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https://github.com/asoplata/open-computational-neuroscience-resources

A publicly-editable collection of open computational neuroscience resources
https://github.com/asoplata/open-computational-neuroscience-resources

List: open-computational-neuroscience-resources

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

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A publicly-editable collection of open computational neuroscience resources

Awesome Lists containing this project

README 

        

# 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](https://github.com/asoplata/open-science-resources).



Contributions are VERY welcome!



-----------------------------------



- Contents:

    - [Meta-resources](#meta-resources)

    - [Markup Languages for Model Specification](#markup-languages-for-model-specification)

    - [Open Code](#open-code)

        - [Analysis Software For Electrophysiology](#analysis-software-for-electrophysiology)

        - [Analysis Software For Imaging](#analysis-software-for-imaging)

        - [Other Analysis Software](#other-analysis-software)

        - [Operating Systems](#operating-systems)

        - [Simulation Software](#simulation-software)

        - [Simulation Data Format and Management Software](#simulation-data-format-and-management-software)

    - [Open Courses and Educational Resources](#open-courses-and-educational-resources)

    - [Open Data](#open-data)

        - [Open Data Schema](#open-data-schema)

        - [Open Model Repositories](#open-model-repositories)

    - [Organizations and Communities](#organizations-and-communities)

    - [Reproducibility and Provenance](#reproducibility-and-provenance)



-----------------------------------



### Meta-resources



- [Allen Institute for Brain

  Science](https://alleninstitute.org/open-science-tools/)

- [COMBINE - Computational modeling in biology network](http://co.mbine.org/standards)

- [Comparison of Neural Network

  Simulators](https://grey.colorado.edu/emergent/index.php/Comparison_of_Neural_Network_Simulators)

- [Computational Neuroscience journals](http://www.cnsorg.org/journals)

- ["Computational Neuroscience on the Web" (Jim Perlewitz) - Probably the most

  comprehensive *curated* list of computational neuroscience modeling tools on

  the internet. HIGHLY recommended.](https://compneuroweb.com/)

- ["Computational Neuroscience Resources" (Dan Goodman)](https://neural-reckoning.org/comp-neuro-resources.html)

- ["Computational Neuroscience Resources" (Fleur Zeldenrust)](https://fleurzeldenrust.nl/computational-neuroscience-resources/)

- [NCBI databases - National Center for Biotechnology Information database

  list, VERY comprehensive!](http://www.ncbi.nlm.nih.gov/guide/all/)

- [neuroshare - Brief list of neuroscience data tools and vendors](http://neuroshare.sourceforge.net/links.shtml)

- [NIF - Neuroscience Infomation Framework - Search for EVERY kind of

  neuroscience data, atlas, software, everything!](https://neuinfo.org/)

    - This is the most comprehensive tool for open neuroscience resources in

      the world. If it exists on the internet, it's probably indexed here.

- [NSG - Neuroscience Gateway - An online resource that allows public usage of

  high performance computing resources for neural

  simulation!](http://www.nsgportal.org/index.html)

- Open Hardware - [see this Open Science Resources

  page](https://github.com/asoplata/open-science-resources#open-diy-hardware)

- [Planet Neuroscience: An aggregation of neuroscience journal RSS feeds](https://neuroblog.fedoraproject.org/planet-neuroscience/)

- [SORTED - a list of interesting science ideas and links (cognitive/neuro & data science)](https://github.com/PTDZ/SORTED)

- [Wikipedia List of Neuroscience Databases](https://en.wikipedia.org/wiki/List_of_neuroscience_databases)



-----------------------------------



### Markup Languages for Model Specification



- [CellML - A model specification language for general biological mathematical

  modeling](https://www.cellml.org/)

- [NESTML - Domain-specific language for neuron models and code generation

  toolchain](https://nestml.readthedocs.io/)

- [NeuroML - A model description language for computational

  neuroscience](https://www.neuroml.org/)

    - Converts to and can be run automatically by different kinds of simulators:

      https://docs.neuroml.org/Userdocs/Software/SupportingTools.html

- [NineML - A model specification language for

  neuroscience](http://incf.github.io/nineml-spec/)

- [SpineML - A declarative XML-based model description language for large scale neural network models](http://spineml.github.io)



-----------------------------------



### Open Code



##### Analysis Software For Electrophysiology



- 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.

