Literature DB >> 29531050

An empirical analysis of journal policy effectiveness for computational reproducibility.

Victoria Stodden1, Jennifer Seiler2, Zhaokun Ma2.   

Abstract

A key component of scientific communication is sufficient information for other researchers in the field to reproduce published findings. For computational and data-enabled research, this has often been interpreted to mean making available the raw data from which results were generated, the computer code that generated the findings, and any additional information needed such as workflows and input parameters. Many journals are revising author guidelines to include data and code availability. This work evaluates the effectiveness of journal policy that requires the data and code necessary for reproducibility be made available postpublication by the authors upon request. We assess the effectiveness of such a policy by (i) requesting data and code from authors and (ii) attempting replication of the published findings. We chose a random sample of 204 scientific papers published in the journal Science after the implementation of their policy in February 2011. We found that we were able to obtain artifacts from 44% of our sample and were able to reproduce the findings for 26%. We find this policy-author remission of data and code postpublication upon request-an improvement over no policy, but currently insufficient for reproducibility.

Keywords:  code access; data access; open science; reproducibility policy; reproducible research

Year:  2018        PMID: 29531050      PMCID: PMC5856507          DOI: 10.1073/pnas.1708290115

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  9 in total

1.  Reproducible research in computational science.

Authors:  Roger D Peng
Journal:  Science       Date:  2011-12-02       Impact factor: 47.728

2.  Certificates of Confidentiality: Protecting Human Subject Research Data in Law and Practice.

Authors:  Leslie E Wolf; Mayank J Patel; Brett A Williams Tarver; Jeffrey L Austin; Lauren A Dame; Laura M Beskow
Journal:  J Law Med Ethics       Date:  2015       Impact factor: 1.718

3.  Repeatability of published microarray gene expression analyses.

Authors:  John P A Ioannidis; David B Allison; Catherine A Ball; Issa Coulibaly; Xiangqin Cui; Aedín C Culhane; Mario Falchi; Cesare Furlanello; Laurence Game; Giuseppe Jurman; Jon Mangion; Tapan Mehta; Michael Nitzberg; Grier P Page; Enrico Petretto; Vera van Noort
Journal:  Nat Genet       Date:  2008-01-28       Impact factor: 38.330

4.  Making data maximally available.

Authors:  Brooks Hanson; Andrew Sugden; Bruce Alberts
Journal:  Science       Date:  2011-02-11       Impact factor: 47.728

5.  Recommendations for utilizing and reporting population genetic analyses: the reproducibility of genetic clustering using the program STRUCTURE.

Authors:  Kimberly J Gilbert; Rose L Andrew; Dan G Bock; Michelle T Franklin; Nolan C Kane; Jean-Sébastien Moore; Brook T Moyers; Sébastien Renaut; Diana J Rennison; Thor Veen; Timothy H Vines
Journal:  Mol Ecol       Date:  2012-09-24       Impact factor: 6.185

6.  Enhancing reproducibility for computational methods.

Authors:  Victoria Stodden; Marcia McNutt; David H Bailey; Ewa Deelman; Yolanda Gil; Brooks Hanson; Michael A Heroux; John P A Ioannidis; Michela Taufer
Journal:  Science       Date:  2016-12-09       Impact factor: 47.728

7.  Reproducing Epidemiologic Research and Ensuring Transparency.

Authors:  Steven S Coughlin
Journal:  Am J Epidemiol       Date:  2017-08-15       Impact factor: 4.897

8.  SCIENTIFIC STANDARDS. Promoting an open research culture.

Authors:  B A Nosek; G Alter; G C Banks; D Borsboom; S D Bowman; S J Breckler; S Buck; C D Chambers; G Chin; G Christensen; M Contestabile; A Dafoe; E Eich; J Freese; R Glennerster; D Goroff; D P Green; B Hesse; M Humphreys; J Ishiyama; D Karlan; A Kraut; A Lupia; P Mabry; T A Madon; N Malhotra; E Mayo-Wilson; M McNutt; E Miguel; E Levy Paluck; U Simonsohn; C Soderberg; B A Spellman; J Turitto; G VandenBos; S Vazire; E J Wagenmakers; R Wilson; T Yarkoni
Journal:  Science       Date:  2015-06-26       Impact factor: 47.728

9.  Toward Reproducible Computational Research: An Empirical Analysis of Data and Code Policy Adoption by Journals.

Authors:  Victoria Stodden; Peixuan Guo; Zhaokun Ma
Journal:  PLoS One       Date:  2013-06-21       Impact factor: 3.240

  9 in total
  53 in total

1.  The rapid proliferation of solicited content online journals: a quest to disseminate knowledge?

Authors:  Richard C Becker; Vlad Cotarlan; Sakthi Sadayappan
Journal:  J Thromb Thrombolysis       Date:  2019-04       Impact factor: 2.300

2.  "Reproducible" Research in Mathematical Sciences Requires Changes in our Peer Review Culture and Modernization of our Current Publication Approach.

