BioMed Central Blog

PMC Biophysics - Open access to biological physics research

 

We are very pleased to announce that our sister site, PhysMath Central, has launched a new open access journal which will should prove interesting to all BioMed Central readers and authors with an interest in the physical processes behind biological systems.

PMC Biophysics aims to cover the whole spectrum of biological physics and publishes articles on theoretical and experimental aspects of; physical concepts with potential applications to biological systems, physical models inspired by biological system, biological problems addressed by physics-based methods and soft condensed matter & mesoscale systems.

Read more on the PhysMath Central blog and journal homepage.

To celebrate the journal's launch, there is no article processing charge for articles submitted before July 30th 2008. Submit here.

Posted by Chris Leonard at 19:08    Comments (0)

 

NIH Public Access Policy becomes mandatory from April 7th

With effect from April 7th 2008, the US National Institutes of Health (NIH) Public Access Policy requires all peer-reviewed articles resulting from research carried out with NIH funding to be deposited in the PubMed Central archive, and to be made freely available within at most 12 months of publication.

If you are an NIH grantee or employee, publishing in one of BioMed Central's 180+ open access journals is an easy and effective way to ensure automatic and optimal compliance with the NIH's policy.

Benefits for NIH-funded researchers of publishing in one of BioMed Central's open access journals

• All peer-reviewed research articles published by BioMed Central are automatically deposited in PubMed Central
• The official final version of the article is made freely available with no delay or embargo period
• Articles published in BioMed Central journals provide true open access thanks to an open access license agreement which allows (and encourages) re-distribution and re-use.

Inconveniences for NIH-funded authors when publishing in a subscription-only journal

• The author will generally be required to manually deposit a pre-publication manuscript version of their article in PubMed Central.
• The article must then go through a separate markup, layout and checking process, resulting in two versions of the article, an "official" Publisher version and an "unofficial" PubMed Central version
• The article will not be freely available during the embargo period following publication (typically 12 months), yet this is the very time when the article is of most interest to other researchers
• Exclusive rights to article generally remain with the publisher and so, even when the embargo is lifted, re-distribution and re-use remain prohibited.

Given these advantages, publishing in one of BioMed Central's open access journal's is a natural choice for NIH-funded researchers. Automatic deposit means you can spend less time depositing your article, and more time on carrying out your research, and immediate open access to the official published version ensures maximum visibility for your research.

Submitting your research to one of BioMed Central's peer reviewed open access journals is easy – find out more by following the link below:

How can I submit a manuscript to a BioMed Central journal?

Posted by Matthew Cockerill at 17:25    Comments (4)

 

BMC Research Notes will free dark data

BMC Research Notes has launched with the aim of helping to complete the scientific record. Many submissions are rejected by journals on grounds of interest, which can mean that valuable data go unpublished, becoming 'dark data'. This can lead to publication bias, and wasted time, effort and resources of researchers and research subjects.

Small studies and confirmatory studies produce a valuable body of work - most science progresses by small advances rather than headline breakthroughs. Replication of results is essential and these studies are included in meta-analyses and systematic reviews. If the results of a study confirm what is already known or a new method or software tool offers an alternative approach rather than a major advance then we want authors to state this rather than being tempted to make exaggerated claims. Negative results may seem disappointing, but support for the null hypothesis is important and publishing such studies is essential to avoid publication bias.

The journal provides a platform for publishing updates to research reports (such as additional controls, extra time points, more patients or animals), updates to software tools and methods (perhaps optimized for ease of use, speed or accuracy, implemented for another operating system, or using a new interface) and updates to databases (maybe introducing a better interface or new sources of data).

BMC Research Notes is encouraging innovative content with:
·    Correspondence articles reporting novel observations deriving from the published literature.
·    Hypotheses that will spur other researchers into testing these ideas and claims.
·    Data Notes to allow authors to describe public data sets or databases (such as those proposed to be hosted by Google), including how they were collected and curated and likely uses of the data.
·    Project Notes to give researchers the chance to describe a research project as a whole, bringing together an overview normally broken into separate publications.

Project Notes also allow researchers to report research projects and trials that did not yield publishable results - this information may prove to be invaluable to other researchers working on related projects and offer a ‘glimpse behind the curtain’ of scientific research, showing how research really proceeds rather than the polished version often reported in the literature. To navigate the maze of science we need to know the cul de sacs as well as the clear runs.

