From 0b0fa53883d3a17393ce8c4d783682fd59027d30 Mon Sep 17 00:00:00 2001 From: Yarmo Mackenbach Date: Wed, 1 Apr 2020 16:01:52 +0200 Subject: [PATCH] Updated documentation --- README.md | 29 ++++++++++++++++++++++++++++- 1 file changed, 28 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 8370653..37ae5f1 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,30 @@ # pricklypear -PricklyPear matlab/neuron model \ No newline at end of file +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 \ No newline at end of file