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Dear colleagues,<br>
<br>
We are happy to announce a new stable release (version 2, beta 3) of
the NeuroML language for model specification in computational
neuroscience.<br>
<br>
<a class="moz-txt-link-freetext"
href="http://www.neuroml.org/getneuroml">http://www.neuroml.org/getneuroml</a><br>
<br>
NeuroML allows specification of models of systems from integrate and
fire cells up to complex 3D networks of multicompartmental neurons.
NeuroML version 2 has been extensively redesigned to be built on a
new language, LEMS, which allows machine readable definitions of
model structure and dynamics. This facilitates model transparency,
portability and code generation. LEMS and NeuroML 2 are described in
detail in:<br>
<br>
Robert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy,
Boris Marin, Eugenio Piasini and R. Angus Silver, <b>LEMS: A
language for expressing complex biological models in concise and
hierarchical form and its use in underpinning NeuroML 2</b>,
Frontiers in Neuroinformatics 2014, doi: 10.3389/fninf.2014.00079<br>
<br>
There are libraries for reading, writing and simulating NeuroML
models in Java (<a class="moz-txt-link-freetext"
href="https://github.com/NeuroML/jNeuroML">https://github.com/NeuroML/jNeuroML</a>)
and Python. The Python APIs for NeuroML and LEMS have recently been
described in:<br>
<br>
Michael Vella, Robert C. Cannon, Sharon Crook, Andrew P. Davison,
Gautham Ganapathy, Hugh P. C. Robinson, R. Angus Silver and Padraig
Gleeson, <b>libNeuroML and PyLEMS: using Python to combine
procedural and declarative modeling approaches in computational
neuroscience</b>, Frontiers in Neuroinformatics 2014, doi:
10.3389/fninf.2014.00038<br>
<br>
The growing number (30+) of tools, libraries and databases
supporting NeuroML v1 and/or NeuroML v2 are listed here:<br>
<br>
<a class="moz-txt-link-freetext"
href="http://www.neuroml.org/tool_support">http://www.neuroml.org/tool_support</a><br>
<br>
Open Source Brain is a repository of models in computational
neuroscience which actively supports open, collaborative development
of models, as well as conversion to simulator independent formats
including NeuroML (over 500 valid NeuroML 2 cells/channels/synapses
on OSB at last count). An overview of the models currently present
and the formats/simulators supported can be found here:<br>
<br>
<a class="moz-txt-link-freetext"
href="http://www.opensourcebrain.org/status">http://www.opensourcebrain.org/status</a><br>
<br>
Regards,<br>
The NeuroML development community<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>
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