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Reproducibility In Biomedical Research
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Author :National Academies of Sciences, Engineering, and Medicine Publisher :National Academies Press ISBN 13 :0309486165 Total Pages :257 pages Book Rating :4.3/5 (94 download)
Book Synopsis Reproducibility and Replicability in Science by : National Academies of Sciences, Engineering, and Medicine
Download or read book Reproducibility and Replicability in Science written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2019-10-20 with total page 257 pages. Available in PDF, EPUB and Kindle. Book excerpt: One of the pathways by which the scientific community confirms the validity of a new scientific discovery is by repeating the research that produced it. When a scientific effort fails to independently confirm the computations or results of a previous study, some fear that it may be a symptom of a lack of rigor in science, while others argue that such an observed inconsistency can be an important precursor to new discovery. Concerns about reproducibility and replicability have been expressed in both scientific and popular media. As these concerns came to light, Congress requested that the National Academies of Sciences, Engineering, and Medicine conduct a study to assess the extent of issues related to reproducibility and replicability and to offer recommendations for improving rigor and transparency in scientific research. Reproducibility and Replicability in Science defines reproducibility and replicability and examines the factors that may lead to non-reproducibility and non-replicability in research. Unlike the typical expectation of reproducibility between two computations, expectations about replicability are more nuanced, and in some cases a lack of replicability can aid the process of scientific discovery. This report provides recommendations to researchers, academic institutions, journals, and funders on steps they can take to improve reproducibility and replicability in science.
Book Synopsis Research in the Biomedical Sciences by : Michael Williams
Download or read book Research in the Biomedical Sciences written by Michael Williams and published by Academic Press. This book was released on 2017-10-20 with total page 382 pages. Available in PDF, EPUB and Kindle. Book excerpt: Research in the Biomedical Sciences: Transparent and Reproducible documents the widespread concerns related to reproducibility in biomedical research and provides a best practices guide to effective and transparent hypothesis generation, experimental design, reagent standardization (including validation and authentication), statistical analysis, and data reporting. The book addresses issues in the perceived value of the existing peer review process and calls for the need for improved transparency in data reporting. It reflects new guidelines for publication that include manuscript checklists, replication/reproducibility initiatives, and the potential consequences for the biomedical research community and societal health and well-being if training, mentoring, and funding of new generations of researchers and incentives for publications are not improved. This book offers real world examples, insights, and solutions to provide a thought-provoking and timely resource for all those learning about, or engaged in, performing and supervising research across the biomedical sciences. Provides a “big picture perspective on the scope of reproducibility issues and covers initiatives that have potential as effective solutions Offers real-world research context for transparent, reproducible experimental design, execution and reporting of biomedical research with the potential to address aspects of the translational gap in drug discovery Highlights the importance of reproducibility and the necessary changes in biomedical and pharmaceutical research training and incentives to ensure sustainability
Author :National Academies of Sciences, Engineering, and Medicine Publisher :National Academies Press ISBN 13 :0309663490 Total Pages :143 pages Book Rating :4.3/5 (96 download)
Book Synopsis Enhancing Scientific Reproducibility in Biomedical Research Through Transparent Reporting by : National Academies of Sciences, Engineering, and Medicine
Download or read book Enhancing Scientific Reproducibility in Biomedical Research Through Transparent Reporting written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2020-05-28 with total page 143 pages. Available in PDF, EPUB and Kindle. Book excerpt: Sharing knowledge is what drives scientific progress - each new advance or innovation in biomedical research builds on previous observations. However, for experimental findings to be broadly accepted as credible by the scientific community, they must be verified by other researchers. An essential step is for researchers to report their findings in a manner that is understandable to others in the scientific community and provide sufficient information for others to validate the original results and build on them. In recent years, concern has been growing over a number of studies that have failed to replicate previous results and evidence from larger meta-analyses, which have pointed to the lack of reproducibility in biomedical research. On September 25 and 26, 2019, the National Academies of Science, Engineering, and Medicine hosted a public workshop in Washington, DC, to discuss the current state of transparency in the reporting of preclinical biomedical research and to explore opportunities for harmonizing reporting guidelines across journals and funding agencies. Convened jointly by the Forum on Drug Discovery, Development, and Translation; the Forum on Neuroscience and Nervous System Disorders; the National Cancer Policy Forum; and the Roundtable on Genomics and Precision Health, the workshop primarily focused on transparent reporting in preclinical research, but also considered lessons learned and best practices from clinical research reporting. This publication summarizes the presentation and discussion of the workshop.
