Preprints in the Spotlight: Establishing Best Practices, Building Trust 1
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Superresolution Microscopy of the Β-Carboxysome Reveals a Homogeneous Matrix
Superresolution microscopy of the β-carboxysome reveals a homogeneous matrix The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Niederhuber, Matthew J., Talley J. Lambert, Clarence Yapp, Pamela A. Silver, and Jessica K. Polka. 2017. “Superresolution microscopy of the β-carboxysome reveals a homogeneous matrix.” Molecular Biology of the Cell 28 (20): 2734-2745. doi:10.1091/ mbc.E17-01-0069. http://dx.doi.org/10.1091/mbc.E17-01-0069. Published Version doi:10.1091/mbc.E17-01-0069 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:34651752 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA M BoC | ARTICLE Superresolution microscopy of the β-carboxysome reveals a homogeneous matrix Matthew J. Niederhubera,b,†, Talley J. Lambertc, Clarence Yappd, Pamela A. Silvera,b, and Jessica K. Polkaa,b,* aDepartment of Systems Biology, cDepartment of Cell Biology, and dImage and Data Analysis Core, Harvard Medical School, Boston, MA 02115; bWyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115 ABSTRACT Carbon fixation in cyanobacteria makes a major contribution to the global carbon Monitoring Editor cycle. The cyanobacterial carboxysome is a proteinaceous microcompartment that protects Benjamin S. Glick and concentrates the carbon-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygen- University of Chicago ase (RuBisCO) in a paracrystalline lattice, making it possible for these organisms to fix CO2 Received: Jan 30, 2017 from the atmosphere. -
The Evolving Preprint Landscape
The evolving preprint landscape Introductory report for the Knowledge Exchange working group on preprints. Based on contributions from the Knowledge Exchange Preprints Advisory Group (see page 12) and edited by Jonathan Tennant ([email protected]). 1. Introduction 1.1. A brief history of preprints 1.2. What is a preprint? 1.3 Benefits of using preprints 1.4. Current state of preprints 1.4.1. The recent explosion of preprint platforms and services 2. Recent policy developments 3. Trends and future predictions 3.1. Overlay journals and services 3.2. Global expansion 3.3. Research on preprints 3.4. Community development 4. Gaps in the present system 5. Main stakeholder groups 6. Business and funding models Acknowledgements References 1. Introduction 1.1. A brief history of preprints In 1961, the USA National Institutes of Health (NIH) launched a program called Information Exchange Groups, designed for the circulation of biological preprints, but this shut down in 1967 (Confrey, 1996; Cobb, 2017). In 1991, the arXiv repository was launched for physics, computer science, and mathematics, which is when preprints (or ‘e-prints’) began to increase in popularity and attention (Wikipedia ArXiv#History; Jackson, 2002). The Social Sciences Research Network (SSRN) was launched in 1994, and in 1997 Research Papers in Economics (Wikipedia RePEc) was launched. In 2008, the research network platforms Academia.edu and ResearchGate were both launched and allowed sharing of research papers at any stage. In 2013, two new biological preprint servers were launched, bioRxiv (by Cold Spring Harbor Laboratory) and PeerJ Preprints (by PeerJ) (Wikipedia BioRxiv; Wikipedia PeerJ). -
Episciences: a Model of Overlay Journals
Episciences: a model of overlay journals COAR 2019 Annual Meeting & General Assembly Lyon (France) 2019-05-22 Raphaël Tournoy <[email protected]> HAL hal.archives-ouvertes.fr HAL is an open archive where authors can deposit scholarly documents from all academic fields Created in 2000 Missions: Development of OA and related services for the higher education and Sciencesconf.org research community www.sciencesconf.org A Web platform available to all organizers of scientific conferences that have calls for communication Partner in European projects: MedOANet, DARIAH-EU, PEER OpenAIRE, Equipex DILOH, ANR Episciences.org Campus AAR