Python utilities for NeuroML
Project description
## pyNeuroML
Under development: subject to change without notice…
### Installation
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](https://github.com/NeuralEnsemble/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:
libNeuroML
PyLEMS
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](https://github.com/NeuroML/pyNeuroML/tree/master/pyneuroml/lib)) or PyLEMS (coming soon…)
Uses similar command line interface to jNeuroML, i.e. based on jnml
Try:
pynml -h
#### 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](https://github.com/NeuroML/pyNeuroML/blob/master/examples/run_jneuroml_plot_matplotlib.py#L21).
#### 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](https://github.com/NeuroML/pyNeuroML/blob/master/examples/analyseNaNml2.sh)):
pynml-channelanalysis NaConductance.channel.nml
Generation of plots of activation rates for ion channels from NEURON mod file ([example](https://github.com/NeuroML/pyNeuroML/blob/master/examples/analyseNaMod.sh)):
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](https://github.com/NeuroML/pyNeuroML/blob/master/examples/export_neuroml2.py).
mod files - make best guess at initial NeuroML2 form
#### View cells in 3D?
Built in viewer of cells in 3D? Mayavi?
#### PyNN?
More closely tied to PyNN?
[](https://travis-ci.org/NeuroML/pyNeuroML)
](https://travis-ci.org/NeuroML/pyNeuroML){kind=link}