Python utilities for NeuroML
Project description
A single package in Python unifying scripts and modules for reading, writing, simulating and analysing NeuroML2/LEMS models.
Builds on: [libNeuroML](https://github.com/NeuralEnsemble/libNeuroML) & [PyLEMS](https://github.com/LEMS/pylems) and wraps functionality from [jNeuroML](https://github.com/NeuroML/jNeuroML).
Installation
### Pip
pyNeuroML can be installed with pip:
sudo pip install pyneuroml
You may need to install lxml on Linux with:
sudo apt-get install python-lxml
### Installation from source
Clone the repository:
git clone https://github.com/NeuroML/pyNeuroML.git cd pyNeuroML
It should be possible to install pyNeuroML using just:
sudo pip install . -r requirements.txt
You may have to install lxml and the development version of [libNeuroML](https://github.com/NeuralEnsemble/libNeuroML) manually:
apt-get install python-lxml cd .. git clone https://github.com/NeuralEnsemble/libNeuroML.git cd libNeuroML git checkout development sudo python setup.py install
Current/planned features
1) 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
2) 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 (todo…)
Uses similar command line interface to jNeuroML, i.e. based on jnml
Try:
pynml -h
to list current options.
3) Access to export & import options of jNeuroML
All export & import options of jNeuroML available through easy command line interface (see [here](https://github.com/NeuroML/pyNeuroML/issues/21) for progress) & 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).
4) Helper Python scripts
Lots of helper scripts for commonly used functions, e.g. [generating a firing frequency vs injected current plot](https://github.com/NeuroML/pyNeuroML/blob/master/pyneuroml/analysis/__init__.py#L8), [generating a LEMS file for use with a NeuroML2 file](https://github.com/NeuroML/pyNeuroML/blob/master/pyneuroml/lems/__init__.py),
5) 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
See [here](http://www.opensourcebrain.org/docs#Converting_To_NeuroML2) for more.
6) Home for existing functionality distributed in various places
Incorporate ChannelML2NeuroML2beta.xsl for updating ChannelML (coming soon…)
7) 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 (todo)
8) Export of images/movies from cell/networks
Files can be generated for [POV-Ray](http://www.povray.org/) which can be used to generate high resolution images and even sequences of images for creating movies. try:
pynml-povray -h
9) Tuning cell models in NeuroML 2
Builds on [Neurotune](https://github.com/NeuralEnsemble/neurotune) and [pyelectro](https://github.com/NeuralEnsemble/pyelectro). See [here](https://github.com/NeuroML/pyNeuroML/blob/master/examples/tuneHHCell.py) for example.
9) Planned functionality
Built in viewer of cells in 3D? Mayavi? More closely tied to PyNN?
[](https://travis-ci.org/NeuroML/pyNeuroML)
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