| |
| Allen Institute for Brain
Science | | | |
| COMBINE - Computational modeling in biology network | | | |
| Comparison of Neural Network
Simulators | | | |
| Computational Neuroscience journals | | | |
| "Computational Neuroscience on the Web" (Jim Perlewitz) - Probably the most
comprehensive curated list of computational neuroscience modeling tools on
the internet. HIGHLY recommended. | | | |
| "Computational Neuroscience Resources" (Dan Goodman) | | | |
| "Computational Neuroscience Resources" (Fleur Zeldenrust) | | | |
| NCBI databases - National Center for Biotechnology Information database
list, VERY comprehensive! | | | |
| neuroshare - Brief list of neuroscience data tools and vendors | | | |
| NIF - Neuroscience Infomation Framework - Search for EVERY kind of
neuroscience data, atlas, software, everything! | | | |
| NSG - Neuroscience Gateway - An online resource that allows public usage of
high performance computing resources for neural
simulation! | | | |
| see this Open Science Resources
page | 113 | about 3 years ago | Open Hardware - |
| Planet Neuroscience: An aggregation of neuroscience journal RSS feeds | | | |
| SORTED - a list of interesting science ideas and links (cognitive/neuro & data science) | 15 | over 1 year ago | |
| Wikipedia List of Neuroscience Databases | | | |
Open Computational Neuroscience Resources / Markup Languages for Model Specification |
| CellML - A model specification language for general biological mathematical
modeling | | | |
| NESTML - Domain-specific language for neuron models and code generation
toolchain | | | |
| NeuroML - A model description language for computational
neuroscience | | | |
Open Computational Neuroscience Resources / 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: |
Open Computational Neuroscience Resources / Markup Languages for Model Specification |
| NineML - A model specification language for
neuroscience | | | |
| SpineML - A declarative XML-based model description language for large scale neural network models | | | |
Open Computational Neuroscience Resources / Open Code |
| Elephant - Software for common electrophysiological data analysis
operations | | | |
Open Computational Neuroscience Resources / 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 Computational Neuroscience Resources / Open Code |
| Neo - Python library for enabling interoperability of electrophysiological
data, including conversion from proprietary file
formats | | | |
| (deprecated) OpenElectrophy - Analysis software for electrophysiological data, built on
Neo | | | |
Open Computational Neuroscience Resources / Open Code / (deprecated) OpenElectrophy - Analysis software for electrophysiological data, built on
Neo |
| OpenElectrophy's README | 31 | over 7 years ago | indicates that it is old, effectively abandoned, and you should use something else |
Open Computational Neuroscience Resources / Open Code |
| Pynapple - "PYthon Neural Analysis Package" for neurophysiological data analysis | 284 | 11 months ago | |
| Spike Sorting Software - VERY good comparison of different spike sorting
software capabilities | | | |
| SpikeInterface - Spike sorting analysis specifically made for compatibility
between different sorting algorithms, part of the Open Ephys project | | | |
| SpykeViewer - Analysis software for spikes of electrophysiological data | | | SpykeViewer can consume electrophysiology data loaded by |
| CaImAn - Calcium Imaging Analysis | 644 | 11 months ago | |
| CATMAID - The Collaborative Annotation Toolkit for Massive Amounts of Image
Data | | | |
| Chronux - MATLAB toolbox for EEG analysis, including some tools for MEG, fMRI, and image data | | | |
| EEGLAB - MATLAB toolbox for EEG, MEG, and ECOG data analysis and
visualization | | | |
| FieldTrip - MATLAB toolbox for EEG, MEG, and ECoG analysis | | | |
| FreeSurfer - Popular open-source MRI processing and analysis
software | | | |
| MNE - MEG + EEG analysis and visualization tool in
Python | | | |
| NiBabel - Python library for enabling interoperability of neuroimaging data,
including conversion from and between many file
formats | | | |
