Ten Simple Rules to Consider Regarding Preprint Submission
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What Is Biomath?
What is Biomath? Summary Biomathematics covers a wide range of activities at the interface between the mathematical and biological sciences. Depending on who you talk to, it might have a different name, including mathematical biology, systems biology, quantitative biology or theoretical biology. The focus of our biomathematics program is on building and using mathematical models to describe and analyze biological systems. Often this involves the analysis of biological data, which typically means using statistical approaches together with the models. In many cases, our models are mechanistic, meaning that their components represent biological processes, although many of us also use models that are more statistical in nature. More In-Depth Biomathematics is the use of mathematical models to help understand phenomena in biology. Modern experimental biology is very good at taking biological systems apart (at all levels of organization, from genome to global nutrient cycling), into components simple enough that their structure and function can be studied in isolation. Dynamic models are a way to put the pieces back together, with equations that represent the system’s components, processes, and the structure of their interactions. Mathematical models are important tools in basic scientific research in many areas of biology, including physiology, cellular biology, developmental biology, ecology, evolution, toxicology, epidemiology, immunology, natural resource management, and conservation biology. The results obtained from analysis and simulation -
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. -
1 the Challenges Facing Genomic Informatics
1 The Challenges Facing Genomic Informatics Temple F. Smith What are these areas of intense research labeled bioinformatics and functional genomics? If we take literally much of the recently published "news and views," it seems that the often stated claim that the last century was the century of physics, whereas the twenty-first will be the century of biology, rests significantly on these new research areas. We might therefore ask: What is new about them? After all, compu- tational or mathematical biology has been around for a long time. Surely much of bioinformatics, particularly that associated with evolution and genetic analyses, does not appear very new. In fact, the related work of researchers like R. A. Fisher, J. B. S. Haldane, and SewellWright dates nearly to the beginning of the 1900s. The modem analytical approaches to genetics, evolution, and ecology rest directly on their and similar work. Even genetic mapping easily dates to the 1930s, with the work of T. S. Painter and his students of Drosophila (still earlier if you include T. H. Morgan's work on X-linked markers in the fly). Thus a short historical review might provide a useful perspective on this anticipated century of biology and allow us to view the future from a firmer foundation. First of all, it should be helpful to recognize that it was very early in the so-called century of physics that modem biology began, with a paper read by Hermann Muller at a 1921meeting in Toronto. Muller, a student of Morgan's, stated that although of submicroscopic size, the gene was clearly a physical particle of complex structure, not just a working construct! Muller noted that the gene is unique from its product, and that it is normally duplicated unchanged, but once mutated, the new form is in turn duplicated faithfully. -
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 “. -
Rapporti ISTISAN 07/12 Istituto Superiore Di Sanità Conference
ISTITUTO SUPERIORE DI SANITÀ Conference Institutional archives for research: experiences and projects in Open Access Istituto Superiore di Sanità Rome, 30 November - 1 December 2006 Proceedings edited by Paola De Castro and Elisabetta Poltronieri Servizio Informatico, Documentazione, Biblioteca ed Attività editoriali ISSN 1123-3117 Rapporti ISTISAN 07/12 Istituto Superiore di Sanità Conference. Institutional archives for research: experiences and projects in Open Access. Istituto Superiore di Sanità. Rome, 30 November-1 December 2006. Proceedings edited by Paola De Castro and Elisabetta Poltronieri 2007, vi, 112 p. Rapporti ISTISAN 07/12 The Congress was organised into four sessions: 1) Open Access (OA) and authors: support from the international community; 2) OA in Italy: knowledge and tools to write and search; 3) institutional policies for OA; 4) opportunities and services to develop OA. It was aimed at achieving the following objectives: a) make authors of biomedical publications aware of the benefits of depositing research material in digital open archives and publishing in OA peer- reviewed journals; b) outline the impact of the OA publishing model on the assessment of research output; c) enhance the adoption of policies encouraging the OA paradigm; d) promote cooperation between research institutions in Italy and abroad to share resources and experiences on institutional repositories. A useful introductory bibliography on the OA publishing model in the biomedical field is included in the Appendix. Key words: Open Access publishing model, Scientific publications, Institutional repositories, Editorial policies, Bibliography Istituto Superiore di Sanità Congresso. Archivi istituzionali per la ricerca: esperienze e progetti di Open Access. Istituto Superiore di Sanità. Roma, 30 novembre-1 dicembre 2006. -
QUANTITATIVE BIOLOGY This Interdiscplinary Major Bridges the Space Between Biology, Chemistry, Data Science, and Engineering