- [Elephant - Software for common electrophysiological data analysis

  operations](http://neuralensemble.org/elephant/)

    - Elephant is the direct successor to [Neurotools](http://neuralensemble.org/NeuroTools/)

    - Elephant can consume electrophysiology data loaded by [Neo](http://neuralensemble.org/neo/)

- [Neo - Python library for enabling interoperability of electrophysiological

  data, including conversion from proprietary file

  formats](http://neuralensemble.org/neo/)

    - Note that Neo does not perform analysis or visualization, but instead is only for loading or converting between electrophysiology data types.

- [(deprecated) OpenElectrophy - Analysis software for electrophysiological data, built on

  Neo](http://neuralensemble.org/OpenElectrophy/)

    - [OpenElectrophy's README](https://github.com/OpenElectrophy/OpenElectrophy) indicates that it is old, effectively abandoned, and you should use something else.

- [Pynapple - "PYthon Neural Analysis Package" for neurophysiological data analysis](https://github.com/pynapple-org/pynapple)

- [Spike Sorting Software - VERY good comparison of different spike sorting

  software capabilities](https://simonster.github.io/SpikeSortingSoftware/)

- [SpikeInterface - Spike sorting analysis specifically made for compatibility

  between different sorting algorithms, part of the Open Ephys project](https://open-ephys.org/spikeinterface)

- [SpykeViewer - Analysis software for spikes of electrophysiological data](http://neuralensemble.org/SpykeViewer/)

      - SpykeViewer can consume electrophysiology data loaded by [Neo](http://neuralensemble.org/neo/)



##### Analysis Software For Imaging



- [CaImAn - Calcium Imaging Analysis](https://github.com/flatironinstitute/CaImAn)

- [CATMAID - The Collaborative Annotation Toolkit for Massive Amounts of Image

  Data](http://catmaid.readthedocs.io/en/stable/)

- [Chronux - MATLAB toolbox for EEG analysis, including some tools for MEG, fMRI, and image data](http://chronux.org/)

- [EEGLAB - MATLAB toolbox for EEG, MEG, and ECOG data analysis and

  visualization](https://sccn.ucsd.edu/eeglab/index.php)

- [FieldTrip - MATLAB toolbox for EEG, MEG, and ECoG analysis](http://www.fieldtriptoolbox.org/)

- [FreeSurfer - Popular open-source MRI processing and analysis

  software](https://surfer.nmr.mgh.harvard.edu/)

- [MNE - MEG + EEG analysis and visualization tool in

  Python](http://martinos.org/mne/stable/index.html)

- [NiBabel - Python library for enabling interoperability of neuroimaging data,

  including conversion from and between many file

  formats](https://nipy.org/nibabel/)

- [NiMARE - NiMARE is a Python package for neuroimaging meta-analyses](https://nimare.readthedocs.io/en/latest/)

- [supereeg - Sparse ECoG analysis](http://supereeg.readthedocs.io/en/latest/)

- [TrakEM2 - Morphological image (histological staining) data mining and analysis

  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/)

- [TREES - MATLAB toolbox for analyzing neuron

  microscopy](http://www.treestoolbox.org/)

- [V-NeuroStack - 3D time stacks for finding patterns in spontaneous activity of

  neurons in mouse brain slices](https://www.evl.uic.edu/entry.php?id=2479)



##### Other Analysis Software



- [bctnet - Brain Connectivity Toolbox for complex-network analysis](https://github.com/brainlife/BCT)

- [Geppetto - Web-based, open-source visualization platform for computational

  biology](http://www.geppetto.org/)

- [NeuronUnit - Data-driven model validation for

  neuroscience](https://github.com/scidash/neuronunit)

- [SpectraVis - Network visualization tool for functional brain connectivity

  in-browser](https://github.com/NeurophysVis/SpectraVis)

- [Vaa3D - 3D Visualization-Assisted

  Analysis](http://www.alleninstitute.org/what-we-do/brain-science/research/products-tools/vaa3d/)



##### Operating Systems



- [NeuroDebian](http://neuro.debian.net/)

- [Comp-Neuro Fedora](https://docs.fedoraproject.org/en-US/neurofedora/install-media/#_fedora_linux_os_for_computational_neuroscience)



##### Simulation Software



- Note: some of these tools are interoperable to some degree.

