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Hi,<br>
<br>
We've been busy in a few different directions recently with
developments for NeuroML 2 and LEMS so probably time for a quick
update.<br>
<br>
LEMS<br>
<br>
- The main specifications for LEMS (Low Entropy Model Specification
language) has been moved here: <a class="moz-txt-link-freetext"
href="https://github.com/LEMS/LEMS">https://github.com/LEMS/LEMS</a>.
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.<br>
<br>
- jLEMS, or the Java reference implementation of LEMS by Robert
Cannon has been moved here: <a class="moz-txt-link-freetext"
href="https://github.com/LEMS/jLEMS">https://github.com/LEMS/jLEMS</a>.
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 (<a class="moz-txt-link-freetext"
href="http://lems.github.com/jLEMS/elements.html">http://lems.github.com/jLEMS/elements.html</a>).<br>
<br>
- PyLEMS (you guessed it, a Python implementation of LEMS) developed
by Gautham Ganapathy is here: <a class="moz-txt-link-freetext"
href="https://github.com/LEMS/pylems">https://github.com/LEMS/pylems</a>,
and uses the same updated version of LEMS as jLEMS and can
parse/validate/simulate most of the same examples.<br>
<br>
NeuroML 2<br>
<br>
- The main repository for NeuroML 2 specifications is here: <a
class="moz-txt-link-freetext"
href="https://github.com/NeuroML/NeuroML2">https://github.com/NeuroML/NeuroML2</a>.
This includes the Schemas, including the <a
href="https://github.com/NeuroML/NeuroML2/blob/master/Schemas/NeuroML2/NeuroML_v2beta.xsd">NeuroML
2 beta schema</a>, and the <a
href="https://github.com/NeuroML/NeuroML2/tree/master/NeuroML2CoreTypes">LEMS
ComponentTypes</a> 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. <a
href="http://www.neuroml.org/NeuroML2CoreTypes/Cells.html#izhikevichCell">izhikevichCell</a>,
<a
href="http://www.neuroml.org/NeuroML2CoreTypes/Synapses.html#nmdaSynapse">nmdaSynapse</a>,
<a
href="http://www.neuroml.org/NeuroML2CoreTypes/Inputs.html#sineGenerator">
sineGenerator</a>, etc.<br>
<br>
- A number of Java packages modules for handling NeuroML have been
created <a href="https://github.com/NeuroML/">here</a>. One of
these, <a href="https://github.com/NeuroML/org.neuroml.model">org.neuroml.model</a>,
is a Java API for reading, writing & validating NeuroML 2.
Others include packages for exporting NeuroML & LEMS models to
various formats. These packages use <a
href="http://maven.apache.org/index.html">Maven</a> to make it
easier to incorporate them into other Java applications. We plan to
gather all these NeuroML/LEMS packages together into a <a
href="https://github.com/NeuroML/jNeuroML">single downloadable
package</a> with a simple command line interface for
reading/writing/executing/converting models.<br>
<br>
- The Python API for NeuroML 2, <a
href="https://github.com/NeuralEnsemble/libNeuroML">libNeuroML</a>,
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, <a
href="https://github.com/vellamike/pyramidal">Pyramidal</a>, which
will further increase interoperability between NeuroML & PyNN.<br>
<br>
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 (<a class="moz-txt-link-freetext"
href="http://opensourcebrain.org">http://opensourcebrain.org</a>).
More exciting announcements about that coming soon!<br>
<br>
Regards,<br>
The NeuroML, LEMS & OSB teams<br>
<br>
<pre class="moz-signature" cols="72">-----------------------------------------------------
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
<a class="moz-txt-link-abbreviated" href="mailto:p.gleeson@ucl.ac.uk">p.gleeson@ucl.ac.uk</a>
----------------------------------------------------- </pre>
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