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...

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Bibliographic Details
Published inFrontiers in neuroinformatics Vol. 7; p. 28
Main Authors McDougal, Robert A, Hines, Michael L, Lytton, William W
Format Journal Article
LanguageEnglish
Published Switzerland Frontiers Research Foundation 01.01.2013
Frontiers Media S.A
Subjects
Algorithms
Binding sites
Bioinformatics
Biology
Cell membranes
computational neuroscience
Kinases
Neurodynamics
Neurons
Neuroscience
Neurosciences
numerical integration
Ordinary differential equations
Partial differential equations
Proteomics
python
Reaction-diffusion
Software
United States > US
neurodynamics
numerical integration
python
reaction-diffusion
computational neuroscience
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Summary: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.
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Reviewed by: Upinder S. Bhalla, National Center for Biological Sciences, India; Padraig Gleeson, University College London, UK; Zbigniew Jedrzejewski-Szmek, George Mason University, USA
This article was submitted to the journal Frontiers in Neuroinformatics.
Edited by: Andrew P. Davison, Centre National de la Recherche Scientifique, France
ISSN:1662-5196
1662-5196
DOI:10.3389/fninf.2013.00028