Editorial: The journey of Diagnostic Pathology in 2009, perspectives for 2010 Diagnostic Pathology is approaching the end of its fourth year of publication. From the beginning, Diagnostic Pathology has operated as an independent scientific journal, allowing the Editor-in-Chief and Editorial Board to control the content of the journal, while the publisher provides support in these activities and regulates other aspects including production and layout of the published articles. The separation of these activities allows the Editorial team to focus on the content and direction for the journal, making it the best home for research in the area.Diagnostic Pathology open access, the journal levies an article-processing charge (APC) for each article accepted for publication. These costs are necessary to continue to provide the production and hosting services as well as additional support, but they remain competitive compared to other open access journals. Many funders support open access by allowing their grants to be used to cover the cost of publishing in open access journals [In order to make journals  and moreThis is primarily a question to the authors, although it is also of importance to the journal Editors. Publishing an article usually requires research investigation which can last for months or years. Results and interpretation are the fruits that are offered to colleagues, and "should be eaten". They have to be "sweet" and to "fit into the taste" of the potential readers. Every successful merchant knows that the wrapping of an article is as important as the content that has to be sold successfully. The main interest of an author in publishing scientific results is a broad access to the corresponding scientific world, and a high reputation of the article (at home and in the scientific environment). Also of interest are the technical publication procedures, such as fast, helpful, non-biased, and reliable review of the article, concrete assistance in improving the paper, and fast publication of the accepted final version.Diagnostic Pathology deal with these reimbursements?How does Diagnostic Pathology offers all these items. With a wide readership, articles are well accessed. A total of six articles were published in November 2009, two of which have already been read by more than 400 colleagues. These articles were submitted to Diagnostic Pathology at the end of August 2009, and published in November 2009, i.e., the time taken from submission, to review, revise and final publication amounts to less than three months. The average time of acceptance was calculated as 74 days (from submission to publication).Open access journals, i.e., those that can be read for free, have a wide reader community. The readers are not limited to colleagues who are working within the same field of the published article. They often visit a journal in search for new ideas or even by chance, for example by coming across relevant articles in PubMed or PubMed Central. In addition, open access journals are embedded in an electronic communication medium that offers several advantages for a fast and "screening-like" visit. They are all provided with a fast search function, adequate links to "related articles", easy to copy functions, or "post a comment" message. Diagnostic Pathology is truely a world-wide and well known scientific journal already in its fourth year of publication.In addition to our standard scientific quality levels it is also our policy to encourage and support colleagues working in developing countries to publish their findings in our journal. Taking out randomly 10 published articles in 2009, two of them were submitted from the USA, one article each from Brazil, China, Egypt, Germany, Iran, Poland, Spain and Turkey. These figures indicate that The scientific quality of a journal can be partly judged by statistical methods such as the impact factor or H-index. Although it is questionable whether these factors reflect to the reputation of a scientific journal in its community, an impact factor is often mandatory if scientists want to publish their results in the selected journal. The main disadvantage of the impact factor is its absolute value, i.e. it depends upon the size of the journal specific scientific community. The impact factor of pathology journals is basically low in comparison to that of molecular biology or biochemistry journals.Diagnostic Pathology received its first official impact factor in 2009, of 1.11 and is now included in the journal citation index. At a starting point the value 1.11 can be regarded as high. It is already above that of several long term established scientific journals in surgical pathology.Both figures, namely the submission of articles written in all parts of the world, the frequent access of interested colleagues, and the newly established citation index contribute to the journal's reputation, and can be considered as a high quality return for the invested time and financial input of the authors.Diagnostic Pathology is coming to its end despite all constraints. A big step forward in reputation and notification has been achieved, which to our satisfaction benefits our authors.In summary, a successful year for We want to express our deep gratitude to, and we wish all our authors, readers, reviewers, and our publication team a Merry Christmas and a Happy and Healthy New Year.Klaus KayserEditor in Chief


This month's editorial discusses ways in which the process of publishing scientific research can be inappropriately influenced by varied forms of bias and the effects of competing interests. The editors propose five ways in which individuals involved in the publication process can mitigate the effects of biased agendas on the published scientific record. A large and growing literature details the many ways by which research and the subsequent published record can be inappropriately influenced, including publication bias , outcomeAny journal has stories to tell of attempts to unduly influence the publication process—such as the author who repeatedly appeals a manuscript's rejection, claiming the reviewers are incompetent and demanding evaluation by a specific list of preferred experts, or the biotech company that refuses to publicly deposit the microarray data underlying their findings. Sometimes distortion of the scientific record may be limited in scope, relating to just one paper. But when a single company funds virtually an entire research agenda on a particular topic, there is the potential for wider and far more damaging distortion. In a detailed analysis of documentation released as part of a class-action lawsuit relating to the drug gabapentin (Neurontin), Kay Dickersin has described “…a remarkable assemblage of evidence of reporting biases that amount to outright deception of the biomedical community, and suppression of scientific truth concerning the effectiveness of Neurontin for migraine, bipolar disorders, and pain…” . At PLoSo much has been published relating to the damaging nature of commercial competing interests  that it Robust journal policies regarding non-commercial competing interests  will atPLoS Medicine opposes the death penalty. It is not our intention to encourage further research to ‘improve’ lethal injection protocols” [In publishing a research article on the unreliability of protocols for execution by lethal injection , we declotocols” . It therPLoS Medicine editors recently handled a manuscript describing the burden of a disease of poverty. The study was designed, and the paper apparently written up, by the manufacturer of a vaccine, but no employees of this company were named in the paper; the authorship byline included only representatives of a health communications company, along with one individual affiliated with the hospitals where the work was done. Had the manufacturer's employees been listed as authors, together with their contributions and competing interests, any role of the company in directing the research project would have been appropriately evident.One of the PLoS Medicine, three viewpoints lay out a variety of approaches for combating ghostwriting . All coMany journals now have policies requiring, or recommending, the submission of original protocol documents before papers reporting the results of clinical trials are peer-reviewed , as wellIn one situation, we received a report of a randomized, placebo-controlled trial of a marketed intervention, funded by the manufacturer of the intervention being studied. On requesting the study protocol, we received an e-mail from an individual affiliated with the company, but who was not listed as an author of the paper, asking us to sign a confidentiality agreement barring us from making the protocol available to reviewers, and from publishing it as supporting material, as is our policy for clinical trial papers. In this situation, we and the reviewers would have been unable to properly evaluate the submitted report; we declined to consider the paper further, based on the journal's policy regarding reporting standards for clinical trials.PLoS ONE (http://www.plosone.org/), which aims to publish all methodologically rigorous, ethically sound, and properly reported work, provide one way to ensure that journals do not become part of the problem of publication bias.The Declaration of Helsinki  emphasizPLoS Medicine's efforts, and those of many other journals, to promote full transparency will ultimately lead to a more rigorous and unbiased knowledge base.Peer-reviewed publication is the final, essential step in any research project, providing legitimization and credit for the work that has been done. It is the responsibility of everyone involved to ensure that the published record is an unbiased, accurate representation of research. We recognize that today there are many, and increasing, pressures on authors and journals to bias this record. If this pressure is not resisted, journals may increasingly become closer to works of fiction telling the stories dictated by various lobbies rather than works of science. We hope that


Current Oncology sees a significant change of direction for the journal—for want of a better word, publication in a “hybrid format.” Although all manuscripts will continue to be published online at www.current-oncology.com as usual, not all will be published in their full form in the hardcopy issue. Papers selected for online publication exclusively will also be presented in an extended (single-page) short version in the print publication. The present hardcopy issue therefore includes two short-form manuscripts with universal resource locaters (URLs) that link to the respective complete online versions.This new issue of Current Oncology will carry full versions of invited editorials, unsolicited manuscripts with a broad-based appeal to readership, and selected sponsored items such as the new “info editorial” series. Conversely, manuscripts for a more specialized audience and those that need exceptional length to demonstrate their theses, may appear in full online only. The cost of publishing colour online is trivial as compared with colour in hard copy, and one interesting (and to date unexplored) asset for online publication is the ability to include selected audio and video formats such as MP3. Although such formats are perhaps more appealing to the various journals of ornithology, they may represent added value for some submissions arriving here!The hardcopy version of Current Oncology is an example), which most major medical publishing companies such as MultiMed are now incorporating. Electronic open-access journals provide speedier turnaround from submission to publication, allow for more interactivity between authors and readers, and comply with the growing demands placed on libraries and other depositories to sustain a wide range of journals in their inventories despite limited space and tight budgets. A hybrid model can only enhance the ability of Current Oncology to maintain the broadest exposure within its operating budget.The publishing world has changed dramatically in the past couple of years—a notable development being the open-access journals  Index Copernicus.