Authors:  Santiago Schnell
Journal:  Bull Math Biol       Date:  2018-09-19       Impact factor: 1.758

3.  Reproducible Research Using Biomodels.

Authors:  Pedro Mendes
Journal:  Bull Math Biol       Date:  2018-09-06       Impact factor: 1.758

4.  Reproducibility of research: Issues and proposed remedies.

Authors:  David B Allison; Richard M Shiffrin; Victoria Stodden
Journal:  Proc Natl Acad Sci U S A       Date:  2018-03-12       Impact factor: 11.205

Review 5.  Open Science principles for accelerating trait-based science across the Tree of Life.

Authors:  Rachael V Gallagher; Daniel S Falster; Brian S Maitner; Roberto Salguero-Gómez; Vigdis Vandvik; William D Pearse; Florian D Schneider; Jens Kattge; Jorrit H Poelen; Joshua S Madin; Markus J Ankenbrand; Caterina Penone; Xiao Feng; Vanessa M Adams; John Alroy; Samuel C Andrew; Meghan A Balk; Lucie M Bland; Brad L Boyle; Catherine H Bravo-Avila; Ian Brennan; Alexandra J R Carthey; Renee Catullo; Brittany R Cavazos; Dalia A Conde; Steven L Chown; Belen Fadrique; Heloise Gibb; Aud H Halbritter; Jennifer Hammock; J Aaron Hogan; Hamish Holewa; Michael Hope; Colleen M Iversen; Malte Jochum; Michael Kearney; Alexander Keller; Paula Mabee; Peter Manning; Luke McCormack; Sean T Michaletz; Daniel S Park; Timothy M Perez; Silvia Pineda-Munoz; Courtenay A Ray; Maurizio Rossetto; Hervé Sauquet; Benjamin Sparrow; Marko J Spasojevic; Richard J Telford; Joseph A Tobias; Cyrille Violle; Ramona Walls; Katherine C B Weiss; Mark Westoby; Ian J Wright; Brian J Enquist
Journal:  Nat Ecol Evol       Date:  2020-02-17       Impact factor: 15.460

6.  Neuroscience Cloud Analysis As a Service: An open-source platform for scalable, reproducible data analysis.

Authors:  Taiga Abe; Ian Kinsella; Shreya Saxena; E Kelly Buchanan; Joao Couto; John Briggs; Sian Lee Kitt; Ryan Glassman; John Zhou; Liam Paninski; John P Cunningham
Journal:  Neuron       Date:  2022-07-22       Impact factor: 18.688

7.  Countering reproducibility issues in mathematical models with software engineering techniques: A case study using a one-dimensional mathematical model of the atrioventricular node.

Authors:  Christopher Schölzel; Valeria Blesius; Gernot Ernst; Alexander Goesmann; Andreas Dominik
Journal:  PLoS One       Date:  2021-07-19       Impact factor: 3.240

8.  Clinical relevance assessment of animal preclinical research (RAA) tool: development and explanation.

Authors:  Kurinchi S Gurusamy; David Moher; Marilena Loizidou; Irfan Ahmed; Marc T Avey; Carly C Barron; Brian Davidson; Miriam Dwek; Christian Gluud; Gavin Jell; Kiran Katakam; Joshua Montroy; Timothy D McHugh; Nicola J Osborne; Merel Ritskes-Hoitinga; Kees van Laarhoven; Jan Vollert; Manoj Lalu
Journal:  PeerJ       Date:  2021-01-27       Impact factor: 2.984

9.  Knowledge and Attitudes Among Life Scientists Toward Reproducibility Within Journal Articles: A Research Survey.

Authors:  Evanthia Kaimaklioti Samota; Robert P Davey
Journal:  Front Res Metr Anal       Date:  2021-06-29

10.  A computational reproducibility study of PLOS ONE articles featuring longitudinal data analyses.

Authors:  Heidi Seibold; Severin Czerny; Siona Decke; Roman Dieterle; Thomas Eder; Steffen Fohr; Nico Hahn; Rabea Hartmann; Christoph Heindl; Philipp Kopper; Dario Lepke; Verena Loidl; Maximilian Mandl; Sarah Musiol; Jessica Peter; Alexander Piehler; Elio Rojas; Stefanie Schmid; Hannah Schmidt; Melissa Schmoll; Lennart Schneider; Xiao-Yin To; Viet Tran; Antje Völker; Moritz Wagner; Joshua Wagner; Maria Waize; Hannah Wecker; Rui Yang; Simone Zellner; Malte Nalenz
Journal:  PLoS One       Date:  2021-06-21       Impact factor: 3.240

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