A310 Computational Neuroscience - Okinawa Institute of Science and Technology, 2022

This repository contains modeling practice materials and homework for the Computational Neuroscience course at Okinawa Institute of Science and Technology in 2022. 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, which uses Python programming language for the interface. We will also cover some basic analysis of neural data, while most of our focus will be constructing the models of neural circuits and running their simulations.

Software

We use NEURON 8.0. Please follow the instruction to install the software before the first exercise class. The following Python packages are also required:

1. Numpy
2. Scipy
3. Matplotlib
4. Pandas
5. JupyterLab

Please install them by following the instructions at their homepage.

Schedule of modeling classes and homework dues

Modeling class introduction — January 24, 2022

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.

Written by Sungho Hong, Computational Neuroscience Unit, Okinawa Institutes of Science and Technology

January 2021