The way science and research is done is rapidly becoming more open and collaborative. The traditional way of publishing new findings in journals is becoming increasingly outdated and no longer serves the needs of much of science. Whilst preprints can bring significant benefits of removing delay and selection, they do not go far enough if simply implemented alongside the existing journal system. We propose that we need a new approach, an Open Science Platform, that takes the benefits of preprints but adds formal, invited, and transparent post-publication peer review. This bypasses the problems of the current journal system and, in doing so, moves the evaluation of research and researchers away from the journal-based Impact Factor and towards a fairer system of article-based qualitative and quantitative indicators. In the long term, it should be irrelevant where a researcher publishes their findings. What is important is that research is shared and made available without delay within a framework that encourages quality standards and requires all players in the research community to work as collaborators. The way science and research is done is evolving rapidly. The change is characterised by more open, collaborative and networked ways of sharing information and making discoveries. This change is being driven by recognition of the profound benefits to the pace of scientific progress that can be brought by collaboration and ready exchange of ideas between and beyond disciplines and sectors. Furthermore, technology can now enable and support collaboration, information sharing and rapid data exchange and analysis. To make science more efficient, we need to remove the waste in the current system, as exemplified by ongoing debates concerning research duplication and the growing doubts about the reproducibility of findings.The goal for open science is to accelerate scientific progress and to turn what is discovered into benefits for all. An essential part of this is to ensure that scientific findings are open and available for scrutiny, rapidly accessible, and easily discoverable for others to use and build upon. The way research findings are currently made available – through journals – is increasingly at odds with the aspirations of open science.2. The current publishing processes bring many problems that are not conducive to the progress of science. These include:There is some recognition amongst the research community that journals are now an outdated method for publishing new research findings and no longer serve the needs of much science•Holding up science. The selection process that journals run to help them decide what to accept is typically done before publication, and hence leads to a delay in the availability of new findings to those who need them3. There are no obvious benefits of such a delay, and indeed it can sometimes cause significant damage when the health of patients are affected4.•Non-transparent. The peer review scheme used by most journals is anonymous . Its current main function is usually to help editors make decisions on what to publish and what to reject, rather than to help the authors improve their article. Furthermore, the readers do not get the benefit of the insight on any outstanding issues the referees may have identified with the article along the way. In a competitive research environment, these non-transparent schemes can lead to abuse of the system in a variety of different ways6 and there is little to stop this from happening.•Much science never shared. Many findings are currently not published , which often leads to significant research waste and potential publication bias9. This is often caused by the fact that journals, in order to maintain their Impact Factor, are keen to attract submissions that bring in more citations10.•Waste in the system. There is significant waste in the publishing system caused by articles moving from journal to journal until they find somewhere that will accept to publish the article. This brings inefficiencies in the system and wasted effort both for the authors and for the referees in repeated refereeing.•Too expensive. Most new scientific findings are still published in subscription journals that are usually expensive. This means that a large proportion of the community (researchers and the public) cannot access the research12. Open access journals certainly enable everyone to have access but their Article Processing Charges are still often very high13. So-called hybrid journals  are even worse, because they create extra costs for the information exchange system and significantly slow the growth of fully open access journals.17, or of the potential of the author(s) as researchers18.Which journal an article is published in is still commonly used as a surrogate quality measure for an individual article and its authors. However, it is well established that such use, specifically of a journal’s Impact Factor (JIF), is an inappropriate and misleading indicator of either the importance and/or quality of a specific articlePubMed  and/orGoogle Scholar,Scopus,Web of Science etc., to help researchers find new articles in an area of interest. Journals survive primarily because they are needed by authors to get the reflected benefit of the JIF. One of the challenges for the future is to develop reliable and effective qualitative assessment of both research articles and an individual researcher’s scientific output.The reality is that journals are not essential anymore (though sometimes useful) for the discovery of research results. Much more efficient tools and services can and are being developed using the information in citation databases such asA new way of publishing, discussing and reviewing new scientific findings is urgently needed to speed up the progression of science, and to improve the fairness of the system used to judge researchers with regards to their next grant or career move. Such a new system should also enable funders to maximise the value of their research investment. The technology to enable such a change is now available. This new approach needs to avoid the significant delays in making new findings visible, and needs to be efficient, easy to use and not expensive.In our view, and as we outline further below, such a new process would only work if driven by the authors within a scientific framework that facilitates self-regulation. There needs to be a generally agreed set of ethical and technical rules, and these should be overseen by bodies directly representing researchers, such as funders, institutions, organisations and societies.21. One of the features of preprints is that authors remain completely in control and no formal refereeing is required. The culture of using preprint servers in physics (arXiv) has established itself well without structured refereeing. It is surprising that preprints and journals have survived alongside each other for so long, and that authors still feel the need to have the preprint converted into an article published in a journal, even though all who need to have already accessed the article from the preprint server. It seems that even here, where the article is published can have a significant impact on the prospects of the authors’ career. This perhaps illustrates the powerful hold that journals and JIFs have on researchers’ careers. Preprints, even when used widely, may not remove this dependence.One idea currently being discussed is the much wider use of preprints in the life sciences, i.e. the online posting of an article to make it openly visible and citable prior to peer reviewPeerJ PrePrints andBioRxiv, the overall use of preprints to-date in the life sciences is still not in significantly large numbers . There have been several attempts to encourage the use of preprint servers, but none has really taken off. In the early days of open access back in the late 1990s, the idea had been to start with a preprint server, but there was such strong objection from some members of the PubMed Central (PMC) National Advisory Committee in its first meeting22, that a decision was taken not to accept preprints. The prevailing culture within the research community at the time was not to recognise preprints as a formal output, and it is not clear how different the culture really is now.Despite a modest increase in the use of preprints in life sciences recently with the launch ofThere are many benefits to authors and to the community of using preprint servers as part of the mix of options in publishing life science research articles. Perhaps most important is the immediacy of placing research findings on public record . Preprints can also be used to gather informal comments from colleagues on possible problems and potential improvements before committing to the non-transparent refereeing as operated by most journals. But preprints solve only some of the problems outlined earlier, and technology now enables us to do much more with findings at the stage that researchers are willing to share them.Many questions have yet to be answered about the adoption of preprints in the life sciences. Among them:•Will a significant proportion of authors opt to post preprints?