- [Arbor - High-performance library for computational neuroscience simulations](https://arbor.readthedocs.io/en/latest/)

- [BindsNET - Simulation of spiking neural networks (SNNs) using PyTorch](https://github.com/Hananel-Hazan/bindsnet)

- [Brain Dynamics Toolbox - Open software for simulating dynamical systems in

  neuroscience using MATLAB](https://bdtoolbox.org/)

- [Brian2 - Powerful, modern neural simulator written in Pythonthat offers

  built-in compilation](http://brian2.readthedocs.io/en/stable/)

- [CoreNeuron - Optimized, simplified NEURON implementation used by the Blue

  Brain Project](https://github.com/BlueBrain/CoreNeuron)

- [DiPDE - Platform for population-level neural

  simulation](http://alleninstitute.github.io/dipde/)

- [DynaSim - Open-source MATLAB/GNU Octave toolbox for neural simulation.

  Offers built-in parallelization, compilation, and batch/cluster simulation

  management.](https://dynasim.github.io/)

- [GENESIS / PGENESIS - Longstanding platform for neural

  simulation](http://www.genesis-sim.org/)

    - [NeuroSpaces - A modular implementation of GENESIS

      components](http://neurospaces.sourceforge.net/)

- [LFPy - Local Field Potential simulator meant for use with NEURON

  models](https://lfpy.readthedocs.io/en/latest/)

- [HNN - Human Neocortical Neurosolver - Simulation of MEG/EEG source waveforms using NEURON](https://hnn.brown.edu/)

  - [HNN (GUI version)](https://jonescompneurolab.github.io/hnn/)

  - [HNN-core (command line version)](https://jonescompneurolab.github.io/hnn-core/)

- [MOOSE - Multiscale Object-Oriented Simulate

  Environment](https://moose.ncbs.res.in/) (Not to be confused with this [Moose

  Simulator](https://www.youtube.com/watch?v=axtA_Bls1ag&t=11s))

- [NEF - Neural Engineering Framework](http://compneuro.uwaterloo.ca/research/nef.html)

- [Nengo - Large-scale neural simulator](https://www.nengo.ai/)

- [NEST - A popular, actively developed neural simulator that can simulate

  large neural systems](http://www.nest-simulator.org/)

- [neurolib - A Python simulation framework for easy whole-brain neural mass modeling](https://caglorithm.github.io/notebooks/neurolib-intro/)

- [NEURON - The most popular computational neuroscience model

  simulator, focusing on biophysical modelling](https://neuron.yale.edu/neuron/)

- [NeuroRD - "A computationally efficient, stochastic reaction-diffusion

  simulator".](http://krasnow1.gmu.edu/CENlab/software.html)

- [PyRhO - Virtual laboratory for optogenetic simulation. Integrates with

  NEURON and Brian2 models.](https://github.com/ProjectPyRhO/PyRhO)

    - [Prometheus - Related docker image for use with PyRhO via "Modelling as a

      Service"](https://github.com/ProjectPyRhO/Prometheus)

- [PSICS - Parallel Stochastic Ion Channel Simulator](http://www.psics.org/)

- [PCSIM - Parallel neural Circuit SIMulator](http://www.lsm.tugraz.at/pcsim/)

  (The successor to [CSIM](http://www.lsm.tugraz.at/csim/))

- [PyNN - Language for building neuronal network models meant for export to

  other simulators](http://neuralensemble.org/docs/PyNN/0.7/)

- [PyPNS - Python Peripheral Nerve Simulator](https://github.com/chlubba/PyPNS)

- [Spike - "A high speed Spiking Neural Network Simulator designed for

  GPGPUs".](http://oftnai.github.io/Spike/)

- [SpineCreator - A cross platform graphical editor for SpineML models with support for running model simulations](http://spineml.github.io/spinecreator/)

