[neuroConstruct] Re: [Neuroml-technology] NeuroML version 2.0
mattioni at ebi.ac.uk
Wed Dec 22 12:28:08 GMT 2010
I was just checking the examples and I have just noticed that the
units in line with the value, sometimes there is a space and sometimes
the space is missing.
Just a small sample from the synapse example from here
<synapse type="nmdaSynapse" id="nmdaSyn" gbase="0.5nS" erev="0mV"
<block type="VoltageConcDepBlock" species="mg"
blockConcentration="1.2 mM" scalingConc="1.920544 mM"
Is the space optional or not?
On Wed, Dec 15, 2010 at 11:21 AM, P Gleeson <p.gleeson at ucl.ac.uk> wrote:
> Hi all,
> A number of activities have been taking place towards NeuroML version 2.
> These have been mentioned in some previous mails and have been in
> development on the Sourceforge SVN repository, but the various threads
> have reached a point where a draft schema for version 2 (NeuroML
> v2alpha) can be used for testing in applications which import/export
> NeuroML 2.
> Full details of the ongoing work are available here:
> Some of the things which are possible with the current version of NeuroML 2:
> * Full 3D networks containing morphologically detailed cells with
> electrical properties, ion channels and synapses can be expressed in
> NeuroML v2alpha and validated according to the new XML Schema (i.e.
> roughly the same scope as version 1.x Level 3)
> * Abstract cell models including the Izhikevich cell and adapting
> exponential integrate & fire can be specified using Robert's LEMS*, and
> instantiated in NeuroML 2 files. These can be executed with the LEMS
> interpreter or NEURON code can be generated.
> * Examples of synapse models including single & double exponential,
> voltage dependent (NMDA-R) and short term plasticity models are
> available, as are HH and kinetic scheme ion channel models. These can be
> extended using the LEMS framework and executed with the interpreter.
> * An initial export of models specified in NeuroML 2 (and many other
> models in LEMS) to SBML is available.
> * Various aspects of NeuroML 2 development have benefited from
> discussions in the INCF Multiscale Modelling Program, and files in the
> emerging NineML language can be generated from many of the NeuroML
> 2/LEMS examples.
> Please look at the provided examples, try out the available tools, try
> building new model components using LEMS (which can subsequently be
> included as core NeuroML 2 types) and give your comments on the main
> NeuroML mailing list. Hopefully we can get some useful feedback on the
> currently proposed structure for NeuroML 2 before the 3rd NeuroML
> development workshop in London at the end of March next year (more
> details to follow).
> The NeuroML Team
> * To summarise the relation between NeuroML 2 and LEMS (Low Entropy
> Model Specification, http://www.neuroml.org/lems): LEMS can be used
> independently as a language for specifying reusable model types, and is
> not really neuroscience specific. NeuroML 2 XML files (very neuroscience
> specific...) can be used without interaction with LEMS, but most of the
> core NeuroML types will be specified in LEMS and applications can
> benefit greatly from the machine readable specification of model
> component behaviour.
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