Literature DB >> 22358837

The case for open computer programs.

Darrel C Ince1, Leslie Hatton, John 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.

Mesh:

Year:  2012        PMID: 22358837     DOI: 10.1038/nature10836

Source DB:  PubMed          Journal:  Nature        ISSN: 0028-0836            Impact factor:   49.962


  6 in total

1.  An invitation to reproducible computational research.

Authors:  David L Donoho
Journal:  Biostatistics       Date:  2010-07       Impact factor: 5.899

2.  Publish your computer code: it is good enough.

Authors:  Nick Barnes
Journal:  Nature       Date:  2010-10-14       Impact factor: 49.962

3.  Computational science: ...Error.

Authors:  Zeeya Merali
Journal:  Nature       Date:  2010-10-14       Impact factor: 49.962

4.  Computer science. Accessible reproducible research.

Authors:  Jill P Mesirov
Journal:  Science       Date:  2010-01-22       Impact factor: 47.728

5.  Devil in the details.

Authors: 
Journal:  Nature       Date:  2011-02-17       Impact factor: 49.962

6.  Making data maximally available.

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

  6 in total
  115 in total

1.  Research priorities. Shining light into black boxes.

Authors:  A Morin; J Urban; P D Adams; I Foster; A Sali; D Baker; P Sliz
Journal:  Science       Date:  2012-04-13       Impact factor: 47.728

2.  A call for bioimaging software usability.

Authors:  Anne E Carpenter; Lee Kamentsky; Kevin W Eliceiri
Journal:  Nat Methods       Date:  2012-06-28       Impact factor: 28.547

3.  Current challenges in open-source bioimage informatics.

Authors:  Albert Cardona; Pavel Tomancak
Journal:  Nat Methods       Date:  2012-06-28       Impact factor: 28.547

4.  Image registration for targeted MRI-guided transperineal prostate biopsy.

Authors:  Andriy Fedorov; Kemal Tuncali; Fiona M Fennessy; Junichi Tokuda; Nobuhiko Hata; William M Wells; Ron Kikinis; Clare M Tempany
Journal:  J Magn Reson Imaging       Date:  2012-05-29       Impact factor: 4.813

5.  Slide Set: Reproducible image analysis and batch processing with ImageJ.

Authors:  Benjamin A Nanes
Journal:  Biotechniques       Date:  2015-11-01       Impact factor: 1.993

6.  Open collaborative writing with Manubot.

Authors:  Daniel S Himmelstein; Vincent Rubinetti; David R Slochower; Dongbo Hu; Venkat S Malladi; Casey S Greene; Anthony Gitter
Journal:  PLoS Comput Biol       Date:  2019-06-24       Impact factor: 4.475

7.  MITK-US: real-time ultrasound support within MITK.

Authors:  K März; A M Franz; A Seitel; A Winterstein; R Bendl; S Zelzer; M Nolden; H-P Meinzer; L Maier-Hein
Journal:  Int J Comput Assist Radiol Surg       Date:  2013-12-17       Impact factor: 2.924

8.  Icy: an open bioimage informatics platform for extended reproducible research.

Authors:  Fabrice de Chaumont; Stéphane Dallongeville; Nicolas Chenouard; Nicolas Hervé; Sorin Pop; Thomas Provoost; Vannary Meas-Yedid; Praveen Pankajakshan; Timothée Lecomte; Yoann Le Montagner; Thibault Lagache; Alexandre Dufour; Jean-Christophe Olivo-Marin
Journal:  Nat Methods       Date:  2012-06-28       Impact factor: 28.547

Review 9.  Deciphering tissue morphodynamics using bioimage informatics.

Authors:  Alexandre C Dufour; Anneliene H Jonker; Jean-Christophe Olivo-Marin
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2017-05-19       Impact factor: 6.237

10.  Free digital image analysis software helps to resolve equivocal scores in HER2 immunohistochemistry.

Authors:  Henrik O Helin; Vilppu J Tuominen; Onni Ylinen; Heikki J Helin; Jorma Isola
Journal:  Virchows Arch       Date:  2015-10-22       Impact factor: 4.064

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