{"id":13688550,"url":"https://github.com/asoplata/open-computational-neuroscience-resources","last_synced_at":"2025-12-30T14:04:40.353Z","repository":{"id":41325627,"uuid":"126888001","full_name":"asoplata/open-computational-neuroscience-resources","owner":"asoplata","description":"A publicly-editable collection of open computational neuroscience resources","archived":false,"fork":false,"pushed_at":"2024-04-11T09:23:03.000Z","size":286,"stargazers_count":596,"open_issues_count":3,"forks_count":91,"subscribers_count":29,"default_branch":"main","last_synced_at":"2025-04-23T00:02:24.062Z","etag":null,"topics":["awesome","awesome-list","brain","computational-biology","computational-neuroscience","electrophysiological-data","neural-simulations","neural-simulators","neuroimaging-data","neuron-models","neuroscience","neuroscience-data","neuroscience-methods","open-science","simulation-neuroscience"],"latest_commit_sha":null,"homepage":"","language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/asoplata.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null}},"created_at":"2018-03-26T20:47:18.000Z","updated_at":"2025-04-21T12:47:28.000Z","dependencies_parsed_at":"2024-01-14T06:04:33.610Z","dependency_job_id":"430089ce-4598-4c1b-b6e8-180c44b996a3","html_url":"https://github.com/asoplata/open-computational-neuroscience-resources","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/asoplata%2Fopen-computational-neuroscience-resources","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/asoplata%2Fopen-computational-neuroscience-resources/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/asoplata%2Fopen-computational-neuroscience-resources/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/asoplata%2Fopen-computational-neuroscience-resources/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/asoplata","download_url":"https://codeload.github.com/asoplata/open-computational-neuroscience-resources/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251932651,"owners_count":21667189,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["awesome","awesome-list","brain","computational-biology","computational-neuroscience","electrophysiological-data","neural-simulations","neural-simulators","neuroimaging-data","neuron-models","neuroscience","neuroscience-data","neuroscience-methods","open-science","simulation-neuroscience"],"created_at":"2024-08-02T15:01:16.395Z","updated_at":"2025-12-30T14:04:40.274Z","avatar_url":"https://github.com/asoplata.png","language":null,"funding_links":[],"categories":["Science","Others","Other Lists","Additional Resources:"],"sub_categories":["TeX Lists","Journals (for Data Notes)"],"readme":"\n# Open Computational Neuroscience Resources\n\nComputational neuroscience means one of two things: \n\n1. Analysis of\nneuroscientific data. Examples: analysis of MRI/fMRI imaging data, invasive intracranial electrode recordings from\na 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!\n\n2. Simulation of neural systems. Examples: simulating (aka \"modeling\") many compartments of a\nsingle neuron, large networks of model neurons with simple individual\nbehavior, dynamical systems analysis of simplified neurons, neural \"mass\" models where only *groups* of neurons (not individual cells) are modeled, and much more!\n\nThese endeavors initially require expensive data from wet-lab\nexperiments to inform parameters, but most of the computational work can be\naccomplished using everyday, consumer-grade laptop and desktop computers!