This model, originally written in NEURON and hoc by van der Velten et al (2012), has been adapted by M. Bezaire to be a hybrid NEURON+Python model for use in a summer course on computational modeling. The original code is available on ModelDB.
This code requires NEURON. To run via Python (optional), this code requires Python 2 or 3 as well as updated environmental variables so that NEURON can be accessed from within Python. Run nrnpyenv for hints.
Download the code as a zip file or, from the terminal with git installed, with the command:
git clone https://github.com/risecourse/lsd_dendritic_complexity.git
Then, in the directory of the model code, compile the *.mod mechanisms by running the following command in a terminal:
- On Windows, run
mknrndll - On Mac and Linux, run
nrnivmodl
The code can be run from within Spyder or via Anaconda Prompt if you want to run in parallel.
In Spyder, simply run the main.py file. It will run slowly, in serial, and plot at the end.
If using Anaconda Prompt, first find out how many cores your computer has, then launch an Anaconda Prompt from the Anaconda application folder. Change directory (cd) to the CA1_Cutsuridis folder and then enter at the command line (replacing 4 with however many cores your computer has):
mpiexec -n 4 python main.py