The case for open computer programs.

Nature
Darrel C InceJohn Graham-Cumming

Abstract

Scientific communication relies on evidence that cannot be entirely included in publications, but the rise of computational science has added a new layer of inaccessibility. Although it is now accepted that data should be made available on request, the current regulations regarding the availability of software are inconsistent. We argue that, with some exceptions, anything less than the release of source programs is intolerable for results that depend on computation. The vagaries of hardware, software and natural language will always ensure that exact reproducibility remains uncertain, but withholding code increases the chances that efforts to reproduce results will fail.

References

Jun 19, 2009·Biostatistics·Roger D Peng
Jan 23, 2010·Science·Jill P Mesirov
Jun 12, 2010·Biostatistics·David L Donoho
Oct 15, 2010·Nature·Nick Barnes
Oct 15, 2010·Nature·Zeeya Merali
Feb 12, 2011·Science·Brooks HansonBruce Alberts
Feb 19, 2011·Nature

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Citations

Apr 17, 2013·International Journal of Computer Assisted Radiology and Surgery·Marco NoldenIvo Wolf
Jun 30, 2012·Nature Methods·Anne E CarpenterKevin W Eliceiri
Jun 30, 2012·Nature Methods·Fabrice de ChaumontJean-Christophe Olivo-Marin
Jun 30, 2012·Nature Methods·Albert Cardona, Pavel Tomancak
Apr 14, 2012·Science·A MorinP Sliz
May 21, 2013·Science·Lucas N JoppaStephen Emmott
Jun 22, 2013·BMC Bioinformatics·Francesco NapolitanoRoberto Tagliaferri
Dec 7, 2013·BMC Bioinformatics·Jason Hennessey, Steven Ge
May 30, 2012·Source Code for Biology and Medicine·Cameron NeylonEgon Willighagen
Mar 2, 2013·Source Code for Biology and Medicine·Karthik Ram
Jan 28, 2014·PLoS Computational Biology·Marc-Oliver Gewaltig, Robert Cannon
Jul 31, 2012·PloS One·Hugues BersiniVéronique Thomas-Vaslin
Jul 5, 2013·PloS One·Michael D Barton, Hazel A Barton
Aug 31, 2013·PloS One·José María Mateos-PérezJuan J Vaquero
Mar 20, 2014·Journal of Proteomics·Mauricio Maldonado-TorresRobert Winkler
Apr 15, 2014·Nature Biotechnology·Hannes L RöstRuedi Aebersold
Dec 18, 2013·International Journal of Computer Assisted Radiology and Surgery·K MärzL Maier-Hein
Oct 3, 2014·Journal of Biomedical Semantics·Kristina M HettneMarco Roos
Jul 16, 2014·Database : the Journal of Biological Databases and Curation·Vincent J HenryArnaud Desfeux
Aug 22, 2014·Journal of the Royal Society, Interface·Mark ReadVipin Kumar
Dec 6, 2014·TheScientificWorldJournal·K Karnavel, R Dillibabu
Oct 6, 2012·Journal of the American Medical Informatics Association : JAMIA·Daniela M Witten, Robert Tibshirani
Jan 16, 2015·Journal of the Royal Society, Interface·Kieran AldenJon Timmis
Mar 16, 2016·BioMed Research International·Francesco RussoClaudia Angelini
Mar 5, 2016·The Review of Scientific Instruments·James P SharkeyRichard W Bowman
Oct 24, 2015·Virchows Archiv : an International Journal of Pathology·Henrik O HelinJorma Isola
Dec 11, 2014·IEEE Transactions on Medical Imaging·Bjoern H MenzeKoen Van Leemput
Mar 26, 2016·Science·Kurt LejaeghereStefaan Cottenier
Oct 22, 2016·Proceedings of the IEEE·Alistair E W JohnsonGari D Clifford
Sep 28, 2015·International Journal of Computer Assisted Radiology and Surgery·Christian AskelandFrank Lindseth
Apr 8, 2016·Science Translational Medicine·Jerôme AboabDavid J Stone
Mar 26, 2015·Frontiers in Human Neuroscience·Michael ZehetleitnerHermann J Müller
Aug 16, 2014·Frontiers in Neuroinformatics·Miriam FriedelJason P Lerch
May 16, 2015·Scientific Data·Brian B AvantsDanny J J Wang
Jun 1, 2016·Frontiers in Psychology·Manuel Rausch, Michael Zehetleitner
Jul 9, 2016·ELife·Erin C McKiernanTal Yarkoni
Sep 10, 2016·Frontiers in Neuroinformatics·Robert Meyer, Klaus Obermayer
Sep 2, 2016·International Journal of Computer Assisted Radiology and Surgery·Simon DrouinD Louis Collins
Apr 2, 2015·GigaScience·Cyril Pernet, Jean-Baptiste Poline
Apr 20, 2017·Proceedings of the National Academy of Sciences of the United States of America·Anders EklundHans Knutsson
May 26, 2017·Nature Neuroscience·Stephen J EglenJean-Baptiste Poline

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