QUANTITATIVE BIOLOGY This interdiscplinary major bridges the space between biology, chemistry, data science, and engineering. It allows students interested in studying the life sciences to achieve a fuller background in the quantitative sciences such as computer science and statistics that are essential for modern data-driven biological science. The Quantitative Biology major is designed to train students to be both high-level biologists and high-level data analysts. Students will take an introductory seminar, participate in undergraduate research, and write an honors thesis. BACHELOR OF SCIENCE (BS) GENERAL OVERVIEW Seven lower division courses: One advanced biology course. Examples include: General Biology — Organismal Biology and Evolution Evolution and Population Genetics General Biology — Cell Biology and Physiology Molecular Biology Introduction to Quantitative Biology Seminar General Chemistry A At least two upper division courses. Examples include: Introduction to Programming Cellular and Molecular Neuroscience Data Structures and Object Oriented Design Mathematics of Machine Learning Calculus I Fundamentals of Physics I Choose one Capstone course from the following: Choose five courses from the following areas: Computational Genome Analysis Structural Bioinformatics: From Atoms to Cells Physics Chemistry Research Experience: Mathematics Students are required to enroll in directed Computer Science research in a lab approved by the Quantitative Biology Executive Committee or assigned faculty adviser EXPERIENTIAL OPPORTUNITIES Freshman -
Publishing Collaborative Studies Between Academics and Industry
Eur Respir J 1997; 10: 2441–2442 Copyright ERS Journals Ltd 1997 DOI: 10.1183/09031936.97.10112441 European Respiratory Journal Printed in UK - all rights reserved ISSN 0903 - 1936 EDITORIAL Publishing collaborative studies between academics and industry P.J. Sterk*, K. Larsson**, R. Naeije+, U. Costabel++ Research partnership should be in accordance with legal and ethical regula- tions, and with the standard rules generally obeyed by During the last decade we have observed a large pro- the scientific community. gress in biomedical research in general, and in the pul- monary field in particular. This is shown by the almost What can go wrong? exponential increase in the quantity of published sci- ence, as well as by the obvious improvement of its over- The editors of the ERJ have recently faced a serious all quality. We are very pleased that this is certainly dilemma as to whether to publish a manuscript submit- apparent from the current submissions to the European ted by PALMQVIST et al. [1]. This is a collaborative study Respiratory Journal (ERJ). between academic researchers and a pharmaceutical Presumably, one of the reasons for this favourable company. Although not innovative in the strict sense, development is the improved exchange of information the study provides useful data on the application of anti- among scientists all over the world. This has been facili- asthma drugs, also to be used for an international regi- tated by modern communication techniques, and seems stration dossier. Even though the manuscript of the to have led to intensive and frank collaboration between study had passed the scientific peer review process after different research groups and institutes. -
Introduction to Open Access
INTRODUCTION TO OPEN ACCESS John Borghi, PhD Manager, Research and Instruction Lane Medical Library Open Access Week OA Week at Lane Library Enhancing Your Researcher Profile with ORCID | October 19, 2:00 pm A Brief Introduction to Preprints October 20, 2:00 pm Introduction to Dryad (Data Sharing) October 22, 2:00 pm Open Science Reading Group October 27, 2:00 pm All events are free of charge and conducted virtually. Visit Lane.Stanford.edu to register for our upcoming classes and events. Today’s Agenda Preprints!? Wrap up 2:00 3:00 What is OA? Breakout Groups Fraser, N., et al. (2020). Preprinting a pandemic: The role of preprints in the COVID-19 Reading for today: pandemic. BioRxiv. https://doi.org/10.1101/2020.05.22.111294 Penfold, N. C., & Polka, J. K. (2020). Technical and social issues influencing the adoption of preprints in the life sciences. PLOS Genetics, 16(4), Additional reading: e1008565. https://doi.org/10.1371/journal.pgen.1008565 Suber, P. (2012). What is Open Access? In Open Access (pp 1-27). MIT Press. https://archive.org/details/9780262517638OpenAccess/page/n13/mode/2up What is Open Access? By "open access" to [peer reviewed] literature, we mean its free availability on the public internet, permitting any users to For a work to be OA, the copyright holder read, download, copy, distribute, print, must consent in advance to let users “copy, search, or link to the full texts of these use, distribute, transmit and display the articles, crawl them for indexing, pass work publicly and to make and distribute them as data to software, or use them for derivative works, in any digital medium for any other lawful purpose, without any responsible purpose, subject to proper financial, legal, or technical barriers other attribution of authorship.” than those inseparable from gaining access to the internet itself. -
Gender Disparity in Computational Biology Research Publications
bioRxiv preprint doi: https://doi.org/10.1101/070631; this version posted August 26, 2016. 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. Gender disparity in computational biology research publications Kevin S. Bonham and Melanie I. Stefan Abstract While women are generally underrepresented in STEM fields, there are noticeable differences between fields. For instance, the gender ratio in biology is more balanced than in computer science. We were interested in how this difference is reflected in the interdisciplinary field of computational/quantitative biology. To this end, we examined the proportion of female authors in publications from the PubMed and arXiv databases. There are fewer female authors on research papers in computational biology, as compared to biology in general. This is true across authorship positions, year, and journal impact factor. A comparison with arXiv shows that quantitative biology papers have a higher ratio of female authors than computer science papers, placing computational biology in between its two parent fields in terms of gender representation. Both in biology and in computational biology, a female last author increases the probability of other authors on the paper being female, pointing to a potential role of female PIs in influencing the gender balance. Intro There is ample literature on the underrepresentation of women in STEM fields and the biases contributing to it. Those biases, though often subtle, are pervasive in several ways: they are often held and perpetuated by both men and women, and they are apparent across all aspects of academic and scientific practice. -