•Will enough colleagues and other researchers comment openly  on articles posted there, to make the effort useful? A quick review of a randomly selected block of 100 articles posted on BioRxiv in June/July 2015 (so over 6 months ago to ensure time to receive comments) showed that there were only two preprints in that selection that had any external comments, each being back and forth with a single commenter.•Will subsequent formal submission to a journal and progress through the lengthy process of official peer review as currently operated by journals still be required, thereby retaining many of the problems outlined earlier?F1000Research) is described below.What we propose here is a scheme that takes full advantage of the benefits that preprints can bring, combined with a new type of invited, formal transparent peer review that differs significantly from the one currently run by most journals, both in its goals and in its processes. The description of this scheme . They can also enable collaborative authoring , and provide formatting tools to simplify the process of structuring an article to ensure all the necessary underlying information has been captured . Submission for posting as a preprint, and/or for formal publication and peer review, should be as simple as a single click.Initial objective checks. We envisage that all submitted articles should be rapidly screened against a set of objective criteria. Such criteria might include checks for obvious non-scientific content, readability, ensuring the work is not plagiarised, that it meets standard ethical requirements, and that the underlying data has been supplied together with detailed methods. They could also include other specifics as agreed by the relevant communities depending on, for example, the type of experimental study being described. The specifics of these checks should be listed transparently.FAIR  data. The need for an open data policy seems undisputable to us: the data underlying the findings presented in the article should be openly accessible, together with information on how the data were analysed such as the software used etc., so that users can fully scrutinise the presented findings and repeat the work, if they wish. The data and any code should be in a form that can be used by the referees and readers, together with detailed methods as to how it was generated. They need to be stored in approved repositories that meet a minimum set of criteria to ensure long-term availability and persistence, with appropriate levels of protection for sensitive data. How much and what data to provide is a highly complex issue and will require specific instructions to be developed by the relevant communities, together with more generalised requirements on data format, structure and associated metadata. There are numerous groups working collaboratively worldwide on these many issues such as theData Fairport Initiative,FORCE11,Research Data Alliance and others.Publication. Any submitted article that passes these rapid checks would then be published (made public) immediately, given a unique identifier (making them permanently citable) and clearly labelled as not yet peer reviewed. Following the initial screening, we think it is important that there is no editorial decision on accepting or rejecting research articles, to remove the inherent biases in having a single Editor making a decision on behalf of the rest of the community, and to help to remove publication bias.Identifying referees. In order to facilitate communication between peers without the interference of editors, and to ensure peer review is carried out by qualified experts, we envisage that authors should select referees from a large community of recognised experts , as long as they abide by a clear set of transparent rules and criteria on how to select suitable referees. Both authors and referees should also transparently declare any conflicts they have with each other or the work being refereed.F1000 Faculty. It would seem that there should be greater collaboration across the key stakeholders involved in research  to work together to resolve these issues.Questions remain around how this community should be defined. Should a database (growing and changing) be created of ‘approved referees’? How does someone qualify to be included in this community of approved referees? How will this database grow, and who will control it? For example, it could comprise grantees of major granting bodies with some minimum experience/publication record. Or it could be constructed like a large virtual faculty like theThe peer review process. Referees should then be invited as requests from the authors, but mediated by the platform. Without the need to select for impact, the peer review process can refocus on its basic goal to help the authors improve their work and to provide valuable context and feedback on the viability and quality of the published research for the reader and for anyone reviewing the work of that individual.Referees should be given a set of clear instructions and guidance on what aspects of the article to assess and what is expected in a referee report (as common practice today). Referees should also be able to benefit from tools similar to those provided to authors, to make the writing of the report more efficient. With the publication of new types of findings, there is an interesting question about whether all findings need to be refereed . There are also many questions about what types of aspects of an article can a referee sensibly be expected to check within a reasonable timeframe, especially with regards to data, code and figures. Should peer review differ for different types of findings?23, but should this always be the same irrespective of the type of finding?Given the open questions about what level of peer review should be required for different article types and for data and software, there are also questions around what constitutes an article being ‘peer reviewed’. PubMed has developed criteria for F1000Research and future publishing platforms25. The authors would drive the process via the platform provider, so that they can engage in open discussion with the referees and can revise their article and publish new findings as and when they feel appropriate. This process should continue until the authors wish to stop. All versions need to be independently citable but connected, and a dynamic citation26 can be used to ensure the reader is always clear about the article version and its peer review status. In addition to formal refereeing, any researcher should be able to openly comment and discuss an article in a transparent way, although this should not impact the formal peer review status of the article.We think it is very important that all peer review reports are published transparently alongside