Python utilities for NeuroML
Under development: subject to change without notice…
Clone the repository:
git clone https://github.com/NeuroML/pyNeuroML.git cd pyNeuroML
It should be possible to install pyNeuroML using just:
sudo python setup.py install
You may have to install the development version of libNeuroML manually:
cd .. git clone https://github.com/NeuralEnsemble/libNeuroML.git cd libNeuroML git checkout development sudo python setup.py install
Some current/planned features
Single Python package for NeuroML2/LEMS
One Python package which can be installed using pip & a user has everything they need to work with NeuroML2/LEMS files:
- A bundled version of jNeuroML which can be used to run simulations
Run models using jNeuroML or PyLEMS
Ability to run NeuroML2/LEMS models using jLEMS/jNeuroML (with bundled jar) or PyLEMS (coming soon…)
Uses similar command line interface to jNeuroML, i.e. based on jnml
Access to export & import options of jNeuroML
All export & import options of jNeuroML available through easy command line interface (coming soon…) & through Python methods.
Example of export of NeuroML2/LEMS to NEURON and execution of generated code using single method is here.
Helper Python scripts
Lots of helper scripts for commonly used NeuroML2 functions, e.g.
Analysis of ion channels
Generation of plots of activation rates for ion channels from NeuroML2 channel file (example):
Generation of plots of activation rates for ion channels from NEURON mod file (example):
pynml-modchananalysis NaConductance -modFile NaConductance.mod
Home for existing functionality distributed in various places
Incorporate ChannelML2NeuroML2beta.xsl for updating ChannelML (coming soon…)
NEURON to NeuroML2
Scripts for converting NEURON to NeuroML2
- Export morphologies (plus channels, soon). See here.
- mod files - make best guess at initial NeuroML2 form
View cells in 3D?
Built in viewer of cells in 3D? Mayavi?