- [STEPS - Parallel stochastic reaction-diffusion and voltage simulator on realistic 3D geometries](http://steps.sourceforge.net)

- [sPyNNaker - A software package for running PyNN simulations on the SpiNNaker million core neuromorphic machine](https://github.com/SpiNNakerManchester/sPyNNaker)



##### Simulation Data Format and Management Software



- [BluePyOpt - Blue Brain Python Optimisation Library, for optimizing

  parameters in neural models](https://github.com/BlueBrain/BluePyOpt)

- [BRAHMS - A modular execution framework for executing integrated systems built from component software processes](https://github.com/BRAHMS-SystemML/brahms)

- [GIMBL-Vis - Multi-dimensional visualization toolbox; integrates with

  DynaSim](https://github.com/erik-roberts/GIMBL-Vis)

- [Lancet - Software for managing large volumes of neural

  simulations](http://ioam.github.io/lancet/)

- [neuroConstruct - Software for developing biologically realistic 3D neural

  networks geometries, for simulation by NEURON, PyNN,

  etc.](http://www.neuroconstruct.org/)

- [Neurofitter - Parameter tuning software for electrophysiological neural

  models like NEURON](http://neurofitter.sourceforge.net)

- [neuroHDF - HDF5 data format for

  neuroscience](https://neurohdf.readthedocs.io/en/latest/)

- [NeuroTools - Collection of tools for "simulation setup, parameterization,

  data management, analysis, and visualization" for many neural simulators

  above.](https://pythonhosted.org/NeuroTools/)

- [NSDF - Neuroscience Simulation Data Format, built on

  HDF5](https://github.com/nsdf/nsdf)

- [ODE-toolbox - Automatic selection and generation of integration schemes

  for systems of ordinary differential equations](https://ode-toolbox.readthedocs.io/)

- [pypet - Python parameter exploration toolkit for managing parameter sweeps

  of simulations in neural simulators like Brian. Has Sumatra

  integration.](http://pypet.readthedocs.io/en/latest/)

- [Sumatra - An "automated electronic lab notebook" for managing simulation and

  analysis projects](http://neuralensemble.org/sumatra/)



-----------------------------------



### Open Courses and Educational Resources



- [Course: Computational Neuroscience at

  Coursera](https://www.coursera.org/learn/computational-neuroscience)

- [Course: Introduction To Modern Brain-Computer Interface Design](https://sccn.ucsd.edu/wiki/Introduction_To_Modern_Brain-Computer_Interface_Design)

- [Course: Computational Neuroscience: Neuronal Dynamics of Cognition at edX](https://www.edx.org/course/computational-neuroscience-neuronal-dynamics-of-cognition)

- [Course/Curriculum: Mathematical Tools for Neuroscientists](https://ebatty.github.io/MathToolsforNeuroscience/intro.html)

- [Courses: Neuromatch Academy hands-on courses in either Computational Neuroscience or Deep Learning](https://academy.neuromatch.io/courses)

- [Course: Neuronal Dynamics at

  edX](https://www.edx.org/course/neuronal-dynamics-epflx-bio465-1x)

    - [Textbook: The open book for this course is available here](http://neuronaldynamics.epfl.ch/online/index.html)

- [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/)

- [Course: Simulation Neuroscience at edX](https://www.edx.org/course/simulation-neuroscience-epflx-simneurox)

- [Encyclopedia of Computational Neuroscience at

  Scholarpedia](http://www.scholarpedia.org/article/Encyclopedia_of_computational_neuroscience)

- [Notebook: Python notebooks from courseware on theoretical/computational neuroscience (for beginners)](https://dabane-ghassan.github.io/ModNeuro/)

- [Textbook: Computational Cognitive

  Neuroscience (maybe 404'd as of 2022-11-21?)](https://grey.colorado.edu/CompCogNeuro/index.php/CCNBook/Main)

- [Textbook (online): Neural Data Science in Python](https://neuraldatascience.io/intro.html)

- [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/)