\nIndeed, the biggest barrier to entry is not hardware, data, or expense, but\nrather time and passion to learn the tools and underlying biology/mathematics\nneeded for such computational science. Coupled with the great tools coming out\nof the modern Data Science movement, new Open Science and Open Data resources make it easier than\never to learn or even contribute to the study of the brain! **The resources\nbelow should be more than enough to provide anyone with the means to begin\nlearning or working in computational neuroscience, at no cost other than time\nand a modern personal computer.**\n\nNote: This is intended as a list of resources to help with *neuroscientific*\npursuits (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\nmade a similar repo-list of general open science resources\nhere](https://github.com/asoplata/open-science-resources).\n\nContributions are VERY welcome!\n\n-----------------------------------\n\n- Contents:\n    - [Meta-resources](#meta-resources)\n    - [Markup Languages for Model Specification](#markup-languages-for-model-specification)\n    - [Open Code](#open-code)\n        - [Analysis Software For Electrophysiology](#analysis-software-for-electrophysiology)\n        - [Analysis Software For Imaging](#analysis-software-for-imaging)\n        - [Other Analysis Software](#other-analysis-software)\n        - [Operating Systems](#operating-systems)\n        - [Simulation Software](#simulation-software)\n        - [Simulation Data Format and Management Software](#simulation-data-format-and-management-software)\n    - [Open Courses and Educational Resources](#open-courses-and-educational-resources)\n    - [Open Data](#open-data)\n        - [Open Data Schema](#open-data-schema)\n        - [Open Model Repositories](#open-model-repositories)\n    - [Organizations and Communities](#organizations-and-communities)\n    - [Reproducibility and Provenance](#reproducibility-and-provenance)\n\n-----------------------------------\n\n### Meta-resources\n\n- [Allen Institute for Brain\n  Science](https://alleninstitute.org/open-science-tools/)\n- [COMBINE - Computational modeling in biology network](http://co.mbine.org/standards)\n- [Comparison of Neural Network\n  Simulators](https://grey.colorado.edu/emergent/index.php/Comparison_of_Neural_Network_Simulators)\n- [Computational Neuroscience journals](http://www.cnsorg.org/journals)\n- [\"Computational Neuroscience on the Web\" (Jim Perlewitz) - Probably the most\n  comprehensive *curated* list of computational neuroscience modeling tools on\n  the internet. HIGHLY recommended.](https://compneuroweb.com/)\n- [\"Computational Neuroscience Resources\" (Dan Goodman)](https://neural-reckoning.org/comp-neuro-resources.html)\n- [\"Computational Neuroscience Resources\" (Fleur Zeldenrust)](https://fleurzeldenrust.nl/computational-neuroscience-resources/)\n- [NCBI databases - National Center for Biotechnology Information database\n  list, VERY comprehensive!](http://www.ncbi.nlm.nih.gov/guide/all/)\n- [neuroshare - Brief list of neuroscience data tools and vendors](http://neuroshare.sourceforge.net/links.shtml)\n- [NIF - Neuroscience Infomation Framework - Search for EVERY kind of\n  neuroscience data, atlas, software, everything!](https://neuinfo.org/)\n    - This is the most comprehensive tool for open neuroscience resources in\n      the world. If it exists on the internet, it's probably indexed here.