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. (2023).

https://github.com/tomko-neuron/etdp-ca1

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Repository

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. (2023).

Basic Info

Host: GitHub
Owner: tomko-neuron
License: mit
Language: Python
Default Branch: main
Size: 2.75 MB

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Created almost 3 years ago · Last pushed about 1 year ago

Metadata Files

Readme License Citation

README.md

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. 2023; Journal of Computational Neuroscience).

To run:

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

install packages in requirements

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. - DisttufLTP_CA1 implements four theta-burst stimulation protocols as in Kim et al. (2015). - SuthresoldLTPCA1 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:

configuration
model instantiation
simulation
saving and plot figures

Owner

Login: tomko-neuron
Kind: user

Repositories: 1
Profile: https://github.com/tomko-neuron

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Tomko"
  given-names: "Matus"
  orcid: "https://orcid.org/0000-0002-2915-1780"
title: "A voltage-based Event-Timing-Dependent Plasticity rule accounts for LTP subthreshold and suprathreshold for dendritic spikes in CA1 pyramidal neurons"
version: 2.0.0
doi: 10.5281/zenodo.8348967
date-released: 2023-09-15
url: "https://github.com/tomko-neuron/ETDP-CA1"

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