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:
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.
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.
Scripts used for the single-compartment simulations of the plasticity in the post-synaptic spine using NeuroRD simulator.
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):
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. 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):
To draw Fig. 3 and 4 and Suppl. Fig. 3.1, run the following commands:
#sh runsteadystate.sh #skip this if you ran it already for Fig. 3
To draw Fig. 5, run the following commands:
To draw Fig. 9 panels A-C, run the following commands: