leon-k-martin / pylems

LEMS interpreter implemented in Python

PyLEMS

A LEMS (http://lems.github.io/LEMS) simulator written in Python which can be used to run NeuroML2 models (see here).

For more about PyLEMS see:

Michael Vella, Robert C. Cannon, Sharon Crook, Andrew P. Davison, Gautham Ganapathy, Hugh P. C. Robinson, R. Angus Silver and Padraig Gleeson, libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience Frontiers in Neuroinformatics 2014, doi: 10.3389/fninf.2014.00038

PLEASE CITE THE PAPER ABOVE IF YOU USE PYLEMS!

For more details on LEMS see:

Robert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy, Boris Marin, Eugenio Piasini and R. Angus Silver, LEMS: A language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2, Frontiers in Neuroinformatics 2014, doi: 10.3389/fninf.2014.00079

Installation

A stable version of PyLEMS is available on PyPI using pip:

pip install pylems

Alternatively, you can obtain the latest version with

git clone https://github.com/LEMS/pylems.git
cd pylems
git checkout development   # optional
pip install .

Usage as a LEMS model simulator

pylems [options] LEMS_file

Options

• -I/-include path - Adds a directory to the model file include search path

Examples

NeuroML examples (from https://github.com/NeuroML/NeuroML2/tree/development/NeuroML2CoreTypes)

• Example 0 -- Working
• Example 1 -- Working
• Example 2 -- Working
• Example 3 -- Working
• Example 4 -- Not working (Unsupported in PyLEMS: KSChannel)
• Example 5 -- Working
• Example 6 -- Working
• Example 7 -- Working
• Example 8 -- Working
• Example 9 -- Working
• Example 10 -- Working
• Example 11 -- Working
• Example 12 -- Not working (Unsupported in PyLEMS: Property)
• Example 13 -- Working
• Example 14 -- Not working (Unsupported in PyLEMS: Property)
• Example 15 -- Working
• Example 16 -- Working (apart from spikeArray)
• Example 17 -- Working
• Example 18 -- Working

LEMS examples (in directory examples)

• example1.xml -- Working
• example2.xml -- Working
• example3.xml -- Working
• example4.xml -- Not working (Unsupported in PyLEMS: KSChannel)
• example5.xml -- Not working (Unsupported in PyLEMS: KSChannel)
• example6.xml -- Working

TODO: Rest of examples require an update to the <Simulation> element, i.e. use <Simulation...> not <SimulationSet...>, to work in PyLEMS

LEMS elements that do not work

• KSChannel
• Property
• XPath based parameters - PathParameter
• Assertions

Tasks TODO

• Implement flattening
• Decouple events from runnables
• Improve dimension-checking on expressions.

This code is distributed under the terms of the GNU Lesser General Public License.