| NiMARE - NiMARE is a Python package for neuroimaging meta-analyses | | | |
| supereeg - Sparse ECoG analysis | | | |
| TrakEM2 - Morphological image (histological staining) data mining and analysis
plugin | | | for use as a including as part of the |
| TREES - MATLAB toolbox for analyzing neuron
microscopy | | | |
| V-NeuroStack - 3D time stacks for finding patterns in spontaneous activity of
neurons in mouse brain slices | | | |
| bctnet - Brain Connectivity Toolbox for complex-network analysis | 19 | almost 5 years ago | |
| Geppetto - Web-based, open-source visualization platform for computational
biology | | | |
| NeuronUnit - Data-driven model validation for
neuroscience | 38 | over 4 years ago | |
| SpectraVis - Network visualization tool for functional brain connectivity
in-browser | 38 | about 3 years ago | |
| Vaa3D - 3D Visualization-Assisted
Analysis | | | |
| NeuroDebian | | | |
| Comp-Neuro Fedora | | | |
| Arbor - High-performance library for computational neuroscience simulations | | | |
| BindsNET - Simulation of spiking neural networks (SNNs) using PyTorch | 1,517 | 11 months ago | |
| Brain Dynamics Toolbox - Open software for simulating dynamical systems in
neuroscience using MATLAB | | | |
| Brian2 - Powerful, modern neural simulator written in Pythonthat offers
built-in compilation | | | |
| CoreNeuron - Optimized, simplified NEURON implementation used by the Blue
Brain Project | 136 | over 2 years ago | |
| DiPDE - Platform for population-level neural
simulation | | | |
| DynaSim - Open-source MATLAB/GNU Octave toolbox for neural simulation.
Offers built-in parallelization, compilation, and batch/cluster simulation
management. | | | |
| GENESIS / PGENESIS - Longstanding platform for neural
simulation | | | |
| |
| NeuroSpaces - A modular implementation of GENESIS
components | | | |
Open Computational Neuroscience Resources / Open Code |
| LFPy - Local Field Potential simulator meant for use with NEURON
models | | | |
| HNN - Human Neocortical Neurosolver - Simulation of MEG/EEG source waveforms using NEURON | | | |
| |
| HNN (GUI version) | | | |
| HNN-core (command line version) | | | |
Open Computational Neuroscience Resources / Open Code |
| MOOSE - Multiscale Object-Oriented Simulate
Environment | | | (Not to be confused with this ) |
| NEF - Neural Engineering Framework | | | |
| Nengo - Large-scale neural simulator | | | |
| NEST - A popular, actively developed neural simulator that can simulate
large neural systems | | | |
| neurolib - A Python simulation framework for easy whole-brain neural mass modeling | | | |
| NEURON - The most popular computational neuroscience model
simulator, focusing on biophysical modelling | | | |
| NeuroRD - "A computationally efficient, stochastic reaction-diffusion
simulator". | | | |
| PyRhO - Virtual laboratory for optogenetic simulation. Integrates with
NEURON and Brian2 models. | 34 | over 2 years ago | |
Open Computational Neuroscience Resources / Open Code / PyRhO - Virtual laboratory for optogenetic simulation. Integrates with
NEURON and Brian2 models. |
| Prometheus - Related docker image for use with PyRhO via "Modelling as a
Service" | 0 | over 2 years ago | |
Open Computational Neuroscience Resources / Open Code |
| PSICS - Parallel Stochastic Ion Channel Simulator | | | |
| PCSIM - Parallel neural Circuit SIMulator | | | (The successor to ) |
| PyNN - Language for building neuronal network models meant for export to
other simulators | | | |
| PyPNS - Python Peripheral Nerve Simulator | 3 | over 2 years ago | |
| Spike - "A high speed Spiking Neural Network Simulator designed for
GPGPUs". | | | |
| 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 | 105 | 11 months ago | |
| BluePyOpt - Blue Brain Python Optimisation Library, for optimizing
parameters in neural models | 204 | 12 months ago | |
| BRAHMS - A modular execution framework for executing integrated systems built from component software processes | 3 | over 6 years ago | |
| GIMBL-Vis - Multi-dimensional visualization toolbox; integrates with
DynaSim | 4 | about 5 years ago | |
| Lancet - Software for managing large volumes of neural
