Literature DB >> 28542156

Toward standard practices for sharing computer code and programs in neuroscience.

Stephen J Eglen1, Ben Marwick2, Yaroslav O Halchenko3, Michael Hanke4,5, Shoaib Sufi6, Padraig Gleeson7, R Angus Silver7, Andrew P Davison8, Linda Lanyon9, Mathew Abrams9, Thomas Wachtler10, David J Willshaw11, Christophe Pouzat12, Jean-Baptiste Poline13.   

Abstract

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Year:  2017        PMID： 28542156      PMCID： PMC6386137          DOI： 10.1038/nn.4550

Source DB:  PubMed          Journal:  Nat Neurosci        ISSN： 1097-6256            Impact factor:   24.884


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  27 in total

1.  The case for open computer programs.

Authors:  Darrel C Ince; Leslie Hatton; John Graham-Cumming
Journal:  Nature       Date:  2012-02-22       Impact factor: 49.962

2.  Social science. Promoting transparency in social science research.

Authors:  E Miguel; C Camerer; K Casey; J Cohen; K M Esterling; A Gerber; R Glennerster; D P Green; M Humphreys; G Imbens; D Laitin; T Madon; L Nelson; B A Nosek; M Petersen; R Sedlmayr; J P Simmons; U Simonsohn; M Van der Laan
Journal:  Science       Date:  2014-01-03       Impact factor: 47.728

3.  A model neuron with activity-dependent conductances regulated by multiple calcium sensors.

Authors:  Z Liu; J Golowasch; E Marder; L F Abbott
Journal:  J Neurosci       Date:  1998-04-01       Impact factor: 6.167

4.  Editorial expression of concern.

Authors:  Jeremy Berg
Journal:  Science       Date:  2016-12-01       Impact factor: 47.728

5.  PyNN: A Common Interface for Neuronal Network Simulators.

Authors:  Andrew P Davison; Daniel Brüderle; Jochen Eppler; Jens Kremkow; Eilif Muller; Dejan Pecevski; Laurent Perrinet; Pierre Yger
Journal:  Front Neuroinform       Date:  2009-01-27       Impact factor: 4.081

6.  An automated and reproducible workflow for running and analyzing neural simulations using Lancet and IPython Notebook.

Authors:  Jean-Luc R Stevens; Marco Elver; James A Bednar
Journal:  Front Neuroinform       Date:  2013-12-30       Impact factor: 4.081

7.  The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments.

Authors:  Krzysztof J Gorgolewski; Tibor Auer; Vince D Calhoun; R Cameron Craddock; Samir Das; Eugene P Duff; Guillaume Flandin; Satrajit S Ghosh; Tristan Glatard; Yaroslav O Halchenko; Daniel A Handwerker; Michael Hanke; David Keator; Xiangrui Li; Zachary Michael; Camille Maumet; B Nolan Nichols; Thomas E Nichols; John Pellman; Jean-Baptiste Poline; Ariel Rokem; Gunnar Schaefer; Vanessa Sochat; William Triplett; Jessica A Turner; Gaël Varoquaux; Russell A Poldrack
Journal:  Sci Data       Date:  2016-06-21       Impact factor: 6.444

8.  A data repository and analysis framework for spontaneous neural activity recordings in developing retina.

Authors:  Stephen John Eglen; Michael Weeks; Mark Jessop; Jennifer Simonotto; Tom Jackson; Evelyne Sernagor
Journal:  Gigascience       Date:  2014-03-26       Impact factor: 6.524

9.  A Practical Guide for Improving Transparency and Reproducibility in Neuroimaging Research.

Authors:  Krzysztof J Gorgolewski; Russell A Poldrack
Journal:  PLoS Biol       Date:  2016-07-07       Impact factor: 8.029

10.  LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2.

Authors:  Robert C Cannon; Padraig Gleeson; Sharon Crook; Gautham Ganapathy; Boris Marin; Eugenio Piasini; R Angus Silver
Journal:  Front Neuroinform       Date:  2014-09-25       Impact factor: 4.081
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  33 in total