the name of the referee – open peer review has been repeatedly shown to be of comparable (if not better) quality, and also often more constructive compared with closed peer reviewBenefits for referees. Referees currently receive very little direct benefit from the process of refereeing and their contribution is currently not visible. We believe referees should receive real benefits for contributing to what is a crucial function in improving the work of others. Referee reports should receive their own persistent identifier  and therefore be independently citable which means that referees can receive their own metrics. Refereeing can now be included as a formal contribution onPublons and on ORCID profiles27 , and we would urge institutions and funders to lay out an expectation , for their grantees to contribute to this important process. Are there other forms of credit that referees could receive for their important role? Should ways be developed to qualitatively assess the work of referees?Access and cost. All articles should be published (made visible and citable) using immediate open access so that everyone has equal access to new findings. The cost of running the process described above is considerably cheaper than the traditional process as it removes the substantial costs associated with editorial decision making. There are of course still costs involved in running the peer review process, conducting the initial set of checks, and building and maintaining the tools required to operate such a system. These cheaper costs would still be covered as now by research funders, and competition between service providers should put further downward pressure on these costs. Where there is no research funding, there needs to be further consideration across all stakeholders as to how best to cover the modest fees, whether through institutional funds or other sources.It remains important that there are indicators of the value, importance, use and re-use of research findings and data. Research outputs, in all their forms, are valuable indicators of research and knowledge progression, as well as of the ‘performance’ and productivity of scientific fields and of the researchers who are generating those outputs. Such indicators are also vital for users of research findings, such as health professionals and policy makers, to help get relevant research findings into policy and practice more effectively and without unnecessary delay.28. The Leiden Manifesto29 recently emphasised the importance of combining quantitative and qualitative indicators in assuring a balanced and robust conclusion about the value of specific research. Furthermore, the selection of indicators that are used in any assessment should be tailored according to the purpose of the assessment. We should all seize the opportunity of working in a different publishing system to respond to recommendations such as those in the Manifesto, and redress our reliance on erroneous and misleading measures of research quality. Improvements in our ability to identify, track and analyse the outputs means that we can also shift our emphasis away from a reliance on ‘metrics’ based solely around the academic citation of a research paper and its hosting journal (e.g. JIF), as supported by signatories of DORA30.The indicators that are adopted to provide a view on research must be meaningful, contextualised and used responsibly31, remembering that citation-based measures take considerable time, which may be an issue particularly for younger researchers. Post-publication identification of interest and importance of an article, and commentary about the context and potential implications of the findings should become a key aspect of science journals in the future, and could of course play a role in this qualitative assessment of research.Open peer review can play an important part in this, as researchers can gain visibility and credit for their contribution to the progression of another’s work. Furthermore, transparent refereeing provides researchers, and potential users of research, with another marker of quality as a peer reviewer’s credentials and what they say about a piece of research can become part of the assessment – instead of hidden and lost from the public record. A more appropriate use of citation-based indicators should also be included in measuring quality, such as the Relative Citation Ratio (RCR) recently proposed by the NIHF1000Prime,PubMed Commons etc).It is, of course, not usually possible to predict the longer term impact or consequence of a new discovery at the time of publication and refereeing , and so it remains important that reflections on the significance of research can be done at any time in the future , with tools to assist in writing in F1000Workspace, and some measures of qualitative assessment of published articles through F1000Prime, both to inform reading and to help assess new findings after publication. Many other publishers have begun to create similar platforms that would compete to provide such services to researchers and funders.However, a widespread change to a new way of publishing is unlikely to happen whilst the research community relies primarily on journals to provide the outlet for research findings. We therefore propose that to enable open science to succeed, researchers should be able to publish any research data and findings that they consider to be useful to others and to publish it without delay. To achieve this, we believe that there needs to be a fundamental shift in the way research findings are shared.Nature magazine’s News & Views section orCurrent Biology’s Dispatches. Funders are perfectly placed to help drive this shift by approving those providers that offer a high quality service that meet the agreed requirements. In time (as with open access), we anticipate that making research findings and data available in this open science way will ultimately become the norm and a requirement of all public funders. Researchers would then be free to choose whichever of the approved services they prefer, and articles would also be available to all on mirrored repositories , together with all their versions, referee reports and others comments, and the supporting data.Publishers and others can support this process by providing services that meet a community-agreed set of rules (such as those suggested above); competition between providers will naturally lead to improved services and reduced costs. Meanwhile, journals could begin to provide qualitative assessment and to encourage discussion of findings published on these platforms, for example likeIn the long term, it should be irrelevant where researchers publish their findings. What is important is that to speed up scientific progress, discovery and impact, research should be shared and made available without delay for others to use and to build upon. Making findings available needs to be done within a framework that encourages quality standards and requires all players in the research community to work as collaborators. The printing press, the disruptive technology of 400 years ago, revolutionized how science was communicated. Journals, along with editors and reviewers—the peer review process--eventually replaced an author-directed process of letter writing. A new disruptive technology has placed us in the midst of another revolution in communication. The power of the internet has enabled communication with a rapidity, connectivity and interactiveness unlike anything possible with print media. It therefore behooves the research community to rethink how the science communication process might be structured.st century life, the internet has enabled the elimination of intermediaries between the end consumer and the producer. Are we at a similar stage for publications?Tracz and Lawrence present to us their rethinking. They consider journals to be an outdated mechanism for publishing science and they enumerate the multiple problems familiar to researchers—the