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A Python library for working with the Low Entropy Model Specification language (LEMS)

Project description


A LEMS ( simulator written in Python which can be used
to run NeuroML2 ( models.

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


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


A stable version of PyLEMS is [available on PyPI]( using [pip](

pip install pylems

To install as root:

sudo pip install pylems

Alternatively, you can obtain the latest version with

git clone
cd pylems
git checkout development # optional
sudo python install

Usage as a LEMS model simulator

pylems [options] LEMS_file


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


**NeuroML examples (from**

- 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.

Travis integration

pylems is integrated with the the [Travis Continuous Integration service](

[![Build Status](](

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

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