www.episciences.org An overlay journal platform www.ccsd.cnrs.fr 2 CONTEXT • Growing number of preprints and servers • No scientific validation in OA repositories • Preprints are less likely to be cited • Subscriptions costs rising • Budgets cuts for libraries • Long delay of publishing in journals 3 PROPOSAL : OVERLAY JOURNALS • Build journals on top of OA repositories • Peer review preprints • Submit revised preprints in repositories • Publish preprints as articles 4 CCSD’S PROPOSAL FOR OVERLAY JOURNALS • Episciences: platform for creating and hosting scientific journals (2013) • Built above open archives, composed of documents deposited in HAL, arXiv,… • From open access (OA preprints) To open access (OA papers) 5 EPISCIENCES ORGANIZATION • The steering committee review general platform orientations and epi-committees • Epi-committees select new journals in their disciplines • Editorials Committees -
Nature Toolbox Leading Mathematician Launches Arxiv 'Overlay' Journal Journal That Reviews Papers from Preprint Server Aims to R
Nature Toolbox Leading mathematician launches arXiv 'overlay' journal Journal that reviews papers from preprint server aims to return publishing to the hands of academics. Philip Ball 15 September 2015 New journals spring up with overwhelming, almost tiresome, frequency these days. But Discrete Analysis is different. This journal is online only — but it will contain no papers. Rather, it will provide links to mathematics papers hosted on the preprint server arXiv. Researchers will submit their papers directly from arXiv to the journal, which will evaluate them by conventional peer review. With no charges for contributors or readers, Discrete Analysis will avoid the commercial pressures that some feel are distorting the scientific literature, in part by reducing its accessibility, says the journal's managing editor Timothy Gowers, a mathematician at the University of Cambridge, UK, and a winner of the prestigious Fields Medal. “Part of the motivation for starting the journal is, of course, to challenge existing models of academic publishing and to contribute in a small way to creating an alternative and much cheaper system,” he explained in a 10 September blogpost announcing the journal. “If you trust authors to do their own typesetting and copy-editing to a satisfactory standard, with the help of suggestions from referees, then the cost of running a mathematics journal can be at least two orders of magnitude lower than the cost incurred by traditional publishers.” Related stories • Open access: The true cost of science publishing • Mathematicians aim to take publishers out of publishing • Open-access deal for particle physics More related stories Discrete Analysis' costs are only $10 per submitted paper, says Gowers; money required to make use of Scholastica, software that was developed at the University of Chicago in Illinois for managing peer review and for setting up journal websites. -
OPENING the RECORD of SCIENCE MAKING SCHOLARLY PUBLISHING WORK for SCIENCE in the DIGITAL ERA 2 International Science Council Opening the Record of Science
OPENING THE RECORD OF SCIENCE MAKING SCHOLARLY PUBLISHING WORK FOR SCIENCE IN THE DIGITAL ERA 2 International Science Council Opening the Record of Science Citation: International Science Council. 2021. Opening the record of science: making scholarly publishing work for science in the digital era. Paris, France. International Science Council. http://doi.org/10.24948/2021.01 Photo credits: Cover by metamorworks on shutterstock.com p10 by Garry Killian on shutterstock.com p15 by Olga Miltsova on shutterstock.com p20 by sdecoret on shutterstock.com p35 by whiteMocca on shutterstock.com p42 by Pixels Hunter on shutterstock.com p53 by SFIO CRACHO on shutterstock.com p60 by Pixels Hunter on shutterstock.com p68 by Pixels Hunter on shutterstock.com p71 by Pixels Hunter on shutterstock.com Design: Alan J. Tait / ajtait.co.uk Work with the ISC to advance science as a global public good. Connect with us at: www.council.science [email protected] International