For submissions to the journal, all relevant data should be made publicly available either in public repositories or in additional files to be published with the article. Authors should follow reporting and deposition guidelines as summarised by the MIBBI project and the EQUATOR Network, for biological and clinical studies respectively. We are working on guidelines for the formatting and reporting of data.

Our large international Editorial Board of Associate Editors and Subject Advisers is ready to handle work from across biology and medicine. We look forward to your submission.

Posted by Matt Hodgkinson at 18:36    Comments (1)

 

Harvard Faculty of Arts and Sciences votes to adopt mandatory open access policy

As discussed in the New York Times and the Harvard Crimson, Harvard's Faculty of Arts and Sciences has just considered, and approved, the adoption of a new policy designed to ensure that the results of work published by members of the Faculty remain openly accessible. The policy is the first of its kind in the US, though similar institutional open access mandates are becoming increasingly common around the world.

A new Office for Scholarly Communication will be responsible for implementing the policy, and for addressing the broader issues to ensure that the results of research carried out at Harvard are made universally accessible.

Harvard University's strong move to encourage open access is not an isolated instance. It is hugely encouraging to note the rapid pace of change in the United States on open access issues since the passing of the bill late last year, which made mandatory the National Institutes of Health's Public Access Policy.

For example, the University of Berkeley recently announced the Berkeley Research Impact Initiative, which sets up a central open access fund to assist Berkeley researchers who wish to publish in open access journals. Later this month, Berkeley will also play host to the inaugural US meeting in relation to the SCOAP3 initiative in particle physics. SCOAP3 is a consortium of the world's major particle physics laboratories which has set itself the ambitious yet achievable aim of switching the whole particle physics literature to an open access model, en masse.

What is clear is that the need for open access, and the failure of the traditional model of scientific publishing to make full use of the internet's potential in this respect, are no longer issues of interest only to librarians or to activists These issues are now recognized to be important ones that all serious research institutions need to consider. The recent steps taken by Harvard and Berkeley show that universities are just as willing as research funders to take a stand on this issue. Open access is no longer just a nice idea, but is a concrete objective and over the course of 2008, the key focus will be not on rhetoric, but on the practical issues necessary to make wide-scale open access a reality.

Update: Here is the official announcement from Harvard 

Posted by Matthew Cockerill at 20:36    Comments (3)

 

UK PubMed Central announces workshop and online survey to shape future development plans

Researchers, librarians and research administrators working in the UK may be interested in the following update from UK PubMed Central:

1. UKPMC Workshop
We are entering the next stage of developing UKPMC into an innovative and useful resource for UK researchers. We want to ensure that your needs and ideas are heard and incorporated at the outset and to this end we are holding a free one-day workshop on the 4th February 2008.
If you have an interest in helping us shape this vision, then please register for this free workshop. Places are limited - so respond today to reserve your place.

2. UKPMC Survey
We would like to know your opinion on the current service and resources you would like to see in
the future.  This is your opportunity to influence the improvements that we make to the site.

Posted by Matthew Cockerill at 18:15    Comments (0)

 

Journal of Cardiovascular Magnetic Resonance publishes first open access articles

The Journal of Cardiovascular Magnetic Resonance (JCMR) has published the first articles on BioMed Central’s open access publishing platform after its move from Taylor & Francis. JCMR, now in its tenth year, is the official journal of the Society of Cardiovascular Magnetic Resonance.

JCMR readers now have free, instant online access to all published articles, not only via BioMed Central’s website but also via  PubMed Central and other open access repositories. “Open access brings benefits to readers that are of utmost importance to science - free, unfettered and widespread access to all research,” says Editor-in-Chief Dudley Pennell. “Authors will benefit from faster publication cycles and a wider readership, leading to increased citation counts.” The online format also allows authors to publish colour images and embed movies at no extra cost, a great advantage in a field that relies heavily on high-quality image reproduction.

For further details regarding the journal’s move to open access publishing with BioMed Central please read the Editorial ‘Journal of Cardiovascular Magnetic Resonance: Open access in 2008.

The first and only journal devoted exclusively to CMR, Journal of Cardiovascular Magnetic Resonance includes basic and clinical research articles, technical notes, review articles, and editorial commentary on the research, design, development, and evaluation of magnetic resonance methods applied to the cardiovascular system.

