NEURON and NeuroML#
NEURON is a widely used simulation environment and is one of the main target platforms for a standard facilitating exchange of neuronal models.
Simulating NeuroML models in NEURON#
jNeuroML or pyNeuroML can be used to convert NeuroML2/LEMS models to NEURON. This involves pointing at a LEMS Simulation file describing what to simulate, and using the
# Simulate the model using NEURON with python/hoc/mod files generated by jNeuroML jnml <LEMS simulation file> -neuron -run # Simulate the model using NEURON with python/hoc/mod files generated by pyNeuroML pynml <LEMS simulation file> -neuron -run
These commands generate a PyNeuron script and run it (a file ending in
So you must have NEURON installed on your system, with its Python bindings (PyNeuron).
-run flag will generate the Python script but will not run it: you can run it manually later.
-nogui will suppress the NEURON graphical elements/menu opening and just run the model in NEURON in the background
You can also run LEMS simulations using the NEURON simulator using the pyNeuroML API:
from pyneuroml.pynml import run_lems_with_jneuroml_neuron ... run_lems_with_jneuroml_neuron(lems_file_name)
NEURON simulations can also be generated from NeuroML model components by neuroConstruct, but most of this functionality is related to NeuroML v1.