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Python utilities for NeuroML

Project Description

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 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) 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.

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):

pynml-channelanalysis NaConductance.channel.nml

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?

PyNN?

More closely tied to PyNN?

Release History

Release History

This version
History Node

0.0.7

Download Files

Download Files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
pyNeuroML-0.0.7.tar.gz (16.3 MB) Copy SHA256 Checksum SHA256 Source Jul 27, 2015

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