-----------------------------------



### Open Data



- This only lists neuroscience-specific open data repositories. For general

  science data repositories that may contain neuroscience data like

  [re3data](https://www.re3data.org/search?query=neuroscience), [see this Open

  Science Resources

  page](https://github.com/asoplata/open-science-resources#open-data-repositories-and-services)

- [3D Brain Atlas Reconstructor](http://www.3dbars.org/)

- [Allen Brain Atlas Data Portal](http://brain-map.org/)

    - [More detail

      here](http://www.alleninstitute.org/what-we-do/brain-science/research/products-tools/)

    - [AllenSDK - How to programmatically download and use Allen data](http://alleninstitute.github.io/AllenSDK/)

- [BODB - Brain Operation Database System](http://bodb.usc.edu/bodb/)

- [BossDB.org — hundreds of terabytes of microscopy](https://bossdb.org/)

- [Brain Slices- Repository of brain tissue images](https://brainslices.org/)

- [C-BIG - Biological Imaging and Genetic

  repository](http://www.mcgill.ca/c-bigneuro/)

- [Channelpedia - Wiki of neuron ion channels, hosted by the Blue Brain

  Project](http://channelpedia.epfl.ch/)

- [Codex: FlyWire - Proofread static snapshots of the FlyWire full-brain connectome](https://codex.flywire.ai/)

- [CRCNS - Collaborative Research in Computational

  Neuroscience](http://crcns.org/data-sets)

- [GIN - Modern Research Data Management for Neuroscience](https://web.gin.g-node.org/)

- [IDA LONI - Image and Data Archive for neuroscience by Laboratory of Neuro

  Imaging](https://ida.loni.usc.edu/login.jsp)

- [INDI - International Neuroimaging Data-Sharing

  Initiative](http://fcon_1000.projects.nitrc.org/)

- [iEEG.org - National Institutes of Neurological Disorders and Stroke EEG data

  repository for epilepsy research](https://www.ieeg.org/)

- [NCBI databases - National Center for Biotechnology Information database

  list, VERY comprehensive!](http://www.ncbi.nlm.nih.gov/guide/all/)

- [NDA - National Institute of Mental Health Data

  Archive](https://data-archive.nimh.nih.gov/)

- [NeuroVault - Public repository of MRI and PET statistical maps,

  parcellations, and atlases](https://neurovault.org/)

- [NIF - Neuroscience Information Framework, massive search engine for

  neuroscience data, tools, etc.](http://www.neuinfo.org/)

- [NITRC - NeuroImaging Tools and Resources

  Collaboratory](https://www.nitrc.org/)

- [NMC - Neocortical Microcircuit Collaboration, part of Blue

  Brain](https://bbp.epfl.ch/nmc-portal/welcome)

- [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.](http://nwb.org/)

- [OpenNeuro - Free and open platform for neuroimaging data (succeeds

  OpenfMRI)](https://openneuro.org/)

- [Whole Brain Catalog - Virtual catalog of a mouse

  brain](https://library.tmc.edu/website/whole-brain-catalog/)

- [WormBase - Database of nematode information](https://www.wormbase.org)

- [ZFIN - Zebrafish Model Organism Database](http://zfin.org/)



##### Open Data Schema



- [Neo - Python library for enabling interoperability of electrophysiological

  data, including conversion from proprietary file

  formats](http://neuralensemble.org/neo/)

- [Neurodata Without Borders: Neurophysiology (NWB:N) data standard for

  neurophysiology, including intracellular, extracellular, optical physiology,

  tracking, and stimulus data](https://www.nwb.org/)

    - [ndx-simulation-output Large-scale simulation data scheme extenstion to

      NWB:N](https://github.com/catalystneuro/ndx-simulation-output)

- [NSDF - Neuroscience Simulation Data Format, built on top of HDF5](https://github.com/nsdf/nsdf)

- [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](https://github.com/AllenInstitute/sonata)



##### Open Model Repositories



- [BioModels - Not neuroscience-specific](https://wwwdev.ebi.ac.uk/biomodels/)

- [ModelDB - Repository of computational neuroscience models for

  simulation](https://senselab.med.yale.edu/modeldb/), built by

  [Senselab](https://senselab.med.yale.edu/)