\n- [NSG - Neuroscience Gateway - An online resource that allows public usage of\n  high performance computing resources for neural\n  simulation!](http://www.nsgportal.org/index.html)\n- Open Hardware - [see this Open Science Resources\n  page](https://github.com/asoplata/open-science-resources#open-diy-hardware)\n- [Planet Neuroscience: An aggregation of neuroscience journal RSS feeds](https://neuroblog.fedoraproject.org/planet-neuroscience/)\n- [SORTED - a list of interesting science ideas and links (cognitive/neuro \u0026 data science)](https://github.com/PTDZ/SORTED)\n- [Wikipedia List of Neuroscience Databases](https://en.wikipedia.org/wiki/List_of_neuroscience_databases)\n\n-----------------------------------\n\n### Markup Languages for Model Specification\n\n- [CellML - A model specification language for general biological mathematical\n  modeling](https://www.cellml.org/)\n- [NESTML - Domain-specific language for neuron models and code generation\n  toolchain](https://nestml.readthedocs.io/)\n- [NeuroML - A model description language for computational\n  neuroscience](https://www.neuroml.org/)\n    - Converts to and can be run automatically by different kinds of simulators:\n      https://docs.neuroml.org/Userdocs/Software/SupportingTools.html\n- [NineML - A model specification language for\n  neuroscience](http://incf.github.io/nineml-spec/)\n- [SpineML - A declarative XML-based model description language for large scale neural network models](http://spineml.github.io)\n\n-----------------------------------\n\n### Open Code\n\n##### Analysis Software For Electrophysiology\n\n- Note: \"electrophysiology of neurons\" (also called \"ephys\") is equivalent to the common term \"neurophysiology\". In neuroscience, unless it is mentioned explicitly, you can safely assume that \"electrophysiology\" is referring to that of *neuron cells* in particular, as opposed to electrophysiology of *non-neuron brain cells* like astrocytes, glia, etc.\n- [Elephant - Software for common electrophysiological data analysis\n  operations](http://neuralensemble.org/elephant/)\n    - Elephant is the direct successor to [Neurotools](http://neuralensemble.org/NeuroTools/)\n    - Elephant can consume electrophysiology data loaded by [Neo](http://neuralensemble.org/neo/)\n- [Neo - Python library for enabling interoperability of electrophysiological\n  data, including conversion from proprietary file\n  formats](http://neuralensemble.org/neo/)\n    - Note that Neo does not perform analysis or visualization, but instead is only for loading or converting between electrophysiology data types.\n- [(deprecated) OpenElectrophy - Analysis software for electrophysiological data, built on\n  Neo](http://neuralensemble.org/OpenElectrophy/)\n    - [OpenElectrophy's README](https://github.com/OpenElectrophy/OpenElectrophy) indicates that it is old, effectively abandoned, and you should use something else.\n- [Pynapple - \"PYthon Neural Analysis Package\" for neurophysiological data analysis](https://github.com/pynapple-org/pynapple)\n- [Spike Sorting Software - VERY good comparison of different spike sorting\n  software capabilities](https://simonster.github.io/SpikeSortingSoftware/)\n- [SpikeInterface - Spike sorting analysis specifically made for compatibility\n  between different sorting algorithms, part of the Open Ephys project](https://open-ephys.org/spikeinterface)\n- [SpykeViewer - Analysis software for spikes of electrophysiological data](http://neuralensemble.org/SpykeViewer/)\n      - SpykeViewer can consume electrophysiology data loaded by [Neo](http://neuralensemble.org/neo/)\n\n##### Analysis Software For Imaging\n\n- [CaImAn - Calcium Imaging Analysis](https://github.com/flatironinstitute/CaImAn)\n- [CATMAID - The Collaborative Annotation Toolkit for Massive Amounts of Image\n  Data](http://catmaid.readthedocs.io/en/stable/)\n- [Chronux - MATLAB toolbox for EEG analysis, including some tools for MEG, fMRI, and image data](http://chronux.org/)\n- [EEGLAB - MATLAB toolbox for EEG, MEG, and ECOG data analysis and\n  visualization](https://sccn.ucsd.edu/eeglab/index.php)\n- [FieldTrip - MATLAB toolbox for EEG, MEG, and ECoG analysis](http://www.fieldtriptoolbox.org/)\n- [FreeSurfer - Popular open-source MRI processing and analysis\n  software](https://surfer.nmr.mgh.harvard.edu/)\n- [MNE - MEG + EEG analysis and visualization tool in\n  Python](http://martinos.org/mne/stable/index.html)\n- [NiBabel - Python library for enabling interoperability of neuroimaging data,\n  including conversion from and between many file\n  formats](https://nipy.org/nibabel/)\n- [NiMARE - NiMARE is a Python package for neuroimaging meta-analyses](https://nimare.readthedocs.io/en/latest/)\n- [supereeg - Sparse ECoG analysis](http://supereeg.readthedocs.io/en/latest/)\n- [TrakEM2 - Morphological image (histological staining) data mining and analysis\n  plugin](https://syn.mrc-lmb.cam.ac.uk/acardona/INI-2008-2011/trakem2.html) for use as a [plugin for ImageJ](https://imagej.net/plugins/trakem2/) including as part of the [Fiji distribution](https://fiji.sc/)\n- [TREES - MATLAB toolbox for analyzing neuron\n  microscopy](http://www.treestoolbox.org/)\n- [V-NeuroStack - 3D time stacks for finding patterns in spontaneous activity of\n  neurons in mouse brain slices](https://www.evl.uic.edu/entry.php?id=2479)\n\n##### Other Analysis Software\n\n- [bctnet - Brain Connectivity Toolbox for complex-network analysis](https://github.com/brainlife/BCT)\n- [Geppetto - Web-based, open-source visualization platform for computational\n  biology](http://www.geppetto.org/)\n- [NeuronUnit - Data-driven model validation for\n  neuroscience](https://github.com/scidash/neuronunit)\n- [SpectraVis - Network visualization tool for functional brain connectivity\n  in-browser](https://github.com/NeurophysVis/SpectraVis)\n- [Vaa3D - 3D Visualization-Assisted\n  Analysis](http://www.alleninstitute.org/what-we-do/brain-science/research/products-tools/vaa3d/)\n\n##### Operating Systems\n\n- [NeuroDebian](http://neuro.debian.net/)\n- [Comp-Neuro Fedora](https://docs.fedoraproject.org/en-US/neurofedora/install-media/#_fedora_linux_os_for_computational_neuroscience)\n\n##### Simulation Software\n\n- Note: some of these tools are interoperable to some degree.\n- [Arbor - High-performance library for computational neuroscience simulations](https://arbor.readthedocs.io/en/latest/)\n- [BindsNET - Simulation of spiking neural networks (SNNs) using PyTorch](https://github.com/Hananel-Hazan/bindsnet)\n- [Brain Dynamics Toolbox - Open software for simulating dynamical systems in\n  neuroscience using MATLAB](https://bdtoolbox.org/)\n- [Brian2 - Powerful, modern neural simulator written in Pythonthat offers\n  built-in compilation](http://brian2.readthedocs.io/en/stable/)\n- [CoreNeuron - Optimized, simplified NEURON implementation used by the Blue\n  Brain Project](https://github.com/BlueBrain/CoreNeuron)\n- [DiPDE - Platform for population-level neural\n  simulation](http://alleninstitute.github.io/dipde/)\n- [DynaSim - Open-source MATLAB/GNU Octave toolbox for neural simulation.\n  Offers built-in parallelization, compilation, and batch/cluster simulation\n  management.](https://dynasim.github.io/)\n- [GENESIS / PGENESIS - Longstanding platform for neural\n  simulation](http://www.genesis-sim.org/)\n    - [NeuroSpaces - A modular implementation of GENESIS\n      components](http://neurospaces.sourceforge.net/)\n- [LFPy - Local Field Potential simulator meant for use with NEURON\n  models](https://lfpy.readthedocs.io/en/latest/)\n- [HNN - Human Neocortical Neurosolver - Simulation of MEG/EEG source waveforms using NEURON](https://hnn.brown.edu/)\n  - [HNN (GUI version)](https://jonescompneurolab.github.io/hnn/)\n  - [HNN-core (command line version)](https://jonescompneurolab.github.io/hnn-core/)\n- [MOOSE - Multiscale Object-Oriented Simulate\n  Environment](https://moose.ncbs.res.in/) (Not to be