NEURON files & Python code from paper:<br>
<br>
Rachel Humphries, Jack R. Mellor, Cian O'Donnell,
Acetylcholine Boosts Dendritic NMDA Spikes in a CA3 Pyramidal Neuron Model,
Neuroscience, 2021,ISSN 0306-4522
https://doi.org/10.1016/j.neuroscience.2021.11.014<br>
<br>
In this paper, this model was used to compare the nonlinearity of NMDA inputs
between dendritic sections in a CA3 pyramidal neuron as well as investigate
the effect of cholinergic modulation/potassium channel inhibition on this 
dendritic NMDA-mediated nonlinearity.<br>
<br>
NEURON and Python 3.8 were used to run the simulations. <br>
<br>
In the folder provided here are the mod files for each of the conductances/synaptic 
mechanisms and the main hoc file (ca3b-cell1zr-fig9b.hoc - adapted from Hemond et al. 
2008 model (accession no.:101629)). <br> 
<br>
The mod files will need to be compiled using the "mknrndll" command (on Windows).<br> 
<br>
**Hoc files** <br>
(adapted from Hemond et al. 2008 (accession no.:101629))<br>
ca3b-cell1zr-fig9b.hoc - main hoc file to set up model and insert conductances<br>
geo-cell1zr.hoc - sets up neuron morphology<br>
fixnseg.hoc - sets number of segments for each section<br>
<br>
Python was used to run simulations, analyse and plot the data.<br> 
<br>
**Python files**<br>
measure_dend_Rin_rest.py - Measures dendritic input resistance at rest.<br>
nonlinearity_all_dends.py - Produces data used in Figures 3 and 4 of the paper. <br>
ach_exp.py - Produces data used in Figures 5 and 6 of the paper. <br>
ca3_synapse_functions.py - additional functions required for running the simulations<br>
Fig5_example_dend_traces.py - Runs the simulation for 6 example dendrites and plots
neuron morphology and example voltages traces from Figure 5A,B+C of the paper. <br>
add_scalebar_func.py & scalebars.py - scalebar functions for plotting<br>
<br>
Simulation outputs are saved in pickle files.<br> 
<br>
**PNG files**<br>
Output from running Fig5_example_dend_traces.py - this will take a couple of hours
to run.<br>
Representative of Figure 5A,B+C from paper - from running the simulation with the 
6 highlighted dendrites.<br>
<br>
**Note** <br>
On a standard PC, ach_exp.py with the default parameters (20 inputs on all 
dendritic sections + all conditions) may take >24 hours to run.<br>