simulations | | | |
| neuroConstruct - Software for developing biologically realistic 3D neural
networks geometries, for simulation by NEURON, PyNN,
etc. | | | |
| Neurofitter - Parameter tuning software for electrophysiological neural
models like NEURON | | | |
| neuroHDF - HDF5 data format for
neuroscience | | | |
| NeuroTools - Collection of tools for "simulation setup, parameterization,
data management, analysis, and visualization" for many neural simulators
above. | | | |
| NSDF - Neuroscience Simulation Data Format, built on
HDF5 | 7 | 12 months ago | |
| ODE-toolbox - Automatic selection and generation of integration schemes
for systems of ordinary differential equations | | | |
| pypet - Python parameter exploration toolkit for managing parameter sweeps
of simulations in neural simulators like Brian. Has Sumatra
integration. | | | |
| Sumatra - An "automated electronic lab notebook" for managing simulation and
analysis projects | | | |
Open Computational Neuroscience Resources / Open Courses and Educational Resources |
| Course: Computational Neuroscience at
Coursera | | | |
| 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 | | | |
| Course: Neuronal Dynamics at
edX | | | |
Open Computational Neuroscience Resources / Open Courses and Educational Resources / Course: Neuronal Dynamics at
edX |
| Textbook: The open book for this course is available here | | | |
Open Computational Neuroscience Resources / Open Courses and Educational Resources |
| Courses: Neuroscience course material from OpenCourseWare (OCW) at MIT Department of Brain and Cognitive Sciences - HUGE list! | | | |
| Course: Simulation Neuroscience at edX | | | |
| Encyclopedia of Computational Neuroscience at
Scholarpedia | | | |
| Notebook: Python notebooks from courseware on theoretical/computational neuroscience (for beginners) | | | |
| Textbook: Computational Cognitive
Neuroscience (maybe 404'd as of 2022-11-21?) | | | |
| Textbook (online): Neural Data Science in Python | | | |
| Webpage: Biological Neural Networks: Part 1, Spiking Neurons - VERY cool webpage with interactive spiking neural models! | | | |
Open Computational Neuroscience Resources / Open Data |
| re3data | | | This only lists neuroscience-specific open data repositories. For general
science data repositories that may contain neuroscience data like
, |
| 3D Brain Atlas Reconstructor | | | |
| Allen Brain Atlas Data Portal | | | |
Open Computational Neuroscience Resources / Open Data / Allen Brain Atlas Data Portal |
| More detail
here | | | |
| AllenSDK - How to programmatically download and use Allen data | | | |
Open Computational Neuroscience Resources / Open Data |
| BODB - Brain Operation Database System | | | |
| BossDB.org — hundreds of terabytes of microscopy | | | |
| Brain Slices- Repository of brain tissue images | | | |
| C-BIG - Biological Imaging and Genetic
repository | | | |
| Channelpedia - Wiki of neuron ion channels, hosted by the Blue Brain
Project | | | |
| Codex: FlyWire - Proofread static snapshots of the FlyWire full-brain connectome | | | |
| CRCNS - Collaborative Research in Computational
Neuroscience | | | |
| GIN - Modern Research Data Management for Neuroscience | | | |
| IDA LONI - Image and Data Archive for neuroscience by Laboratory of Neuro
Imaging | | | |
| INDI - International Neuroimaging Data-Sharing
Initiative | | | |
| iEEG.org - National Institutes of Neurological Disorders and Stroke EEG data
repository for epilepsy research | | | |
| NCBI databases - National Center for Biotechnology Information database
list, VERY comprehensive! | | | |
| NDA - National Institute of Mental Health Data
Archive | | | |
| NeuroVault - Public repository of MRI and PET statistical maps,
parcellations, and atlases | | | |
| NIF - Neuroscience Information Framework, massive search engine for
neuroscience data, tools, etc. | | | |
| NITRC - NeuroImaging Tools and Resources
Collaboratory | | | |
| NMC - Neocortical Microcircuit Collaboration, part of Blue
Brain | | | |
| NWB - Neurodata Without Borders - A standardized format for
electrophysiological, and in the future other, neuroscience data. Some data
