Zobrazit v EDS

PyFibers: An open-source NEURON-Python package to simulate responses of model nerve fibers to electrical stimulation.

Uloženo v:
Podrobná bibliografie
Název: PyFibers: An open-source NEURON-Python package to simulate responses of model nerve fibers to electrical stimulation.
Autoři: Marshall, Daniel P., Farah, Elie S., Musselman, Eric D., Pelot, Nicole A., Grill, Warren M.
Zdroj: PLoS Computational Biology; 12/12/2025, Vol. 21 Issue 12, p1-30, 30p
Témata: NERVE fibers, ELECTRIC stimulation, OPEN source software, PYTHON programming language, COMPUTER simulation, NEURONS, NEUROMODULATION
Abstrakt: Computational modeling of peripheral nerve fibers is a key tool for designing improved neuromodulation therapies. The NEURON software is commonly used to create biophysical simulations of nerve fibers, often in the outdated HOC language. Whether written in HOC or Python, implementing fiber simulations involves a steep learning curve and requires a large amount of standard, boilerplate code that is typically written anew for each project. There is a need for a code package that standardizes and simplifies the creation of model fibers, the execution of simulations of electrical stimulation, and the analysis of the resulting data. We created PyFibers, a NEURON-Python package that provides tools for accomplishing all these tasks and supports the development of new fiber models and stimulation protocols. PyFibers includes 11 fiber models from prior publications under a shared framework, and we validated each model's implementation in PyFibers against the original results. Our open-source tool simplifies and standardizes computational modeling of peripheral nerve fiber responses to electrical stimulation, providing a platform for the development of novel therapies using electrical stimulation, block, and recording. Author summary: Electrical stimulation of peripheral nerves can treat conditions such as epilepsy, paralysis, bladder dysfunction, and sleep apnea. Improving the design of these nerve stimulation therapies can increase efficacy and reduce side effects. Computational models of nerve fibers (axons) provide a rapid approach to study many different device designs and parameters. However, present nerve fiber modeling tools focus primarily on modeling of entire nerves, and researchers often need to create and run nerve fiber models on their own. We created PyFibers, an open-source Python package that makes it easy to implement and simulate computational models of stimulation, block, and recording of single nerve fibers. With PyFibers, users can quickly create nerve fiber models, apply electrical stimulation, and examine the responses in detail. PyFibers runs on top of a widely used neuron modeling program (NEURON) and can plug into larger simulation pipelines, enabling researchers to test new electrode designs and stimulation strategies to complement preclinical or clinical studies. [ABSTRACT FROM AUTHOR]
Copyright of PLoS Computational Biology is the property of Public Library of Science and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Databáze: Complementary Index
Popis
Abstrakt:Computational modeling of peripheral nerve fibers is a key tool for designing improved neuromodulation therapies. The NEURON software is commonly used to create biophysical simulations of nerve fibers, often in the outdated HOC language. Whether written in HOC or Python, implementing fiber simulations involves a steep learning curve and requires a large amount of standard, boilerplate code that is typically written anew for each project. There is a need for a code package that standardizes and simplifies the creation of model fibers, the execution of simulations of electrical stimulation, and the analysis of the resulting data. We created PyFibers, a NEURON-Python package that provides tools for accomplishing all these tasks and supports the development of new fiber models and stimulation protocols. PyFibers includes 11 fiber models from prior publications under a shared framework, and we validated each model's implementation in PyFibers against the original results. Our open-source tool simplifies and standardizes computational modeling of peripheral nerve fiber responses to electrical stimulation, providing a platform for the development of novel therapies using electrical stimulation, block, and recording. Author summary: Electrical stimulation of peripheral nerves can treat conditions such as epilepsy, paralysis, bladder dysfunction, and sleep apnea. Improving the design of these nerve stimulation therapies can increase efficacy and reduce side effects. Computational models of nerve fibers (axons) provide a rapid approach to study many different device designs and parameters. However, present nerve fiber modeling tools focus primarily on modeling of entire nerves, and researchers often need to create and run nerve fiber models on their own. We created PyFibers, an open-source Python package that makes it easy to implement and simulate computational models of stimulation, block, and recording of single nerve fibers. With PyFibers, users can quickly create nerve fiber models, apply electrical stimulation, and examine the responses in detail. PyFibers runs on top of a widely used neuron modeling program (NEURON) and can plug into larger simulation pipelines, enabling researchers to test new electrode designs and stimulation strategies to complement preclinical or clinical studies. [ABSTRACT FROM AUTHOR]
ISSN:1553734X
DOI:10.1371/journal.pcbi.1013764