Last September, US Congressman John Conyers introduced the Fair Copyright in Research Works Act. John Willinsky explains how the bill's Orwellian title obscures its true aim: to derail the new policy implemented by the National Institutes of Health to open access to publicly funded research, amid talk of sustainability that cuts both ways. The dying light of the George W. Bush presidency was marked by, among other things, a legislative move to derail recent gains in the federal government's opening of science. In particular, the innocuous sounding “Fair Copyright in Research Works Act” (HR 6845) introduced into the House by John Conyers, Jr. (DEM-MI), on 9 September 2008  was poisCertainly, the Obama presidency promises, among so many things, an improved regard for science. Yet I can't help but agree with Peter Suber's prediction that Congress will see the likes of the Fair Copyright in Research Works Act again, though perhaps not from Conyers, who was an early supporter of Obama . The bacConyers' bill, with strong backing from both the profit and nonprofit scholarly publishing organizations, would preclude federal agencies from retaining any claim on research articles in which the work had been government funded, specifically targeting any right that “involves the availability to the public of that work” . What isWhat the NIH's Public Access Policy—which had been supported by no less than 33 Nobel Prize laureates, the Taxpayers Alliance for Access, and leading research libraries—had established was a public exception to that monopoly. It was a trade-off that protected the initial intent of the constitutional sense of copyright, as greater access contributes to the progress of science and such useful arts as medicine.What is strangely amiss in the publishers' support for outlawing the NIH Public Access Policy is that they support the upshot of this initiative with their own current copyright policies. While a growing number of open-access journals provide immediate access to the published version, even subscription-based publishers had originally been happy enough to grant authors the right to do what they were already doing, which was putting PDFs of their articles up on their websites. Still, it was not long before the publishers began to limit authors' archiving rights, imposing an embargo period of perhaps a year following publication after which the author is permitted to archive the final peer-reviewed draft (rather than the published version) . Now, asOne reason for the publishers' change of heart is that archiving is catching on, amid growing public expectations that research is a public good that should be made freely available online. Research libraries are setting up dedicated archives for just such purposes. Funding agencies, foundations, and institutions are putting in place policies supporting archiving as a duty and point of pride. Still, when the NIH established its Public Access Policy in April of 2008, the terms carefully reflected the publisher's own archiving policies. Authors were asked to deposit the “final peer-reviewed manuscript” in PubMed Central on publication, which would then be made public no later than 12 months after publication  should 12 months prove disadvantageous to the Society's business model” [Frank's stance makes it clear that s model” . The pois model” . The assFor STM publishers, the NIH mandate “puts at risk a system which has enabled more research to be available to more scientists in more countries than at any point in the history of science” . But is At the root of the problem is the current cost of access to knowledge and how those costs have come to differ so radically from journal to journal that one has to wonder about whether the progress of science is being served. This is the result of the scholarly publishing economy that emerged during the last half of the twentieth century. In that time, the commercial scholarly publishers adeptly served the greatly expanding scale of government-sponsored research by providing many new journal titles in new areas that soon became a critical part of scholarly communication. It was a move that also enabled commercial publishers to run subscription prices up each year well over the rate of inflation, with some nonprofit societies following suit. The result is a publishing system in which subscription prices no longer correspond to the quantity or quality of the work. The price per page charged by commercial publishers averaged six and seven times that of nonprofit society publishers across a number of disciplines in one study of journal subscriptions pricing . This isWhich is only to say that the real battle for the future of science is not about NIH's provision of delayed access to author's drafts. It is about efforts to protect unsustainable revenue streams amid the capitalization of a public good to a degree that arguably undermines what is basic to the progress of science and useful arts. If the publishers' exclusive ownership of this body of work enables them to charge what they will, on their own terms, then what is at risk is the delicate-at-best balance between public interests in such learning and private investments in bringing it to the widest possible audience.The NIH Public Access Policy stands as an expression of interest in righting the imbalance. It is a transition point, a step toward establishing a new economy of openness for the progress of science. No one has made that more clear than NIH director Elias A. Zerhouni in his testimony against the Fair Copyright bill . ZerhounZerhouni spoke, as well, of public interest in this knowledge, pointing to how the majority of patients now turn up at the doctor's office having visited medical Web sites. This interest in access to knowledge is bound to spread to the other professions and their clients as well. Publishers, who could once count on no one giving a second thought, least of all researchers, to transferring to them the copyright for the entire research corpus, article by article, should have sufficient vision to see that a new civil rights issue is emerging over access to, as well as control over, such knowledge.Now may be the time to step back from these time-consuming legislative skirmishes over who should determine rights of access to this knowledge. What makes far more sense at this point, as we move into a new publishing medium, is for journal publishers, scholarly societies, and research libraries to come to the table, to rethink cost structures, to collaborate on publishing platforms and systems, and to explore new ways of justifying, rationalizing, and allocating what is well over a US$7 billion investment in the circulation of knowledge  . What isYou may find the prospects of such coordinated and cooperative approaches to advancing this public good hopelessly naive, even in this time of renewed hope and economic reconstruction. If so, then I can only advise constant, if not increased, vigilance on behalf of those with an interest in the openness of science. It will be a long road forward of strategic incremental measures, such as the NIH Public Access Policy, with carefully orchestrated counter-measures, even as a number of us within the academic community seek ways to extend this vision of public access to all that we do in the name of research and scholarship.


Welcome to PMC Biophysics, an international, peer-reviewed, open access journal devoted to biological physics in all its myriad forms. The journal has been launched in response to two significant trends in publishing and research.Firstly, the open access movement is gathering strength. Pioneered by PMC Biophysics's parent company, BioMed Central, open access allows any reader immediate free access to published articles, encouraging the widest possible spread of knowledge. Archiving in multiple repositories ensures the long-term preservation of scientific research, and electronic publication enables the inclusion of multimedia content and the dissemination of raw data - allowing other researchers to exploit them. All these features serve to enhance the impact of published articles.The strength and future success of open access are heralded by two major recent developments. The US National Institutes of Health, the largest public funding agency for biomedical research, now requires that all peer-reviewed journal articles arising from NIH funding be made open access within 12 months of publication. In addition, BioMed Central has recently been acquired by Springer, the world's second largest publisher of scientific journals.The second trend concerns the multidisciplinary nature of research in biological physics.Over the past 40 years, the field of biological physics has been shaped by forces from two directions. On one hand, the study of biological systems has become less and less descriptive and more and more quantitative. It has become more compelling to model biological systems and rationalise or predict behaviours from physical principles, such as in protein folding.On the other hand, it has been discovered time and again that models and techniques developed for simple physical systems eventually become powerful tools for studying biological systems – Born's model for ion solvation and Kramers' rate theory for barrier crossing being classic examples. X-ray crystallography and computer simulations both started from humble beginnings, but are now used to study ever larger biomacromolecular complexes. The end result is that biological physics is now a thriving area for researchers from a wide variety of backgrounds, united by their interest in, or their work's application to, biological systems.With the help of the distinguished members of our editorial board and our colleagues who willingly serve as reviewers, I hope that PMC Biophysics will become a powerful voice in biological physics, and your first choice when considering venues for publishing your work.