Book Synopsis Introduction to the Responsible Conduct of Research (rev. Ed. ) by : Nicholas H. Steneck
Download or read book Introduction to the Responsible Conduct of Research (rev. Ed. ) written by Nicholas H. Steneck and published by DIANE Publishing. This book was released on 2009-09 with total page 182 pages. Available in PDF, EPUB and Kindle. Book excerpt: This report seeks to supplement existing resources by making a comprehensive overview of basic rules of the road for responsible research available to all U.S. Public Health Service-funded researchers. It has been prepared with the needs of small and mid-size research and institutions and beginning researchers in mind, but it may be used in other settings. Illustrations.
Book Synopsis Reproducibility in Biomedical Research by : Erwin B. Montgomery Jr.
Download or read book Reproducibility in Biomedical Research written by Erwin B. Montgomery Jr. and published by Elsevier. This book was released on 2024-04-26 with total page 464 pages. Available in PDF, EPUB and Kindle. Book excerpt: Reproducibility in Biomedical Research: Epistemological and Statistical Problems, 2nd Ed. explores the ideas and conundrums inherent in scientific research. Reproducibility is one of the biggest challenges in biomedical research. It affects not only the ability to replicate results, but the very trust in the findings. Since published in 2019, Reproducibility of Biomedical Research: Epistemological and Statistical Problems established itself as a solid ethical reference in the area, leading to significant reflection on biomedical research. The second edition addresses new challenges to reproducibility in biosciences, namely reproducibility of machine learning Artificial Intelligence (AI), reproducibility of translation from research to medical care, and the fundamental challenges to reproducibility. All current chapters will be expanded to cover advances in the topics previously addressed. Reproducibility in Biomedical Research: Epistemological and Statistical Problems, 2nd Ed. provides biomedical researchers with a framework to better understand the reproducibility challenges in the area. Newly introduced interactive exercises and updated case studies help students understand the fundamental concepts involved in the area. Includes four new chapters and updates across the book, covering recent developments of issues affecting reproducibility in biomedical researchCovers reproducibility of results from machine learning AI algorithmsPresents new case studies to illustrate challenges in related fieldsIncludes a companion website with interactive exercises and summary tables
Book Synopsis Reproducible Research with R and RStudio by : Christopher Gandrud
Download or read book Reproducible Research with R and RStudio written by Christopher Gandrud and published by CRC Press. This book was released on 2020-02-21 with total page 299 pages. Available in PDF, EPUB and Kindle. Book excerpt: Praise for previous editions: "Gandrud has written a great outline of how a fully reproducible research project should look from start to finish, with brief explanations of each tool that he uses along the way... Advanced undergraduate students in mathematics, statistics, and similar fields as well as students just beginning their graduate studies would benefit the most from reading this book. Many more experienced R users or second-year graduate students might find themselves thinking, ‘I wish I’d read this book at the start of my studies, when I was first learning R!’...This book could be used as the main text for a class on reproducible research ..." (The American Statistician) Reproducible Research with R and R Studio, Third Edition brings together the skills and tools needed for doing and presenting computational research. Using straightforward examples, the book takes you through an entire reproducible research workflow. This practical workflow enables you to gather and analyze data as well as dynamically present results in print and on the web. Supplementary materials and example are available on the author’s website. New to the Third Edition Updated package recommendations, examples, URLs, and removed technologies no longer in regular use. More advanced R Markdown (and less LaTeX) in discussions of markup languages and examples. Stronger focus on reproducible working directory tools. Updated discussion of cloud storage services and persistent reproducible material citation. Added discussion of Jupyter notebooks and reproducible practices in industry. Examples of data manipulation with Tidyverse tibbles (in addition to standard data frames) and pivot_longer() and pivot_wider() functions for pivoting data. Features Incorporates the most important advances that have been developed since the editions were published Describes a complete reproducible research workflow, from data gathering to the presentation of results Shows how to automatically generate tables and figures using R Includes instructions on formatting a presentation document via markup languages Discusses cloud storage and versioning services, particularly Github Explains how to use Unix-like shell programs for working with large research projects
Book Synopsis The Practice of Reproducible Research by : Justin Kitzes
Download or read book The Practice of Reproducible Research written by Justin Kitzes and published by Univ of California Press. This book was released on 2018 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Practice of Reproducible Research presents concrete examples of how researchers in the data-intensive sciences are working to improve the reproducibility of their research projects. In each of the thirty-one case studies in this volume, the author or team describes the workflow that they used to complete a real-world research project. Authors highlight how they utilized particular tools, ideas, and practices to support reproducibility, emphasizing the very practical how, rather than the why or what, of conducting reproducible research. Part 1 provides an accessible introduction to reproducible research, a basic reproducible research project template, and a synthesis of lessons learned from across the thirty-one case studies. Parts 2 and 3 focus on the case studies themselves. The Practice of Reproducible Research is an invaluable resource for students and researchers who wish to better understand the practice of data-intensive sciences and learn how to make their own research more reproducible.
