Numerical Integration of Izhikevich and HH model neurons (Stewart and Bair 2009)

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Accession:117361
The Parker-Sochacki method is a new technique for the numerical integration of differential equations applicable to many neuronal models. Using this method, the solution order can be adapted according to the local conditions at each time step, enabling adaptive error control without changing the integration timestep. We apply the Parker-Sochacki method to the Izhikevich ‘simple’ model and a Hodgkin-Huxley type neuron, comparing the results with those obtained using the Runge-Kutta and Bulirsch-Stoer methods.
Reference:
1 . Stewart RD, Bair W (2009) Spiking neural network simulation: numerical integration with the Parker-Sochacki method. J Comput Neurosci [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
Cell Type(s): Hodgkin-Huxley neuron;
Channel(s):
Gap Junctions:
Receptor(s): AMPA; Glutamate;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: C or C++ program; MATLAB;
Model Concept(s): Simplified Models; Detailed Neuronal Models; Methods;
Implementer(s): Stewart, Robert [Robert.Stewart at pharm.ox.ac.uk];
Search NeuronDB for information about:  AMPA; Glutamate; Gaba; Glutamate;
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hh
iz
mex
readme.txt
                            
Readme for the model code associated with the paper:

Stewart RD, Bair W. (2009)
Spiking neural network simulation: numerical integration with the Parker-Sochacki method.
J Comput Neurosci
ISSN:	0929-5313 (Print) 1573-6873 (Online)
DOI:	10.1007/s10827-008-0131-5
Springer Netherlands
SpringerLink Date: Saturday, January 17, 2009

The article is freely available through Springer's Open Access program. It can be downloaded from here:
http://www.springerlink.com/content/8q431074727r41h2/

The code was uploaded to the ModelDB database on 13/02/09. It is divided into three folders:

1) mex - contains all the c code, plus compiled mex files of the top-level simulation functions iz_ps.c 
and tm_ps.c (both 64-bit Windows and 64-bit Linux versions). Instructions for compiling are given in the 
comments at the top of the .c files.

2) iz - contains the matlab code for the Izhikevich model simulations.
iz_bench.m is the top level script for running all experiments.

3) tm - contains the matlab code for the Traub-Miles HH neuron simulations.
tm_bench.m is the top level script for running all experiments.

Also included in both iz and tm folders are .mat files with results from the injection current simulations. 
The Izhikevich recurrent network simulation results take up GBs of space and have not been uploaded. 
To generate them locally, you need to run iz_bench and select simulation type 4.