Sir,Once you replace negative thoughts with positive ones, you’ll start having positive results.”“Willie NelsonDrug discovery nowadays is a highly innovative process by which new drugs are discovered and/or designed. It is expected that in the year 2010, at least 50% of all new approved drugs will come from the biopharmaceutical sector. The discovery and validation process is mostly carried out by new innovative and medium-sized companies. But, despite advances in technology and greater understanding of biological systems, drug discovery is still a lengthy process. Specialized drug discovery companies need an ideal business climate, that is, political, economic, and social conditions, to be able to cope with the entrepreneurial risks of drug development.Global pharmaceutical industry is at the crossroads. On one side, market demand for novel and better medicines is getting redefined and growing due to demographic, economic, and epidemiologic trends, but at the same time, pharmaceutical companies are finding it difficult to survive because they are unable to innovate and discover new molecules. The pipeline of the new drug molecules is drying fast due to poor R&D productivity, high failure rate, and generic competition.Scientific research proceeds with an infinite variety in the availability of data, the maturity of conceptions, and the mix of conviction and uncertainty. Often a major discovery is the culmination of a process with numerous blunders, wrong turns, false hypotheses, missed opportunities, persistent hard work, lucky breaks, rational arguments, insightful conjectures, and accumulation of knowledge over decades. But none of the failures are being reported or published in the journals and other resources. This part is always ignored because of the publishing style of most of the journals in the pharmaceutical field.Journal of Pharmaceutical Negative Results (PNR). We are proud to introduce you to a new home for negative results focused on all aspects of Pharmacy. Journal of Pharmaceutical Negative Results[Welcome to the e Results represenJournal of Pharmaceutical Negative Results is a peer-reviewed journal developed to publish original, innovative, and novel research articles with negative results. This peer-reviewed scientific journal publishes theoretic and empiric papers that report negative findings and research failures in the pharmaceutical field. Submissions should have a negative focus, which means the output of research yielded in negative results is given more preference. All theoretic and methodologic perspectives are welcomed. We also encourage the submission of short papers/communications presenting counter-examples to usually accepted conjectures or to published articles.[articles.3The main aim of the journal is to publish negative results so that newer generation of researchers should not waste their time and money repeating the same studies and finding the same unpublishable results. Most of the journals have published only the positive results and findings; however, they do not publish negative results. We believe that negative results are also a part of quality research. Thus, the journal focus is not only limited to negative issues but will also address advances in pharmaceutical research leading to failures. This journal will provide multilateral coverage of numerous applied and basic aspects of current pharmaceutical research.Taking into account the growing number of pharmaceutical journals available, one can argue whether we need another one like this. However, any scientist working on theoretic and practical aspects of the pharmaceutical field would undoubtedly agree that there are few or no journals covering or boldly accepting negative results, and that there are no journals providing immediate open access. We performed an informal analysis Figure  and 2 thJournal of Pharmaceutical Negative Results aims to become a significant international participant in this field. The purpose of the journal is, therefore, to publish timely and high-quality articles  concerning failures in techniques and negative or unexpected results in all areas of pharmacy. To achieve this, the Editorial Board of PNR journal gathers well-known experts from all over the world.[journal, the Editor-in-Chief or corresponding specialists from the Editorial Board will immediately screen a submission and appropriate manuscripts will be sent for peer review to two independent reviewers. Based on their reports and scoring, a final decision will be made regarding the acceptance of manuscripts. Editor-in-Chief reserves the right to make final decisions concerning each manuscript submitted to the journal. At the first sight, our peer-review system does not significantly differ from that proposed by other journals. However, we encourage our Editorial Board members as well as reviewers to be motivated critical advisers for improving a manuscript rather than suggesting rejection, which is unfortunately a common experience for anyone who has ever tried to publish his or her original negative research results.he world. To make Journal of Pharmaceutical Negative Results is published by the open access publisher, Medknow Publications and Media Pvt. Ltd., India.[., India. When subConsidering all the advantages of this journal, we believe this journal to be of great benefit to the field of pharmacy. We invite you to work together with us to create this new and high-visibility open access forum for the pharmaceutical sciences.


Angiogenesis is the growth of new blood vessels and is a key process which occurs during both physiological and pathological disease processes. Knowledge of the mechanisms through which this process is initiated and maintained will have a significant impact on the treatment of these diseases. Pathological angiogenesis occurs in major diseases such as cancer, diabetic retinopathies, age-related macular degeneration and atherosclerosis. In other diseases such as stroke and myocardial infarction, insufficient or improper angiogenesis results in tissue loss and ultimately higher morbidity and mortality. The concept of tumor angiogenesis and therapy was proposed by Dr. Judah Folkman, who published the first and probably one of the most cited articles in 1971 [Journal of Angiogenesis Research.Over the last couple of decades scientists have identified the importance of angiogenesis in determining disease development in association with tissue remodelling. It is now established that therapeutic modulation of the "angiogenic switch", may be a key mechanism for the treatment of these diseases. For these reasons and due to the continual expansion of this area of biomedical research, we are proud to announce the launch of Journal of Angiogenesis Research aims to publish articles from all areas of the 'broad spectrum' of vascular research and from the bench to the bed-side. All submitted articles will be screened initially by a member of the journal's Editorial Board and if found to be suitable will be sent out for peer-review to internationally recognised experts in the field of angiogenesis research. The journal aims for the review process to be rapid and once accepted, the manuscripts will be published online immediately in a provisional format. Once an article is accepted for publication, the publisher will levy an Article Processing Charge which is a flat rate fee used to cover the article handling costs. Since articles are published online, there are no restrictions on size and number of figures that can be included. Articles will be immediately submitted to public repositories and will be freely available to read or down-load to readers world-wide.Accepted articles will be of the highest quality and can take the form of original research articles, reviews and commentaries (some commissioned) providing pertinent, cutting edge up-dates in a focussed area of research. These can be in any field of research related to angiogenesis, from identification of novel mechanisms and signalling factors associated with angiogenesis, in vitro and in vivo disease models, results from pre-clinical trials, novel imaging modalities and nano-biological approaches. Please see the journal website for a more complete list of topics .Journal of Angiogenesis Research welcomes your submissions, and hopes you will visit the website often to stay up-to-date with the latest articles.


Over two decades ago the first electronic databases which systematically collected protein and nucleic acid sequence and structure data came into existence. This period also saw the emergence of the first algorithms and their implementations to query these databases for sequence and structure similarities, to align sequences, and to identify of compositional features in sequences. A parallel advance was the integration of these disparate data collections into strongly interconnected databases, which included repositories of biomedical literature (e.g. Entrez). It would be no exaggeration to state that these computational developments played a role comparable to that of the polymerase chain reaction in the rise of modern molecular biology.The essential philosophy of this new movement within biology – computational biology – has been the use of computational methods to explore repositories of biological information to make new scientific discoveries. An early example of the success of these methods was the identification of the helix-turn-helix domain as a determinant of DNA-protein interaction . This alBiology Direct is to augment the process of discovery in light of the unprecedented accumulation of biological data. The articles submitted to this section aim to occupy a specific niche in the already rich menagerie of publications. Papers announcing the sequencing of a particular genome or a high-throughput genome-scale analysis hardly do justice to all that can be inferred from the data presented in them. Especially in the case of the high-profile scientific magazines with a space-crunch, much is relegated to supplementary material and may not necessarily hit the target audience. Likewise, comprehensive papers discussing the evolution of particular biological systems might contain many specific findings that are lost in the bulk of the article. In light of this, we feel that key findings that are likely to elucidate previously obscure issues, provide novel connections or spur experimental investigations in new and unexpected directions are best published separately as succinct publications. Such publications would do greater justice to such discoveries that might not require a full-scale paper by making the key findings more accessible to the relevant audience. The value of such publications can be easily discerned by considering exemplars from the field of protein sequence analysis. For example, the papers announcing the identification of the UBA domain [The principal idea behind announcing the Discovery Notes section of A domain , or the A domain  or the PA domain ,14 have TiBS [TIG and the Discovery Note section of Bioinformatics. Beyond the two above-mentioned venues, there are hardly any regular venues for such publications. The above venues employ the conventional peer review model involving three or more anonymous referees providing reports to the authors and confidential recommendations to the editors. As result, the usual vagaries of the process and the concomitant delays affect these publications. Given the swell in the data, and the high significance of some of these computational discoveries, we believe that the research community would benefit both from an additional forum for such publications, as well as a modified system of peer-review that would allow greater speed and openness.The goal of the new 'Discovery Notes' section of Biology Direct is to publish brief reports of specific discoveries made by computational analysis of nucleic acid and/or protein sequences, structures or other data, with novel observations and conclusions about the function, organization, or evolution of proteins, genes or genomes. In format it will be comparable to the now discontinued Protein Sequence Motifs column in TiBS , and theBiology Direct, the Discovery Notes section will follow the open peer-review format. However, there will be some key differences in the peer review process for the Discovery Notes section relative to conventional articles:In the original spirit of • Only two Editorial Board members are required for review of the manuscript.• Referees should be selected from the Editorial Board that is specifically set up for discovery notes.Reviewers would primarily assess the validity of the findings in the article, and have a right to veto publication if the findings are incorrect or trivial. The reviewers need not provide full comments/details of revisions, but are welcome to do so whenever they deem it fit. If reviewers see no requirement for additional comments, their report would merely indicate support for the publication of the manuscript. If either or both referees veto publication, the author should consider the manuscript rejected.Biology Direct. Central to the success of such a process is an Editorial Board with a strong track record in computational analysis of biological data. Approximately 40 excellent researchers have accepted our invitation to join the Editorial Board of Discovery Notes at Biology Direct. While such a starting base is encouraging, it is clear that the ultimate success of this section would depend on the authors submitting their interesting findings for publication. We do hope that this section provides a venue for fostering an active community of explorers seeking biological discoveries in silico.Given the nature of the peer-review of these articles, we believe it should not tax the reviewer excessively and he/she could return a review relatively quickly (~2 weeks). All other aspects of the peer review process remain the same as for research articles submitted to


