Literature DB >> 32440654

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

Russell A Poldrack1, Franklin Feingold1, Michael J Frank2, Padraig Gleeson3, Gilles de Hollander4, Quentin Jm Huys3, Bradley C Love3, Christopher J Markiewicz1, Rosalyn Moran5, Petra Ritter6, Timothy T Rogers7, Brandon M Turner8, Tal Yarkoni9, Ming Zhan10, Jonathan D Cohen11.   

Abstract

The Target Article by Lee et al. (2019) highlights the ways in which ongoing concerns about research reproducibility extend to model-based approaches in cognitive science. Whereas Lee et al. focus primarily on the importance of research practices to improve model robustness, we propose that the transparent sharing of model specifications, including their inputs and outputs, is also essential to improving the reproducibility of model-based analyses. We outline an ongoing effort (within the context of the Brain Imaging Data Structure community) to develop standards for the sharing of the structure of computational models and their outputs.

Entities:  

Year:  2019        PMID: 32440654      PMCID: PMC7241435          DOI: 10.1007/s42113-019-00062-x

Source DB:  PubMed          Journal:  Comput Brain Behav        ISSN: 2522-0861


  12 in total

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

Authors:  Stephen J Eglen; Ben Marwick; Yaroslav O Halchenko; Michael Hanke; Shoaib Sufi; Padraig Gleeson; R Angus Silver; Andrew P Davison; Linda Lanyon; Mathew Abrams; Thomas Wachtler; David J Willshaw; Christophe Pouzat; Jean-Baptiste Poline
Journal:  Nat Neurosci       Date:  2017-05-25       Impact factor: 24.884

2.  A Commitment to Open Source in Neuroscience.

Authors:  Padraig Gleeson; Andrew P Davison; R Angus Silver; Giorgio A Ascoli
Journal:  Neuron       Date:  2017-12-06       Impact factor: 17.173

3.  Approaches to Analysis in Model-based Cognitive Neuroscience.

Authors:  Brandon M Turner; Birte U Forstmann; Bradley C Love; Thomas J Palmeri; Leendert Van Maanen
Journal:  J Math Psychol       Date:  2016-02-17       Impact factor: 2.223

4.  Diffusion versus linear ballistic accumulation: different models but the same conclusions about psychological processes?

Authors:  Chris Donkin; Scott Brown; Andrew Heathcote; Eric-Jan Wagenmakers
Journal:  Psychon Bull Rev       Date:  2011-02

5.  Individual Differences and Fitting Methods for the Two-Choice Diffusion Model of Decision Making.

Authors:  Roger Ratcliff; Russ Childers
Journal:  Decision (Wash D C )       Date:  2015

6.  A comparative study of drift diffusion and linear ballistic accumulator models in a reward maximization perceptual choice task.

Authors:  Stephanie Goldfarb; Naomi E Leonard; Patrick Simen; Carlos H Caicedo-Núñez; Philip Holmes
Journal:  Front Neurosci       Date:  2014-08-05       Impact factor: 4.677

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.  Re-run, Repeat, Reproduce, Reuse, Replicate: Transforming Code into Scientific Contributions.

Authors:  Fabien C Y Benureau; Nicolas P Rougier
Journal:  Front Neuroinform       Date:  2018-01-04       Impact factor: 4.081

9.  The Virtual Brain: a simulator of primate brain network dynamics.

Authors:  Paula Sanz Leon; Stuart A Knock; M Marmaduke Woodman; Lia Domide; Jochen Mersmann; Anthony R McIntosh; Viktor Jirsa
Journal:  Front Neuroinform       Date:  2013-06-11       Impact factor: 4.081

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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