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Hi all,<br>
<br>
A few points... Please remember to come along to the workshop at
CNS*2011 on "<a
href="http://incf.org/programs/modeling/projects/standards/cns-2011-workshop-emerging-standards-for-network-modeling-in-neuroscience">Emerging
standards for network modeling in neuroscience</a>" on June 27th
(first workshop day), where there will be presentations on NeuroML
v2/LEMS and the relationship with other initiatives such as
libNineML/PyNN/CSA.<br>
<br>
The code for NeuroML v2 and LEMS has been refactored recently to
reflect the distinction between the core language for describing
generic dynamical models using component definitions (LEMS, a term
which is used for the language itself, and the reference
implementation in Java) and all neuroscience specific component
classes (NeuroML) and the neuroscience/systems biology import/export
extensions to LEMS (libNeuroML).<br>
<br>
The LEMS code base is currently here: <a
class="moz-txt-link-freetext"
href="http://sourceforge.net/apps/trac/neuroml/browser/LEMS">http://sourceforge.net/apps/trac/neuroml/browser/LEMS</a>
(but may move to its own domain in time), together with some
examples. The jar file generated by the Ant script lems-x.x.x.jar,
can be run standalone (see lems/lems.bat scripts in that folder) or
be used to add LEMS functionality to any Java application.<br>
<br>
The NeuroML specific extensions are here: <a
class="moz-txt-link-freetext"
href="http://sourceforge.net/apps/trac/neuroml/browser/NeuroML2">http://sourceforge.net/apps/trac/neuroml/browser/NeuroML2</a>.
The core definitions of neuroscience component classes (e.g.
ionChannelHH, izhikevichCell, synapse) are in NeuroML2CoreTypes.
Note that ComponentType and Behaviour have been renamed
ComponentClass and Dynamics in these definitions. This is due to the
start of a process to harmonise a core language for component
definitions with the libNineML developers, and is an ongoing process
which should stabilise in the next few months. The core of LEMS will
always support the format used in these files. The jar file,
libNeuroML-x.x.x.jar, can be used to run any LEMS file or a
combination of NeuroML2 core components with LEMS simulation run
settings (see examples folder) using the nml2/nml2.bat scripts. This
jar/script can also be used for generating scripts for other formats
(e.g. NEURON, see ./nml2 -help).<br>
<br>
A new version of neuroConstruct has been released (v1.5.1, <a
class="moz-txt-link-freetext"
href="http://www.neuroconstruct.org/download">http://www.neuroconstruct.org/download</a>)
which uses the updated jars for NeuroML 2 support. More details on
the updates in this release are here: <a
class="moz-txt-link-freetext"
href="http://www.neuroconstruct.org/RELEASE_NOTES">http://www.neuroconstruct.org/RELEASE_NOTES</a>.<br>
<br>
A screenshot is included of a network generated with neuroConstruct
of 24 excitatory & inhibitory Adaptive Exponential Integrate
& Fire cells (project nCexamples/Ex10_NeuroML2). The cell models
are specified with NeuroML 2 adExIaFCell components, and the full
network can be generated in NML2, and run on the LEMS interpreter.
The network can also be generated as NEURON hoc/mod, and run with
that simulator, with good agreement for the spike times and sub
threshold behaviour of the cells.<br>
<br>
Regards,<br>
Padraig<br>
<br>
<br>
<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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