confused with this [Moose\n  Simulator](https://www.youtube.com/watch?v=axtA_Bls1ag\u0026t=11s))\n- [NEF - Neural Engineering Framework](http://compneuro.uwaterloo.ca/research/nef.html)\n- [Nengo - Large-scale neural simulator](https://www.nengo.ai/)\n- [NEST - A popular, actively developed neural simulator that can simulate\n  large neural systems](http://www.nest-simulator.org/)\n- [neurolib - A Python simulation framework for easy whole-brain neural mass modeling](https://caglorithm.github.io/notebooks/neurolib-intro/)\n- [NEURON - The most popular computational neuroscience model\n  simulator, focusing on biophysical modelling](https://neuron.yale.edu/neuron/)\n- [NeuroRD - \"A computationally efficient, stochastic reaction-diffusion\n  simulator\".](http://krasnow1.gmu.edu/CENlab/software.html)\n- [PyRhO - Virtual laboratory for optogenetic simulation. Integrates with\n  NEURON and Brian2 models.](https://github.com/ProjectPyRhO/PyRhO)\n    - [Prometheus - Related docker image for use with PyRhO via \"Modelling as a\n      Service\"](https://github.com/ProjectPyRhO/Prometheus)\n- [PSICS - Parallel Stochastic Ion Channel Simulator](http://www.psics.org/)\n- [PCSIM - Parallel neural Circuit SIMulator](http://www.lsm.tugraz.at/pcsim/)\n  (The successor to [CSIM](http://www.lsm.tugraz.at/csim/))\n- [PyNN - Language for building neuronal network models meant for export to\n  other simulators](http://neuralensemble.org/docs/PyNN/0.7/)\n- [PyPNS - Python Peripheral Nerve Simulator](https://github.com/chlubba/PyPNS)\n- [Spike - \"A high speed Spiking Neural Network Simulator designed for\n  GPGPUs\".](http://oftnai.github.io/Spike/)\n- [SpineCreator - A cross platform graphical editor for SpineML models with support for running model simulations](http://spineml.github.io/spinecreator/)\n- [STEPS - Parallel stochastic reaction-diffusion and voltage simulator on realistic 3D geometries](http://steps.sourceforge.net)\n- [sPyNNaker - A software package for running PyNN simulations on the SpiNNaker million core neuromorphic machine](https://github.com/SpiNNakerManchester/sPyNNaker)\n\n##### Simulation Data Format and Management Software\n\n- [BluePyOpt - Blue Brain Python Optimisation Library, for optimizing\n  parameters in neural models](https://github.com/BlueBrain/BluePyOpt)\n- [BRAHMS - A modular execution framework for executing integrated systems built from component software processes](https://github.com/BRAHMS-SystemML/brahms)\n- [GIMBL-Vis - Multi-dimensional visualization toolbox; integrates with\n  DynaSim](https://github.com/erik-roberts/GIMBL-Vis)\n- [Lancet - Software for managing large volumes of neural\n  simulations](http://ioam.github.io/lancet/)\n- [neuroConstruct - Software for developing biologically realistic 3D neural\n  networks geometries, for simulation by NEURON, PyNN,\n  etc.](http://www.neuroconstruct.org/)\n- [Neurofitter - Parameter tuning software for electrophysiological neural\n  models like NEURON](http://neurofitter.sourceforge.net)\n- [neuroHDF - HDF5 data format for\n  neuroscience](https://neurohdf.readthedocs.io/en/latest/)\n- [NeuroTools - Collection of tools for \"simulation setup, parameterization,\n  data management, analysis, and visualization\" for many neural simulators\n  above.](https://pythonhosted.org/NeuroTools/)\n- [NSDF - Neuroscience Simulation Data Format, built on\n  HDF5](https://github.com/nsdf/nsdf)\n- [ODE-toolbox - Automatic selection and generation of integration schemes\n  for systems of ordinary differential equations](https://ode-toolbox.readthedocs.io/)\n- [pypet - Python parameter exploration toolkit for managing parameter sweeps\n  of simulations in neural simulators like Brian. Has Sumatra\n  