From djaeger at emory.edu  Thu Mar  3 14:49:55 2011
From: djaeger at emory.edu (Dieter Jaeger)
Date: Thu, 03 Mar 2011 09:49:55 -0500
Subject: [neuroConstruct] Fwd: FW: Neuron Ontology Workshop
Message-ID: <4D6FAA93.4040903@emory.edu>

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From p.gleeson at ucl.ac.uk  Mon Mar 28 18:26:45 2011
From: p.gleeson at ucl.ac.uk (Padraig Gleeson)
Date: Mon, 28 Mar 2011 18:26:45 +0100
Subject: [neuroConstruct] neuroConstruct version 1.5.0 with initial support
 for NeuroML v2alpha & LEMS
Message-ID: <4D90C4D5.10709@ucl.ac.uk>

Hi,

A new release of neuroConstruct, v1.5.0 is available here: 
http:www.neuroConstruct.org.

The full details of changes in this release are here: 
http://www.neuroconstruct.org/nCinfo/RELEASE_NOTES.

The main change in this release is the initial support for NeuroML 
v2alpha & LEMS.  Morphologies can be exported to NeuroML v2 format, and 
some simple (e.g. HH Na & K) ChannelML files can be translated to the 
equivalent entities in NeuroML v2alpha. Networks files can be generated 
with simple <population> elements, and the temporary 
<explicitConnection> and <explicitInput> elements. The NeuroML 2/LEMS 
code which is being developed on the NeuroML SVN rep (see 
http://sourceforge.net/apps/trac/neuroml/browser/DemoVer2.0/lems) is 
included in this release. This can be automatically updated when using 
nC from the SVN repository by running updatenC.sh/updatenC.bat.

Some simple models in NeuroML 2 can now be run through nC using the LEMS 
interpreter. Note the LEMS interpreter does not yet support 
multicompartmental cells. Try Ex4_HHCells for a network of 2 HH cells
with a simple synapse. Results of a successful simulation on the LEMS 
interpreter should be listed in the Simulation Browser & can be 
reloaded/replayed in the usual way.

There are many more possibilities which will over time be enabled 
through NML2/LEMS support: export to any format supported by the LEMS 
interpreter (NEURON, SBML, Brian, CellML, Matlab & NineML are in the 
pipeline); support for any generic dynamical model that can be expressed 
as a LEMS ComponentType; support for SBML components in simulations; 
support for multicompartmental NML2 cells if a simulator can natively 
read the morphology file (planned for NEURON).

Regards,
Padraig

-----------------------------------------------------
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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