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Loading a NeuroML Network does not work properly #50

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mattions opened this Issue Jul 6, 2012 · 7 comments

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mattions commented Jul 6, 2012

Neuronvisio uses the NEURON readxml parser to load NeuroML file and does not deal with it directly.

Single Cell works ok, however Network doesn't. Check the example @ https://github.com/mattions/neuronvisio/blob/master/examples/cerebellum_network/NeuroML/Ex6_Cerebellum_networks.xml where there is a NeuroML Network file version 1.8

The plan is to switch to https://github.com/NeuralEnsemble/libNeuroML and NeuroML 2.0 when ready, in the mean-time we still using NEURON.

This issue is more to highlight the problem and keep track of it. It should live in the NEURON Issue tracker, but they don't have one.

I'll try to raise this in the NEURON forum and put the link here and get Padraig (@pgleeson) attention on this one

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pgleeson commented Jul 10, 2012

Haven't forgotten about this, am looking into the various NeuroML import
functions of NEURON and hope to have some updated working examples
across versions soon...

On 06/07/12 15:00, Michele Mattioni wrote:

Neuronvisio uses the NEURON readxml parser to load NeuroML file and does not deal with it directly.

Single Cell works ok, however Network doesn't. Check the example @ https://github.com/mattions/neuronvisio/blob/master/examples/cerebellum_network/NeuroML/Ex6_Cerebellum_networks.xml where there is a NeuroML Network file version 1.8

The plan is to switch to https://github.com/NeuralEnsemble/libNeuroML and NeuroML 2.0 when ready, in the mean-time we still using NEURON.

This issue is more to highlight the problem and keep track of it. It should live in the NEURON Issue tracker, but they don't have one.

I'll try to raise this in the NEURON forum and put the link here and get Padraig (@pgleeson) attention on this one


Reply to this email directly or view it on GitHub:
#50


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@ucl.ac.uk

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pgleeson commented Jul 13, 2012

Quick update:

Regarding the issue with loading NeuroML cells into NEURON version 7.2, the API hasn't really changed much, it's just that the neuron.neuroml (containing rdxml.py etc.) wasn't included in setup.py. This can be fixed with something like:
cp -r /home/padraig/nrn2make/nrn/share/lib/python/neuron/neuroml/ /usr/local/lib/python2.7/dist-packages/neuron

This has been fixed in the latest version of setup.py in the mercurial repo, and the xml files can successfully load with test.py here:
http://sourceforge.net/apps/trac/neuroml/browser/NeuroML2nrn

There are some remaining issues with that import, which I'll have to look in to, but I will get any updates integrated into Mike Hines' main branch

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pgleeson commented Jul 13, 2012

Just saw that @mattions pointed this out in issue#48...

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mattions commented Jul 30, 2012

+1 to get this with NEURON branch. Would be cool to know when this happens and in which release of NEURON, so we can point people properly.

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mattions commented Mar 5, 2013

Do we know if NEURON Devs fixed this one or not?

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pgleeson commented Mar 5, 2013

Don't think much has happened here yet, but it should.. Out of the office for the rest of the week, but I'll look at this next week..

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mattions commented Mar 7, 2013

@pgleeson thanks! This is just to get this out of the way if it has been done

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