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. 

![The first 0.25s under normoxic conditions.](plot_CA1Pyr_isch_0.05.png)
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For questions/comments please email:  
  adam.newton at neurosim dot downstate dot edu