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NeuroML Documentation

User documentation

  • Mission and Aims
  • How to use this documentation
  • 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
  • Finding and sharing NeuroML models
  • Creating NeuroML models
  • Validating NeuroML Models
  • Visualising NeuroML Models
  • Simulating NeuroML Models
  • Schema/Specification
    • NeuroML v2
      • NeuroMLCoreDimensions
      • NeuroMLCoreCompTypes
      • Cells
      • Channels
      • Synapses
      • Inputs
      • Networks
      • PyNN
      • Simulation
    • NeuroML v1
  • Using NeuroML 2 and LEMS
    • Conventions
    • Units and dimensions
    • Paths
    • Quantities and recording
    • LEMS Simulation files
    • Extending NeuroML with LEMS
  • Software and Tools
    • pyNeuroML
    • libNeuroML
    • pyLEMS
    • NeuroMLlite
    • jNeuroML
    • jLEMS
    • NeuroML C++ API
    • MatLab NeuroML Toolbox
    • Tools and resources with NeuroML support
  • Frequently asked questions (FAQ)

NeuroML events

  • August 2021: NeuroML tutorial at INCF Training Weeks
  • July 2021: NeuroML tutorial at CNS*2021
  • March 2021: NeuroML hackathon at HARMONY 2021
  • 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
  • NeuroML contributors
  • Code of Conduct

Developer documentation

  • Overview
    • Release Process
  • Interaction with other languages and standards

Reference

  • Glossary
  • Bibliography
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Using NeuroML 2 and LEMSΒΆ

While the tutorials cover many of the key points of using LEMS with NeuroML, there are some points which require further explanation:

  • What are the conventions/best practices to follow in naming NeuroML/LEMS files/elements?

  • How are units and dimensions handled in NeuroML and LEMS?

  • How do I use a LEMS Simulation file to specify how to execute a NeuroML model?

  • How can I extend NeuroML model to include new types using LEMS?

  • What is the correct format/usage of paths and quantities in NeuroML and LEMS?

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NeuroML v1

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Conventions

By NeuroML contributors
© Copyright 2021.