This repository contains modeling exercise materials and homework for the Computational Neuroscience course at Okinawa Institute of Science and Technology in 2023. In our modeling exercises, we explore physiological concepts about how neural systems function via computer simulations. Our goal is to learn how computational models can help us understand how diverse phenomena in real neural systems arise from the underlying physical principles.
We will build models on the NEURON simulation platform and use Python programming language to write models using NEURON. While most of our focus will be constructing the models of neural circuits and running their simulations, we will also cover some basic analysis of neural data.
We use NEURON 8.2. Please follow the instruction to install the software before the first exercise class.
The following Python packages are also required:
Please install them by following the instructions at their homepages.
Modeling class introduction — February 2, 2023
In this introduction class, we will go through an overview of building the models of neurons. We will dicuss fundamental concepts such as the compartmental representation of a neuron as a spatially extended electrophysiological device. We will also discusse steps to construct those model neurons and simulate them in the NEURON simulator.
Modeling class 1 — Febuary 16, 2023
In this class, we will work with a neuron model reconstructed from an experimentally measured morphology. We will discuss how to build/run the simulations of electrophysiology experiments and analyze how their responses to inputs are governed by their biophysical properties.
Modeling class 2 — March 16, 2023
In this class, we will use the lessons from a previous class to understand the integration fo synaptic inputs in model neurons. We will also learn about active mechanisms and how they impact the input integration and output generation.
Modeling class 3 — April 6, 2023
In this class, we will learn more about modeling active mechanisms. We will also discuss the basics of building network models and analyzing neural data.
Modeling class 4 — April 20, 2023
In the last class, we will go through the examples and use cases of network models.
Homework 1 — Febraury 27, 2023
Homework 2 — March 24, 2023
Homework 3 — April 24, 2023
Written by Sungho Hong, Computational Neuroscience Unit, Okinawa Institutes of Science and Technology
January 2023