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Open Computational Neuroscience Resources

Computational neuroscience means one of two things:

  1. Analysis of neuroscientific data. Examples: analysis of MRI/fMRI imaging data, invasive intracranial electrode recordings from a mouse running in a maze or performing a task, calcium-sensitive fluorescent dye imaging data, human EEG data, computer-vision analysis of post-mortem histology stains, statistical modeling of such data, and much more!

  2. Simulation of neural systems. Examples: simulating (aka "modeling") many compartments of a single neuron, large networks of model neurons with simple individual behavior, dynamical systems analysis of simplified neurons, neural "mass" models where only groups of neurons (not individual cells) are modeled, and much more!

These endeavors initially require expensive data from wet-lab experiments to inform parameters, but most of the computational work can be accomplished using everyday, consumer-grade laptop and desktop computers! Indeed, the biggest barrier to entry is not hardware, data, or expense, but rather time and passion to learn the tools and underlying biology/mathematics needed for such computational science. Coupled with the great tools coming out of the modern Data Science movement, new Open Science and Open Data resources make it easier than ever to learn or even contribute to the study of the brain! The resources below should be more than enough to provide anyone with the means to begin learning or working in computational neuroscience, at no cost other than time and a modern personal computer.

Note: This is intended as a list of resources to help with neuroscientific pursuits (trying to understand the brain as it exists), as opposed to artificial intelligence or machine learning pursuits (using brain-inspired mathematics and properties to engineer systems meant to accomplish a particular task). More broadly, I've made a similar repo-list of general open science resources here.

Contributions are VERY welcome!



Meta-resources


Markup Languages for Model Specification


Open Code

Analysis Software For Imaging
Analysis Software For Everything Except Imaging
Operating Systems
Simulation Software
Simulation Data Format and Management Software

Open Courses and Educational Resources


Open Data

Open Data Schema
Open Model Repositories

Organizations and Communities


Reproducibility