Open Computational Neuroscience Resources Save
A publicly-editable collection of open computational neuroscience resources
Project README
Open Computational Neuroscience Resources
Computational neuroscience means one of two things:
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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!
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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.
Contributions are VERY welcome!
- Contents:
Meta-resources
- 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
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NIF - Neuroscience Infomation Framework - Search for EVERY kind of
neuroscience data, atlas, software, everything!
- 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!
- Open Hardware - see this Open Science Resources page
- 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
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
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NeuroML - A model description language for computational
neuroscience
- 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
- SpineML - A declarative XML-based model description language for large scale neural network models
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
- Elephant is the direct successor to Neurotools
- Elephant can consume electrophysiology data loaded by Neo
-
Neo - Python library for enabling interoperability of electrophysiological
data, including conversion from proprietary file
formats
- Note that Neo does not perform analysis or visualization, but instead is only for loading or converting between electrophysiology data types.
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(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.
- Pynapple - "PYthon Neural Analysis Package" for neurophysiological data analysis
- 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 Neo
Analysis Software For Imaging
- CaImAn - Calcium Imaging Analysis
- 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 plugin for ImageJ including as part of the Fiji distribution
- TREES - MATLAB toolbox for analyzing neuron microscopy
- V-NeuroStack - 3D time stacks for finding patterns in spontaneous activity of neurons in mouse brain slices
Other Analysis Software
- bctnet - Brain Connectivity Toolbox for complex-network analysis
- Geppetto - Web-based, open-source visualization platform for computational biology
- NeuronUnit - Data-driven model validation for neuroscience
- SpectraVis - Network visualization tool for functional brain connectivity in-browser
- Vaa3D - 3D Visualization-Assisted Analysis
Operating Systems
Simulation Software
- Note: some of these tools are interoperable to some degree.
- Arbor - High-performance library for computational neuroscience simulations
- BindsNET - Simulation of spiking neural networks (SNNs) using PyTorch
- 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
- 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
- LFPy - Local Field Potential simulator meant for use with NEURON models
- HNN - Human Neocortical Neurosolver - Simulation of MEG/EEG source waveforms using NEURON
- MOOSE - Multiscale Object-Oriented Simulate Environment (Not to be confused with this Moose Simulator)
- 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.
- PSICS - Parallel Stochastic Ion Channel Simulator
- PCSIM - Parallel neural Circuit SIMulator (The successor to CSIM)
- PyNN - Language for building neuronal network models meant for export to other simulators
- PyPNS - Python Peripheral Nerve Simulator
- 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
Simulation Data Format and Management Software
- BluePyOpt - Blue Brain Python Optimisation Library, for optimizing parameters in neural models
- BRAHMS - A modular execution framework for executing integrated systems built from component software processes
- GIMBL-Vis - Multi-dimensional visualization toolbox; integrates with DynaSim
- 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
- 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 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
- 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 Data
- This only lists neuroscience-specific open data repositories. For general science data repositories that may contain neuroscience data like re3data, see this Open Science Resources page
- 3D Brain Atlas Reconstructor
- Allen Brain Atlas Data Portal
- 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
Open Data Schema
- 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
- NSDF - Neuroscience Simulation Data Format, built on top of HDF5
- 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
Open Model Repositories
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ModelDB - Repository of computational neuroscience models for simulation, built by Senselab
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Senselab 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.
- 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.
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NeuroElectro - Repository of data-mined and human-curated neuron celltype electrophysiological data
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NeuroMorpho - Curated repository of digitally reconstructed neuron geometries
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OpenWorm - Popular platform for simulation and analysis of nematode neuroscience models!
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"Integrated Models" RRID on SciCrunch - Compilation of model sources
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
Reproducibility and Provenance
Open Source Agenda is not affiliated with "Open Computational Neuroscience Resources" Project. README Source: asoplata/open-computational-neuroscience-resources
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