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User documentation
Mission and Aims
How to use this documentation
Get NeuroML
Getting started with NeuroML
Simulating a regular spiking Izhikevich neuron
Interactive single Izhikevich neuron NeuroML example
A two population network of regular spiking Izhikevich neurons
Interactive two population network example
Simulating a single compartment Hodgkin-Huxley neuron
Interactive single compartment HH example
Simulating a multi compartment OLM neuron
Interactive multi-compartment OLM cell example
Create novel NeuroML models from components on NeuroML-DB
Finding and sharing NeuroML models
Creating NeuroML models
Converting models to NeuroML and sharing them on Open Source Brain
Handling Morphology Files
HDF5 support
Maintaining provenance in NeuroML models
Validating NeuroML Models
Visualising NeuroML Models
Visualising and analysing ion channel models
Visualising and analysing cell models
Simulating NeuroML Models
Optimising/fitting NeuroML Models
Testing/validating NeuroML Models
LEMS: Low Entropy Model Specification
Model structure overview
Example 1: Dimensions, Units, ComponentTypes and Components
Example 2: tidying up example 1
Example 3: Connection dependent synaptic components
Example 4: Kinetic schemes
Example 5: References and paths
Example 6: User defined types for simulation and display
Example 7: User defined types for networks and populations
Example 8: Regimes in Dynamics definitions
Schema/Specification
NeuroML v2
NeuroMLDocument
NeuroMLCoreDimensions
NeuroMLCoreCompTypes
Cells
Channels
Synapses
Inputs
Networks
PyNN
Simulation
Index
NeuroML v1
LEMS
Model structure
Units and dimensions
Defining component types
Dynamics
Structure
Simulation
Procedure
Defining Components
Geometry
NeuroML 2 and LEMS
Conventions
Units and dimensions
Paths
Quantities and recording
LEMS Simulation files
Extending NeuroML
Software and Tools
pyNeuroML
libNeuroML
pyLEMS
NeuroMLlite
jNeuroML
jLEMS
NeuroML C++ API
MatLab NeuroML Toolbox
Tools and resources with NeuroML support
Approaches to adding NeuroML support
NEURON and NeuroML
NetPyNE and NeuroML
PyNN and NeuroML
Brian and NeuroML
MOOSE and NeuroML
EDEN and NeuroML
Arbor and NeuroML
N2A and NeuroML
NEST and NeuroML
SWC and NeuroML
Citing NeuroML and related publications
Frequently asked questions (FAQ)
Walk throughs
Converting Ray et al 2020 to NeuroML
Setting up
Converting to NeuroML
Adding OMV tests
NeuroML events
NeuroML outreach and events
July 2024: NeuroML tutorial at CNS 2024
April 2024: NeuroML hackathon at HARMONY 2024
June 2022: NeuroML tutorial at CNS*2022 satellite tutorials
April 2022: NeuroML development workshop at HARMONY 2022
October 2021: NeuroML development workshop at COMBINE meeting
August 2021: NeuroML tutorial at INCF Training Weeks
July 2021: NeuroML tutorial at CNS*2021
March 2021: NeuroML hackathon at HARMONY 2021
March 2012: Fourth NeuroML Development Workshop
Past NeuroML Events
The NeuroML Initiative
Getting in touch
Overview of standards in neuroscience
A brief history of NeuroML
NeuroML Editorial Board
History of the NeuroML Editorial Board
Workshop and Meeting reports
NeuroML Scientific Committee
Funding and Acknowledgements
Outreach and training
NeuroML contributors
NeuroML repositories
Code of Conduct
Developer documentation
Overview
Contribution guidelines
Release Process
Making changes to the NeuroML standard
Interaction with other languages and standards
Reference
Glossary
Bibliography
Repository
Open issue
Index
