PyLEMS

A 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.

Metadata

Release files for PyLEMS 0.6.9

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for PyLEMS 0.6.9
File	Size	Uploaded
pylems-0.6.9.tar.gz	72.4 kB	Nov 26, 2025	Details

Built distribution (wheel)

Table of built distributions (wheels) for PyLEMS 0.6.9
File	Interpreter	ABI	Platform	Reset
pylems-0.6.9-py3-none-any.whl 67.6 kB Nov 26, 2025	Python 3	none	any	Details

Total release size: 140.0 kB

Release files / pylems-0.6.9.tar.gz

Download URL	pylems-0.6.9.tar.gz
Size	72.4 kB
Tags	Source
SHA-256 checksum How to use checksums	`01b47e60ec1fc4896e9cf69c15160012148202547a9cf6759a93828abdcd738a`
BLAKE2b-256 checksum How to use checksums	`b40bb5d0800c3ae8aecf4ac0ab415537643e8a1fff138f6a282409f23e4906cd`
Upload date	Nov 26, 2025
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.9.25`

Release files / pylems-0.6.9-py3-none-any.whl

Download URL	pylems-0.6.9-py3-none-any.whl
Size	67.6 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`2c4346da61f1e312c7eeb6d3f98922854b6674391648aaf4c9c5c8d0e3977beb`
BLAKE2b-256 checksum How to use checksums	`f7c524fa6d73081f592b7008806c3e20ad6633ae12c8e2d56bc78f14a19d68c2`
Upload date	Nov 26, 2025
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.9.25`