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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

#### View cells in 3D?

Built in viewer of cells in 3D? Mayavi?

#### PyNN?

More closely tied to PyNN?

[![Build Status](https://travis-ci.org/NeuroML/pyNeuroML.svg?branch=master)](https://travis-ci.org/NeuroML/pyNeuroML)

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