Download or read book Rigor Mortis written by Richard Harris and published by Hachette UK. This book was released on 2017-04-04 with total page 288 pages. Available in PDF, EPUB and Kindle. Book excerpt: An essential book to understanding whether the new miracle cure is good science or simply too good to be true American taxpayers spend $30 billion annually funding biomedical research, but over half of these studies can't be replicated due to poor experimental design, improper methods, and sloppy statistics. Bad science doesn't just hold back medical progress, it can sign the equivalent of a death sentence for terminal patients. In Rigor Mortis, Richard Harris explores these urgent issues with vivid anecdotes, personal stories, and interviews with the top biomedical researchers. We need to fix our dysfunctional biomedical system -- before it's too late.
Book Synopsis Good Research Practice in Non-Clinical Pharmacology and Biomedicine by : Anton Bespalov
Download or read book Good Research Practice in Non-Clinical Pharmacology and Biomedicine written by Anton Bespalov and published by Springer Nature. This book was released on 2020-01-01 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access book, published under a CC BY 4.0 license in the Pubmed indexed book series Handbook of Experimental Pharmacology, provides up-to-date information on best practice to improve experimental design and quality of research in non-clinical pharmacology and biomedicine.
Book Synopsis Implementing Reproducible Research by : Victoria Stodden
Download or read book Implementing Reproducible Research written by Victoria Stodden and published by CRC Press. This book was released on 2018-12-14 with total page 450 pages. Available in PDF, EPUB and Kindle. Book excerpt: In computational science, reproducibility requires that researchers make code and data available to others so that the data can be analyzed in a similar manner as in the original publication. Code must be available to be distributed, data must be accessible in a readable format, and a platform must be available for widely distributing the data and code. In addition, both data and code need to be licensed permissively enough so that others can reproduce the work without a substantial legal burden. Implementing Reproducible Research covers many of the elements necessary for conducting and distributing reproducible research. It explains how to accurately reproduce a scientific result. Divided into three parts, the book discusses the tools, practices, and dissemination platforms for ensuring reproducibility in computational science. It describes: Computational tools, such as Sweave, knitr, VisTrails, Sumatra, CDE, and the Declaratron system Open source practices, good programming practices, trends in open science, and the role of cloud computing in reproducible research Software and methodological platforms, including open source software packages, RunMyCode platform, and open access journals Each part presents contributions from leaders who have developed software and other products that have advanced the field. Supplementary material is available at www.ImplementingRR.org.
Book Synopsis Towards Bayesian Model-Based Demography by : Jakub Bijak
Download or read book Towards Bayesian Model-Based Demography written by Jakub Bijak and published by Springer Nature. This book was released on 2021-12-09 with total page 277 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access book presents a ground-breaking approach to developing micro-foundations for demography and migration studies. It offers a unique and novel methodology for creating empirically grounded agent-based models of international migration – one of the most uncertain population processes and a top-priority policy area. The book discusses in detail the process of building a simulation model of migration, based on a population of intelligent, cognitive agents, their networks and institutions, all interacting with one another. The proposed model-based approach integrates behavioural and social theory with formal modelling, by embedding the interdisciplinary modelling process within a wider inductive framework based on the Bayesian statistical reasoning. Principles of uncertainty quantification are used to devise innovative computer-based simulations, and to learn about modelling the simulated individuals and the way they make decisions. The identified knowledge gaps are subsequently filled with information from dedicated laboratory experiments on cognitive aspects of human decision-making under uncertainty. In this way, the models are built iteratively, from the bottom up, filling an important epistemological gap in migration studies, and social sciences more broadly.