sets available on the site in this format. | | | |
| OpenNeuro - Free and open platform for neuroimaging data (succeeds
OpenfMRI) | | | |
| Whole Brain Catalog - Virtual catalog of a mouse
brain | | | |
| WormBase - Database of nematode information | | | |
| ZFIN - Zebrafish Model Organism Database | | | |
| Neo - Python library for enabling interoperability of electrophysiological
data, including conversion from proprietary file
formats | | | |
| Neurodata Without Borders: Neurophysiology (NWB:N) data standard for
neurophysiology, including intracellular, extracellular, optical physiology,
tracking, and stimulus data | | | |
Open Computational Neuroscience Resources / Open Data / Neurodata Without Borders: Neurophysiology (NWB:N) data standard for
neurophysiology, including intracellular, extracellular, optical physiology,
tracking, and stimulus data |
| ndx-simulation-output Large-scale simulation data scheme extenstion to
NWB:N | 4 | almost 5 years ago | |
Open Computational Neuroscience Resources / Open Data |
| NSDF - Neuroscience Simulation Data Format, built on top of HDF5 | 7 | 12 months ago | |
| SONATA format for large-scale, efficient model specification and output data
schema of neural simulations, co-developed by Allen Institute for Brain
Sciences and Blue Brain Project | 55 | over 1 year ago | |
| 3DModelDB - A collection of 3D printable versions of published neuron
morphologies, both traced and
artificial. | | | |
| CellPropDB - Cellular Properties Database provides a simple repository
for data regarding membrane channels, receptor and neurotransmitters that
are expressed in specific types of
cells. | | | |
| MicrocircuitDB - Provides an accessible location for storing and
efficiently retrieving realistic computational models of brain
microcircuits and
networks. | | | |
| NeuronDB - Provides a dynamically searchable database of three types of
neuronal properties: voltage gated conductances, neurotransmitter
receptors, and neurotransmitter
substances. | | | |
| OdorDB - Odor Molecules DataBase | | | |
| OdorMapDB - Olfactory Bulb Odor Map
DataBase | | | |
| ORDB - Olfactory Receptor DataBase | | | |
| ORModelDB - A resource that is a repository of the results of the
efforts of the community is computationally elucidating the structure of
the olfactory receptor with a view to establishing a mechanistic basis
for OR-odorant binding. | | | |
Open Computational Neuroscience Resources / Organizations and Communities |
| CodeNeuro - Bringing neuroscience and data science together | | | |
| OCNS - Organization for Computational Neuroscience | | | |
| G-NODE - German Informatics Node | | | |
| INCF - International Neuroinformatics Coordinating
Facility | | | |
| NeuralEnsemble, focused on software development in
neuroscience | | | |
| NeuroFedora, Fedora community special interest group | | | |
| Neuroinformatics Research Group at Harvard | | | |
| Neurostars - Neuroscience Q and A website | | | |
| NIMH - National Institute of Mental
Health | | | |
| An Open Computational Neuroscience list I've made on
Twitter | | | |
| Organization for Human Brain Mapping | | | |
| Reddit /r/Neuroscience
resources | | | |
| SFN - Society for Neuroscience | | | |
| Funding research software development | | | |
Open Computational Neuroscience Resources / Reproducibility and Provenance |
| Tutorial on reproducible computational neuroscience research, from CNS 2012
by author of Sumatra | | | |
| Alpaca - Provenance for data analysis in Python | | | |
Open Computational Neuroscience Resources / Reproducibility and Provenance / Alpaca - Provenance for data analysis in Python |
| Neo | | | Provides examples for use with and |
Open Computational Neuroscience Resources / Reproducibility and Provenance |
| Snakemake - Scalable, reproducible workflows using a Python-like language | | | |
open-computational-neuroscience-resources 
0ex/more-awesome
ptdz/sorted
openlists/otherlists
alejoe91/multimodalfitting
nds-org/ndslabs
matomatical/remarkable-kaitai
after-eight/regitable
deap/deap
bluebrain/brayns
jamesf91/remarkablesync
ds160/remarkable-remember