Science Council 5 rue Auguste Vacquerie 75116 Paris, France www.twitter.com/ISC www.facebook.com/InternationalScience www.instagram.com/council.science www.linkedin.com/company/international-science-council 3 International Science Council Opening the Record of Science CONTENTS Preface 5 Summary 6 1. SCIENCE AND PUBLISHING 10 1.1 Why science matters 11 1.2 The record of science 11 1.3 Diverse publishing traditions 14 2. PRINCIPLES FOR SCIENTIFIC PUBLISHING 15 2.1 Principles and their rationales 16 2.2 Responses from the scientific community 19 3. THE EVOLVING LANDSCAPE OF SCHOLARLY AND SCIENTIFIC 20 PUBLISHING 3.1 The commercialization of scientific publishing 21 3.2 The reader-pays model 24 3.3 The open access movement 24 3.4 The author-pays models 26 3.5 Learned society publishing 28 3.6 Institutionally-based repositories and infrastructures 28 3.7 Preprint repositories 29 3.8 ‘Public infrastructures’ – publicly funded and scholar-led 31 3.9 Books and monographs 33 3.10 ‘Predatory’ publishing 34 4. -
Opening up Peer-Review Policies
FEATURE Opening Up Peer-Review Policies Jessica Polka, Tony Ross-Hellauer, and Gary McDowell Authors in many disciplines favor1 peer review moving out of the shadows and becoming a more transparent practice. Accordingly, platforms and publishers are increasingly implementing open peer review (OPR) to enable new kinds of discourse within the publishing process. Yet, these systems differ in what is revealed when and to whom. OPR can operate on many different parts of the review process. It can infl uence the process of peer review (who can comment on the manuscript, and whether they can communicate with one another) as well as the transparency of information about peer review (the visibility of the manuscript or reviewer names, reports), and it can operate at Photo by Javier Allegue Barros (https://unsplash.com/photos/ many different times, from before submission (i.e., preprints) C7B-ExXpOIE?utm_source=unsplash&utm_medium=referral&utm_ to after publication (i.e., post-publication commenting). One content=creditCopyText) on Unsplash. of us undertook a systematic analysis2 of defi nitions of OPR; this uncovered 7 core traits, which were used in 22 distinct Scholarly activity in open peer review has also made confi gurations. The most frequently used elements of OPR signifi cant progress. In January 2019, results were released were revealing reviewer identities (open identities) and from a trial in which 5 Elsevier journals6 began publishing all publishing reviews (open reports). peer reviews. It showed that each journals’ submission rates increased during the trial. While the rate at which reviewers Growth in open peer-review accepted invitations to review declined, these declines implementations and experiments matched global trends, so may not have been caused by the While open peer review has been practiced by publishers review model. -
Downloads Have Grown Commen- Surately with Their Uploads [10]
Neuroanatomy and Behaviour, 2020, 2(1), e9. Neuroanatomy ISSN: 2652-1768 and H doi: 10.35430/nab.2020.e9 ε Behaviour PROFESSIONALPERSPECTIVES Enhancing scientific dissemination in neuroscience via preprint peer-review: “Peer Community In Circuit Neuroscience” Marion S. Mercier1, Vincent Magloire1 and Mahesh Karnani2,* 1Institute of Neurology, UCL, London, United Kingdom and 2Institute for Neuroscience, ETH Zürich, Switzerland *[email protected] Abstract The dissemination of scientific results and new technologies in biomedical science is rapidly evolving from an exclusive and fee-oriented publishing system towards more open, free and independent strategies for sharing knowledge. In this context, preprint servers such as bioRxiv answer a very real scientific need by enabling the rapid, free and easy dissemination of findings, regardless of whether these are novel, replicated, or even showcasing negative results. Currently, thousands of manuscripts are being shared via bioRxiv each month, and neuroscience is the largest and fastest growing subject category. However, commenting on bioRxiv is declining and no structured scientific validation such as peer-review is currently available. The Peer Community In (PCI) platform addresses this unmet need by facilitating the rigorous evaluation and validation of preprints, and PCI Circuit Neuroscience (PCI C Neuro) aims to develop and extend this tool for the neuroscience community. Here we discuss PCI C Neuro’s mission, how it works, and why it is an essential initiative in this -