Book Synopsis A Survey of Nature by : George Rex Green
Download or read book A Survey of Nature written by George Rex Green and published by . This book was released on 1926 with total page 158 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author :National Academies of Sciences, Engineering, and Medicine Publisher :National Academies Press ISBN 13 :0309392020 Total Pages :133 pages Book Rating :4.3/5 (93 download)
Book Synopsis Statistical Challenges in Assessing and Fostering the Reproducibility of Scientific Results by : National Academies of Sciences, Engineering, and Medicine
Download or read book Statistical Challenges in Assessing and Fostering the Reproducibility of Scientific Results written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2016-03-29 with total page 133 pages. Available in PDF, EPUB and Kindle. Book excerpt: Questions about the reproducibility of scientific research have been raised in numerous settings and have gained visibility through several high-profile journal and popular press articles. Quantitative issues contributing to reproducibility challenges have been considered (including improper data measurement and analysis, inadequate statistical expertise, and incomplete data, among others), but there is no clear consensus on how best to approach or to minimize these problems. A lack of reproducibility of scientific results has created some distrust in scientific findings among the general public, scientists, funding agencies, and industries. While studies fail for a variety of reasons, many factors contribute to the lack of perfect reproducibility, including insufficient training in experimental design, misaligned incentives for publication and the implications for university tenure, intentional manipulation, poor data management and analysis, and inadequate instances of statistical inference. The workshop summarized in this report was designed not to address the social and experimental challenges but instead to focus on the latter issues of improper data management and analysis, inadequate statistical expertise, incomplete data, and difficulties applying sound statistic inference to the available data. Many efforts have emerged over recent years to draw attention to and improve reproducibility of scientific work. This report uniquely focuses on the statistical perspective of three issues: the extent of reproducibility, the causes of reproducibility failures, and the potential remedies for these failures.
Author :National Academies of Sciences, Engineering, and Medicine Publisher :National Academies Press ISBN 13 :0309391253 Total Pages :327 pages Book Rating :4.3/5 (93 download)
Book Synopsis Fostering Integrity in Research by : National Academies of Sciences, Engineering, and Medicine
Download or read book Fostering Integrity in Research written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2018-01-13 with total page 327 pages. Available in PDF, EPUB and Kindle. Book excerpt: The integrity of knowledge that emerges from research is based on individual and collective adherence to core values of objectivity, honesty, openness, fairness, accountability, and stewardship. Integrity in science means that the organizations in which research is conducted encourage those involved to exemplify these values in every step of the research process. Understanding the dynamics that support â€" or distort â€" practices that uphold the integrity of research by all participants ensures that the research enterprise advances knowledge. The 1992 report Responsible Science: Ensuring the Integrity of the Research Process evaluated issues related to scientific responsibility and the conduct of research. It provided a valuable service in describing and analyzing a very complicated set of issues, and has served as a crucial basis for thinking about research integrity for more than two decades. However, as experience has accumulated with various forms of research misconduct, detrimental research practices, and other forms of misconduct, as subsequent empirical research has revealed more about the nature of scientific misconduct, and because technological and social changes have altered the environment in which science is conducted, it is clear that the framework established more than two decades ago needs to be updated. Responsible Science served as a valuable benchmark to set the context for this most recent analysis and to help guide the committee's thought process. Fostering Integrity in Research identifies best practices in research and recommends practical options for discouraging and addressing research misconduct and detrimental research practices.
Book Synopsis Experimental Design for Laboratory Biologists by : Stanley E. Lazic
Download or read book Experimental Design for Laboratory Biologists written by Stanley E. Lazic and published by Cambridge University Press. This book was released on 2016-12-08 with total page 429 pages. Available in PDF, EPUB and Kindle. Book excerpt: Specifically intended for lab-based biomedical researchers, this practical guide shows how to design experiments that are reproducible, with low bias, high precision, and widely applicable results. With specific examples from research using both cell cultures and model organisms, it explores key ideas in experimental design, assesses common designs, and shows how to plan a successful experiment. It demonstrates how to control biological and technical factors that can introduce bias or add noise, and covers rarely discussed topics such as graphical data exploration, choosing outcome variables, data quality control checks, and data pre-processing. It also shows how to use R for analysis, and is designed for those with no prior experience. An accompanying website (https://stanlazic.github.io/EDLB.html) includes all R code, data sets, and the labstats R package. This is an ideal guide for anyone conducting lab-based biological research, from students to principle investigators working in either academia or industry.
