This is a single-compartment model of cortical synapse and the intracellular signaling within as described in

Mäki-Marttunen T, Iannella N, Edwards AG, Einevoll GT, Blackwell KT: A unified computational model for cortical post-synaptic plasticity. eLife 2020;9:e55714

Three folders are included in this ModelDB entry: L23PC

A model from NMC portal: https://bbp.epfl.ch/nmc-portal/downloads. Includes scripts used for calculation of the Ca2+ transients through NMDA receptors in the paired-stimulus experiment. Pre-calculated data included for running the scripts needed for reproduction of Figure 5.

NEURON

Scripts used for the single-compartment simulations of the plasticity in the post-synaptic spine using NEURON RxD simulator. Contains also the scripts for drawing the Figures of the paper.

NeuroRD

Scripts used for the single-compartment simulations of the plasticity in the post-synaptic spine using NeuroRD simulator.

Software:

The scripts assume the command "python" runs Python 2.7 with packages neuron (v7.5), numpy, scipy, and matplotlib installed. For Python 3, the print commands should be reformatted to have parentheses and the "<>" signs in model_nrn*.py and simsteadystate_flexible.py should be replaced by "!=", and possibly some other changes to pickle and scipy.io commands.
The NeuroRD simulations worked with Java version 1.8.0_131

To draw Fig. 11 (Model calibration figure; Methods), run the following commands (if you get errors see NEURON/README.html for issues with NEURON RxD version):


cd NEURON
sh runfig11.sh     
python drawfig11.py
cd ..

To draw Fig. 2 (Activation of PKA, PKC, and CaMKII pathways with varying Ca input), run the following commands (if you get errors see NeuroRD/README.html for issues with the java command):


cd NeuroRD
sh runsteadystate.sh
sh runfig2_nrd.sh
cd ../NEURON
sh runfig2.sh
python drawfig2.py
cd ..

To draw Fig. 3 and 4 and Suppl. Fig. 3.1, run the following commands:


cd NeuroRD
#sh runsteadystate.sh #skip this if you ran it already for Fig. 3
sh runfig3-4_nrd.sh
cd ../NEURON
sh runfig3-4.sh
sh runfig3_1.sh
python drawfig3.py
python drawfig4.py
python drawfig3_1.py
cd ..

To draw Fig. 5, run the following commands:


cd NEURON
sh runfig5.sh
python drawfig5.py
cd ..

To draw Fig. 9 panels A-C, run the following commands:


cd NEURON
sh runfig9.sh
python drawfig9abc.py
cd ..