The Evolving Preprint Landscape
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Open Access Publishing
Open Access The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Suber, Peter. 2012. Open access. Cambridge, Mass: MIT Press. [Updates and Supplements: http://cyber.law.harvard.edu/hoap/ Open_Access_(the_book)] Published Version http://mitpress.mit.edu/books/open-access Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:10752204 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 OPEN ACCESS The MIT Press Essential Knowledge Series Information and the Modern Corporation, James Cortada Intellectual Property Strategy, John Palfrey Open Access, Peter Suber OPEN ACCESS PETER SUBER TheMIT Press | Cambridge, Massachusetts | London, England © 2012 Massachusetts Institute of Technology This work is licensed under the Creative Commons licenses noted below. To view a copy of these licenses, visit creativecommons.org. Other than as provided by these licenses, no part of this book may be reproduced, transmitted, or displayed by any electronic or mechanical means without permission from the publisher or as permitted by law. This book incorporates certain materials previously published under a CC-BY license and copyright in those underlying materials is owned by SPARC. Those materials remain under the CC-BY license. Effective June 15, 2013, this book will be subject to a CC-BY-NC license. MIT Press books may be purchased at special quantity discounts for business or sales promotional use. -
Preprints in the Spotlight: Establishing Best Practices, Building Trust 1
ISSUE BRIEF Preprints in the Spotlight Establishing Best Practices, Building Trust May 27, 2020 Oya Y. Rieger Ithaka S+R provides research and Copyright 2020 ITHAKA. This work is strategic guidance to help the licensed under a Creative Commons Attribution-NonCommercial 4.0 academic and cultural communities International License. To view a copy of serve the public good and navigate the license, please see http://creative- economic, demographic, and commons.org/licenses/by-nc/4.0/. technological change. Ithaka S+R is ITHAKA is interested in disseminating part of ITHAKA, a not-for-profit this brief as widely as possible. Please organization that works to advance contact us with any questions about using and preserve knowledge and to the report: [email protected]. improve teaching and learning through the use of digital technologies. Artstor, JSTOR, and Portico are also part of ITHAKA. PREPRINTS IN THE SPOTLIGHT: ESTABLISHING BEST PRACTICES, BUILDING TRUST 1 Introduction Preprints have been getting a lot of attention recently. The COVID-19 pandemic—the first major health crisis since medical and biomedical preprints have become widely available online—has further underscored the importance of speedy dissemination of research outcomes. Preprints allow researchers to share results with speed, but raise questions about accuracy, misconduct, and our reliance on the “self-correcting” nature of the scientific enterprise. As scientists and health care professionals, as well as the general public, look for information about the pandemic, preprint services are growing in importance. So too are the policy decisions preprint platform leaders make. Even before the crisis struck, it was clear that 2020 would be a year of reckoning for preprints. -
Consistent Variations in Personality Traits and Their Potential for Genetic Improvement in The
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.21.257881. this version posted August 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Consistent variations in personality traits and their potential for genetic improvement in the 2 biocontrol agent Trichogramma evanescens 3 4 Silène Lartiguea,b,c, Myriam Yalaouib, Jean Belliardb, Claire Caravelb, Louise Jeandrozb, 5 Géraldine Groussierb, Vincent Calcagnob, Philippe Louâprec, François-Xavier Dechaume- 6 Moncharmontd, Thibaut Malausab and Jérôme Moreauc, e 7 8 a ENGREF AgroParisTech, Paris, France 9 10 b UMR Institut Sophia Agrobiotech, INRAE, UCA, CNRS, 06903 Sophia Antipolis, France 11 12 c UMR CNRS 6282 Biogéosciences, Université Bourgogne Franche-Comté, 6 Boulevard 13 Gabriel, 21000 Dijon, France 14 15 d Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, 69622 16 Villeurbanne, France 17 18 e Centre d'Études Biologiques de Chizé, UMR 7372, CNRS & La Rochelle Université, 79360 19 Villiers-en-bois, France 20 21 * Corresponding author: S. Lartigue, UMR Institut Sophia Agrobiotech, INRAE, UCA, 22 CNRS, Sophia Antipolis, France. E-mail address: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.21.257881. this version posted August 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 23 Abstract 24 Improvements in the biological control of agricultural pests require improvements in the 25 phenotyping methods used by practitioners to select efficient biological control agent (BCA) 26 populations in industrial rearing or field conditions. -
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). -
Open Science in Archaeology
