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open-computational-neuroscience-resources
A publicly-editable collection of open computational neuroscience resources
https://github.com/asoplata/open-computational-neuroscience-resources
- COMBINE - Computational modeling in biology network
- Computational Neuroscience journals
- "Computational Neuroscience Resources" (Dan Goodman)
- "Computational Neuroscience Resources" (Fleur Zeldenrust)
- neuroshare - Brief list of neuroscience data tools and vendors
- Planet Neuroscience: An aggregation of neuroscience journal RSS feeds
- SORTED - a list of interesting science ideas and links (cognitive/neuro & data science)
- Wikipedia List of Neuroscience Databases
- SpineML - A declarative XML-based model description language for large scale neural network models
- Neurotools
- Neo
- OpenElectrophy's README
- Pynapple - "PYthon Neural Analysis Package" for neurophysiological data analysis
- SpykeViewer - Analysis software for spikes of electrophysiological data
- Neo
- CaImAn - Calcium Imaging Analysis
- Chronux - MATLAB toolbox for EEG analysis, including some tools for MEG, fMRI, and image data
- FieldTrip - MATLAB toolbox for EEG, MEG, and ECoG analysis
- NiMARE - NiMARE is a Python package for neuroimaging meta-analyses
- supereeg - Sparse ECoG analysis
- bctnet - Brain Connectivity Toolbox for complex-network analysis
- NeuroDebian
- Comp-Neuro Fedora
- Arbor - High-performance library for computational neuroscience simulations
- BindsNET - Simulation of spiking neural networks (SNNs) using PyTorch
- HNN - Human Neocortical Neurosolver - Simulation of MEG/EEG source waveforms using NEURON
- HNN (GUI version)
- HNN-core (command line version)
- NEF - Neural Engineering Framework
- Nengo - Large-scale neural simulator
- neurolib - A Python simulation framework for easy whole-brain neural mass modeling
- PSICS - Parallel Stochastic Ion Channel Simulator
- PCSIM - Parallel neural Circuit SIMulator
- PyPNS - Python Peripheral Nerve Simulator
- SpineCreator - A cross platform graphical editor for SpineML models with support for running model simulations
- STEPS - Parallel stochastic reaction-diffusion and voltage simulator on realistic 3D geometries
- sPyNNaker - A software package for running PyNN simulations on the SpiNNaker million core neuromorphic machine
- BRAHMS - A modular execution framework for executing integrated systems built from component software processes
- Course: Introduction To Modern Brain-Computer Interface Design
- Course: Computational Neuroscience: Neuronal Dynamics of Cognition at edX
- Course/Curriculum: Mathematical Tools for Neuroscientists
- Courses: Neuromatch Academy hands-on courses in either Computational Neuroscience or Deep Learning
- Textbook: The open book for this course is available here
- Courses: Neuroscience course material from OpenCourseWare (OCW) at MIT Department of Brain and Cognitive Sciences - HUGE list!
- Course: Simulation Neuroscience at edX
- Notebook: Python notebooks from courseware on theoretical/computational neuroscience (for beginners)
- Textbook (online): Neural Data Science in Python
- Webpage: Biological Neural Networks: Part 1, Spiking Neurons - VERY cool webpage with interactive spiking neural models!
- 3D Brain Atlas Reconstructor
- Allen Brain Atlas Data Portal
- AllenSDK - How to programmatically download and use Allen data
- BODB - Brain Operation Database System
- BossDB.org — hundreds of terabytes of microscopy
- Brain Slices- Repository of brain tissue images
- Codex: FlyWire - Proofread static snapshots of the FlyWire full-brain connectome
- GIN - Modern Research Data Management for Neuroscience
- WormBase - Database of nematode information
- ZFIN - Zebrafish Model Organism Database
- NSDF - Neuroscience Simulation Data Format, built on top of HDF5
- BioModels - Not neuroscience-specific
- Senselab
- OdorDB - Odor Molecules DataBase
- ORDB - Olfactory Receptor DataBase
- NeuroElectro - Repository of data-mined and human-curated neuron celltype electrophysiological data
- NeuroML-db - Curated database of NeuroML models
- NeuroMorpho - Curated repository of digitally reconstructed neuron geometries
- OSB - Open Source Brain
- OSBv2 - Open Source Brain version 2.0
- OpenWorm - Popular platform for simulation and analysis of nematode neuroscience models!
- "Integrated Models" RRID on SciCrunch - Compilation of model sources
- CodeNeuro - Bringing neuroscience and data science together
- OCNS - Organization for Computational Neuroscience
- G-NODE - German Informatics Node
- NeuroFedora, Fedora community special interest group
- Neuroinformatics Research Group at Harvard
- Neurostars - Neuroscience Q and A website
- Organization for Human Brain Mapping
- SFN - Society for Neuroscience
- Funding research software development
- Alpaca - Provenance for data analysis in Python
- Neo
- Snakemake - Scalable, reproducible workflows using a Python-like language
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Keywords
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