[neuroConstruct] Update on LEMS & NeuroML 2 developments

[Padraig Gleeson]

Hi,

We've been busy in a few different directions recently with developments 
for NeuroML 2 and LEMS so probably time for a quick update.

     LEMS

- The main specifications for LEMS (Low Entropy Model Specification 
language) has been moved here: https://github.com/LEMS/LEMS. This 
currently consists of the XML Schema for LEMS, but the documentation, 
core examples etc. will be moved here also from the Java & Python 
repositories below.

- jLEMS, or the Java reference implementation of LEMS by Robert Cannon 
has been moved here: https://github.com/LEMS/jLEMS. This includes a 
number of examples which can be read in & executed by jLEMS and has the 
most up to date documentation for LEMS elements 
(http://lems.github.com/jLEMS/elements.html).

- PyLEMS (you guessed it, a Python implementation of LEMS) developed by 
Gautham Ganapathy is here: https://github.com/LEMS/pylems, and uses the 
same updated version of LEMS as jLEMS and can parse/validate/simulate 
most of the same examples.

     NeuroML 2

- The main repository for NeuroML 2 specifications is here: 
https://github.com/NeuroML/NeuroML2. This includes the Schemas, 
including the NeuroML 2 beta schema 
<https://github.com/NeuroML/NeuroML2/blob/master/Schemas/NeuroML2/NeuroML_v2beta.xsd>, 
and the LEMS ComponentTypes 
<https://github.com/NeuroML/NeuroML2/tree/master/NeuroML2CoreTypes> 
which define the structure and behaviour of elements of NeuroML 2. These 
definitions can be viewed online for a (hopefully) clearer view of their 
structure, e.g. izhikevichCell 
<http://www.neuroml.org/NeuroML2CoreTypes/Cells.html#izhikevichCell>, 
nmdaSynapse 
<http://www.neuroml.org/NeuroML2CoreTypes/Synapses.html#nmdaSynapse>, 
sineGenerator 
<http://www.neuroml.org/NeuroML2CoreTypes/Inputs.html#sineGenerator>, etc.

- A number of Java packages modules for handling NeuroML have been 
created here <https://github.com/NeuroML/>. One of these, 
org.neuroml.model <https://github.com/NeuroML/org.neuroml.model>, is a 
Java API for reading, writing & validating NeuroML 2. Others include 
packages for exporting NeuroML & LEMS models to various formats. These 
packages use Maven <http://maven.apache.org/index.html> to make it 
easier to incorporate them into other Java applications. We plan to 
gather all these NeuroML/LEMS packages together into a single 
downloadable package <https://github.com/NeuroML/jNeuroML> with a simple 
command line interface for reading/writing/executing/converting models.

- The Python API for NeuroML 2, libNeuroML 
<https://github.com/NeuralEnsemble/libNeuroML>, is undergoing major 
refactoring, but the existing version should still work fine for 
reading/writing NML2. Please get in contact with Mike Vella or myself if 
you're keen to use this. This initiative is closely linked to a Python 
API for multicompartmental modelling, Pyramidal 
<https://github.com/vellamike/pyramidal>, which will further increase 
interoperability between NeuroML & PyNN.

Hope that provides a good overview of what's available at the moment. As 
suggested most of these initiatives are under active development, and 
offers of help or just feedback are more than welcome! These 
developments are also closely related to our work for the Open Source 
Brain repository (http://opensourcebrain.org). More exciting 
announcements about that coming soon!

Regards,
The NeuroML, LEMS & OSB teams

-----------------------------------------------------
Padraig Gleeson
Room 321, Anatomy Building
Department of Neuroscience, Physiology&  Pharmacology
University College London
Gower Street
London WC1E 6BT
United Kingdom

+44 207 679 3214
p.gleeson at ucl.ac.uk
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