Journal of General Internal Medicine (JGIM).Editorial peer review is universally used but little studied. We examined the relationship between external reviewers' recommendations and the editorial outcome of manuscripts undergoing external peer-review at the not be rejected (48% of manuscripts) (p<0.01).We examined reviewer recommendations and editors' decisions at JGIM between 2004 and 2008. For manuscripts undergoing peer review, we calculated chance-corrected agreement among reviewers on recommendations to reject versus accept or revise. Using mixed effects logistic regression models, we estimated intra-class correlation coefficients (ICC) at the reviewer and manuscript level. Finally, we examined the probability of rejection in relation to reviewer agreement and disagreement. The 2264 manuscripts sent for external review during the study period received 5881 reviews provided by 2916 reviewers; 28% of reviews recommended rejection. Chance corrected agreement (kappa statistic) on rejection among reviewers was 0.11 (p<.01). In mixed effects models adjusting for study year and manuscript type, the reviewer-level ICC was 0.23  and the manuscript-level ICC was 0.17 . The editors' overall rejection rate was 48%: 88% when all reviewers for a manuscript agreed on rejection (7% of manuscripts) and 20% when all reviewers agreed that the manuscript should Reviewers at JGIM agreed on recommendations to reject vs. accept/revise at levels barely beyond chance, yet editors placed considerable weight on reviewers' recommendations. Efforts are needed to improve the reliability of the peer-review process while helping editors understand the limitations of reviewers' recommendations. Journal of General Internal Medicine (JGIM) is a peer-reviewed journal focusing on clinical care, education, and research in general internal medicine and primary care. Like many of their peers, JGIM editors claim that “the quality of the papers published in the Journal depends on both the authors and the external reviewers who help the editors select the best papers and improve their presentation.”Editorial peer review is widely regarded as the cornerstone of quality assurance in academic medical scholarship.recommendations (i.e. accept/revise vs. reject) and reviewer comments (narrative assessment and suggestions for improvement). To the extent that JGIM editors are influenced in their decisions by reviewer recommendations, “it is reasonable to expect that experts' judgment[s] be somewhat concordant.” We distinguish here between reviewer Journal of Clinical Anesthesia found moderate levels of reviewer concordance .Do peer reviewers assigned the same manuscript tend to issue similar judgments? Data are conflicting. One early study from the While perfect agreement among reviewers is arguably unnecessary (implying redundancy of effort) or undesirable (perhaps suggesting excessive cognitive homogeneity in the reviewer pool), editors should expect reviewer recommendations to be substantially more consistent than mere chance. How much more consistent? The answer may depend on a particular journal's target acceptance rate and decision structure. Hargens suggests that editors of more selective journals put greater credence in negative reviews, whereas editors of less selective journals assign greater weight to positive reviews. These editorial predispositions may influence who is asked to review, how many reviews are requested, and how discordant recommendations are reconciled.recommendations (though not their comments) are not meaningful and should therefore be ignored – or at least steeply discounted – in making editorial decisions. Second, to what extent do JGIM editors incorporate reviewer recommendations into their decisions? For example, do they place more weight on reviewer recommendations than the data warrant? Finally, to what extent does reviewer style influence recommendations? The results have implications for the editorial process, and in particular how journal editors should collect, assess, and act on reviewer recommendations.We conducted the current study to address three questions. First, to what extent do peer reviewers at JGIM agree with each other in their manuscript recommendations? Poor agreement would suggest that reviewer Information on all 6213 manuscripts received by JGIM between 2004 and 2008 (inclusive) were stored in a central database at the Regenstrief Institute . Each submitted manuscript underwent two levels of initial internal editorial screening. First, one of the Co-Editors-in-Chief read the abstract. Articles felt to be inconsistent with the journal's mission were rejected. The remainder were assigned to a Deputy Editor with expertise relevant to the content of the article. The Deputy Editor then decided whether to reject the article without external review or to send the article out for external peer-review. JGIM routinely sought three peer-reviewers for each manuscript. We analyzed results for the 2264 manuscripts (36%) that were sent out for external review. Sources of data included structured forms completed by peer reviewers (1–4 per manuscript) and final editorial decisions made by JGIM's Editors (including Editors-in-Chief and Deputy Editors)) (1 per manuscript). Neither the Co-Editors-in-Chief nor Deputy Editors were blinded to the manuscripts' authors or institutions. For the first three years of this study, reviewers were not provided with manuscript authors or institutions, although no other efforts were made to blind the reviewers . In the fourth year of this study, the authors and their institutions were provided to the reviewers to give reviewers the opportunity to comment on possible conflicts of interest.Data were analyzed using Stata . We used kappa statistics to evaluate chance-corrected agreement among reviewers' recommendations to reject vs. accept/revise specific manuscripts. We used mixed model logistic regression analyses, with individual reviewer recommendation as the unit of analysis, to adjust reviewers' recommendations for review year and manuscript type . We used random effects models to account for nesting of reviews by manuscript and by reviewer and to calculate the intra-cluster correlation coefficients (ICCs) for manuscripts and reviewers. Because of the cross-nested nature of reviewers and manuscripts, simultaneous consideration of these variables as crossed random effects within the same logistic regression using the entire dataset exceeded the available computing capacity. Therefore, the reported ICCs are based on considering manuscripts and reviewers as the random effect in separate analyses. The results were consistent with those based on two other models using a 10% random sample of the data; each model treated one of the variables as a fixed effect and the other variable, in turn, as a random effect. We conducted supplementary analyses to examine possible Deputy Editor effects.  In these supplementary analyses, the unit of analysis was the manuscript, the dependent variable was the Deputy Editor decision (reject vs. not reject), and Deputy Editor was treated as a random effect.The 2264 manuscripts sent for external review during the study period received 5881 reviews provided by 2916 reviewers; 3.5% received one review, 34.6% received two reviews, 60.6% received three reviews, and 1% received four reviews. . Each reThe kappa statistic for inter-reviewer agreement on reject vs. accept/revise for each manuscript was 0.11 (p<.001); it was 0.14 when there were 4 reviews, 0.12 when there were 3 reviews, and 0.08 when there were 2 reviews. In a mixed effects logistic regression  the rho coefficient (ICC) for manuscript identity was 0.17 (95% CI 0.13–0.22), confirming modest inter-reviewer agreement. The mixed effects model using reviewer identity as the random effect yielded a reviewer ICC of 0.23  Assuming an ICC of 0.17 (i.e. the manuscript-level ICC observed in the current study), 7 reviewers would be required to achieve a Cronbach's alpha reliability of 0.6 and 18 reviewers would be needed to yield an alpha of 0.8. With a 50% increase in the manuscript-level ICC, 4 reviewers would suffice for an alpha of 0.6 and 10 for an alpha of 0.8. With a 100% increase in ICC, the requisite number of required reviewers would be 2  and 6 .not to reject , less than 10% received reviews that were in complete agreement to reject, and the balance received reviews with conflicting recommendations . In an analysis using manuscript as the unit of analysis and the assigned Deputy Editor as a random effect, taking initial editorial decision (reject or not) as the dependent variable, and no independent variables, the Deputy Editor ICC was 0.02 . When this model adjusted also for reviewer agreement , manuscript year and article type, the Deputy Editor ICC increased to 0.03 .The results of this analysis suggest that reviewers for JGIM agreed on the disposition of manuscripts at a rate barely exceeding what would be expected by chance. Nevertheless, JGIM editor's decisions appeared to be significantly influenced by reviewer recommendations. In particular, agreement by all reviewers that a manuscript should be rejected (an uncommon occurrence in our data) essentially sealed its fate. Consensus among reviewers that a manuscript deserved further consideration  reduced the likelihood of rejection from approximately half  to about one in five. These results challenge biomedical journal editors to reconsider what is now standard practice: asking reviewers to provide recommendations to accept, revise, or reject submitted manuscripts.http://www.plosone.org/static/information.action). For the time being, however, placement of a manuscript within a particular journal is of great significance to readers, authors, and authors' institutions. Busy clinician-readers fix their attention on a limited number of journals, chosen according to the journals' clinical focus and impact.Of the two instrumental purposes served by peer review , filtering is arguably less important to the biomedical enterprise as a whole, since most rejected manuscripts eventually get published. In this light, the results of this study are provocative. Reliability is a pre-requisite for validity, and the reliability of reviewer recommendations at JGIM  is low. Peer review serves multiple purposes, including social functions such as managing the process by which a “community certifies additions to its body of accepted knowledge”Several solutions might be entertained. First, editors might solicit more reviewers per manuscript; however, given ICCs in the range reported here, it would take 18 reviews per manuscript to push the coefficient alpha above 0.8. Given the difficulty JGIMrequire attendance. JGIM also provides guidelines for reviewers on its website (http://jgim.iusm.iu.edu/) but does not monitor website traffic nor formally certify reviewer competence. More formal attempts at reviewer training have met with mixed results.A second solution is to improve the process of peer review by providing more effective guidance to reviewers or by working to enhance the psychometric properties of the questions that are posed to them. JGIM hosts an annual peer review workshop at a national meeting but (for obvious reasons) does not Finally, journal editors could consider a break with tradition by dispensing with reviewer recommendations altogether, asking them to focus instead on evaluating the strengths and weaknesses of manuscripts across multiple dimensions and particularly on suggestions for improvement. Under this approach, the role of the reviewer would be realigned to emphasize evaluation and constructive criticism rather than decision-making. Again, such an approach should undergo a formal evaluation.It is interesting to note that recommendations were more consistent for multiple manuscripts assigned to the same reviewer (intra-class correlation coefficient rho = 0.23) than for multiple reviewers assessing the same manuscript (rho = 0.17). These results provide evidence that reviewers have an evaluation style that exerts itself across manuscripts. Any college undergraduate knows that there are hard and easy graders among professors, but it is still surprising that the propensity of reviewers to be generous or tough is quantitatively larger than the tendency of different raters to recommend rejection (vs. further consideration) of the same manuscript. In a study conducted at the American Journal of Radiology, Siegelman identified 8 “zealots” (very easy graders) and 9 “assassins” (very hard ones) among 660 reviewers who had reviewed at least 10 manuscripts. Our data indicate that inter-reviewer variability is much more pervasive; it is not just outliers who adopt a particular “style.” The existence of such a style effect and its potential arbitrary influence on the fate of manuscripts also raises questions about the probative value of reviewer recommendations.In contrast to the evidence for a modest reviewer style effect, there was little evidence for a substantive Deputy Editor style effect on initial rejection decisions. While the Deputy Editor rho was statistically significant, it was small (0.02) and increased only to 0.03 after adjusting for the effect of reviewer agreement, manuscript year and article type. It remains possible that editors exert a style effect through their selection of specific reviewers.This report has certain limitations. Most importantly, the data were obtained from a single general medical journal, and generalizability is therefore limited. However, manuscripts submitted to JGIM encompass a wide array of topics including clinical and health services research, clinical medicine, medical education, and health policy, so these findings may be relevant to a wide array of general medical journals. Moreover, many JGIM reviewers are academic general internists with extensive training in clinical epidemiology, health services research, critical appraisal, and biostatistics. Concordance within this methodologically minded cohort of reviewers might be expected to be, if anything, higher than for the average clinical journal. Other limitations include the relatively short evaluation period, likely non-random assignment of manuscripts to reviewers (editors may choose “hard graders” to review papers they don't like), and lack of data on outcomes . Further, we did not investigate the informational content of reviewers' narrative comments nor their impact on editorial decision-making. It remains possible that such comments drive editorial decisions in a more reliable and valid fashion than reviewers' summary recommendations. Finally, there is no guarantee that any of the potential solutions discussed here will work better than the current system. A Cochrane review concluded there is scant evidence to support the current process of editorial peer review.Journal of General Internal Medicine showed scant agreement but were nonetheless accorded considerable weight by the editors. Reviewers appear to have a relatively stable style that influences their recommendations over time and across manuscripts. Biomedical journal editors should look carefully at their own data – and pool data across journals – in an effort to create a more reliable and valid review process.In summary, reviewer publication recommendations over a five-year period at the