delay, the non-transparency, the tussles with reviewers and editors, the jockeying for high-impact journals. Tracz and Lawrence ask if journals are really necessary anymore. In so many other areas of 21Tracz and Lawrence propose an Open Science Platform that enables authors to publish essentially immediately after they consider their work ready to be shared with the scientific community. The work is then subjected to a post-publication review process which is transparent because the reviewers are not anonymous and their critiques as well as the authors responses are posted as an integral part of the publication process.A key issue is how the reviewers will be selected. Tracz and Lawrence propose that the authors be empowered to select and invite reviewers from a pool of qualified researchers. Of course, this shifts the question to how the reviewers become qualified and who makes this decision. The authors suggest that a virtual faculty such as that of F1000 could serve this function. Researchers would be incentivized to deliver thoughtful reviews not only because they would be identified but because their reviews would be citable documents in their own right. This would provide a benefit to reviewers which is lacking in the current system.  A question that will spring to the lips of every researcher is how, in such a system, will we find the important publications. Tracz and Lawrence say that, in the long run, it should be irrelevant where authors publish their findings. But there are so many publications and so little time. Don’t journals with their editorial boards serve as key gatekeepers? Doesn’t the much-maligned impact factor nevertheless serve as a helpful guide? The Open Access movement has greatly facilitated the dissemination of research results but it has had the unintended consequence of also facilitating the emergence of predatory journals whose business model is to provide publication for pay with only the appearance, not the reality, of bona fide editorial quality control. This only compounds the problem.Indicators of the importance of publications will remain necessary. The Open Science Platform does not, per se, provide the indicators but it does provide a framework in which quantitative and qualitative metrics of importance such as citations, downloads, blogs and commentary can be incorporated into the platform. In principle, these article-based metrics can be made discoverable and substitute for the classic journal gatekeepers.st century and there is no turning back.Tracz and Lawrence have done the research community a service by proposing this bold, new Open Science Platform. Apprehensions aside, we have crossed into the 21I have read this submission. I believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. This article outlines a new model to making scientific findings public. It argues that typical journal publishing processes are no longer fit for purpose and discusses pros and cons of preprints, before describing "Open Science Platform". The article is very timely given the latest discussions around preprints in biology, stimulated by Ron Vale's preprint, then article on the subject (Ref. 19 in this article).Open Science Platform is in essence a nose-to-tail set of services that enable researchers to collaboratively write, publish, openly peer review, revise, credit, evaluate and archive scientific articles with minimal friction. The philosophy is that anything we think would be useful to publish should be published, and we will organize this bulk by devising better filtering/discovery mechanisms and reward systems post publication. While quite a few journals have touched many parts of this particular elephant, there is not to my knowledge an existing public platform that offers all these steps aside from the one described here. F1000 has developed such a platform, but the authors note that many other publishers are probably also building similar platforms to provide some healthy competition on the services provided.I have no major criticisms of the article itself - it is not overly pushing a particular (F1000) product but rather painting a picture of what open science publishing might look like, reviewing challenges and possible solutions to the sub-optimal aspects of our current publishing systems. Frequent reference is made to many of the on-going efforts in this area and the authors clearly state their roles at F1000.An important issue that was given only brief attention is the matter of data and other research objects associated with articles. Open science extends to many aspects other than article publishing. The authors acknowledged that data underling assertions in articles are critical, as is the need to deposit data in community-supported repositories with data-appropriate access, but delegates this particular challenge to other groups. Clearly research communities and resources need to lead from different angles - but nevertheless in a more rapid and expansive publishing mode, new mechanisms will be required to ensure rigour, and support the desired behaviour around data deposition and archiving. One of the key points of open science is to enable reuse of data and other outputs in other contexts. Therefore an open science platform for articles will need to operate in a well-coordinated fashion with data archives and processes to ensure that the gains in article publishing also apply to related data and other research objects (and the emerging credit systems for those too).One aspect I would have liked to have seen the authors explore more is the fundamental matter of how to stimulate uptake of open science platforms by the key target audience: researchers. The technical challenges are tractable, the social ones the blocker. For many researchers, deeply engaged in their work at the bench, such open science systems are a long way from current operating practices, so adoption may take a while and many incentives along the way required.I have read this submission. I believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.


Genes and Environment unique in the Asian environmental mutagen research community.Genes and Environment is now at the start of a new era of publication as an open access journal. I believe that open access publication marks a turning point that will make  Genes and Environment is at the start of a new era of publication as an open access journal. The transformation of Genes and Environment, the official journal of the Japanese Environmental Mutagen Society (JEMS), to open access is the beginning of a great epoch for JEMS. I would like to especially thank Dr. Takashi Yagi Editor-in-Chief, for his tireless efforts in this process, which was planned in May 2014 by the Editorial Committee. After discussions among Editorial Committee members and Council members, JEMS chose BioMed Central as the journal’s open access publisher. Articles in Genes and Environment are now accessible via the journal’s homepage at BioMed Central, and previous content can be accessed on the JEMS homepage.In 2015 Genes and Environment has published many outstanding articles in the field of mutation research, including articles on the mechanisms by which environmental agents induce mutations. I believe that open access publication marks a turning point that will make Genes and Environment unique in the Asian environmental mutagen research community. Asian countries share issues that need to be resolved; for example, the people of Asia are concerned that diseases such as cancers may be caused by agents in environmental media such as the air or water, or in food, and this concern will be an important topic in the new Genes and Environment.Genes and Environment into a mainstream journal in the field of mutation research. All mutation researchers are invited to submit their latest manuscripts to Genes and Environment.JEMS plans for growing


