Instructions for running simulations with the set of GP neuron models from
Edgerton JR, Hanson JE, Gunay C, Jaeger D (2010). Dendritic sodium channels
regulate network integration in globus pallidus neurons: a modeling study.
J Neurosci 30: 15146-59.
DIRECTORY STRUCTURE:
common: contains the model description files and some utility functions for
setting up a simulation.
common/biophysics: ion channel, synapse and passive biophysics descriptions
common/morphol: cell morphology descriptions
common/library: scripts to create a library of template objects during the
simulation
common/functions: various implementation scripts for the simulations
common/comptlists: lists of model compartments for various purposes such
as where to put synapses, which compartments to save outputs from, etc.
shellscripts: linux shell scripts to help run the simulations
run_example: scripts to run two different types of example simulations
run_example/run_slice.g: example simulations with no synaptic inputs but
with somatic current injections like those often used in slice
experiments.
run_example/run_vivo.g: example simulations with synaptic inputs active
throughout the dendritic tree. Synapses have random timing in these
simulations.
matlab_reader: a plugin written in C that enables you to load the
output data into Matlab.
--> compile using the Matlab mex compiler in a Linux shell:
> mex -output readgenesis readgenesis.c
TUTORIAL:
First, you must have genesis 2.3 installed on your machine.
Download and unzip the model files.
Navigate to the run_example directory.
To run the "slice" simulations, execute the following commands:
> ../shellscripts/create_perlhash_param_db pars_slice.par
> ../shellscripts/runbatch_local_perlhash.sh run_slice_example.g pars_slice.par 1 1
This command runs a simulation using the first row of parameters listed
in the pars_slice.par file. If it runs without any problem you
should see a data file appear in the data_slice directory named
1_mtype_1_scaleMeth_0_sclTau_-200_pAinjected_slice_example_run_v.bin
> ../shellscripts/runbatch_local_perlhash.sh run_slice_example.g pars_slice.par 2 72
This command runs each of the remaining 71 parameter combinations in the
pars_slice.par file sequentially. Once complete, there should be
72 data files in the data_slice directory, one for each parameter
set.
To run the "vivo" simulations, simply repeat the same steps with the vivo
example scripts.
> ../shellscripts/create_perlhash_param_db pars_vivo.par
> ../shellscripts/runbatch_local_perlhash.sh run_vivo_example.g pars_vivo.par 1 1
> ../shellscripts/runbatch_local_perlhash.sh run_vivo_example.g pars_vivo.par 2 18
To visualize the data in Matlab:
First compile the reader:
> mex -output readgenesis readgenesis.c
Add the reader directory to your Matlab path, then run the following
commands from within Matlab:
% Load the data into the workspace
>> tdat = readgenesis('data_slice/1_mtype_1_scaleMeth_0_sclTau_-200_pAinjected_slice_example_run_v.bin', 1);
% Change the y-scale from volts to millivolts
>> tdat = tdat .* 1e3;
% Plot the data
>> figure; plot([1e-4:1e-4:5], tdat);
Submitted by:
Jeremy R. Edgerton < jeremy.edgerton AT gmail.com >, 12/2010
Co-authors:
Jesse E. Hanson < hanson.jesse AT gene.com >
Cengiz Gunay < cgunay AT emory.edu >
Dieter Jaeger < djaeger AT emory.edu >
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