Innovation in computational biology research is predicated on the availability of published methods and computational resources. These resources facilitate the generation of new hypotheses and observations both on the part of the creators and the scientists who use them. These methods and resources include Web servers, databases, and software, both complex and simple, that implement a specific procedure or algorithm. Usually, a resource is maintained by the laboratory in which it was initially developed. We would assert that there is a growing level of frustration among scientists who attempt to use many of these resources and find that they no longer exist or are not properly maintained. Whether you agree or disagree with this statement and the evidence that follows, we welcome your thoughts and invite you to add a Comment to this article to share your own experiences and perspectives.It is timely to visit this situation in more detail. The International Society for Computational Biology (ISCB) is reviewing its position on software sharing, and this journal is now doing the same . To help us gain a better understanding of the resource situation, we took on two simple experiments: first, a review of the persistence of Web servers, and, second, an experience creating a metaserver—a Web site where users can come and run a variety of methods to compare results. Here is what we found.To evaluate the persistence of biology Web servers, we extracted all the URLs from the Nucleic Acids Research (NAR) Web server issues over the past four years since its inception . We thenOf those servers published four years ago, 14% no longer appear to be active, and a significant number of those published two and three years ago were similarly unavailable. One can speculate as to the reasons for these findings. The sites may have been down when we tried to access them but are available most of the time . More likely, they are no longer maintained either because of a lack of funding to support maintenance, the responsible parties have left the laboratory, or there simply has been a shift in emphasis by the laboratory and/or the community. For example, a newer resource may provide a more recent and well-accepted development. Given that journals describing these resources are more dynamic than they used to be, for example in adding commentary to a paper, these findings beg the question: Should journals report when the resource appears to become unavailable? This might encourage authors to keep the server operating or to not publish the resource at all if they are not inclined to maintain it. Your thoughts on this would be welcome.It is difficult to acquire quantitative information describing software availability. Rather than attempting to perform a comprehensive survey, we describe a specific experience from our own laboratory.Decomposition of protein structures into domains is one of the oldest and still active areas of research in computational biology. As soon as a few dozen structures were solved, methods for partitioning these structures into compact, globular units (coined domains) appeared. The complexity and sophistication of the methods increased as more structures and more powerful computers became available, and this trend still continues today. More than 30 methods have been published in the last 30 or so years, with two new methods being reported in 2007. This information might lead one to believe that there are now a large number of computational methods from which to choose. Our experience indicates otherwise.Many of the methods published since 1995 are difficult or impossible to obtain. The description of each new method's publication points out how its method is better than the previous ones. However, it is hard to objectively evaluate these claims because the software is simply unavailable. In addition, new methods are often tested using different sets of data than previously published methods, so a direct quantitative comparison cannot be made.In our attempt to analyze and benchmark methods for domain assignments, we are continuously working (or attempting to work) with the authors of the methods. With few exceptions, the software is not submitted along with article. When we contact the authors to obtain the software implementation of their published method and to run that software locally, one of the following scenarios takes place (ranked from worst to best).The authors of the paper do not respond. Authors rarely respond after the first request, but some do not respond no matter how many times we contact them.Authors of the software engage in a dialog and promise to provide the software. In the end, however, they never provide the code due to lack of time, resources, and (we suspect) lack of incentive.The student or postdoctoral fellow who wrote the software has since left the group, and the author, who has started new projects, has no time or interest in providing the software. Sometimes, it is also revealed that the software requires subjective manual post-processing, and it could thus be argued that the published results are irreproducible.The software is eventually provided, but it cannot be made to run, and the authors are not eager to help.Authors say they need to work further on the software, and eventually (over months or years) we receive it, it works, and if we have problems authors continue to collaborate with us.The authors provide their software immediately, assist us with our local installation, and even improve usability of their software upon our suggestions.Of 14 methods we attempted to obtain, some over a period of four years, we gained access to six methods (covering the period from 1994 to 2008) that we can run locally or remotely on a consistent basis.Based on our experience, it can be said that the notion of what constitutes “software” in the field of computational biology is variable. Many programs/Websites are developed as part of a graduate student's thesis without any forethought given for their future maintenance. Should these be published in peer-reviewed journals and presented as legitimate resources to the scientific community? Certainly there is pressure to do so as part of the academic process. But in the longer term are we doing the scientific community a disservice?Currently, there is little incentive to encourage a responsible approach to software/Website support. Extreme demands on scientists' time and the constant push toward novel research make it difficult to maintain existing resources. Funding agencies seem willing to fund new developments of resources but not their ongoing maintenance, unless they are known to be vital to the field at large. Journals may or may not review resources described in the submitted paper, and there does not seem to be a business model accepted by the academic community by which these resources can be maintained. Open sourcing seems to be the most viable solution at this time.The issue of resource persistence and usability would seem to be of particular importance to the field of computational biology. This issue plays a significant role in how our discipline is perceived by the broader scientific community. As such, we suggest that, as a community and as individual scientists, we must be more vigilant and responsible when we publish new resources. It would seem no longer sufficient to write in a paper that “software is available from the authors upon request” or to publish a Web server that will quickly become obsolete.By way of full disclosure, we (the authors) admit that we have all been guilty of poor software support and the creation of transient Web servers  The important issue to consider is how all of us can do better in the future. We list a few possible scenarios that might improve the availability and usefulness of published computational methods and resources and invite your comment.Authors should not be able to publish a method or relevant performance statistics without providing the software and tested datasets to the journal or to a stable, publicly available third-party repository. The goal here is to support reproducibility at any time subsequent to the paper being published. Furthermore, documented software should be submitted as part of the peer review process.Authors, or at least the primary author, of the method, should sign an agreement at the time their paper is accepted for publication that they will actively maintain the software and make it available for a specified period.Since authors of the methods are often graduate students or postdoctoral fellows, the head of the laboratory, as mentor, should insist on better standards of software practice and take responsibility for support and maintenance. Perhaps maintenance of the computational resources should be treated similarly to the author's publications, where status and level of use of each resource is reported as a prerequisite for publication. At the very least, the time the resource was last updated should be displayed prominently.The computational biology research community  should develop standards for software and Web servers, including guidelines on adequate testing, documentation, and the provision of benchmark datasets. In addition, the community should mandate the deposition of software in a publicly available open source repository.Such scenarios may be thwarted by institutional copyright issues that complicate deposition of software to open source or publicly available repositories. While a complex and contentious subject, it could be overcome in many cases by more insistent policies by funding agencies before the resource is developed and by scientists requesting from their institutions that the resources they develop be fully open prior to accepting funding. Certainly only a small percentage of the software currently in use by computational biologists is available from an open source archive. Beyond institutional and copyright issues, there are the scientists themselves who publish the work but do not want to go to the trouble of making the resource easy to use. Wouldn't it seem that evidence of usability through suitable documentation and accessibility should be prerequisite to publishing a paper when that paper is about such a resource?What do you, as members of the computational biology research community, think, and what are you willing to do? Is our integrity being compromised by the resources we are making public? Is this concern overstated? Are there other approaches to solving the problem? Please post a Comment to this article to make your views known.


