Skip to main content
This is a pre-production deployment of Warehouse. Changes made here affect the production instance of PyPI (
Help us improve Python packaging - Donate today!

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]( & [PyLEMS]( and wraps functionality from [jNeuroML](


### 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 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]( manually:

apt-get install python-lxml cd .. git clone cd libNeuroML git checkout development sudo python 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]( or PyLEMS (todo…)

Uses similar command line interface to jNeuroML, i.e. based on jnml


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]( for progress) & through Python methods.

Example of export of NeuroML2/LEMS to NEURON and execution of generated code using single method is [here](

4) Helper Python scripts

Lots of helper scripts for commonly used functions, e.g. [generating a firing frequency vs injected current plot](, [generating a LEMS file for use with a NeuroML2 file](,

5) 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

See [here]( 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

8) Export of images/movies from cell/networks

Files can be generated for [POV-Ray]( 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]( and [pyelectro]( See [here]( for example.

9) Planned functionality

Built in viewer of cells in 3D? Mayavi? More closely tied to PyNN?

[![Build Status](](

Release History

Release History

This version
History Node


History Node


History Node


History Node


History Node


History Node


History Node


History Node


History Node


History Node


History Node


History Node


History Node


History Node


History Node


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-0.3.0.tar.gz (27.1 MB) Copy SHA256 Checksum SHA256 Source Jul 7, 2017

Supported By

WebFaction WebFaction Technical Writing Elastic Elastic Search Pingdom Pingdom Monitoring Dyn Dyn DNS Sentry Sentry Error Logging CloudAMQP CloudAMQP RabbitMQ Heroku Heroku PaaS Kabu Creative Kabu Creative UX & Design Fastly Fastly CDN DigiCert DigiCert EV Certificate Rackspace Rackspace Cloud Servers DreamHost DreamHost Log Hosting