open-computational-neuroscience-resources
by asoplata
A publicly-editable collection of open computational neuroscience resources
AI summary
Brain analysis toolkit
A collection of resources and tools for analyzing and simulating brain data and neural systems
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What's in the list
165 links in 27 sections, with live GitHub stats.activeno commit in 2y
Meta-resources
see this Open Science Resources page
Open Hardware -
Markup Languages for Model Specification
Markup Languages for Model Specification / NeuroML - A model description language for computational neuroscience
- https://docs.neuroml.org/Userdocs/Software/SupportingTools.html
Converts to and can be run automatically by different kinds of simulators:
Markup Languages for Model Specification
Open Code
Open Code / Elephant - Software for common electrophysiological data analysis operations
- Neurotools
Elephant is the direct successor to
- Neo
Elephant can consume electrophysiology data loaded by
Open Code
Open Code / (deprecated) OpenElectrophy - Analysis software for electrophysiological data, built on Neo
OpenElectrophy's README
indicates that it is old, effectively abandoned, and you should use something else
Open Code
- SpykeViewer - Analysis software for spikes of electrophysiological data
SpykeViewer can consume electrophysiology data loaded by
- TrakEM2 - Morphological image (histological staining) data mining and analysis plugin
for use as a including as part of the
Open Code / GENESIS / PGENESIS - Longstanding platform for neural simulation
Open Code
Open Code / HNN - Human Neocortical Neurosolver - Simulation of MEG/EEG source waveforms using NEURON
Open Code
- MOOSE - Multiscale Object-Oriented Simulate Environment
(Not to be confused with this )
Open Code / PyRhO - Virtual laboratory for optogenetic simulation. Integrates with NEURON and Brian2 models.
Open Code
- PCSIM - Parallel neural Circuit SIMulator
(The successor to )
Open Courses and Educational Resources
Open Courses and Educational Resources / Course: Neuronal Dynamics at edX
Open Courses and Educational Resources
Open Data
- re3data
This only lists neuroscience-specific open data repositories. For general science data repositories that may contain neuroscience data like ,
Open Data / Allen Brain Atlas Data Portal
Open Data
Open Data / Neurodata Without Borders: Neurophysiology (NWB:N) data standard for neurophysiology, including intracellular, extracellular, optical physiology, tracking, and stimulus data
Open Data
Organizations and Communities
Reproducibility and Provenance
Reproducibility and Provenance / Alpaca - Provenance for data analysis in Python
- Neo
Provides examples for use with and
Reproducibility and Provenance
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Featured in 2 awesome lists
Each link jumps to the spot where the list mentions open-computational-neuroscience-resources.