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Guidance for sharing computational models of neural stimulation: from project planning to publication.

Publication ,  Journal Article
Pelot, NA; Wang, B; Marshall, DP; Hussain, MA; Musselman, ED; Yu, GJ; Dale, J; Baumgart, IW; Dardani, D; Zamani, PT; Chang Villacreses, D ...
Published in: Journal of neural engineering
March 2025

Objective. Sharing computational models offers many benefits, including increased scientific rigor during project execution, readership of the associated paper, resource usage efficiency, replicability, and reusability. In recognition of the growing practice and requirement of sharing models, code, and data, herein, we provide guidance to facilitate sharing of computational models by providing an accessible resource for regular reference throughout a project's stages.Approach. We synthesized literature on good practices in scientific computing and on code and data sharing with our experience in developing, sharing, and using models of neural stimulation, although the guidance will also apply well to most other types of computational models.Main results. We first describe the '6 R' characteristics of shared models, leaning on prior scientific computing literature, which enforce accountability and enable advancement: re-runnability, repeatability, replicability, reproducibility, reusability, and readability. We then summarize action items associated with good practices in scientific computing, including selection of computational tools during project planning, code and documentation design during development, and user instructions for deployment. We provide a detailed checklist of the contents of shared models and associated materials, including the model itself, code for reproducing published figures, documentation, and supporting datasets. We describe code, model, and data repositories, including a list of characteristics to consider when selecting a platform for sharing. We describe intellectual property (IP) considerations to balance permissive, open-source licenses versus software patents and bespoke licenses that govern and incentivize commercialization. Finally, we exemplify these practices with our ASCENT pipeline for modeling peripheral nerve stimulation.Significance. We hope that this paper will serve as an important and actionable reference for scientists who develop models-from project planning through publication-as well as for model users, institutions, IP experts, journals, funding sources, and repository platform developers.

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Published In

Journal of neural engineering

DOI

EISSN

1741-2552

ISSN

1741-2560

Publication Date

March 2025

Volume

22

Issue

2

Related Subject Headings

  • Software
  • Publishing
  • Models, Neurological
  • Information Dissemination
  • Humans
  • Computer Simulation
  • Biomedical Engineering
  • 4003 Biomedical engineering
  • 3209 Neurosciences
  • 1109 Neurosciences
 

Citation

APA
Chicago
ICMJE
MLA
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Pelot, N. A., Wang, B., Marshall, D. P., Hussain, M. A., Musselman, E. D., Yu, G. J., … Grill, W. M. (2025). Guidance for sharing computational models of neural stimulation: from project planning to publication. Journal of Neural Engineering, 22(2). https://doi.org/10.1088/1741-2552/adb997
Pelot, Nicole A., Boshuo Wang, Daniel P. Marshall, Minhaj A. Hussain, Eric D. Musselman, Gene J. Yu, Jahrane Dale, et al. “Guidance for sharing computational models of neural stimulation: from project planning to publication.Journal of Neural Engineering 22, no. 2 (March 2025). https://doi.org/10.1088/1741-2552/adb997.
Pelot NA, Wang B, Marshall DP, Hussain MA, Musselman ED, Yu GJ, et al. Guidance for sharing computational models of neural stimulation: from project planning to publication. Journal of neural engineering. 2025 Mar;22(2).
Pelot, Nicole A., et al. “Guidance for sharing computational models of neural stimulation: from project planning to publication.Journal of Neural Engineering, vol. 22, no. 2, Mar. 2025. Epmc, doi:10.1088/1741-2552/adb997.
Pelot NA, Wang B, Marshall DP, Hussain MA, Musselman ED, Yu GJ, Dale J, Baumgart IW, Dardani D, Zamani PT, Chang Villacreses D, Wagenaar JB, Grill WM. Guidance for sharing computational models of neural stimulation: from project planning to publication. Journal of neural engineering. 2025 Mar;22(2).
Journal cover image

Published In

Journal of neural engineering

DOI

EISSN

1741-2552

ISSN

1741-2560

Publication Date

March 2025

Volume

22

Issue

2

Related Subject Headings

  • Software
  • Publishing
  • Models, Neurological
  • Information Dissemination
  • Humans
  • Computer Simulation
  • Biomedical Engineering
  • 4003 Biomedical engineering
  • 3209 Neurosciences
  • 1109 Neurosciences