These simulations were used in the following article:
Newton AJH, Lytton WW, DiStasio M, McDougal RA. Computational modeling predicts spatial variation of dendritic vulnerability to ischemia.
The code in this folder runs the simulations and generates a simple plot of the concentrations an membrane potential for the neuron model under specified conditions.
The code uses NEURON and RxD. To run the simulation first extract the files, install the required Python packages and compile the mod files.
```
unzip CA1PyrIschemicModel.zip
cd CA1PyrIschemicModel
pip install -r requirements.txt
nrnivmodl mod
```
The model is run in python with various arguments to specify the conditions to simulation and where to save or load the data.
```
usage: CA1pyr.py [-h] [--tstop TSTOP] [--O2 O2] [--saveint SAVEINT]
[--mode MODE] [--path PATH] [--cao CAO] [--ko KO] [--nmda]
[--glu] [--mglur] [--nax] [--load] [--plot]
optional arguments:
-h, --help show this help message and exit
--tstop TSTOP time (in seconds) to run the simulation. Default 60s
--O2 O2 O2 'steady-state' concentration in mM. Default 0.05mM
--saveint SAVEINT Interval (in seconds) at which to save the results.
Default 10s
--mode MODE Run 'isch' or 'penumbra' simulation
--path PATH path of the directory to save the data
--cao CAO extracellular Ca2+ concentration in mM
--ko KO extracellular K+ concentration in mM
--nmda block NMDA receptors
--glu block all glutamate
--mglur block mGluR
--nax block mGluR
--load load previous results instead of running the simulation.
Default False
--plot Plot the results.
```
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For example to run the simulation in normoxic conditions for 0.25s, save the data to current directory and plot the results;
```python CA1Pyr.py --tstop 0.25 --saveint 0.25 --plot```
This example simulation took 6m23s to run in Linux on an Intel(R) Core(TM) i7-7700HQ CPU.
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For questions/comments please email:
adam.newton at neurosim dot downstate dot edu