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mattions / neuronvisio

A Graphical User Interface with 3D Visualization features for NEURON simulation enviroment
https://neuronvisio.readthedocs.io
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Loading a NeuroML Network does not work properly #50

Open mattions opened 12 years ago

mattions commented 12 years ago

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

pgleeson commented 12 years ago

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: https://github.com/mattions/neuronvisio/issues/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

pgleeson commented 12 years ago

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

pgleeson commented 12 years ago

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

mattions commented 12 years ago

+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.

mattions commented 11 years ago

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

pgleeson commented 11 years ago

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..

mattions commented 11 years ago

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