Regenerative Medicine Research. In this open access, online journal, we aim to publish research relating to both the fundamental and practical aspects of regenerative medicine, with a particular emphasis on translational research.I am, as an Editor-in-Chief joining BioMed Central, so excited to announce the launch of a new biomedical journal, Regenerative medicine is an emerging field with the potential to empower medical research and practice. The process of tissue regeneration is essential to many organisms for a healthy life, from the highly studied axolotl, to us as human beings. In many ways regenerative medicine has become the leading edge of biomedical research and clinical practice, due to its key implications for the treatment of increasingly prevalent diseases, such as heart disease.Regenerative Medicine Research takes place.The field is in the infant stage of its development but it is growing at an impressively fast pace. For instance, based on a PubMed search, there were less than 200 articles relating to regenerative medicine published in 2002, but more than 3,000 articles published in 2012. However, comprehensive information or research data on regenerative medicine cannot presently be efficiently gathered, but can only be scrutinized through a diversity of different journals in various fields. Regenerative medicine is, by current definition, the process of creating living, functional tissues to repair or replace tissue or organ function lost due to age, disease, damage, or congenital defects [et al.[et al.[et al. [We hope to publish articles that shed light on the signalling pathways involved in cell/tissue regeneration, as well as those that address how biomaterials and stem cells can be adapted or integrated into the failing organ system. Two of the first articles published in the journal today focus on the effects of chronic alcohol consumption on tissue repair and regeneration; Dekeyser et al. study thl.[et al. look at .[et al.  provide Regenerative Medicine Research are made rapidly available online following acceptance. This ensures efficient dissemination of information and experimental data to scientific communities and the medical practice field. Furthermore, a highly respected Editorial Board composed of internationally well-recognized experts in the field facilitates a fair, timely and rigorous peer review process.As an open access journal, articles accepted for publication in Regenerative Medicine Research a preeminent platform for exchanging research protocols and experimental data in this exciting, emerging field. We look forward to receiving your high quality contributions to the journal.The Editorial Board, Publisher, and myself assure the authors and readers that we are committed to making


In the present issue of Theoretical Biology and Medical Modelling (TBioMed), it is a pleasure to present you a selection of 8 extended versions of selected papers from the International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2013) held in Granada (Spain) during March 18-20, 2013. IWBBIO 2013 seeks to provide a discussion forum for scientists, engineers, educators and students about the latest ideas and realizations in the foundations, theory, models and applications for interdisciplinary and multidisciplinary research encompassing disciplines of computer science, mathematics, statistics, biology, bioinformatics, and biomedicine. The aims of IWBBIO 2013 is to create a friendly environment that could lead to the establishment or strengthening of scientific collaborations and exchanges among attendees, and therefore, IWBBIO 2013 solicited high-quality original research papers (including significant work-in-progress) on any aspect of Bioinformatics, Biomedicine and Biomedical Engineering.New computational techniques and methods in machine learning, data mining, text analysis, pattern recognition, data integration, genomics and evolution, next generation sequencing data, protein and RNA structure, protein function and proteomics, medical informatics and translational bioinformatics, computational systems biology, modelling and simulation and their application in the life science domain, biomedicine and biomedical engineering were especially encouraged.At the end of the submission process of IWBBIO 2013, and after a careful peer review and evaluation process , 122 papers were accepted for oral or poster presentation, according to the recommendations of reviewers and the authors' preferences.A number of authors were invited to submit an extended version of their conference paper to be considered for special publication in this issue of Theoretical Biology and Medical Modelling (TBioMed). These authors were selected after the recommendation of the reviewers of the conference papers, the opinion of the chairs of the different sessions and the guest editors. The extended versions were again carefully reviewed by at least two independent and anonymous experts and the accepted papers, after this new review process, are presented in this issue.The first paper by Jose J. Castro et al.  proposesThe paper by J. Zyla et al.  has as tThe paper titled “A flowgraph model for bladder carcinoma” , focusesIn the paper titled “Improvement of Design of a Surgical Interface using an Eye Tracking Device” , the autThe paper by Alfredo Benso et al.  presentsThe paper by José Carlos Santos et al.  presentsIn the paper titled “Application of genetic algorithms and constructive neural networks for the analysis of microarray cancer data” , the autFinally, the last selected paper titled “Pathway landscapes and epigenetic regulation in breast cancer and melanoma cell lines”  performsThe Guest Editors would like to express their gratitude to all the contributing authors for their submissions and to the anonymous reviewers for their comments and useful suggestions in order to improve the quality of the papers. They would also like to express their gratitude to Hiroshi Nishiura, Edward Rietman and Rongling Wu, Editors-in-Chief of Theoretical Biology and Medical Modelling (TBioMed), for providing the opportunity to publish this set of selected papers in the present issue. Finally, they are also very thankful to Chantal Stilwell, Assistant Project Manager for Supplements of this journal, for thoroughly helping with the edition and publication of this special issue.http://iwbbio.ugr.es.It is a pleasure for us to invite all authors and interested readers of this issue to future IWBBIO conferences, which will be announced at The authors of this introductory article and guest editors of the special issue declare that they have no competing interests.


Plain English summaries (PESs) are a valuable tool for making research findings available and accessible to patients and the public. They provide brief descriptions of research written in non-specialist language. The National Institute for Health Research Journals Library (NIHRJL) currently requires authors to provide a 250 word PES. This is published online as part of the final, open-access report. Practice varies among other funders and journals, some of whom employ independent external writers (IEWs) for this purpose.To compare ease of reading and understanding of PESs written by clinical trial teams and an IEW.Forty reports undergoing the editorial process for the NIHRJL will be included in the study. The PES for each report will be revised by authors in line with detailed guidance and edited by an IEW.Ease of reading will be measured using the Flesch Reading Ease score. Scores range from 0-100; higher scores indicate text that is easier to read. Ease of understanding will be assessed by asking public reviewers to read a selection of PESs and rate them from 1 (did not understand) to 4 . Statistical comparison of group scores will be reported.High quality PESs are a priority for dissemination of clinical trial results to patients and the public but it is currently unclear who is best placed to produce them. Results of this study will inform future practice for the NIHRJL and will be relevant to all agencies communicating trial findings to patients and the public.


