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Yarmo Mackenbach 2020-04-01 16:01:52 +02:00
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# 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 and rename it to `pp_dir.txt`
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