Marwick, B. et al. (2017) Open science in archaeology. SAA Archaeological Record, 17(4), pp. 8-14. There may be differences between this version and the published version. You are advised to consult the publisher’s version if you wish to cite from it. http://eprints.gla.ac.uk/148887/ Deposited on: 29 September 2017 Enlighten – Research publications by members of the University of Glasgow http://eprints.gla.ac.uk Open Science in Archaeology Ben Marwick*, Jade d’Alpoim Guedes, C. Michael Barton, Lynsey A. Bates, Michael Baxter, Andrew Bevan, Elizabeth A. Bollwerk, R. Kyle Bocinsky, Tom Brughmans, Alison K. Carter, Cyler Conrad, Daniel A. Contreras, Stefano Costa, Enrico R. Crema, Adrianne Daggett, Benjamin Davies, B. Lee Drake, Thomas S. Dye, Phoebe France, Richard Fullagar, Domenico Giusti, Shawn Graham, Matthew D. Harris, John Hawks, Sebastian Heath, Damien Huffer, Eric C. Kansa, Sarah Whitcher Kansa, Mark E. Madsen, Jennifer Melcher, Joan Negre, Fraser D. Neiman, Rachel Opitz, David C. Orton, Paulina Przystupa, Maria Raviele, Julien Riel-Salvatore, Philip Riris, Iza Romanowska, Néhémie Strupler, Isaac I. Ullah, Hannah G. Van Vlack, Ethan C. Watrall, Chris Webster, Joshua Wells, Judith Winters, Colin D. Wren * corresponding author, [email protected] Introduction In archaeology, we are accustomed to investing great effort into collecting data from fieldwork, museum collections, and other sources, followed by detailed description, rigorous analysis, and in many cases ending with publication of our findings in short, highly concentrated reports or journal articles. Very often, these publications are all that is visible of this lengthy process, and even then, most of our journal articles are only accessible to scholars at institutions paying subscription fees to the journal publishers. -
Ten Simple Rules to Consider Regarding Preprint Submission
EDITORIAL Ten simple rules to consider regarding preprint submission Philip E. Bourne1*, Jessica K. Polka2, Ronald D. Vale3, Robert Kiley4 1 Office of the Director, The National Institutes of Health, Bethesda, Maryland, United States of America, 2 Whitehead Institute, Cambridge, Massachusetts, United States of America, 3 Department of Cellular and Molecular Pharmacology and the Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California, United States of America, 4 Wellcome Library, The Wellcome Trust, London, United Kingdom * [email protected] For the purposes of these rules, a preprint is defined as a complete written description of a body of scientific work that has yet to be published in a journal. Typically, a preprint is a research article, editorial, review, etc. that is ready to be submitted to a journal for peer review or is under review. It could also be a commentary, a report of negative results, a large data set and its description, and more. Finally, it could also be a paper that has been peer reviewed and either is awaiting formal publication by a journal or was rejected, but the authors are willing to make the content public. In short, a preprint is a research output that has not completed a typi- cal publication pipeline but is of value to the community and deserving of being easily discov- ered and accessed. We also note that the term preprint is an anomaly, since there may not be a a1111111111 print version at all. The rules that follow relate to all these preprint types unless otherwise a1111111111 noted. -
Do You Speak Open Science? Resources and Tips to Learn the Language
Do You Speak Open Science? Resources and Tips to Learn the Language. Paola Masuzzo1, 2 - ORCID: 0000-0003-3699-1195, Lennart Martens1,2 - ORCID: 0000- 0003-4277-658X Author Affiliation 1 Medical Biotechnology Center, VIB, Ghent, Belgium 2 Department of Biochemistry, Ghent University, Ghent, Belgium Abstract The internet era, large-scale computing and storage resources, mobile devices, social media, and their high uptake among different groups of people, have all deeply changed the way knowledge is created, communicated, and further deployed. These advances have enabled a radical transformation of the practice of science, which is now more open, more global and collaborative, and closer to society than ever. Open science has therefore become an increasingly important topic. Moreover, as open science is actively pursued by several high-profile funders and institutions, it has fast become a crucial matter to all researchers. However, because this widespread interest in open science has emerged relatively recently, its definition and implementation are constantly shifting and evolving, sometimes leaving researchers in doubt about how to adopt open science, and which are the best practices to follow. This article therefore aims to be a field guide for scientists who want to perform science in the open, offering resources and tips to make open science happen in the four key areas of data, code, publications and peer-review. The Rationale for Open Science: Standing on the Shoulders of Giants One of the most widely used definitions of open science originates from Michael Nielsen [1]: “Open science is the idea that scientific knowledge of all kinds should be openly shared as early as is practical in the discovery process”. -
Whither the Ingelfinger Rule? an Editor’S Perspective