There has never been a more exciting time to study the science of living systems. Contemporary biology is a vibrant field which grows stronger year on year. Biological scientists have access to powerful new tools and techniques that even recently would have seemed like science fiction. We are enjoying ‘a wellspring of technical advancements’ . The conThe revolutions taking place result in part from technological advances in our ability to undertake ever larger-sized analyses at all scales from the sub-atomic to the global. Thus, for example, more and more genomes are being sequenced and compared, large global scale datasets are being analyzed and more and bigger biological structures are being solved. In almost every area of biological investigation larger datasets are available; this can be from wider, often unbiased, data harvesting, such as genome sequencing, or from highly focused, data-rich studies, such as real-time neurophysiological monitoring. The huge advances in biology are far from sterile. They are already influencing the present and will continue to shape the future in diverse areas such as medicine, food production, synthetic biology and environmental care. Enormous effort is being invested into translating these advances for global benefit and it is difficult to overestimate the impact that the study of biology has already had and will continue to have. This translational work is biology too and rightly so. Biology will be (Biology, the subject, is at the forefront of scientific progress and this is where the journal  will be . BiologiBiology is a new journal and its launch offers an exciting possibility to create a journal that reflects this diversity within biological science. The journal will bring together studies employing the varied experimental and theoretical approaches that are fuelling biological discovery. Biology will be an inclusive journal that embraces all these disciplines and sub-disciplines. With the explosion of biological discovery, there is an explosion in publication. The rate of discovery in most scientific groups is accelerating and there is a pressing need to simplify and accelerate the process of publication. Biology, the journal, will do this. It will be a fully peer-reviewed publication with a rapid and economical route to open access publication.We regard biology as the study of any biological system at any scale from the global to the sub-atomic. Biology encompasses the diversity that constitutes the living world in its myriad manifestations. We make no distinction between biology, biochemistry, genetics, immunology, paleontology, zoology, biophysics, neuroscience, developmental biology, mathematical biology, bacteriology, systems biology, virology, botany, genomics, medicine, parasitology, pharmacology, proteomics or any other biological disciplines. They are all part of the same subject, the study of life.Both the subject and the approaches to its study are exciting and diverse. Bringing all these studies together in a multi-disciplinary manner should drive the field forward by providing an overview that may not be possible from studies conducted only at a particular scale or using only one modality of investigation.Biology, the journal, will capture this diversity and publish across the spectrum of the field. As well as standard research articles we will also publish reviews, commentaries, hypotheses and descriptions of new methods.Biologists study amazing and complex systems using an incredibly wide repertoire of approaches. Biology will provide very rapid dissemination of robust scientific findings. All articles will be peer-reviewed, but the focus will be on determining that the work is scientifically sound rather than trying to predict its future impact. Good results will stand the test of time and the priority for scientists now is to disseminate their findings.Writing in 1974, Francis Crick, reflecting on the impact of the publication of the work on the structure of DNA that won him the Nobel Prize, suggested that it would be for historians to decide the impact of this work . He noteBiology will not waste your time or their time trying to assess the impact of your article. We will assess whether it is scientifically sound and properly written. If work is well conducted and properly documented, then it is necessarily a contribution to the field and only the future can determine its true impact or significance.The editorial panel and the referees of the journal Biology has a streamlined publications process that uses technology to keep the price of publication down. Editors offer their services without payment. The result is that our charges are low and some of the most economical available. Indeed submission is free until 2013. The less money that is spent on publishing, the more there is to spend on discovery.We are an open access journal. When most research is funded by tax payers or charitable donors, it seems appropriate that the reports of this research should be freely available to all. However, open access comes with a price tag as researchers have to fund the publications. We want to accelerate the progress from discovery to dissemination. Review and a decision on publication will be rapid. The time that scientists have is precious and is better spent on discovery than on rewriting articles or trying to persuade journals of their potential impact.Biology are simple. Firstly, is the work scientifically robust? Secondly, is the paper sensibly argued and properly written? We have no limit to the number of papers that we can publish and there is no minimum or maximum page length for a Biology article. If you feel something is ready for dissemination please submit it and we will aim to give you a rapid peer-reviewed decision and fast publication if accepted.The key tests for publication in Biology now.Biology has a superb and diverse editorial team, which includes a Nobel laureate. We are committed to making the journal a success. Our aim is to promote research by reducing the time that publishing results takes out of busy research schedules. The journal will in time be indexed in Pubmed and other standard search and indexing services. It will benefit from the publisher’s experience over more than ten years with a range of successful online journals and the crisp web interface and submission procedure. The launch of a new journal is an exciting moment and we encourage you to submit your articles to


Now it is my great pleasure and honor to serve as editor in chief of this new promising journal.Asia Oceania Journal of Nuclear Medicine & biology (AOJNMB) is the official publication of Asia Oceania Federation of Nuclear Medicine & Biology (AOFNMB). When publication of an official journal of AOFNMB was suggested in 10AOJNMB focuses on issues of interest of scientists and physicians working in the field of nuclear medicine and biology and publishes a variety of articles including original research, technical notes, case reports, review articles and meta-analysis. Although the journal tries to provide a platform for communication between the scientists (in particular from the region) and give them an opportunity to publish their work free of charge, manuscripts from all around the world is most welcome.AOJNMB is an open access journal with absolutely no costs to authors and their institution. Although open access policy is getting popularity in recent years, the current situation is not in the best interest of authors . In someThe journal will be published biannually (in May and November each year) for the first two years and may increase the number of issues per year later. The journal uses a standard peer review process and all manuscripts are reviewed by two reviewers for the originality, relevance, quality and integrity of the manuscript. The revised manuscript is sent to a comparative reviewer for further evaluation. Final decision on acceptance or rejection of the article is done by editor in chief based on these expert opinions. Three experienced associate editors and a group of well known editorial board members are serving the journal, which are mainly from Asia Oceania region. I would like to thanks all my colleagues and editors that helped us in this way, especially Prof. Henry Bom and Prof. Seigo Kinuya for their enthusiastic support.To the extent of my search, 24 journals are published in the field of nuclear medicine and at least 20 are indexed in Scopus or Science citation index. Journal of Nuclear Medicine from North America and European Journal of Nuclear Medicine & Molecular Imaging (EJNMMI) from Europe have the highest impact factors among all nuclear medicine journals(Asia Oceania region as the largest continent with largest population could have a bigger impact on the scientific progress in nuclear medicine. AOJNMB could play an important role in this way and could provide a new opportunity for researchers in developing countries for free publication of their works. It could also potentially make more communication between the scientists of the region with subsequent multicenter research projects and collaborative efforts. Nuclear medicine facilities and resources are not uniform in this region, neither is the scientific publications . A quickThe first issue of the journal enjoys from different variety of articles including 4 original clinical studies, 1 original article in radiopharmacy, one review article and one case report. Also an editorial is written by the president of AOFNMB about history and perspectives of the AOFNMB as well as another editorial by editor in chief.It is clear that willingness of each member of the Asia Oceania Federation of Nuclear Medicine and Biology is the main requirement for success of this journal. I am confident that AOJNMB will grow to be one of the most important journals in the field of nuclear medicine and biology. Let’s turn it to reality.


