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.

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 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

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 (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.

3) Helper Python scripts

Lots of helper scripts for commonly used NeuroML2 functions, e.g.

4) 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

5) Home for existing functionality distributed in various places

Incorporate ChannelML2NeuroML2beta.xsl for updating ChannelML (coming soon...)

6) 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

7) Planned functionality

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