Challenges and Changing Roles for Medical Journals in the Cyberspace Age: Electronic Pre-Prints and E-Papers
JOURNAL OF MEDICAL INTERNET RESEARCH Eysenbach Editorial Challenges and changing roles for medical journals in the cyberspace age: Electronic pre-prints and e-papers Gunther Eysenbach (J Med Internet Res 1999;1(2):e9) doi: 10.2196/jmir.1.2.e9 "We are in the business of revealing, not suppressing for the very purpose of open peer-review and in an effort to information." improve the manuscript are routinely rejected by these journals, with the argument that the public shall in this manner be J. P. Kassirer, N. Eng. J. Med. 327, 1238 (1992). protected from non-peer-reviewed, low-quality information. It In May 1999, the Director of the US National Institutes of shows the paternalistic concern of these journals, their belief Health (NIH), Harold Vermus, proposed a project, then dubbed that the public cannot discriminate between the different levels "E-biomed" [1] (now called "PubMed Central" [2]). In this of credibility of a manuscript. Another explanation for this proposal, the National Institutes of Health - through the National unwillingness to embrace electronic advance publication could Center for Biotechnology Information, a component of the be that traditional paper journals attempt to preserve their National Library of Medicine - proposed to establish an priority, newsworthiness, and exclusive access to research papers Internet-accessible database of full electronic papers, which (which has long been a guarantee for circulation, attention, and would be submitted directly by their authors. The original paid advertisements for their journals). However, this race of E-biomed plan [1] envisaged two sections in this system: one traditional journals against the Internet for priority and that allowed authors to submit papers which would only be exclusivity of research reports cannot be won by the journals. -
The Center for Quantitative Biology at Peking University
Quantitative Biology 2015, 3(1): 1–3 DOI 10.1007/s40484-015-0041-2 INTRODUCING A CENTER The Center for Quantitative Biology at Peking University Jing Yuan*, Luhua Lai and Chao Tang Center for Quantitative Biology, Peking University, Beijing 100871, China * Correspondence: [email protected] Received January 30, 2014; OVERVIEW biology; (ii) synthetic biology; (iii) computational biology and bioinformatics; (iv) disease mechanism and drug In the 21st century, scientific research is becoming more design from a system biology perspective. The goal of and more interdisciplinary. New discoveries are often CQB is to become a leading research center in the field of made at the boundaries of different disciplines. Biology is system biology and to promote the development of entering a new era in which quantitative measurements quantitative life sciences. In recent years, CQB received a and mathematical modeling play increasingly important number of major funding supports from the Ministry of roles in understanding and predicting biological behavior. Science and Technology of China and the National Facing this challenge and opportunity, the Center for Natural Science Foundation of China. Exciting and Quantitative Biology (CQB, formally the Center for cutting-edge researches are being carried out at CQB, Theoretical Biology) was established in 2001, with the some of which have been published in prestigious support of the Nobel Laureate Prof. T. D. Lee and the journals such as Cell, Science, Nature Chemistry, PNAS, leadership of Peking University. As part of PKU’s PRL, JACS, Angew Chem. strategic initiative in enhancing interdisciplinary research, CQB is dedicated to research and education at the EDUCATION interface between the traditional more quantitative disciplines (such as mathematics, physical sciences, Education has always been a priority of CQB. -
Scientific Autonomy, Public Accountability, and the Rise of “Peer Review” in the Cold War United States
Scientific Autonomy, Public Accountability, and the Rise of “Peer Review” intheColdWar United States Melinda Baldwin, American Institute of Physics Abstract: This essay traces the history of refereeing at specialist scientific jour- nals and at funding bodies and shows that it was only in the late twentieth cen- tury that peer review came to be seen as a process central to scientific practice. Throughout the nineteenth century and into much of the twentieth, external referee reports were considered an optional part of journal editing or grant making. The idea that refereeing is a requirement for scientific legitimacy seems to have arisen first in the Cold War United States. In the 1970s, in the wake of a series of attacks on scientific funding, American scientists faced a dilemma: there was increasing pressure for science to be accountable to those who funded it, but scientists wanted to ensure their continuing influence over funding decisions. Scientists and their supporters cast expert refereeing—or “peer review,” as it was increasingly called—as the crucial process that ensured the credibility of science as a whole. Taking funding decisions out of expert hands, they argued, would be a corruption of science itself. This public elevation of peer review both reinforced and spread the belief that only peer-reviewed science was scientifically legitimate. y the time this essay reaches print, it will have passed through a gauntlet familiar to scholars Bin every discipline. The editor of this journal will have sent it to two or three anonymous referees. If the referees deemed the contents potentially worthy of publication (and this article could have been rejected once, twice, or many times before finding a home), they will have offered comments on how it should be improved before publication.