EHP’s Instructions to Authors states that “Contributions submitted to EHP must be original works of the authors(s) and must not have been previously published in print or online or simultaneously submitted to another publication.” According to the International Committee of Medical Journal Editors  the potential for disagreement when two (or more) journals claim the right to publish a manuscript that has been submitted simultaneously to more than one; and 2) the possibility that two or more journals will unknowingly and unnecessarily undertake the work of peer review, edit the same manuscript, and publish the same article.Therefore, a policy on originality of submissions helps to protect against copyright infringements, prevent the waste of valuable resources related to the review and publication process, and guard against possible double counting of a specific set of data or ideas.EHP has utilized an online search engine to help identify material that may have been published elsewhere. As a result, we discovered several manuscripts that drew heavily from reports or documents already published online by groups such as the World Health Organization, the U.S. Environmental Protection Agency, or state health or regulatory agencies. Based on our experience with these submissions, we have come to recognize that online publication of internal reports, dissertations, and other documents is not necessarily equivalent to prior publication in a peer-reviewed journal. Clearly, our policy concerning the originality of the submission needs to be updated.Over the last two years, EHP will accept manuscripts based on materials that have been published online or in print elsewhere, we offer the following guidance. Much of the guidance is based on criteria developed by the EHP has two different standards, one for commentaries and review articles, and one for original research papers. Previously published material may be included in commentaries and review articles, assuming that the original authors have given permission to reproduce the material and all copyright issues have been resolved. For original research articles, previously published schemata or illustrative figures are acceptable with the proper attribution; however, figures or tables of data reproduced exactly from previously published reports or other documents are not acceptable. Text or narrative from previously published reports or documents should also include new information. EHP will consider a) manuscripts from dissertations that have been published in their entirety by a university in partial fulfillment of a degree; b) manuscripts based on preliminary reports, such as an abstract or poster displayed at a professional meeting; and c) manuscripts based on papers presented at a scientific meeting but not published in full, or those that are being considered for publication in a proceedings or similar format. Previously published material may be included in the Supplemental Materials of the paper (peer reviewed but published online only).To help clarify the conditions under which As indicated in the guidance by the EHP acknowledges the fact that considerable time and original thought is involved in producing guidance documents, technical reports, and position papers by various government and non-government organizations. Materials included in these documents may under certain circumstances be included in commentaries, reviews, and original research articles submitted to EHP. Hopefully, the guidance provided here will help authors in the preparation of their manuscripts. Of course, authors may wish to contact the Editor-in-Chief or Science Editor of the journal for additional guidance or information.


Journal of Cheminformatics. We are proud to be associated with a field that has a history longer than most applied computational disciplines; that has elegantly solved so many basic (and not so basic) problems; that has a reputation for intellectual rigor and good-naturedness; that has hundreds of scholarly articles published; and that has impacted fields as diverse as drug discovery, library science and database searching. Every time an HIV patient takes a life-saving protease inhibitor, a synthetic chemist finds a needed journal article through a substructure search, or a medicinal chemist finds a new, promising set of compounds through a virtual screening experiment, they have good reason to thank the practitioners of the field we now call cheminformatics.Welcome to the But therein lies a problem. We have impacted a diverse group of people and domains that defy a single categorization. We have done so with a small, scattered academic presence in very different environments . We only settled on a name for the field less than a decade ago, and we still struggle with its spelling. Much research has been carried out in pharmaceutical companies or with industry support, so is not as visible or accessible as comparable research in related fields such as bioinformatics. Unlike biology, academic chemistry traditionally has a much different scope than industrial and pharmaceutical chemistry.So are we all about Library & Information Science or Computational Drug Discovery? Is our work theoretical or pragmatic? Are our "customers" biologists or chemists? Do we have an academic or industry focus? Historically, the answer to these questions is "both". Those of us who care about the future of this field need to honestly ask whether cheminformatics is a bona-fide discipline in its own right, or whether it is a loose collection of practitioners without a single, definable focus. How we answer this question will determine the approach we should take to research, funding, publication, and education in the future.st century, and we need to find our place in relation to our sister field of bioinformatics. We can no longer point backwards to our prior successes, and potential marginal improvements on our successes, but must as a community prioritize our efforts for the future and change some our strategies for research and education accordingly.We firmly believe that Cheminformatics needs to be centered and cemented as a true, distinct discipline, with explicit funding support, dedicated journals and conferences, more visibility in the academic community, strengthened ties to related fields, and a mechanism to educate the next generation of researchers. To maximize our chances of this happening, we need to be clear about what we can contribute to the world in the future, we need to apply ourselves to some of the grand challenges of the 21We identify four "grand challenge" areas that we think should be an important focus for cheminformatics.After the impressive successes in drug discovery toward the end of the last century, productivity in the pharmaceutical industry has declined as expenses have gone up. Cheminformatics can help by enabling fast, cheap virtual experiments to prioritize real experiments. As more drug discovery research is carried out in academia, institutes and small companies, and solutions will require pieces from cheminformatics, bioinformatics and other disciplines, cheminformatics knowledge and tools should be made as widely available as possible.Global warming and preserving the environment will be one of the biggest challenges for mankind this century. Fundamental to this will be finding chemicals which are less polluting or less toxic to the environment, or improving chemical use to minimize environmental impact . Cheminformatics already has much to offer through computational toxicology and predictive modeling.Chemicals are being found to be increasingly important in cellular functions, for example through small molecule modulators and epigenetics. This has led to fields such as chemical biology, and more recently systems chemistry  and systWe have seen huge leaps forward in the provision of freely accessible chemical databases such as PubChem  and ChemJournal of Cheminformatics is to be a small but significant part in this process. Our name reflects our commitment to cheminformatics as a distinct discipline. Because we are an Open Access journal, our published work is immediately accessible through the web in a form which encourages propagation into other disciplines (such as being referenced in blog entries). We stand on the shoulders of BioMed Central, which contains some of the most highly cited journals in related fields such as Bioinformatics. We are committed to publishing only the highest quality research and insightful opinion that is most relevant to 21st century science.But of course these are just our thoughts. We need a discussion about priorities, and we need high quality research to point us in the right direction. Our aim in launching the Journal of Cheminformatics a vibrant continuation into the 21st century of a very important discipline.So welcome to the journal. In an editorial, we have the luxury of airing grand ideas but they may only be realized through the hard work of authors committed to this vision. So we thank the authors of articles already contributed, and we encourage you to help make the


