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CA1_plasticity

Code repository of the dissertation thesis: Computational model of synaptic plasticity in CA1 region of hippocampus.

To run:

git clone https://github.com/tomko-neuron/CA1_plasticity.git

CA1 pyramidal cell model

In simulations is used a reduced-morphology model for CA1 pyramidal cells. The model was optimized and tested using HippoUnit. The model is associated with a paper: A new reduced-morphology model for CA1 pyramidal cells and its validation and comparison with other models using HippoUnit and GitHub repository.

To21 model

Synaptic plasticity experiments

There are three defined experiments on synaptic plasticity. In all experiments, the voltage-based meta-STDP synaptic plasticity rule described in Jedlicka et al. (2015) was employed.

  • Experiment 1 implements the sequentional stimulation protocol as in Dong et al. (2008) under the pentobarbital anesthesia.
  • Experiment 2 implements the high-frequency stimulation protocol and the paired-pulses stimulation protocol as in Pavlowsky and Alarcon (2012).
  • Experiment 3 implements the theta burst stimulation protocol as in Kim et al. (2015).

Code organization

CA1_plasticity.experiments

This directory contains user-defined experiments. Each experiment has a defined directory that contains all the necessary files and scripts. A typical experiment directory structure is illustrated for our “experiment1”.

CA1_plasticity.experiments.experiment1

The directory contains the main.py script that is used to run a simulation. The figures subdirectory contains saved figures, the recordings subdirectory contains saved recordings, the settings subdirectory contains all settings. This subdirectory contains setting.json and synapses.json files needed for the simulation configuration and add synapses to the model.

CA1_plasticity.io

This directory contains two classes used for data processing. The IOHelper class is used to load and save the settings and recordings. The FigureShower class is used to visualize the recorded data. Several methods are defined in the FigureShower class to plot the evolution of voltages, synaptic weights and ionic currents over time.

CA1_plasticity.model

This directory contains the classes and files needed to work with the model. TheCA1PyramidalCell class represents a model of the CA1 pyramidal cell. The constructor loads the model from a .hoc file. The class defines methods for adding synapses, setting recording vectors and setting spontaneous activity. The StimulationProtocol class is used to set a stimulation protocol. Each stimulation protocol is defined by its own method and the parameters are defined in the setting.json file in the experiment directory (see above). The mods directory contains additional .mod files that must be precompiled. They are loaded when the model is loaded. The hoc_models directory contains the models defined in HOC.

Typical workflow

A typical workflow consists of four main stages:

  1. configuration
  2. model instantiation
  3. simulation
  4. saving and analysis

Typical workflow