BioMed Central publishes a growing number of journals affiliated with learned societies. In addition to the transfer of existing society journals, BioMed Central is also working with societies to launch new journals such as the forthcoming Journal of Foot & Ankle Research, the official journal of the Australasian Podiatry Council and the Society of Chiropodists and Podiatrists (UK).

Posted by Stefan Busch at 10:32    Comments (0)

 

SCImago – a new source of journal metrics offering a wealth of free data on open access journals

Bibliometrics (the measurement of scholarly citation) has long been dominated by the Science Citation Index. Created by Eugene Garfield in the 1960s, the SCI is now made available online as Web of Science by Thomson Scientific. In the last few years however two new services, Scopus and Google Scholar, have created competition for Web of Science, providing an alternative means to discover which articles have cited a particular research article. Scopus, a paid for service, offers an attractive user interface that is arguably easier to use and in some ways more powerful than that of Web of Science, while Google Scholar, though more limited in functionality, has the significant benefit of being free.

Until very recently, though, one area of Thomson Scientific's monopoly has remained essentially unchallenged – that of journal metrics. Thomson's Journal Citation Reports service (JCR), whilst frequently criticized, has been the unchallenged de facto standard for the comparison of journals, and the "impact factor" metric used in the JCR to rank journals has acquired almost mystical importance within the scientific community as a measure and signifier of the kudos associated with publication in a particular journal. For this reason, the announcement of SCImago Journal and Country Rank, a alternative database of journal citation metrics developed by researchers in Spain, is highly significant for the communication and evaluation of scholarly research.

Unlike the JCR (which is available to subscribers only), SCImago is freely available online, but in addition to being free, SCImago offers important improvements, compared to the JCR:

• Perhaps the most fundamental improvement, compared to the JCR, is the breadth of SCImago's scientific, technical and medical journal coverage. SCImago makes use of data supplied by Scopus which covers 13,000 journals, including many STM journals not tracked by Thomson Scientific. Thomson Scientific often wait several years before including new journals in, and in some cases (see below) may not track journals at all, even though they are highly cited. As a result of this, although those BioMed Central's journals which are listed in the JCR have impressive impact factors, many other high calibre BioMed Central journals are not currently listed in the JCR. In contrast, Scopus has a more systematic policy on content inclusion and adds all new BioMed Central titles to its database on an annual basis, and so SCImago contains reliable bibliometric data and rankings for around 100 BioMed Central journals that are not yet listed in the JCR.
• The SCImago Journal Rank (SJR) is used as an alternative to the impact factor, as the primary measure of a journal's citation impact. One of the major criticisms of the impact factor algorithm is that it gives equal weight to all citations – a citation from a very obscure journal is weighted as being just as important as a citation that occurs in the New England Journal of Medicine, or Nature. This is a problem, as it seems intuitively clear that a citation from a journal that is itself highly cited is a more reliable and significant indicator of importance and impact. To address this weakness, SCImago have taken the mathematical approach behind the PageRank algorithm that has been central to Google's success as an internet search engine, and have adapted it to journal metrics in order to create the SCImago Journal Rank. The PageRank-style approach weights citations from journals according to how highly cited the journal itself it, using an iterative approach. Details of the SJR algorithm are available here.
  [SCImago is not the first group to apply a PageRank style algorithm to bibliometrics - Eigenfactor.org launched last year with a similar approach, and the Eigenfactor.org methodology page provides a good overview of the mathematical background and previous work in this area. However, because Eigenfactor.org relies solely on Thomson Scientific data, it does not offer the same breadth of coverage of new open access journals as SCImago].
• One additional point of note is that while impact factors are derived from citations in a single year to articles from the two preceding years, the SJR calculation looks at citations made in a three year period, of articles published in an earlier, but overlapping, three year period. This makes the SJR a more stable indicator of trends than impact factors, which often fluctuate substantially from year to year.

How do SJR rankings for BioMed Central journals compare with JCR rankings?

The SJR algorithm, combined with the more comprehensive pool of citation data provided by Scopus, leads to many significant changes in the relative ranking of journals. A few examples of this are identified below:

• Genome Biology is ranked 54th of all the 13,000+ journals listed by SCImago, outranking journals such as PLoS Biology (which is ranked 60th). In fact, excluding review journals, Genome Biology is the 29th most highly ranked title in SCImago, putting it in an elite club of the most influential research journals.
• Arthritis Research & Therapy is ranked 2nd of 37 in Rheumatology by SCImago, outranking journals such as Annals of Rheumatic Disease, Current Opinion in Rheumatology, Rheumatology, and Osteoarthritis and Cartilage even though those journals have higher impact factors according to the JCR.
• Breast Cancer Research, which ranks 26th of 139 journals in Cancer Research similarly leapfrogs its competitor Breast Cancer Research and Treatment (which is ranked 43rd in this category).