Chemical Information Science channel ofF1000Research.Compared to the traditional anonymous peer review process, open post-publication peer review provides additional opportunities -and challenges- for reviewers to judge scientific studies. In this editorial, we comment on the open peer review culture and provide some guidance for reviewers of manuscripts submitted to the Chemical Information Science (CIS) channel ofF1000Research has been introduced as a publication platform1 that covers all aspects of chemical information science2 and positions the full spectrum of chemoinformatics approaches3 within this broader context. TheCIS channel specifically aims to attract high-quality manuscripts. Therefore, submissions to theCIS channel undergo a two-layer expert review, as described below. This editorial is intended to provide specific guidance for reviewers of studies published in theCIS channel.TheCIS channel takes place in two stages, an initial pre-review by members of the channel Editorial Board, followed by open peer review. Once a submission has been processed byF1000Research editorial staff and passed on to the guest editors, members of the channel Editorial Board evaluate a manuscript on the basis of its scientific potential to advance the field. This initial assessment (pre-review) is not meant to result in formal reviews, but a collection of expert opinions. The conclusions of the channel Editorial Board are then forwarded to the authors. If a positive pre-review consensus is reached or if views of the channel Editorial Board on a submission remain controversial, the paper is published in theCIS channel and reaches the stage of open peer review. If a negative pre-review consensus is reached by the channel Editorial Board, the manuscript is not published in theCIS channel (but the authors have still the opportunity to publish their work inF1000Research).The review of papers submitted to theCIS channel the authors are asked to make reviewer suggestions; members of the channel Editorial Board may suggest additional reviewers. Authors must agree with the final reviewer line-up beforeF1000Research editorial staff initiates the post-publication review. The review, approval, and indexing process ofCIS channel publications follows standardF1000Research procedures.Upon publication of a paper in theThe general philosophy of open peer review is that the reviewer identity will be disclosed and the review directly presented to the scientific community including the authors . In addition, authors and readers have the opportunity to comment on reviews. In the following, we provide some specific comments and guidelines for reviewers ofCIS channel publications.The open post-publication peer review presents referees with different opportunities and challenges compared to the conventional anonymous peer review process.scientifically sound,understandably presented, andreproducible. Frequent lack of reproducibility is a major issue concerning chemoinformatics publications in many journals4. Reviewers ofCIS channel publications must determine whether data and methods used in a given study are accessible to the scientific community and that sufficient details are provided to reproduce reported calculations and re-implement a method (provided an implementation of the method is not made available as part of the study). Answering these key questions should directly lead the reviewer to conclude that a study should be “approved”, “approved with reservations”, or “not approved”.The reviews can be brief as long as they clearly address the key questions.(1) The primary function of a review is to evaluate whether a given study ismembers of the channel Editorial Board are encouraged to convert/extend pre-review comments into a post-publication review. This will inevitably reduce the time required for aCIS channel publication to reach approval status (or a status requiring revisions).(2) Because these questions are among those already considered during the pre-review,CIS channel and spark the interest of the scientific community. As such, these reviews and subsequent on-line discussions become an essential part of a publication.An open review process can also dramatically reduce the time between submission, publication, and indexing of a paper, thus supporting its dissemination. Short review times are highly desired and particularly important forData orMethod articles, which often report tools made freely available to the scientific community. In addition, short review times are an additional attraction for authors to submit their work to theCIS channel.(3) Open peer reviews not only provide feedback for authors, they also help to position a paper within theprovide detailed reviews, which might also suggest more or less extensive revisions. This particularly applies toResearch Articles orReviews. It is also appropriate to further extend reviews of a paper after approval status is reached. This can be accomplished, for example, byadding comments to initial reviews. We expect that diligent authors will take reviewer comments seriously and submit revisions and/or responses. If authors disagree with review conclusions or requests, they can comment on them and articulate their viewpoints. Authors are specifically encouraged to publish appropriate revisions in a second version of their manuscript. If they do or do not take reviews seriously will be clearly visible to the scientific community; another bonus of an open review culture.(4) Of course, reviewers are at liberty -and encouraged- toAnswering the key questions if a study is scientifically sound, clearly presented, and reproducible in a timely manner becomes especially important for off-the-beaten path contributions, which are explicitly encouraged by theCIS channel. For example, such papers might introduce novel, provocative, and/or controversial concepts that are far from being established, report negative results, or principal shortcomings of current methods. In such cases, views of authors, reviewers, and readers might often differ. Regardless, conceptually novel or controversial investigations that are viewed differently must still be scientifically sound. Even in the presence of different opinions, a careful assessment of the key questions is an essential task for reviewers of suchCIS channel publications.(5)CIS channel and beyond. As discussed, open peer reviews are not written for editors but directly address authors and the scientific community. As such, they become a part of a publication and are thought to make important contributions to the further scientific development of our field. Open peer reviews must evaluate the key questions whether a publication isscientifically sound,understandably presented, andreproducible and may go well beyond answering these questions. Short review times are important when a paper is presented to the scientific community. Timely reviews, be they positive or negative, indicate that studies are taken seriously, make publications more interesting to readers, and help to disseminate them. Open peer review catalyzes scientific perception. The scientific community has the last word.We hope that our comments will help to foster a culture of open peer review, for the


