens have migrated, last night, onto...

Open access mandates from the National Institutes of Health and the European Research Council

Mark Patterson — Mon, 14 Jan 2008 03:29:56 -0800

On January 11th, the NIH announced their new public access policy, which has now been strengthened to a mandate as required by the appropriations bill signed by President Bush in December.

The new NIH policy requires all NIH-funded research articles to be deposited into PubMed Central (PMC) and to be made publicly available within 12 months of the official date of publication. Articles must be submitted to PMC upon acceptance for publication. The policy comes into effect on April 7th this year.

The NIH has produced an extensive and very informative FAQ page, which indicates amongst other things that an estimated 80,000 articles will be published each year as a result of NIH funding – and public access to these articles is now assured (albeit after a delay). In another FAQ, it is stated that the NIH will reimburse publication fees, which also helps to reduce any financial burden on authors who wish to publish in open access journals such as those of PLoS. And publishing in such journals is of course an easy way to comply with the NIH policy – we automatically deposit all articles accepted in PLoS journals into PMC, where they are also publicly available immediately upon publication.

While all this activity has been taking place in the United States, another significant development has happened in Europe. On January 10th, the European Research Council (ERC) issued a new position statement on open access. The ERC is also now mandating public access, and requires "all peer-reviewed publications from ERC-funded research projects [to] be deposited on publication into an appropriate research repository…, and subsequently made Open Access within 6 months of publication". As pointed out by Peter Suber, the ERC has also indicated that it will cover publication fees in open access journals. The ERC is responsible for around €7.5 billion of the Framework Programme 7 which will be supporting research activity in Europe from 2007-2013.

With these positive developments in the US and Europe, that’s a pretty good start to 2008.

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Public Access to Research Funded by National Institutes of Health – Now Law

Mark Patterson — Fri, 28 Dec 2007 09:58:31 -0800

On Dec 26th, 2007, President Bush signed the Bill that requires all NIH-funded research to be made available to the public.

This is wonderful news. The NIH funds research to the tune of $29billion, and all of the published output of this work will now be freely and publicly available within 12 months of publication. In practical terms, this means that any researcher funded by the NIH has to ensure that their papers are deposited at the NIH-funded digital archive called PubMed Central, and are released to the public within 12 months.

One of the most effective ways to comply with this new requirement is for researchers to publish their work in fully open access journals such as those of PLoS. As part of the service we provide to authors, we deposit every article in PubMed Central so that it can be a part of this evolving and important online archive. And this happens as soon as the article is published – so that anyone with an interest in the work can immediately read it and build on it.

Many individuals and organizations have worked very hard to help make the new law happen – none harder than the great people at SPARC and the Alliance for Taxpayer access. You can read the ATA press release here, look at some of the reaction in the blogosphere here, and read a terrific summary of the background to the whole story in recent issues of Peter Suber’s newsletter (in November and December).

There’s still a way to go before we get close to the goal that inspired visionaries such as Harold Varmus, chairman of the PLoS Board of Directors, who envisions comprehensive, unfettered access to research literature coupled with new tools and mechanisms for knowledge mining and discovery. But the new law in the US is a very significant step in the right direction. Happy New Year!

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Roll Credits: Sometimes the Authorship Byline Isn’t Enough. Guest Blog by Michael Molla and Tim Gardner.

Mark Patterson — Tue, 6 Nov 2007 03:49:55 -0800

Concept: Michael Molla (1) and Tim Gardner (2)
Writer: M. Molla
Editor: T. Gardner
Readers: Jeff Hasty (3) Jeremiah Faith (4)

(1) Research Associate, Biomedical Engineering, Boston University
(2) Assistant Professor, Biomedical Engineering, Boston University
(3) Associate Professor, Department of Bioengineering, University of California, San Diego
(4) Ph.D. Candidate, Bioinformatics Program, Boston University

Authorship is the "currency" of science. It is not simply a matter of ego. The inclusion or exclusion of names is a serious issue with ramifications for careers and funding. However, the contributions implied by authorship assignments are often unclear to the reader -- especially for the middle authors. The recent additions of contribution statements by PLoS journals and PNAS are a step in the right direction, but lack sufficient detail and academic value.

In the current system, the only job explicitly described by the author list is that of "author". In general, authorship is not just writing, but the entire multi-faceted research process. Important contributions might be made by wet-lab scientists, technicians, statisticians, theorists, computational biologists, and others. The author list is opaque to these distinctions.

The confusion is increased in the case of interdisciplinary research. The need for experts in each discipline multiplies the length of the contributor list. Published work with dozens of authors is common; over 100 authors is not unheard-of. Disciplines and laboratories may even have conflicting customs as to what constitutes authorship.