Writing a research article and getting it published is an appropriate and acceptable means of reporting new information to the scientific community. It is also the stepping stone for the professional career of a research scientist. However, scientific writing is not all that easy! The journey of scientific writing starts with planning and execution of research. Often the experience is not satisfactory. An attempt to publish the research results in a reputed journal is an arduous task for postgraduates and junior faculty members. The quality of manuscripts submitted at Indian Journal of Pharmacology (IJP) and the efforts made in revising them have been a matter of frequent discussion among the editors. We would like to share some of these thoughts which may help the prospective authors. Rarely a manuscript submitted is ‘too good’ to be accepted immediately or ‘too bad’ to be rejected obviously. Most of the manuscripts stand in between ‘too good’ and ‘too bad’. Although peer reviewers provide the scientific opinion about the manuscript, the final decision of acceptance or rejection depends upon the editors. Besides the scientific content, the editors are also concerned about few ‘little things’ which ultimately shape a manuscript for publishing. What are these ‘little things’ that editors look for? The format, novelty of research subject, brevity, language, clarity, message and quality of presentation do matter for the editors.At submission, the editors consider the relevance of the manuscript for the journal and send it to the appropriate reviewers. Articles not relevant to the journal's area of interest are obviously sent back without any external review. While all the original research articles, reviews etc. are always sent for external review, those like case-reports, letter to editor are often reviewed in-house. We have often observed manuscripts having either a long, overstated title along with adjectives and abbreviations or having an unclear, ambiguous meaning. The title should be simple but eye-catchy, brief but convey essence of the study along with important key phrases. The title and the structured abstract should draw the attention of the prospective reader. Avoid including points in the abstract which have not been mentioned in the text.Most of the research articles submitted to IJP follow the IMRAD format aFurther, the editors always look for the novelty of the work. If the research area is novel and of current interest or is involving an uncommon method, unusual study design or an uncommon topic, it certainly generates interest. Editors always look at the manuscript from the readership point of view and judge whether such an article published in the journal, will be useful and interesting to the readers or not? An interventional study or a study providing additional information on economic impact or quality of life would definitely generate interest among readers and editors as compared to the conventional reports. Due consideration is given to a manuscript even with uninteresting or negative results if the topic or methods are instructive and novel. A clear presentation helps reviewers and editors to understand what has been done and this saves their time. The editors match the objectives with concluding remarks and the discrepancies are pointed out, if any. The speculations beyond the results (findings at cellular level and use in human beings) should be avoided.English is an important barrier in writing a manuscript especially if the formal education of the authors has been in vernacular language. However, editors always look for brief and simple words and not really the linguistic expertise. Use of long and complex sentences should be avoided. All that is required is to write simple English with an attempt to inform and educate the readers rather than to impress them. A manuscript with poor language, spelling mistakes or grammatical errors will probably never cause a rejection. But, the amount of revision, rewriting required for accepting that paper will always be considered in making the decision to accept or reject.P  value. Typographical errors and spelling mistakes are considered unprofessional by reviewers and editors. The authors need to take extra care and be consistent with the use of capital letters, abbreviations and spellings. One should also avoid using abbreviations and adjective in the title. The word ‘significant’ should not be used loosely and if used it should be followed by A manuscript which is accurate and concise with a clear message conveyed in a crisp way certainly impresses the editors. Several other factors may be considered by editors before accepting or rejecting a manuscript which is beyond the scope of this editorial to discuss. The ‘little things’ mentioned above are equally important for a good manuscript. These skills need to be cultivated, refined and improved by writing, rewriting and carefully examining the good quality paper paying particular attention to their style rather than just reading the contents. Introduction of scientific communication skills in the post graduate curriculum may help the beginners in this regard.


After publication of this work , we noteFinancial support was provided by the National Modern Meat Caprine Industrial Technology System (nycytx-39), and the Integration and demonstration of foot-and-mouth disease comprehensive prevention and control of national technological support project (2006BAD06A17). Corresponding author is the unique person responsible for these projects.All authors belongs to the same research unit(Lanzhou Veterinary Research Institute), so they have no conflicts of interest.KZ: carried out most of the studies and drafted the manuscript. YS: Study coordination and preparation of the final report. JY, JH: amplified the complete B2L gene. GW: Clinical investigation and sampling. HZ, ZL: consultation. XL: Idea, the leader of the project.All authors read and approved the final manuscript.


Rohrich suggested that the primary role is to represent plastic surgery societies as the “primary source for surgeons to keep current on the latest techniques, trends, and technologies.” Lineaweaver claimed that a journal, independent of any affiliated societies, should present a peer reviewed, selected “finite amount of information at regular intervals.” Both editors speculate on the role of Web-based journalism and mention open access (OA) publishing as a potential avenue for disseminating scientific information.During the past year, 2 of the major plastic surgery journals have published editorials summarizing the various perceived roles of a plastic surgery journal. ePlasty is the embodiment of the OA mission. Our mission statement is the “Open Access Journal of Plastic Surgery…. Committed to the free exchange of knowledge in a global community.” My personal goal in establishing this journal was to bring current scientific information and educational resources to all plastic surgeons throughout the world without the traditional price and transportation barriers  is a paper-restricted system, requires a complex distribution system, and is expensive for readers. Furthermore, authors do the work, write the papers, submit their graphics, illustrations and photos, and then sign over their copyright and licensing control to the publishers. OA publishing breaks down price barriers, allowing “free availability and unrestricted use” (open access overview). TP is costly to libraries and potential readers and establishes price barriers to access scientific literature  and permission barriers (licensing and copyright limitations). OA publishing is Internet based, allowing immediate worldwide availability of publications. TP literature is paper bound and distribution is limited depending on the mail system in place. This may be relatively efficient if mailed within one country's postal boundaries (3–7 days). However, international mailing can delay delivery for weeks to months , Bethesda (June 2003), and Berlin (October 2003) form the common ground of the OA movement. The Budapest convention stated:There are many degrees and kinds of wider and easier access to this literature. By “Open Access” to this literature, we mean its free availability on the public internet, permitting any users to read, download, copy, distribute, print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself. The only constraint on reproduction and distribution, and the only role for copyright in this domain, should be to give authors control over the integrity of their work and the right to be properly acknowledged and cited.The Bethesda and the Berlin conferences stated that in OA publishing authors hold the copyright and must agree in advance to let readers “copy, use, distribute, transmit and display the work publicly and to make and distribute derivative works in any digital medium for any reasonable purpose, subject to proper attribution of authorship.” The importance of a free exchange of scholarly work is now recognized by the National Institutes of Health (NIH), which instituted a mandatory public access policy in April 2008. The NIH policy requiresthat 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.Both publishing systems require revenue to operate. However, the primary difference between OA and TP is that revenue in the OA system is not a barrier to readers. Authors publish their work in OA journals such as ePlasty without monetary expectation. Suber refers to this as “royalty-free literature.” Plastic surgeons do not write articles for dollars, but are motivated to advance knowledge accompanied by the expectation of prestige and career advancement. It is important to realize the OA literature is not free to produce or publish; it simply removes the price barriers to readers. Revenue is a requirement and various OA journals have adopted different models to raise operating funds. Some charge authors to publish. ePlasty has created an Exhibit Hall where sponsors can place multimedia descriptions of their products, link to their own Web sites, and exhibit much the same as they would at a large meeting. The Exhibit Hall has the potential to evolve into an industry-based depot of product descriptions and technical instructions, as well as a vehicle for introducing new technology.Three major OA initiatives in ePlasty has elected to have an educational section extrinsic to the peer-reviewed journal. In the Education Section interesting cases, lectures, and multimedia presentations will be available to readers at no charge. A portion of this section will be devoted to program directors to facilitate their work. The CORE curriculum will evolve into a free “living textbook” of the essential knowledge base of plastic surgery. Additional free “living texts” will be introduced on other specific topics as well. In addition to all of these educational features, an interactive Forum is available for direct interchange of ideas, concepts, and questions. All of this is to promote a free exchange of knowledge for all plastic surgeons.The OA model provides for a repository of ideas, concepts, and all sorts of educational materials. ePlasty. All are invited to participate.Medical publishing has slowly evolved over 400 years to its current TP mode; that is, until now. The digital era is upon us and OA literature is burgeoning due to the ability and need to share knowledge, experience, and expertise at a global level without the traditional constraints. The survival of our specialty is going to depend on the immediate free access by all plastic surgeons to the vast scholarly literature and wide array of educational resources. The worldwide community of plastic surgeons now has an OA vehicle in