What about BioMed Central journals that are not yet listed in the JCR?

Here are a few examples of the journal metric data available from SCImago for BioMed Central journals which do not yet have official impact factors:

• Journal of Biology, which Thomson Scientific strangely do not track due to its small publication volume, confirms its status as a journal of the very highest quality. It ranks 44th of all 13,000+ journalss in SCImago (21st if review journals are excluded).
• BMC Biology, the flagship biology journal in the BMC-series, ranks 227th of all 13,000+ journals listed in SCImago – i.e. one of the top 2%
  (BMC Biology is expected to receive its first impact factor in June 2008)
• BMC Medicine, the flagship medical title in the BMC-series, is ranked 3rd of 241 titles in SCIMago's Public Health, Environmental and Occupational Health category and 532nd in the overall database - a very high ranking for a medical journal.
  (BMC Medicine was recently accepted for tracking by Thomson Scientific, but will not appear in the JCR until June 2009)  
• BMC Medical Education, not yet accepted for tracking by Thomson Scientific, ranks 14th of the  249 journals in SCImago that include 'Education' in their title. (i.e. it is one of the top 6% of such journals)
• Retrovirology, due to receive its first impact factor in June 2008, ranks 5th of 46 in Virology.

Posted by Matthew Cockerill at 14:40    Comments (5)

 

NIH Public Access Policy to become mandatory

Many open access advocates will already have heard that NIH's Public Access Policy, until now voluntary, is set to become mandatory following President Bush's approval on Dec 26th 2007 of the latest NIH appropriations bill, which includes the following wording:

"The Director of the National Institutes of Health shall require that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine's PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication to be made publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law."

This is great news both for researchers and for the general public. Peter Suber's January SPARC Open Access Newsletter contains a detailed analysis of what the change means, and identifies some of the key issues that remain to be resolved.

Perhaps predictably, the publishing organizations who had lobbied strenuously but unsuccessfully against the new policy have lost no time in issuing statements condemning it and forecasting dire consequences. Statements from the Association of American Publishers  and STM appear to take the curious position that it is the publishing organizations who are the rightful owners of the intellectual results of scientific research, and that the NIH is taking an appalling liberty by asserting, on behalf of the public, any rights at all over these results.

According to the AAP:

"[C]hanging to a new mandatory policy that will ‘require’ such submission eliminates the concept of permission, and effectively allows the agency to take important publisher property interests without compensation, including the value added to the article by the publishers’ investments in the peer review process and other quality-assurance aspects of journal publication. It undermines publishers’ ability to exercise their copyrights in the published articles, which is the means by which they support their investments in such value-adding operations"

According to STM, meanwhile:

"The legislation neither provides compensation for the added-value of services that these manuscripts have received from publishers nor does it earmark funds to ensure the economic sustainability of the broad and systematic archiving this sort of project requires. It also undermines a key intellectual property right known as copyright - long a cornerstone used to foster creativity and innovation."

Mind boggling stuff...

The first point to make, in response, is to note the matter of timing. A potential author signs an agreement with NIH concerning the conditions of their grant funding long before any manuscript resulting from that funding is submitted to a publisher. If a publisher does not like the NIH policy, they are within their rights to choose not to consider submissions from NIH-funded authors. But a publisher cannot reasonably claim that NIH is appropriating its intellectual property, since the author's pre-existing contractual agreement, at the point of manuscript submission, is entirely with NIH, not with the publisher. The publisher has no claim whatsoever over the research at that point.

Secondly, copyright, far from being threatened by open access, is the essential legal framework that makes open access possible. The Creative Commons open access license, under which all BioMed Central research articles are distributed, depends entirely on copyright for its legal validity. Traditional publishers may not like an arrangement in which they are no longer the exclusive copyright owners, but that hardly means that such a situation 'undermines' copyright.

Thirdly, and finally: in financial terms the investment made by a publisher in managing the peer-review and publication process for a typical biomedical research publication amounts to roughly 1% of what was invested by the funder in carrying out the research. (i.e. a few thousand dollars of input by the publisher, compared to a few hundred thousand dollars spent by the funder). In such circumstances, it is quite something for the publishers to claim that they are hard done by if they do not receive exclusive rights to the resulting research article in return for their efforts...

