Open Computational Neuroscience Resources

Computational neuroscience means one of two things: 1. analysis of neuroscientific data, whether it be fMRI imaging data, electrode recordings from a mouse running in a maze, statistical modeling of that data, or something else, and 2. simulation of neural systems, including modeling many compartments of a single neuron, or large networks of model neurons with simple individual behavior. 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, open data, open simulation models, and open analysis and simulation tools for computational neuroscience 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, as opposed to artificial intelligence pursuits. More broadly, I've made a similar repo-list of general open science resources here.

Contributions are VERY welcome!

• Contents:
  • Meta-resources
  • Markup Languages for Model Specification
  • Open Code
  • Open Courses
  • Open Data
  • Open Textbooks
  • Organizations and Communities
  • Reproducibility

Meta-resources

• Allen Institute for Brain Science
• COMBINE - Computational modeling in biology network
• Comparison of Neural Network Simulators
• Computational Neuroscience journals
• Jim Perlewitz' "Computational Neuroscience on the Web" - Probably the most comprehensive curated list of computational neuroscience modeling tools on the internet. HIGHLY recommended.
  • Website may be offline now, but you can access an archived version here at the Internet Archive
• 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!
  • 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
• Wikipedia List of Neuroscience Databases
• An aggregation of neuroscience journal RSS feeds

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 specification language for computational neuroscience
  • Converts to and can be run automatically by different kinds of simulators: https://www.neuroml.org/tool_support
• NineML - A model specification language for neuroscience
• SpineML - A declarative XML-based model description language for large scale neural network models

Open Code

• Funding research software development

Non-imaging Analysis

• bctnet - Brain Connectivity Toolbox for complex-network analysis
• 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
• Elephant - Software for common electrophysiological data analysis operations, built on the Neo data format
• FieldTrip - MATLAB toolbox for EEG, MEG, and ECoG analysis
• Geppetto - Web-based, open-source visualization platform for computational biology
• OpenElectrophy - Analysis software for electrophysiological data, built on the Neo data format
• MNE - MEG + EEG analysis and visualization tool in Python
• NeuronUnit - Data-driven model validation for neuroscience
• SpectraVis - Network visualization tool for functional brain connectivity in-browser
• 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, built on the Neo data format
• supereeg - Sparse ECoG analysis
• Vaa3D - 3D Visualization-Assisted Analysis

Imaging Analysis

• Allen SDK - Allen (Institute) Software Development Kit for Allen Brain Atlas
• CaImAn - Calcium Imaging Analysis
• CATMAID - The Collaborative Annotation Toolkit for Massive Amounts of Image Data
• FreeSurfer - Popular open-source MRI processing and analysis software
• NiBabel - Python library for enabling interoperability of neuroimaging data, including conversion from and between many file formats
• TrakEM2 - Morphological data mining and analysis tool
• TREES - MATLAB toolbox for analyzing neuron microscopy
• V-NeuroStack - 3D time stacks for finding patterns in spontaneous activity of neurons in mouse brain slices

Simulation

• 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
  • NeuroSpaces - A modular implementation of GENESIS components
• LFPy - Local Field Potential simulator meant for use with NEURON models
• 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.
  • Prometheus - Related docker image for use with PyRhO via "Modelling as a Service"
• 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
• 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

Auxiliary Simulator 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

• Computational Neuroscience at Coursera
• Computational Neuroscience: Neuronal Dynamics of Cognition at edX
• Neuronal Dynamics at edX
  • The open book for this course is available here
• Neuroscience course material from OpenCourseWare (OCW) at MIT Department of Brain and Cognitive Sciences - HUGE list!
• Simulation Neuroscience at edX
• Interactive webpage illustrating spiking neural models
• A series of notebooks that serves as an introduction to theoretical/computational neuroscience (for beginners)

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
  • More detail here
  • Associated software here
• 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
• 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
  • ndx-simulation-output Large-scale simulation data scheme extenstion to NWB:N
• 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

• BioModels - Not neuroscience-specific
• ModelDB - Repository of computational neuroscience models for simulation, built by Senselab
• Senselab hosts several other databases, but ModelDB is the most popular:
  • CellPropDB - Cellular Properties Database provides a simple repository for data regarding membrane channels, receptor and neurotransmitters that are expressed in specific types of cells.
  • NeuronDB - Provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances.
  • MicrocircuitDB - Provides an accessible location for storing and efficiently retrieving realistic computational models of brain microcircuits and networks.
  • 3DModelDB - A collection of 3D printable versions of published neuron morphologies, both traced and artificial.
  • 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.
  • OdorMapDB - Olfactory Bulb Odor Map DataBase
  • OdorDB - Odor Molecules DataBase
  • ORDB - Olfactory Receptor DataBase
• NeuroElectro - Repository of data-mined and human-curated neuron celltype electrophysiological data
• NeuroMorpho - Curated repository of digitally reconstructed neuron geometries
• OSB - Open Source Brain
• OpenWorm - Popular platform for simulation and analysis of nematode neuroscience models!
• "Integrated Models" RRID on SciCrunch - Compilation of model sources

Open Textbooks

• Computational Cognitive Neuroscience
• Encyclopedia of Computational Neuroscience at Scholarpedia
• Neuronal Dynamics: From single neurons to networks and models of cognition

Organizations and Communities

• CodeNeuro - Bringing neuroscience and data science together
• CNS - Organization for Computational Neuroscience
• G-NODE - German Informatics Node
• INCF - International Neuroinformatics Coordinating Facility
• NeuralEnsemble, focused on software development in neuroscience
• 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

Reproducibility

• Tutorial on reproducible computational neuroscience research, from CNS 2012 by author of Sumatra