More critically, the assignment of authorship has a real impact on the effective execution of research. Middle authorship is often dismissed by readers or employers as insignificant. Thus collaborations are impeded because scientists are more concerned about their position on the paper than about solving research questions. Young scientists may not contribute adequate time or resources to a collaborative effort because they won't gain a first or last authorship. They'd rather work on their own first- author paper.

There is a better system, and it's already in use in the film industry -- a credit list. Each person who contributed to a movie has a specific credit describing his or her contribution. If one's contribution fills more than one role, that person's name can appear more than once. In science, the "first author" position has, over time, come to mean something analogous to a film's "director". The "last author" position is usually filled by a job roughly similar to "producer". But a film also has actors, special-effects artists, stunt people, etc. A would-be movie mogul conveys a much clearer description of her role on a project with an "associate producer" credit on a major film, for example, than a young scientist does with her "third author" status on a major paper.

The contribution statements of PNAS and PLoS are a good start, but authorship is still a predicate for describing one’s contribution to the work. Other contributions are relegated to an acknowledgment, which carries virtually no material value. Moreover, the current contribution statements are uneven and not necessarily informative.

What we are proposing is a detailed, standardized and trackable contribution statement; a statement that would be given equal credence as the author byline. A set of job-based contributions to the research process would be a great deal easier to understand on a person's C.V., and would make it easier to understand the process by which a particular piece of research came to be.

Such a research credit system would have huge benefits for one's career prospects; and it might encourage more effective collaborations. Moreover, these credits could easily be tracked by scientist or project in a database akin to the Internet Movie Database (IMDB). It could provide an alternative to the ever-so-important citation factors as a means of assessing one's scientific impact. And maybe one day there will even be an Academy Awards of Science.

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Bringing Peer Review Out of the Shadows

Mark Patterson — Sat, 27 Oct 2007 02:28:59 -0700

An interesting collection of reader comments has accumulated in response to the PLoS Biology article by Hauser and Fehr, entitled “An incentive solution to the peer review problem”, published earlier this year.

Hauser and Fehr propose a system for holding late reviewers to account by penalizing them when it’s their turn to be an author. A slow reviewer’s paper would be “held in editorial limbo” for a length of time that reflects their own tardiness as a reviewer. The short article was intended to provoke a discussion about how to improve peer review – an opening card as Hauser and Fehr put it.

So far, 16 responses have been added from readers, and the general view seems to be that incentives would be more effective than the punishment that Hauser and Fehr propose. As for an incentive, quite a number of respondents favour a system whereby reviewers are paid for their efforts – although not to a level that would fully reimburse the time spent.

It’s interesting to consider this payment idea in light of the publication fee model that many open access journals use. The essence of this model is that the publication fees cover the costs of the publishing process. So if we were to add to those costs by paying reviewers, then the publication fee would need to be raised as well. Given that the author and reviewer populations overlap to a large extent, this approach would end up shuffling money around within the community of researchers—not a particularly attractive solution to the problem.

But maybe money isn’t the best incentive anyway. And in any case, the challenges facing peer review aren’t just about the speed of the process. Several of the respondents to the discussion emphasize the importance of the quality of the reviews; it’s worth waiting a while longer if the end result is a more considered set of comments on the article. To focus any incentive system on speed alone won’t necessarily improve the quality of peer review one jot.

Maybe a different way to think about the question is to consider who should be the judge of whether or not a reviewer does a good job. As an editor, I’ve been privileged to be party to some incredibly thoughtful and constructive discussions between authors and reviewers. It’s not always that way of course, but when it works, it’s fantastic. I’ve often felt that it’s a pity that these exchanges haven’t been shared more broadly, and as pointed out by others in the discussion, there are many who feel that greater transparency in peer review is the way to go – pre- and post-publication. We are seeing more and more experiments in this arena – PLoS ONE being the obvious example close to home, and Atmospheric Chemistry and Physics being one of the trailblazers – and one can certainly envisage incentives being developed in these more transparent systems. Researchers who add their thoughts to published articles can be rated by other members of their community on the basis of the quality and usefulness of their comments. Their comments can be cited in their own right, ultimately adding to their scientific reputation and credentials – a powerful incentive indeed.

The formula for more transparent peer review might not be perfect yet, but there is great potential and further experimentation is a must. Ultimately, improving the peer review process will take the same kind of thoughtful and constructive discussions that help researchers identify the extra step that will maximize the significance of their results. We invite you to join in that discussion.

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Mandate for public access to NIH-funded research has taken a further step towards becoming law.

Mark Patterson — Thu, 25 Oct 2007 14:30:56 -0700

We are delighted that U.S. Senate has just passed the Labor-HHS appropriations bill containing the provision to mandate public access to NIH-funded research.

We would like to thank the many members of the scientific community who have helped to achieve this important landmark. Your support has played a major role in ensuring that the mandate for public access to NIH-funded research has taken a further step towards becoming law.

But there’s still a lot to do! In anticipation that President Bush will veto this bill, it is as important as ever for the research community to continue to voice support for public access to scientific and medical literature. We will provide more information as this situation develops.

Here’s the press release from the Alliance for Taxpayer Access (ATA).

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2006 impact factors for PLoS journals

Mark Patterson — Wed, 20 Jun 2007 08:39:29 -0700

The 2006 impact factors have just been released by Thompson ISI. The first two PLoS journals continue to perform very well: 14.1 for PLoS Biology (14.7 in 2006); 13.8 for PLoS Medicine (8.4 in 2006). The PLoS community-run journals also received their first impact factors: 4.9 for PLoS Computational Biology; 7.7 for PLoS Genetics; and 6.0 for PLoS Pathogens. (Note that the latter impact factors are based on only around six months worth of publications in 2005, and are likely to increase next year.)

Although the impact factor is an over-used and abused measure of scientific quality, it is a journal metric that is important for the research community, and so until there are alternatives, PLoS has to pay attention to the impact factor.

We are delighted in particular for the authors, editors-in-chief and editorial boards whose hard work and commitment to PLoS and open access has resulted in a tangible measure of success.

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Paying for open access publishing - a role for institutions

Mark Patterson — Sun, 17 Jun 2007 15:33:04 -0700

Nottingham University has recently established a fund of £20,000 to help researchers pay open access publishing fees. Although £20,000 doesn't sound like a lot relative to the estimated value of the entire scientific, technical and medical journals market (thought to be around $5billion), the creation of the fund at Nottingham is significant. This was announced at the recent Association of Research Managers and Administrators conference as described by Natasha Robshaw.

The money in Nottingham University’s fund comes from the indirect expenses associated with grants that have been awarded to researchers at Nottingham. The allocation of these indirect expenses (or overhead) is determined by the university research administration, and they are intended to cover the costs of the infrastructure required to support research (equipment, facilities, libraries and so on). In its position statement on open access last year, the umbrella organization of the Research Councils in the UK indicated that publication fees for open access journals would be a legitimate use of indirect research expenses.

Of course, many funding agencies have indicated that open access fees can be included within the research grant itself, but publications might often arise after the grant has terminated, and this is where an institutional fund might prove particularly helpful (as well as for researchers who have insufficient funds). This practical approach to covering publication fees was suggested previously in a briefing note from the Research Information Network as also discussed here.

Why is all this so significant? Institutions are one of the major stakeholders in publishing, but the creation of the dedicated fund by Nottingham is a new approach to help fund open access publication fees. It should inspire many other institutions to take similar action, and potentially, it’s a scalable way to fund open access publishing. Indirect costs, like research grants scale with research activity, and therefore with publishing output. The funds to cover open access publication fees will therefore grow naturally with the funds for research itself.

It’s fair to say that Nottingham’s action was probably inspired by the policies of the Wellcome Trust in the UK – the Trust has provided money to all major UK institutions to cover open access publishing fees for Trust-funded researchers. Each institution has to administer its fund, and it seems like a logical step to extend that fund using other financial sources to help all researchers publish in open access journals.

The move by Nottingham reflects the ongoing support of the institution for open access. For example, Nottingham is the home of the SHERPA partnership, which runs the ROMEO project, summarizing publisher open access and copyright policies, and the more recent JULIET project which covers funding agency policy.

Bravo, Nottingham!

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A trio of open access policies from UK funders

Mark Patterson — Thu, 24 May 2007 07:38:39 -0700

Over the past week or so, three major funding agencies in the UK have announced their policies on open access. The Department of Health, the British Heart Foundation and Cancer Research UK all now require their grantholders to make their research articles available in UK PubMed Central (UKPMC) as soon as possible (and no later than six months) after publication. The policies apply to newly awarded grants (awarded or applied for after a certain date this year).

It's also encouraging that the British Heart Foundation in particular has pledged to provide additional funds for authors to cover publication fees in open access journals. Although Cancer Research UK will not provide additional funds this year, their policy states that "the situation will be closely monitored and actual costs to researchers will be reviewed in summer 2008." The Department of Health policy currently does not mention publication fees.

The three agencies who have made the recent announcements are all members of the group of funders who have supported the development of UKPMC - the free full-text archive of research literature - which was launched back in January. In sum this group, which also includes the Wellcome Trust and the Medical Research Council, funds around 90% of UK biomedical research. So we are well on the way to providing comprehensive public access to biomedical research publications in the UK.

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