Run this script to plot the current traces across somatic and dendritic compartments in the OLMng models (see https://github.com/FKSkinnerLab/OLMng). Note that this code was written for use with python 2.7 and will require some minimal alterations for use in python 3. Edit "init_model.py" to change from model 1 (i.e. Gormadoc) to model 2 (i.e. Isembard). In the plotting codes the "Cell_Name" variable also needs to be changed to either 'Gormadoc' or 'Isembard'.
Before running the simulations you must first compile the mod files using the following command:
nrnivmodl
To run simulations use python as a command-line argument as follows:
python init.py
After running the simulations npy files will save the current traces to the NPY_files folder and the following additional options will be available.
To plot current traces:
python PlotCurrentPairs.py
To plot current X current cross-correlations:
python PlotCurrentXCorrs.py
To plot current X voltage cross-correlations:
python PlotVoltageXCorrs.py
To plot cross-correlations across compartments (currents):
python PlotMorphXCorrs.py
To plot cross-correlations across compartments (voltage):
python PlotMorphXCorrsV.py
The cells currently available are:
1 Gormadoc
2 Isembard
Most parameters are found in either the sim_params.hoc file or in the per-cell parameter files within the "param_files" directory. The ones in sim_params.hoc are particularly relevant for global aspects of operation such as length of simulation, integration method, current clamp injection parameters, etc.