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ETDP-CA1

This repository contains the code for the models used in A voltage-based Event-Timing-Dependent Plasticity rule accounts for LTP subthreshold and suprathreshold for dendritic spikes in CA1 pyramidal neurons Tomko et al. (preprint, Journal of Computational Neuroscience, 2023).

To run:

git clone https://github.com/tomko-neuron/ETDP-CA1.git

CA1 pyramidal cell models

Two compartmental models of CA1 pyramidal cells are used:

  • CA1 pyramidal neuron: Dendritic Na+ spikes are required for LTP at distal synapses ​(Kim et al. (2015)
  • Global and multiplexed dendritic computations under in vivo-like conditions (Ujfalussy et al 2018)

Synaptic plasticity experiments

There are two defined experiments on synaptic plasticity. In all experiments, the voltage-based ETDP synaptic plasticity rule described in Benuskova and Abraham (2007) was employed.

  • Dist_tuf_LTP_CA1 implements four theta-burst stimulation protocols as in Kim et al. (2015).
  • Suthresold_LTP_CA1 implements four low-frequency stimulation protocols as in Magó et al. (2020).

Code organization

CA1_plasticity

This directory contains the classes and files needed to work with models, run simulations, save records and plot figures.

Dist_tuft_LTP_CA1

The directory includes files and directories from ModelDB necessary for running the model, along with additional resources:

  • libcell.py: This file contains the CA1 class, representing the model.
  • main.py: This script is used to run simulations and plot figures.
  • figures subdirectory: It contains saved figures used in the paper.
  • recordings subdirectory: This contains saved records (not included).
  • settings subdirectory: Here, you'll find setting.json and synapses.json files required for configuring the simulation and adding synapses to the model.

Subthreshold_LTP_CA1

The directory includes files and directories from ModelDB necessary for running the model, along with additional resources:

  • libcell.py: This file contains the CA1 class, representing the model.
  • main.py: This script is used to run simulations and plot figures.
  • figures subdirectory: It contains saved figures used in the paper.
  • recordings subdirectory: This contains saved records (not included).
  • settings subdirectory: Here, you'll find setting.json and synapses.json files required for configuring the simulation and adding synapses to the model.

Typical workflow

A typical workflow consists of four main stages:

  1. configuration
  2. model instantiation
  3. simulation
  4. saving and plot figures