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Reaction-diffusion in the NEURON simulator
In order to support research on the role of cell biological principles (genomics, proteomics, signaling cascades and reaction dynamics) on the dynamics of neuronal response in health and disease, NEURON's Reaction-Diffusion (rxd) module in Python provides specification and simulation for these...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2013
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3828620/ https://www.ncbi.nlm.nih.gov/pubmed/24298253 http://dx.doi.org/10.3389/fninf.2013.00028 |
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author | McDougal, Robert A. Hines, Michael L. Lytton, William W. |
author_facet | McDougal, Robert A. Hines, Michael L. Lytton, William W. |
author_sort | McDougal, Robert A. |
collection | PubMed |
description | In order to support research on the role of cell biological principles (genomics, proteomics, signaling cascades and reaction dynamics) on the dynamics of neuronal response in health and disease, NEURON's Reaction-Diffusion (rxd) module in Python provides specification and simulation for these dynamics, coupled with the electrophysiological dynamics of the cell membrane. Arithmetic operations on species and parameters are overloaded, allowing arbitrary reaction formulas to be specified using Python syntax. These expressions are then transparently compiled into bytecode that uses NumPy for fast vectorized calculations. At each time step, rxd combines NEURON's integrators with SciPy's sparse linear algebra library. |
format | Online Article Text |
id | pubmed-3828620 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-38286202013-12-02 Reaction-diffusion in the NEURON simulator McDougal, Robert A. Hines, Michael L. Lytton, William W. Front Neuroinform Neuroscience In order to support research on the role of cell biological principles (genomics, proteomics, signaling cascades and reaction dynamics) on the dynamics of neuronal response in health and disease, NEURON's Reaction-Diffusion (rxd) module in Python provides specification and simulation for these dynamics, coupled with the electrophysiological dynamics of the cell membrane. Arithmetic operations on species and parameters are overloaded, allowing arbitrary reaction formulas to be specified using Python syntax. These expressions are then transparently compiled into bytecode that uses NumPy for fast vectorized calculations. At each time step, rxd combines NEURON's integrators with SciPy's sparse linear algebra library. Frontiers Media S.A. 2013-11-15 /pmc/articles/PMC3828620/ /pubmed/24298253 http://dx.doi.org/10.3389/fninf.2013.00028 Text en Copyright © 2013 McDougal, Hines and Lytton. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Neuroscience McDougal, Robert A. Hines, Michael L. Lytton, William W. Reaction-diffusion in the NEURON simulator |
title | Reaction-diffusion in the NEURON simulator |
title_full | Reaction-diffusion in the NEURON simulator |
title_fullStr | Reaction-diffusion in the NEURON simulator |
title_full_unstemmed | Reaction-diffusion in the NEURON simulator |
title_short | Reaction-diffusion in the NEURON simulator |
title_sort | reaction-diffusion in the neuron simulator |
topic | Neuroscience |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3828620/ https://www.ncbi.nlm.nih.gov/pubmed/24298253 http://dx.doi.org/10.3389/fninf.2013.00028 |
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