1.  Integrating molecular, histopathological, neuroimaging and clinical neuroscience data with NeuroPM-box.

Authors:  Yasser Iturria-Medina; Félix Carbonell; Atousa Assadi; Quadri Adewale; Ahmed F Khan; Tobias R Baumeister; Lazaro Sanchez-Rodriguez
Journal:  Commun Biol       Date:  2021-05-21

2.  Brian 2, an intuitive and efficient neural simulator.

Authors:  Romain Brette; Dan Fm Goodman; Marcel Stimberg
Journal:  Elife       Date:  2019-08-20       Impact factor: 8.140

3.  Reply to Brown and Behrmann, Cox, et al., and Kessler et al.: Data and code sharing is the way forward for fMRI.

Authors:  Anders Eklund; Thomas E Nichols; Hans Knutsson
Journal:  Proc Natl Acad Sci U S A       Date:  2017-04-18       Impact factor: 11.205

4.  The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services.

Authors:  Paolo Avesani; Brent McPherson; Soichi Hayashi; Cesar F Caiafa; Robert Henschel; Eleftherios Garyfallidis; Lindsey Kitchell; Daniel Bullock; Andrew Patterson; Emanuele Olivetti; Olaf Sporns; Andrew J Saykin; Lei Wang; Ivo Dinov; David Hancock; Bradley Caron; Yiming Qian; Franco Pestilli
Journal:  Sci Data       Date:  2019-05-23       Impact factor: 6.444

5.  The importance of standards for sharing of computational models and data.

Authors:  Russell A Poldrack; Franklin Feingold; Michael J Frank; Padraig Gleeson; Gilles de Hollander; Quentin Jm Huys; Bradley C Love; Christopher J Markiewicz; Rosalyn Moran; Petra Ritter; Timothy T Rogers; Brandon M Turner; Tal Yarkoni; Ming Zhan; Jonathan D Cohen
Journal:  Comput Brain Behav       Date:  2019-10-07

6.  Teaching with Big Data: Report from the 2016 Society for Neuroscience Teaching Workshop.

Authors:  William Grisham; Joshua C Brumberg; Terri Gilbert; Linda Lanyon; Robert W Williams; Richard Olivo
Journal:  J Undergrad Neurosci Educ       Date:  2017-11-15

7.  Everything Matters: The ReproNim Perspective on Reproducible Neuroimaging.

Authors:  David N Kennedy; Sanu A Abraham; Julianna F Bates; Albert Crowley; Satrajit Ghosh; Tom Gillespie; Mathias Goncalves; Jeffrey S Grethe; Yaroslav O Halchenko; Michael Hanke; Christian Haselgrove; Steven M Hodge; Dorota Jarecka; Jakub Kaczmarzyk; David B Keator; Kyle Meyer; Maryann E Martone; Smruti Padhy; Jean-Baptiste Poline; Nina Preuss; Troy Sincomb; Matt Travers
Journal:  Front Neuroinform       Date:  2019-02-07       Impact factor: 4.081

Review 8.  International data governance for neuroscience.

Authors:  Damian O Eke; Amy Bernard; Jan G Bjaalie; Ricardo Chavarriaga; Takashi Hanakawa; Anthony J Hannan; Sean L Hill; Maryann E Martone; Agnes McMahon; Oliver Ruebel; Sharon Crook; Edda Thiels; Franco Pestilli
Journal:  Neuron       Date:  2021-12-15       Impact factor: 18.688

9.  A descriptive analysis of the data availability statements accompanying medRxiv preprints and a comparison with their published counterparts.

Authors:  Luke A McGuinness; Athena L Sheppard
Journal:  PLoS One       Date:  2021-05-13       Impact factor: 3.240

10.  Bridging the Brain and Data Sciences.

Authors:  John Darrell Van Horn
Journal:  Big Data       Date:  2020-11-18       Impact factor: 4.426
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