In the context of the publication of original scientific and medical research articles, publishers are not the content creators, nor should they be the content owners. Publishers are service providers, and should compete to provide the best service to the scientific community on that basis. 180+ open access journals from BioMed Central and around 3000 more listed in the Directory of Open Access Journals demonstrate the appeal and viability of this approach.

[Peter Suber has posted detailed rebuttals of the AAP and  STM statements, here and here respectively.]

Update: 14th Jan 2008 
The NIH has released the text of its new policy, and has also created an accompanying Public Access FAQ. 

Posted by Matthew Cockerill at 19:52    Comments (11)

 

Society journals take a fresh look at open access publishing

A notable trend at BioMed Central during 2007 has been the increasing number of inquiries from scientific societies interested in starting new open access journals or transferring their existing journals to BioMed Central, in many cases converting to open access from a previous subscriber-only model.

Society journals that have recently signed transfer agreements with  BioMed Central include Journal of the International Society of Sports Nutrition and the Journal of Cardiovascular Magnetic Resonance. Several further such transfers are in the pipeline.

This surge in interest seems to result from a combination of factors. Firstly, the so-called 'serials crisis' continues to bite, in that subscription costs are rising faster than library budgets, and so many libraries find they need to cancel journal subscriptions each year. This has hit smaller society journals hard – especially those which do not form part of one of the major commercial publisher 'Big Deal' arrangements.

Secondly, open access publishing has now established itself as a viable and attractive alternative to the traditional model – it is no longer a new-fangled experiment. Learned societies are rightly cautious about change, and wish to avoid risk, but the risk of moving to the open access model now seems more and more attractive compared to risks of sticking to what is in many cases the increasingly unsustainable subscription-based model.

Lastly, but not least, there is the underlying mission of scientific societies, which is typically to support and promote research and researchers in a given field. As the open access publishing model becomes more familiar, it is more and more widely recognized that open access journals can provide a natural and financially sustainable means for societies to achieve their objectives, and increasing numbers of societies are seizing that opportunity.

Of course, change does not happen overnight, not least because societies are often signed-up to multi-year publishing arrangements with their existing publishers. But a recent study by Peter Suber and Caroline Sutton has revealed the surprisingly large number of scientific society journals (collated here as a spreadsheet) that already operate on an open access or hybrid open access model. BioMed Central looks forward to working with many more societies in 2008, to bring the benefits of open access to their society journals.

Posted by Stefan Busch at 12:39    Comments (1)

 

Canadian TV provides excellent coverage of open access research on superbug afflicting soliders in Afghanistan

It's always nice to see research from BioMed Central journals covered in the mainstream media, and  Soldiers bringing superbug back from Kandahar from Canadian broadcaster CTV is an excellent example, featuring research recently published by Dr Homer Tsien and colleages in BMC Infectious Diseases.

It is currently the top story on the CTV website, and the story includes a video of the newscast concerned, along with a more in-depth interview with Dr Tsien.

Perhaps most impressively, CTV have done a great job of providing a route for readers to find out more by linking directly to the open access research article concerned. It's surprisingly rare that news outlets provide such links, but kudos to the CTV team for doing so. BioMed Central is working with other news organizations to encourage them to do the same.

Posted by Matthew Cockerill at 13:19    Comments (0)

 

Forest fires and their impact on CO2 - global press coverage for open access research

A recent article published in Carbon Balance and Management entitled ‘Estimates of CO₂ from fires in the United States: implications for carbon management’ has received widespread, global coverage in the media.

The article by Christine Wiedinmyer and Jason Neff focuses on CO₂ emissions from fires across the US, how these emissions compare to anthropogenic emissions of CO₂ and Net Primary Productivity, and the potential implications for monitoring programs and policy development.

The article was press released by BioMed Central, and has since been highlighted in news coverage around the world including USA Today, Forbes, The Sydney Morning Herald, CBS News, The Times of India and Pollution Online, and more. With the recent forest fires in California, and significant public interest in the effects of carbon emissions on climate, this is a great example of the benefits of open access in making research accessible to all who are interested.

Posted by Charlotte Hubbard at 20:18    Comments (0)

 

Enthusiasm for open access on the Harvard campus

 

 

 

 

 

 

Posted by Matthew Cockerill at 22:57    Comments (0)