Code for the V1 plasticity disruption experiment (prospective experiment 2) in the Cleo publication. Original model from Wilmes and Clopath 2019. Adapted here by Nathan Cruzado to add closed-loop optogenetic control with Cleo.
Research was conducted in the SIPLab, led by Chris Rozell and Sankar Alagapan at Georgia Tech.
Install the conda environment:
mamba env create -f environment.yml
mamba activate wcm(wcm refers to Wilmes-Clopath Model)
To replicate results in the paper, simply run Task:
task
While Task will orchestrate needed runs to form plots, it unfortunately does not detect when a repeated task needs to be rerun when they share a source (in this case the source code Spiking_model_cleo.py).
So if you change that file and need to rerun everything, you'll need to delete the previous results for Task to handle it intelligently.
Snakemake would be the better choice in the future.
This code has not been thoroughly tested, so please report any issues you encounter.