# pricklypear

PricklyPear matlab/neuron model

## Installation

1. Clone this repository or download and unzip on your computer
2. Install [Neuron][neuron homepage] from their website
3. Compile the .mod files using [nmodl][neuron nmodl]
4. In the `pricklypear/matlab` directory, make a copy of the `pp_dir.template.txt` file, rename it to `pp_dir.txt` and edit the contents to reflect the location of the pricklypear directory

To test your installation:

1. Test neuron
  - Copy the files from the `neuron/eventtimes` directory into the `neuron` directory
  - Double click on the `msomodel_default.hoc`
  - If the command window does not give any errors and the `data/_direct` directory contains multiple files named like `run_00001__vm_ad.txt`, the neuron part of the pricklypear model is working
2. Test Matlab
  - Start Matlab and set the working directory to `pathto/pricklypear/matlab` directory or add the `pathto/pricklypear/matlab` to the Matlab path
  - Execute `PP = pricklypear('debug');`
  - Execute `run(PP);`
  - Execute `plot(PP(0));`
  - If you see a stacked plot of electrophysiology-like data, the Matlab part of the pricklypear model is working

## Usage

1. Start Matlab and set the working directory to `pathto/pricklypear/matlab` directory or add the `pathto/pricklypear/matlab` to the Matlab path

[neuron homepage]: https://www.neuron.yale.edu/neuron/
[neuron nmodl]: https://www.neuron.yale.edu/neuron/static/docs/nmodl/mswin.html