The first issue of Philosophical Transactions from the Royal Society published in 1665 is widely regarded as the beginning of modern academic communication through journal articles. This form of presentation was an alternative to books for facilitating the exchange of ideas among scholarly circles. Soon journal collections and scientific libraries were created and eventually an evaluation of the quality of research activity was sought through noting the impact of their publications® of the United States (US-NLM® is the English acronym) articles were indexed from medical journals in the Index Medicus, which went out of circulation due to the impossibility of managing the voluminous information generated in the form of a bookIncreased specialization, experimentation and an interdisciplinary approach to science dramatically increased academic productivity. In the last two centuries, the number of scientific articles has doubled every 10-15 years. From 1879-2004, in the National Library of MedicineThe eruption of digital and electronic formats and public use of the internet in the first half of the nineties changed the manner for disseminating scientific production. Commercial publishing houses proliferated and offered services that the scientific community and universities were unable to assume. Researchers freely ceded their copyrights and donated their writings to the publishers for the objective of having it published. Paradoxically, the university again paid for knowledge which it already owned and in some cases its own researchers had to pay the journals for its work to be published.http://creativecommons.org/about), the least restrictive among those adopted by publishers with open policies. Unfortunately, some traditional subscription journals created an open access system for some articles whose authors were paid a certain amount of money. This practice increases the appearance of predatory publishers of "Open-Access" that are more focused on making money than on spreading academic knowledgeIn response to the abuse by commercial publishing houses, the Open Access movement appeared as an alternative way for disseminating academic productions in which the journal guarantees free, irrevocable, unrestrictive access to the article from the date of its online publication. Reuse is regulated by Creative Commons (CC) licenses  to centers for the administration and management of information and medical knowledge. At the US-NLM significant changes were produced: the The dissemination of scientific information on the Internet requires prompt adoption of Web technologies by publishers to achieve a complete archive of the journals and ensure that the metadata used to describe the articles incorporates the best available technology. The full text of the journal and metadata should be encoded in a standardized manner to achieve interoperability among the different actors in global scientific productivity. The US-NLM in collaboration with Harvard University created a document type definition (DTD for its English acronym) for journal archives and later for use by publishers and authors. After the first users´ conference, the NISO-JATS standard  was adopted in 2011® (PMC), a free archival system for complete texts of biomedical and biological science journals created by the US-NLM in 2000. PMC is the largest digital library in the world that serves as a digital counterpart to the extensive collections of printed journals in the US-NLM.This standard defines a set of elements and attributes in XML format for describing the full narrative content and metadata for a journal article where "journal article" has been broadly defined to include articles differing from those of research. This process has been essential for the consolidation of PubMed CentralThe transfer and implementation of these standards in Latin America has been possible thanks to BIREME, Brazil, the Specialized Center of PAHO/WHO that has fully adapted to the Internet as a production medium for sources and the flow of regional scientific and technical information. Since 1997, the current process began with the creation of SCIELO, a virtual library of scientific journals in electronic format which currently accommodates 967 journals from 12 Ibero-American countries. The library works with SCIELO methodology, a set of rules, guidelines, manuals and software for preparing, storing, disseminating and evaluating electronic publications. It organizes and publishes entire texts from online journals, plus producing and publishing indicators of its use and impact® in 2011. Print journals formalized its entry in MEDLINE® with the periodic shipment of a copy of each issue of the journal to the US-NLMColombia Médica (CM) is at the top of the classification of the Colombian bibliographic index (Publindex) and has been accepted in several important global databases, including SciELO and HINARI. These achievements have been possible thanks to the dedication and generous efforts by the authors, peer reviewers and editorial groups led by Rodrigo Guerrero between 1970 and 1972; Francisco Falabella between 1973 and 1998; Pablo Barreto, Guillermo Llanos and Francisco Falabella from 1998 to 2001; Guillermo Llanos from 2002 to 2009 and Julian Herrera from 2010 to the present time. After 40 years of continuous effort and after complying with all quality standards, it entered the ISI citation index (Science Citation Index - Web of Science) in 2008 and MEDLINE® is more demanding and costly because the journal must provide the US-NLM the complete content of the articles in the XML format with tags for bibliographic citations and a guarantee of access to all its content through a robust system that allows access and permanent preservation of its contents. In Latin America there are no certified digital repositories. The alternative is PMC, which in addition to ensuring free and unrestricted access, offers the archive free to journals that have their complete texts in English. For journals in an exclusively electronic format, such as CM, definitive indexing with MEDLINEColombia Médica faces these demands with the institutional support of the Faculty of Health, Universidad del Valle, who determines the composition, functions and competencies of the Editorial and Scientific Committee of the journal, allowing the appointment of journal committees and internal calls for the appointment of Editor-in-Chief and Associate Editors® was attained. Colombia Médica´s retention over time is guaranteed by the US-NLM; as of 2014 it will become part of PubMed Central®, the free digital archive of biomedical and biological sciences of the U.S. National Institute of Health, which is considered to be the most important digital library in the world.With guidance from the National University of Colombia and support from Scielo Brazil, in 2013 the standards of the US-NLM were implemented and technical endorsement by Pubmed CentralThe guidance of the journals by multidisciplinary teams, the policy of free access to its contents, and the technological transfer with the use of free software will help the journals of middle and low-income countries to overcome barriers to diffusion and to maintain technological independence from commercial publishers. Colombia Médica makes an impassioned plea to WHO/PAHO to support BIREME, Brazil and convert SciELO into a certified digital repository.


Reason for Corrigendum:Chlamydomonas reinhardtii originally published in Molecular Systems Biology in 2011 (Chang et al., iCR1080, however the correct name should be iRC1080, named after the initials of the researcher who reconstructed it. The authors apologize for the mistake. This error does not affect the scientific conclusions of the article in any way.There was a mistake with the naming of the genome-scale metabolic model of All authors listed have made substantial, direct and intellectual contribution to the work, and approved it for publication.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.