Whither the Ingelfinger rule? An editor’s perspective Dr Trish Groves Deputy editor, BMJ [email protected] The problem The Food and Drug Amendments Act 2007 requires pharmaceutical companies to register nearly all trials and to disclose their results publicly within a timeframe dictated by the new legislation or pay penalties of $10K a time Will this infringe the Ingelfinger rule and make it impossible to publish trials in medical journals? What results have to be disclosed for FDA? Four tables: • demographic and baseline data collected overall and for each arm of the trial, including patients dropped out and excluded from analysis • raw data and stats tests for each of the primary and secondary outcome measures for each arm of the trial • anticipated and unanticipated serious adverse events grouped by organ system, with number and frequency of such event in each arm of the clinical trial • anticipated and unanticipated adverse events exceeding 5% frequency in any arm of the trial, grouped by organ system What I aim to cover • International Committee of Medical Journal Editors (ICMJE) policy • BMJ policy • what investigators and authors need to know to continue publishing clinical trial results in top-tier journals and comply with the new law ICMJE policy ICMJE said in June 2007 that member journals * will not consider results posted in a clinical trials register as previous publications if presented in the form of a brief, structured (<500 words) abstract or table. ICMJE meets next in May: will this policy change to cover FDAA’s required four tables? * Annals of Internal Medicine, BMJ, Canadian Medical Association Journal, Croatian Medical Journal, JAMA, Nederlands Tijdschrift voor Geneeskunde, New England Journal of Medicine, New Zealand Medical Journal, The Lancet, The Medical Journal of Australia,Tidsskrift for Den Norske Llegeforening, and Ugeskrift for Laeger ICMJE left door open “. -
Downloads Presented on the Abstract Page
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.27.063578; this version posted April 28, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. A systematic examination of preprint platforms for use in the medical and biomedical sciences setting Jamie J Kirkham1*, Naomi Penfold2, Fiona Murphy3, Isabelle Boutron4, John PA Ioannidis5, Jessica K Polka2, David Moher6,7 1Centre for Biostatistics, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom. 2ASAPbio, San Francisco, CA, USA. 3Murphy Mitchell Consulting Ltd. 4Université de Paris, Centre of Research in Epidemiology and Statistics (CRESS), Inserm, Paris, F-75004 France. 5Meta-Research Innovation Center at Stanford (METRICS) and Departments of Medicine, of Epidemiology and Population Health, of Biomedical Data Science, and of Statistics, Stanford University, Stanford, CA, USA. 6Centre for Journalology, Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, Canada. 7School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Canada. *Corresponding Author: Professor Jamie Kirkham Centre for Biostatistics Faculty of Biology, Medicine and Health The University of Manchester Jean McFarlane Building Oxford Road Manchester, M13 9PL, UK Email: [email protected] Tel: +44 (0)161 275 1135 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.27.063578; this version posted April 28, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
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. -
Peer Review Fails Equity Test Analysis of Submissions to Elife Reveals a Gender Gap in Whom Journals Invite to Do Reviews
IN FOCUS NEWS Micrograph of yttrium studied images of the The technique could eventually help barium copper oxide, pseudogap. Patterns physicists to understand high-temperature a high-temperature in the images, taken superconductivity, says Allan, although he superconductor. with a scanning cautions that the paper is far from definitive tunnelling micro- and that debate about what the pseudogap is scope, often seem disordered to the human eye will continue. because of the material’s naturally chaotic and The work is an impressive, original fluctuating nature, and noise in the measure- application of machine-learning algorithms to ments. The advantage of machine learning in this type of experimental data, says Tremblay. this situation is that algorithms can learn to But the algorithm can only distinguish recognize patterns that are invisible to people. between the various hypotheses it is given, he says, rather than find entirely new patterns. PATTERN RECOGNITION During her talk, Kim said that work is under To train the algorithms, the team fed neural way to apply the technique to rapidly make networks examples of rippled patterns that sense of data from the X-ray diffraction of corresponded to different theoretical predic- quantum materials — a technique that uses the tions. Having learnt to recognize these exam- scattering of electromagnetic waves to reveal ples, each algorithm applied this learning to a mater ial’s 3D physical structure, but which real data from cuprates in the pseudogap. Over creates patterns so rich that they can take 81 iterations, the algorithms repeatedly identi- months to unravel by conventional means. In fied one modulating pattern that corresponded this case, the AI must draw out similarities and to the particle-like description of electrons, classifications itself, rather than be given pre- which dates back to the 1990s.