- [Senselab](https://senselab.med.yale.edu/) hosts several other databases, but

  ModelDB (above) is the most popular:

    - [3DModelDB  - A collection of 3D printable versions of published neuron

      morphologies, both traced and

      artificial.](https://senselab.med.yale.edu/3DModelDB/)

    - [CellPropDB - Cellular Properties Database provides a simple repository

      for data regarding membrane channels, receptor and neurotransmitters that

      are expressed in specific types of

      cells.](https://senselab.med.yale.edu/CellPropDB/)

    - [MicrocircuitDB - Provides an accessible location for storing and

      efficiently retrieving realistic computational models of brain

      microcircuits and

      networks.](https://senselab.med.yale.edu/MicroCircuitDB/)

    - [NeuronDB - Provides a dynamically searchable database of three types of

      neuronal properties: voltage gated conductances, neurotransmitter

      receptors, and neurotransmitter

      substances.](https://senselab.med.yale.edu/NeuronDB/)

    - [OdorDB - Odor Molecules DataBase](https://senselab.med.yale.edu/OdorDB/)

    - [OdorMapDB - Olfactory Bulb Odor Map

      DataBase](https://senselab.med.yale.edu/OdorMapDB/)

    - [ORDB - Olfactory Receptor DataBase](https://senselab.med.yale.edu/OrDB/)

    - [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.](https://senselab.med.yale.edu/OrModelDB/)



- [NeuroElectro - Repository of data-mined and human-curated neuron celltype electrophysiological data](https://neuroelectro.org/)

- [NeuroML-db - Curated database of NeuroML models](https://neuroml-db.org/)

- [NeuroMorpho - Curated repository of digitally reconstructed neuron geometries](http://neuromorpho.org/)

- [OSB - Open Source Brain](http://www.opensourcebrain.org/)

- [OSBv2 - Open Source Brain version 2.0](https://v2.opensourcebrain.org/)

- [OpenWorm - Popular platform for simulation and analysis of nematode neuroscience models!](http://openworm.org/)

- ["Integrated Models" RRID on SciCrunch - Compilation of model sources](https://scicrunch.org/scicrunch/Resources/record/nlx_144509-1/SCR_001481/resolver)



-----------------------------------



### Organizations and Communities



- [CodeNeuro - Bringing neuroscience and data science together](http://codeneuro.org/)

- [OCNS - Organization for Computational Neuroscience](http://www.cnsorg.org/)

- [G-NODE - German Informatics Node](http://www.g-node.org/)

- [INCF - International Neuroinformatics Coordinating

  Facility](https://www.incf.org/about)

- [NeuralEnsemble, focused on software development in

  neuroscience](http://neuralensemble.org/)

- [NeuroFedora, Fedora community special interest group](https://neuro.fedoraproject.org)

- [Neuroinformatics Research Group at Harvard](http://neuroinformatics.harvard.edu/)

- [Neurostars - Neuroscience Q and A website](https://neurostars.org/)

- [NIMH - National Institute of Mental

  Health](https://www.nimh.nih.gov/index.shtml)

- [An Open Computational Neuroscience list I've made on

  Twitter](https://twitter.com/austinsoplata/lists/opencompneuroscience)

- [Organization for Human Brain Mapping](https://www.humanbrainmapping.org)

- [Reddit /r/Neuroscience

  resources](https://www.reddit.com/r/neuroscience/comments/2u87cl/rneuroscience_resource_compilaton/)

- [SFN - Society for Neuroscience](https://www.sfn.org/)



##### Funding



- [Funding research software development](https://www.software.ac.uk/how-fund-research-software-development)



-----------------------------------



### Reproducibility and Provenance



- [Tutorial on reproducible computational neuroscience research, from CNS 2012

  by author of Sumatra](https://rrcns.readthedocs.io/en/cns2012/)

- [Alpaca - Provenance for data analysis in Python](https://alpaca-prov.readthedocs.io/en/latest/)

    - Provides examples for use with [Neo](https://neuralensemble.org/neo/) and [Elephant](http://neuralensemble.org/elephant/)

- [Snakemake - Scalable, reproducible workflows using a Python-like language](https://snakemake.readthedocs.io/en/stable/)