Book Synopsis Reproducibility by : Edo D. Pellizzari
Download or read book Reproducibility written by Edo D. Pellizzari and published by RTI Press. This book was released on 2017 with total page 75 pages. Available in PDF, EPUB and Kindle. Book excerpt: Science is allegedly in the midst of a reproducibility crisis, but questions of reproducibility and related principles date back nearly 80 years. Numerous controversies have arisen, especially since 2010, in a wide array of disciplines that stem from the failure to reproduce studies or their findings:biology, biomedical and preclinical research, business and organizational studies, computational sciences, drug discovery, economics, education, epidemiology and statistics, genetics, immunology, policy research, political science, psychology, and sociology. This monograph defines terms and constructs related to reproducible research, weighs key considerations and challenges in reproducing or replicating studies, and discusses transparency in publications that can support reproducible research goals. It attempts to clarify reproducible research, with its attendant (and confusing or even conflicting) lexicon and aims to provide useful background, definitions, and practical guidance for all readers. Among its conclusions: First, researchers must become better educated about these issues, particularly the differences between the concepts and terms. The main benefit is being able to communicate clearly within their own fields and, more importantly, across multiple disciplines. In addition, scientists need to embrace these concepts as part of their responsibilities as good stewards of research funding and as providers of credible information for policy decision making across many areas of public concern. Finally, although focusing on transparency and documentation is essential, ultimately the goal is achieving the most rigorous, high-quality science possible given limitations on time, funding, or other resources. “The authors have written a nuanced and thoughtful primer on scientific reproducibility. By highlighting the social, political, and technical importance of reproducibility, together with a precise description of the related concepts of reproducibility, replicability, and repeatability, this primer provides a significant resource that all practicing researchers should read.” Daniel Reed, Vice President for Research and Economic Development, University of Iowa and former Corporate Vice President, Microsoft “This is a well-written, clearly articulated, and timely primer on the developing and evolving rich terminology of reproducible research. The primer, put together by authors with deep experience and expertise in the topic area, focuses primarily on human-centric research in biomedicine, medicine, and the social sciences as well as reproducibility issues in analytics and computational science. The growing focus on reproducibility will open new vistas in research methodologies, meta analysis, comparative studies of research results, and reuse and adaptation of results from prior research. This primer provides an excellent overview of the subject area, and I would recommend it to anyone interested in coming up to speed on current issues in reproducible research.” Chaitan Baru, Distinguished Scientist and Associate Director for Data Initiatives, San Diego Supercomputing Center; current appointment as Senior Advisor for Data Science, Computer and Information Science and Engineering Directorate, National Science Foundation “Pellizzari et al. have taken on the Herculean task of collecting, synthesizing, and relating the various interpretations of reproducibility used in the research community today, and turned the result into an accessible must-read guide. This important work provides a Rosetta Stone for various stakeholders to discuss and implement solutions that make real progress toward a research enterprise that routinely produces reproducible findings.” Victoria Stodden, Associate Professor at the School of Information Sciences, University of Illinois at Urbana Champaign and co-editor of the books Implementing Reproducible Research and Privacy, Big Data, and the Public Good: Frameworks for Engagement
Book Synopsis Basic Science Methods for Clinical Researchers by : Morteza Jalali
Download or read book Basic Science Methods for Clinical Researchers written by Morteza Jalali and published by Academic Press. This book was released on 2017-03-31 with total page 382 pages. Available in PDF, EPUB and Kindle. Book excerpt: Basic Science Methods for Clinical Researchers addresses the specific challenges faced by clinicians without a conventional science background. The aim of the book is to introduce the reader to core experimental methods commonly used to answer questions in basic science research and to outline their relative strengths and limitations in generating conclusive data. This book will be a vital companion for clinicians undertaking laboratory-based science. It will support clinicians in the pursuit of their academic interests and in making an original contribution to their chosen field. In doing so, it will facilitate the development of tomorrow’s clinician scientists and future leaders in discovery science. Serves as a helpful guide for clinical researchers who lack a conventional science background Organized around research themes pertaining to key biological molecules, from genes, to proteins, cells, and model organisms Features protocols, techniques for troubleshooting common problems, and an explanation of the advantages and limitations of a technique in generating conclusive data Appendices provide resources for practical research methodology, including legal frameworks for using stem cells and animals in the laboratory, ethical considerations, and good laboratory practice (GLP)