Open Access + Preprints
Open Access + Preprints Journals and scholars take action Presented by: Contents Open Access + Preprints, pg. 3 Preprints and Modern Publishing, pg. 4 •The origin of scholarly journals: 300 years with little change •Preprints and the modern web •What researchers are saying about preprints •Preprints reshaping the research experience The Role of Preprints in Journal Publishing, pg. 8 •Preprints and Green OA •How journals can facilitate Green OA via preprints •Importance of clear preprint policies •Questions surrounding preprint publications •Journals pioneering new preprint publishing models Looking to the Future of Preprints and OA Publishing, pg. 13 OpenTitle Accessof Ebook + Preprints 2 Open Access + Preprints As academics transition to digital journal publishing, the Open Access (OA) movement, which aims to make research freely available at or soon after publication, is picking up record speed. According to a recent Simba report titled Open Access Journal Publishing 2016-2020, “the number of OA research articles published annually is growing at double the rate of the complete spectrum of research articles.” The report also found that about a third of all research articles currently published are OA, when factoring in those with complete embargo periods. The rise in OA publishing comes as a result of scholars banding together to reveal the mounting cost of research access for institutions and individuals, such as those behind The Cost of Knowledge who started a boycott of monolith publisher Elsevier, which now has profit margins exceeding 30%. At the same time governments and funding bodies have introduced new OA mandates and calls for early sharing of research, such as the Wellcome Trust, Bill & Melinda Gates Foundation, and others who this February urged journals and funding agencies to sign a pledge to make all Zika virus research OA in the wake of the public health crisis. -
Accelerating Scientific Publication
Accelerating scientific publication Thierry Galli INSERM & Aviesan ITMO BCDE Ambassador, ASAPbio Twitter: #ASAPbio @jessicapolka 1 Publication is essential to scientific progress Adapted from http://asapbio.org/survey Twitter: #ASAPbio @jessicapolka 3 Publishing isn’t what it used to be Ron Vale, bioRxiv/PNAS 2015 Twitter: #ASAPbio @jessicapolka 4 What to do about it? Problem: fast and open venues are not always ‘impactful’ venues Twitter: #ASAPbio @jessicapolka 5 A preprint is a manuscript posted online before journal-organized peer review Twitter: #ASAPbio @jessicapolka 6 Preprints & journals are compatible Berg et al Science7 2016 Preprint servers have existed for 25 years arXiv: 100,000 manuscripts per year In Biology 8 Preprints are taking off inbiology off taking are Preprints Version 1000 100 200 300 400 500 600 700 800 900 0 1 | asapbio.org janv.-03 juil.-03 janv.-04 arXiv (q-bio w/cross-lists, from arxiv.org stats) bioRxiv (from bioRxiv) PeerJ Preprints (bio/med/life) F1000 Research The Winnower Nature Precedings (manuscripts, from search results) Preprints.org (articles/reviews bio/life/med) in figshare by (filtered PrePubMed) juil.-04 janv.-05 juil.-05 janv.-06 juil.-06 janv.-07 juil.-07 janv.-08 juil.-08 janv.-09 juil.-09 janv.-10 juil.-10 janv.-11 juil.-11 janv.-12 juil.-12 janv.-13 juil.-13 janv.-14 juil.-14 janv.-15 juil.-15 janv.-16 juil.-16 9 •Benefits of preprints •Concerns surrounding preprints •Taking action •Recent updates 10 Problem: Lack of access to literature Preprints are immediately available to everyone around -
Can Open Access Repositories and Peer-Reviewed Journals Coexist?