integration.](http://pypet.readthedocs.io/en/latest/)\n- [Sumatra - An \"automated electronic lab notebook\" for managing simulation and\n  analysis projects](http://neuralensemble.org/sumatra/)\n\n-----------------------------------\n\n### Open Courses and Educational Resources\n\n- [Course: Computational Neuroscience at\n  Coursera](https://www.coursera.org/learn/computational-neuroscience)\n- [Course: Introduction To Modern Brain-Computer Interface Design](https://sccn.ucsd.edu/wiki/Introduction_To_Modern_Brain-Computer_Interface_Design)\n- [Course: Computational Neuroscience: Neuronal Dynamics of Cognition at edX](https://www.edx.org/course/computational-neuroscience-neuronal-dynamics-of-cognition)\n- [Course/Curriculum: Mathematical Tools for Neuroscientists](https://ebatty.github.io/MathToolsforNeuroscience/intro.html)\n- [Courses: Neuromatch Academy hands-on courses in either Computational Neuroscience or Deep Learning](https://academy.neuromatch.io/courses)\n- [Course: Neuronal Dynamics at\n  edX](https://www.edx.org/course/neuronal-dynamics-epflx-bio465-1x)\n    - [Textbook: The open book for this course is available here](http://neuronaldynamics.epfl.ch/online/index.html)\n- [Courses: Neuroscience course material from OpenCourseWare (OCW) at MIT Department of Brain and Cognitive Sciences - HUGE list!](https://ocw.mit.edu/courses/brain-and-cognitive-sciences/)\n- [Course: Simulation Neuroscience at edX](https://www.edx.org/course/simulation-neuroscience-epflx-simneurox)\n- [Encyclopedia of Computational Neuroscience at\n  Scholarpedia](http://www.scholarpedia.org/article/Encyclopedia_of_computational_neuroscience)\n- [Notebook: Python notebooks from courseware on theoretical/computational neuroscience (for beginners)](https://dabane-ghassan.github.io/ModNeuro/)\n- [Textbook: Computational Cognitive\n  Neuroscience (maybe 404'd as of 2022-11-21?)](https://grey.colorado.edu/CompCogNeuro/index.php/CCNBook/Main)\n- [Textbook (online): Neural Data Science in Python](https://neuraldatascience.io/intro.html)\n- [Webpage: Biological Neural Networks: Part 1, Spiking Neurons - VERY cool webpage with interactive spiking neural models!](http://jackterwilliger.com/biological-neural-networks-part-i-spiking-neurons/)\n\n-----------------------------------\n\n### Open Data\n\n- This only lists neuroscience-specific open data repositories. For general\n  science data repositories that may contain neuroscience data like\n  [re3data](https://www.re3data.org/search?query=neuroscience), [see this Open\n  Science Resources\n  page](https://github.com/asoplata/open-science-resources#open-data-repositories-and-services)\n- [3D Brain Atlas Reconstructor](http://www.3dbars.org/)\n- [Allen Brain Atlas Data Portal](http://brain-map.org/)\n    - [More detail\n      here](http://www.alleninstitute.org/what-we-do/brain-science/research/products-tools/)\n    - [AllenSDK - How to programmatically download and use Allen data](http://alleninstitute.github.io/AllenSDK/)\n- [BODB - Brain Operation Database System](http://bodb.usc.edu/bodb/)\n- [BossDB.org — hundreds of terabytes of microscopy](https://bossdb.org/)\n- [Brain Slices- Repository of brain tissue images](https://brainslices.org/)\n- [C-BIG - Biological Imaging and Genetic\n  repository](http://www.mcgill.ca/c-bigneuro/)\n- [Channelpedia - Wiki of neuron ion channels, hosted by the Blue Brain\n  Project](http://channelpedia.epfl.ch/)\n- [Codex: FlyWire - Proofread static snapshots of the FlyWire full-brain connectome](https://codex.flywire.ai/)\n- [CRCNS - Collaborative Research in Computational\n  Neuroscience](http://crcns.org/data-sets)\n- [GIN - Modern Research Data Management for Neuroscience](https://web.gin.g-node.org/)\n- [IDA