As open access grows in prominence, so too has confusion about what open access means; such confusion arises from a genuine misunderstanding of open access by funders, authors, editors, and publishers alike. PLoS Biology was launched, there has been a spectacular growth in “open-access” journals. The Directory of Open Access Journals (http://www.doaj.org/), hosted by Lund University Libraries, lists 2,816 open-access journals as this article goes to press (and probably more by the time you read this). Authors also have various “open-access” options within existing subscription journals offered by traditional publishers . In return for a fee to the publisher, an author's individual article is made freely available and (sometimes) deposited in PubMed Central (PMC). But, as open access grows in prominence, so too has confusion about what open access means, particularly with regard to unrestricted use of content—which true open access allows. This confusion is being promulgated by journal publishers at the expense of authors and funding agencies wanting to support open access.Since 2003, when http://ukpmc.ac.uk/), a free digital archive of biomedical and life sciences journal literature, which aims to mirror that created and hosted by the National Institutes of Health in the United States . European funding agencies are already responding to this resource. For example, within the United Kingdom, the Medical Research Council, the Department of Health, the British Heart Foundation, and Cancer Research UK all now require their grant holders to make their research articles available in UKPMC as soon as possible (and no later than six months) after publication. (Regular updates on open-access mandates and policies are available at http://www.eprints.org/openaccess/policysignup/).Research funding agencies have been instrumental in driving the change toward open-access publishing. Many agencies now require the researchers they fund to make their articles freely available on publication, or within 6 or 12 months of publication , use it for educational purposes —permits derivative reuse, as long as the author is correctly cited and attributed for the work. It is the most liberal of the available Creative Commons licenses (there are six), which are now applied widely to books, music, videos, etc., as well as scholarly works. It is important to note that of the six different Creative Commons licenses, only those that permit unrestricted derivative use  truly equate with open access.All these initiatives signal the ongoing transition from subscription-based to open-access publishing of the scholarly research. It seems we are finally witnessing a sea change in scientific communication. But with this welcome trend comes a more insidious one to obscure the true meaning of open access by confusing it with free access. As the original Bethesda definition makes clear  Box 1),,Box 1), s , or, mohttp://www.earlham.edu/~peters/fos/bethesda.htm.This is taken from 1 is one that meets the following two conditions:An Open Access Publication2, as well as the right to make small numbers of printed copies for their personal use.The author(s) and copyright holder(s) grant(s) to all users a free, irrevocable, worldwide, perpetual right of access to, and a license to copy, use, distribute, transmit and display the work publicly and to make and distribute derivative works, in any digital medium for any responsible purpose, subject to proper attribution of authorshipA complete version of the work and all supplemental materials, including a copy of the permission as stated above, in a suitable standard electronic format is deposited immediately upon initial publication in at least one online repository that is supported by an academic institution, scholarly society, government agency, or other well-established organization that seeks to enable open access, unrestricted distribution, interoperability, and long-term archiving .1Open access is a property of individual works, not necessarily journals or publishers.2Community standards, rather than copyright law, will continue to provide the mechanism for enforcement of proper attribution and responsible use of the published work, as they do now.New York Times science writer Carl Zimmer demonstrated the distinction succinctly . He disc“Compare Shelley's experience to what I'm about to do. I'm going to—shudder—reprint a diagram from a journal. Just lift it straight out. ….And what do I now hear from PLOS? Do I hear the grinding of lawyerly knives? No. I hear the blissful silence of Open Access, a slowly-spreading trend in the journal world. PLOS makes it very clear on their web site that “everything we publish is freely available online throughout the world, for you to read, download, copy, distribute, and use (with attribution) any way you wish.” No muss, no fuss. If I want to blog about this paper right now, I can grab a relevant image right now from it. In fact, I just did.” Subsequent to an outcry within the blogoshpere , Wiley Molecular Systems Biology. This is listed as an open-access journal by the DOAJ and published by the Nature Publishing Group. On the journal website (http://www.nature.com/msb/index.html), there is a prominent link in the left hand column titled “open access.” Here, you are informed that the journal “makes primary research freely available to all researchers worldwide, ensuring maximum dissemination of content through the nature.com platform.” The publisher charges a publication fee (like PLoS) and publishes their content under a Creative Commons license . But that's where the similarities end. The Creative Commons license used is actually very different, despite the fact that at the bottom of the HTML version of any of their articles, there is a statement that the article is licensed under the “Attribution” license. However, when you click through to the full version, you are presented with the most restrictive Creative Commons license available, the “Attribution-Noncommercial-No Derivative Works” license. The article can still be downloaded and redistributed , but permission from the publisher is required for any additional derivative use . Of these, PLoS Biology, BMC Biology, and Nucleic Acids Research conform to open access, as defined by the Bethesda Statement (PLoS Biology and BMC Biology apply the Creative Commons “Attribution” (by) license to their articles, whereas Nucleic Acids Research applies the Creative Commons “Attribution Non-commercial” (by-nc) license.Four of the five journals, whose license statements are listed below, use a Creative Commons license  license.Proceedings of the National Academy of Sciences (PNAS) does not use a Creative Commons license, but they do have a free access option. Their articles can be used for a wide range of purposes without permission, but the creation of derivative works is still restricted so this option is also not open access.The journal Open Access (Permits Unrestricted Derivative Use):PLoS Biology (http://plosbiology.org)Copyright: © 2007 Jetz et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.BMC Biology © 2007 Hoffman and Goodisman; licensee BioMed Central Ltd.http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.This is an Open Access article distributed under the terms of the Creative Commons Attribution License  © 2007 The Author(s)http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (Free Access (Does Not Permit Unrestricted Derivative Use):Molecular Systems Biology (http://www.nature.com/msb/index.html)This license does not permit commercial exploitation or the creation of derivative works without specific permission.This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits distribution, and reproduction in any medium, provided the original author and source are credited. © 2007 EMBO and Nature Publishing Group All rights reserved (on the pdf).PNAS (http://www.pnas.org/)Freely available online through the PNAS open access option.© 2007 by The National Academy of Sciences of the USA.Some journals do not claim to be fully open access but provide an “open-access option” that permits articles to be deposited in PMC and thus conforms to the minimum guidelines set by, e.g., the Wellcome Trust. But confusion abounds here as well. If you search various journal sites for “open-access” options, you'll find it enormously difficult to obtain clearly labeled information describing how you can use the article. Often an article is free to read, and has been deposited in the US PMC, but it's not clear from the terms on the article that it can be distributed freely to others or reused without explicit permission from the appropriate permissions department. Again, this is not open access.Journal of Biological Chemistry (JBC). The JBC website states that it is an “open-access” journal and that their publisher—the American Society for Biochemistry and Molecular Biology (ASBMB)—is an “open-access” publisher (http://www.jbc.org/misc/JBC_Open_Access.shtml). They don't charge a publication fee as such but do have page charges like many traditional journals (US$75 per published page). What you actually find is that manuscripts that are currently in press are available for free but those published in the current issue are not. On the table of contents of the current issue, there is a helpful permissions button next to each article that links to a webpage that helps you calculate the charges for different uses (even for posting on the internet). It is unclear how this qualifies as open access.A particularly befuddling example comes from the Does the distinction between free and open access really matter if anyone can read the article for free? Isn't open access just about making the literature available? Well, yes and no. Free access is certainly important, but it's only the starting point. At least of equal importance is the potential for innovation. We don't know yet what innovation means with regards to the full text of an article—who could have predicted the impact GenBank would have or the uses that sequences are now being put to? As one colleague put it, free access is like giving a child a Lego car and telling her that she can look at it, perhaps touch it, but certainly not take it apart and make an airplane from it. The full potential of the work cannot be realized .http://ukpmc.ac.uk/ppmc-localhtml/not_in_ukpmc.html). It's hard to understand the reasoning for this limitation—after all, the articles are freely available from the US site. But what's disturbing is that publishers can act like this because the articles themselves are not truly open access—who knows what further restrictions might be placed on these articles in the future.What's worrying is that there are already examples of publishers restricting use of their “free-access” articles, even in international repositories. For example, some of the publishers that currently allow their articles to be deposited in the US PMC will not allow those same articles to be mirrored and made available from the UK site ; much arises from a genuine misunderstanding of open access by funders, authors, editors, and publishers alike. However, no matter how unintentional such obfuscation might be, it is detrimental to the free exchange and use of scholarly research. It is now time for all publishers to tighten the definition and application of open access and be clearer about the uses and restrictions applied to their articles. Open access is a term that should only be used when the license permits both free access and unrestricted derivative use (and gives appropriate attribution). Authors and funders need to be much more aware of the small print before inadvertently signing away their rights and those of their readers and, even worse, paying good money for the privilege.—the “Lego factor.” If certain work is not included in these resources because of restrictive license agreements, authors will probably pay much closer attention to the claim that a publisher is “open access.” Enlightened self-interest can be a powerful force.Perhaps the real key to establishing a broad consensus around the meaning of open access will be the development of resources that demonstrate the potential of unrestricted reuse of the literature