Serials – 20(3), November 2007 Stephen Pinfield Can repositories and journals coexist? Can open access repositories and peer-reviewed journals coexist? Based on a paper presented at the 30th UKSG Conference,Warwick,April 2007 It is often assumed that open access repositories and peer-reviewed journals are in competition with each other and therefore will in the long term be unable to coexist. This paper takes a critical look at that assumption. It draws on the available evidence of actual practice which indicates that coexistence is possible at least in the medium term. It discusses possible future models of publication and dissemination which include open access, repositories, peer review and journals. The paper suggests that repositories and journals may coexist in the long term but that both may have to undergo significant changes. Important areas where changes need to occur include: widespread deployment of repository infrastructure, development of version identification standards, development of value-added features, new business models, STEPHEN PINFIELD new approaches to quality control and adoption of digital preservation as Chief Information Officer a repository function. University of Nottingham Introduction It is often assumed that open access (OA) management of digital objects, and where those repositories and peer-reviewed journals are in objects can than be freely and immediately accessed competition. In this competitive situation, it is and reused in an unrestricted way. Repositories suggested, coexistence in the long term will be may be maintained by and serve different com- impossible and only one of the two will exist in the munities, such as institutions or subject groupings. -
Copy of RIOJA Survey
RIOJA Survey ABOUT YOU Q1. Please let us know the primary area of your research: Astrophysics Cosmology Early universe cosmology Galactic astrophysics High-energy astrophysics Observational cosmology Particle astrophysics Solar system astrophysics Solar system physics Stellar astrophysics Other (please specify) Q2. From the following options, please select the one that best describes your current role: Professor/Full Professor Reader Senior Lecturer/Associate Professor Lecturer/Assistant Professor Senior Research Fellow Research Fellow Research Associate/Research Assistant Other Q3. From the following options, please select those that best describe your current responsibilities (tick all boxes that apply): Editor/member of editorial board of peer reviewed journal Head of department Head of research unit/group Publisher - commercial Publisher - not for profit Publisher - University press Research Teaching Other (please specify) Q4. Please let us know how for many years (post Ph.D.) you have been engaged in reseach: More than 10 years 6-10 years 0-5 years Q5. Is English your first language? Yes No PUBLISHING YOUR RESEARCH Q6. In which form is your research most commonly written up? Book(s) Chapter(s) in book(s) Papers for submission to peer reviewed journals Papers included in conference proceedings Workshop papers Other (please specify) Q7. Approximately, how many papers for submission to refereed journals have you produced in the last 2 years? Q8. In which of the following peer reviewed journals have you published your papers? Annual Review of Astronomy and Astrophysics Annual Review of Earth and Planetary Sciences Astronomical Journal Astronomy and Astrophysics Astronomy and Astrophysics Review Astrophysical Journal Astrophysical Journal Supplement Series Journal of Cosmology and Astroparticle Physics Monthly Notices of the Royal Astronomical Society Nature New Journal of Physics Physical Review D Physical Review Letters Science Other (please specify) Q9. -
Building Synthetic Cellular Organization
M BoC | PERSPECTIVE Building synthetic cellular organization Jessica K. Polka and Pamela A. Silver Department of Systems Biology, Harvard Medical School, Boston, MA 02115; Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115 ABSTRACT The elaborate spatial organization of cells enhances, restricts, and regulates pro- Monitoring Editor tein–protein interactions. However, the biological significance of this organization has been Keith G. Kozminski difficult to study without ways of directly perturbing it. We highlight synthetic biology tools University of Virginia for engineering novel cellular organization, describing how they have been, and can be, used Received: Jul 30, 2013 to advance cell biology. Revised: Sep 19, 2013 Accepted: Sep 24, 2013 INTRODUCTION Synthetic biology seeks to use cellular modularity to predictably WHY ORGANIZE? build living systems that do useful things. Historically, many of the Specifying molecular localization provides a powerful way of fruits of the field have been genetic circuits—elements that can re- selecting for and against biological interactions resulting in member, report on stimuli, and perform simple computational tasks. tunable mechanisms for regulation (Figure 1). Thus, confining Other engineered products include synthetic genomes, as well as free diffusion, either by reducing its dimensionality or by corral- proteins endowed by design with novel functions. ling it in a physical compartment, not only can protect proteins Synthetic biology’s engineering principles can also be ap- from off-target effects, but also can enhance desirable interac- plied to interrogate and perturb natural cellular function. In fact, tions. For example, the reduction of diffusion dimensionality can nearly every article published in Molecular Biology of the Cell reduce the search time for finding an on-target interaction.