LONI - Image and Data Archive for neuroscience by Laboratory of Neuro\n  Imaging](https://ida.loni.usc.edu/login.jsp)\n- [INDI - International Neuroimaging Data-Sharing\n  Initiative](http://fcon_1000.projects.nitrc.org/)\n- [iEEG.org - National Institutes of Neurological Disorders and Stroke EEG data\n  repository for epilepsy research](https://www.ieeg.org/)\n- [NCBI databases - National Center for Biotechnology Information database\n  list, VERY comprehensive!](http://www.ncbi.nlm.nih.gov/guide/all/)\n- [NDA - National Institute of Mental Health Data\n  Archive](https://data-archive.nimh.nih.gov/)\n- [NeuroVault - Public repository of MRI and PET statistical maps,\n  parcellations, and atlases](https://neurovault.org/)\n- [NIF - Neuroscience Information Framework, massive search engine for\n  neuroscience data, tools, etc.](http://www.neuinfo.org/)\n- [NITRC - NeuroImaging Tools and Resources\n  Collaboratory](https://www.nitrc.org/)\n- [NMC - Neocortical Microcircuit Collaboration, part of Blue\n  Brain](https://bbp.epfl.ch/nmc-portal/welcome)\n- [NWB - Neurodata Without Borders - A standardized format for\n  electrophysiological, and in the future other, neuroscience data. Some data\n  sets available on the site in this format.](http://nwb.org/)\n- [OpenNeuro - Free and open platform for neuroimaging data (succeeds\n  OpenfMRI)](https://openneuro.org/)\n- [Whole Brain Catalog - Virtual catalog of a mouse\n  brain](https://library.tmc.edu/website/whole-brain-catalog/)\n- [WormBase - Database of nematode information](https://www.wormbase.org)\n- [ZFIN - Zebrafish Model Organism Database](http://zfin.org/)\n\n##### Open Data Schema\n\n- [Neo - Python library for enabling interoperability of electrophysiological\n  data, including conversion from proprietary file\n  formats](http://neuralensemble.org/neo/)\n- [Neurodata Without Borders: Neurophysiology (NWB:N) data standard for\n  neurophysiology, including intracellular, extracellular, optical physiology,\n  tracking, and stimulus data](https://www.nwb.org/)\n    - [ndx-simulation-output Large-scale simulation data scheme extenstion to\n      NWB:N](https://github.com/catalystneuro/ndx-simulation-output)\n- [NSDF - Neuroscience Simulation Data Format, built on top of HDF5](https://github.com/nsdf/nsdf)\n- [SONATA format for large-scale, efficient model specification and output data\n  schema of neural simulations, co-developed by Allen Institute for Brain\n  Sciences and Blue Brain Project](https://github.com/AllenInstitute/sonata)\n\n##### Open Model Repositories\n\n- [BioModels - Not neuroscience-specific](https://wwwdev.ebi.ac.uk/biomodels/)\n- [ModelDB - Repository of computational neuroscience models for\n  simulation](https://senselab.med.yale.edu/modeldb/), built by\n  [Senselab](https://senselab.med.yale.edu/)\n- [Senselab](https://senselab.med.yale.edu/) hosts several other databases, but\n  ModelDB (above) is the most popular:\n    - [3DModelDB  - A collection of 3D printable versions of published neuron\n      morphologies, both traced and\n      artificial.](https://senselab.med.yale.edu/3DModelDB/)\n    - [CellPropDB - Cellular Properties Database provides a simple repository\n      for data regarding membrane channels, receptor and neurotransmitters that\n      are expressed in specific types of\n      cells.](https://senselab.med.yale.edu/CellPropDB/)\n    - [MicrocircuitDB - Provides an accessible location for storing and\n      efficiently retrieving realistic computational models of brain\n      microcircuits and\n      networks.](https://senselab.med.yale.edu/MicroCircuitDB/)\n    - [NeuronDB - Provides a dynamically searchable database of three types of\n      neuronal properties: voltage gated conductances, neurotransmitter\n      receptors, and neurotransmitter\n      substances.](https://senselab.med.yale.edu/NeuronDB/)\n    - [OdorDB - Odor Molecules DataBase](https://senselab.med.yale.edu/OdorDB/)\n    - [OdorMapDB - Olfactory Bulb Odor Map\n      DataBase](https://senselab.med.yale.edu/OdorMapDB/)\n    - [ORDB - Olfactory Receptor DataBase](https://senselab.med.yale.edu/OrDB/)\n    - [ORModelDB - A resource that is a repository of the results of the\n      efforts of the community is computationally elucidating the structure of\n      the olfactory receptor with a view to establishing a mechanistic basis\n      for OR-odorant binding.](https://senselab.med.yale.edu/OrModelDB/)\n\n- [NeuroElectro - Repository of data-mined and human-curated neuron celltype electrophysiological data](https://neuroelectro.org/)\n- [NeuroML-db - Curated database of NeuroML models](https://neuroml-db.org/)\n- [NeuroMorpho - Curated repository of digitally reconstructed neuron geometries](http://neuromorpho.org/)\n- [OSB - Open Source Brain](http://www.opensourcebrain.org/)\n- [OSBv2 - Open Source Brain version 2.0](https://v2.opensourcebrain.org/)\n- [OpenWorm - Popular platform for simulation and analysis of nematode neuroscience models!](http://openworm.org/)\n- [\"Integrated Models\" RRID on SciCrunch - Compilation of model sources](https://scicrunch.org/scicrunch/Resources/record/nlx_144509-1/SCR_001481/resolver)\n\n-----------------------------------\n\n### Organizations and Communities\n\n- [CodeNeuro - Bringing neuroscience and data science together](http://codeneuro.org/)\n- [OCNS - Organization for Computational Neuroscience](http://www.cnsorg.org/)\n- [G-NODE - German Informatics Node](http://www.g-node.org/)\n- [INCF - International Neuroinformatics Coordinating\n  Facility](https://www.incf.org/about)\n- [NeuralEnsemble, focused on software development in\n  neuroscience](http://neuralensemble.org/)\n- [NeuroFedora, Fedora community special interest group](https://neuro.fedoraproject.org)\n- [Neuroinformatics Research Group at Harvard](http://neuroinformatics.harvard.edu/)\n- [Neurostars - Neuroscience Q and A website](https://neurostars.org/)\n- [NIMH - National Institute of Mental\n  Health](https://www.nimh.nih.gov/index.shtml)\n- [An Open Computational Neuroscience list I've made on\n  Twitter](https://twitter.com/austinsoplata/lists/opencompneuroscience)\n- [Organization for Human Brain Mapping](https://www.humanbrainmapping.org)\n- [Reddit /r/Neuroscience\n  resources](https://www.reddit.com/r/neuroscience/comments/2u87cl/rneuroscience_resource_compilaton/)\n- [SFN - Society for Neuroscience](https://www.sfn.org/)\n\n##### Funding\n\n- [Funding research software development](https://www.software.ac.uk/how-fund-research-software-development)\n\n-----------------------------------\n\n### Reproducibility and Provenance\n\n- [Tutorial on reproducible computational neuroscience research, from CNS 2012\n  by author of Sumatra](https://rrcns.readthedocs.io/en/cns2012/)\n- [Alpaca - Provenance for data analysis in Python](https://alpaca-prov.readthedocs.io/en/latest/)\n    - Provides examples for use with [Neo](https://neuralensemble.org/neo/) and [Elephant](http://neuralensemble.org/elephant/)\n- [Snakemake - Scalable, reproducible workflows using a Python-like language](https://snakemake.readthedocs.io/en/stable/)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fasoplata%2Fopen-computational-neuroscience-resources","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fasoplata%2Fopen-computational-neuroscience-resources","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fasoplata%2Fopen-computational-neuroscience-resources/lists"}