Failure to load models in moose-examples [docker]

Created by: lungsi

My environment is bhallalab/moose docker. Using moosegui when I try to load moose-examples I fail to load any of the models shown in the documentation.

When I follow the instruction

Cerebellar granule cell File -> Load -> ~/moose/moose-examples/neuroml/GranuleCell/GranuleCell.net.xml This is a single compartment Cerebellar granule cell with a variety of channels Maex, R. and De Schutter, E., 1997 (exported from http://www.neuroconstruct.org/). Click on its soma, and See children for its list of channels. Vary the Gbar of these channels to obtain regular firing, adapting and bursty behaviour (may need to increase tau of the Ca pool).

I get

For

Pyloric rhythm generator in the stomatogastric ganglion of lobster File -> Load -> ~/moose/moose-examples/neuroml/pyloric/Generated.net.xml

I get

For

Purkinje cell File -> Load -> ~/moose/moose-examples/neuroml/PurkinjeCell/Purkinje.net.xml This is a purely passive cell, but with extensive morphology [De Schutter, E. and Bower, J. M., 1994] (exported from http://www.neuroconstruct.org/). The channel specifications are in an obsolete ChannelML format which MOOSE does not support.

I get

For

Olfactory bulb subnetwork File -> Load -> ~/moose/moose-examples/neuroml/OlfactoryBulb/numgloms2_seed100.0_decimated.xml This is a pruned and decimated version of a detailed network model of the Olfactory bulb [Gilra A. and Bhalla U., in preparation] without channels and synaptic connections. We hope to post the ChannelML specifications of the channels and synapses soon.

I get

For

All channels cell File -> Load -> ~/moose/moose-examples/neuroml/allChannelsCell/allChannelsCell.net.xml This is the Cerebellar granule cell as above, but with loads of channels from various cell types (exported from http://www.neuroconstruct.org/). Play around with the channel properties to see what they do. You can also edit the ChannelML files in ~/moose/moose-examples/neuroml/allChannelsCell/cells_channels/ to experiment further.

I get

Created by: hrani

Hi, To load neuroml model you need to install moogli,

“Moogli is a independent openGL based visualization tool for neural simulations. Moogli can visualize morphology of single/multiple neurons or network of neurons, and can also visualize activity in these cells.” But this project is not maintained for long time I need to install first on the system and test... Will look into this as soon as possible But there is other alternative also give me a Day will get back.

Regards HarshaRani

On Wed, 31 Oct 2018 at 10:42 PM, lungsi notifications@github.com wrote:

My environment is bhallalab/moose docker. Using moosegui when I try to load moose-examples https://moose.ncbs.res.in/readthedocs/user/py/cookbook/elec_GUI.html I fail to load any of the models shown in the documentation.

When I follow the instruction

Cerebellar granule cell File -> Load -> ~/moose/moose-examples/neuroml/GranuleCell/GranuleCell.net.xml This is a single compartment Cerebellar granule cell with a variety of channels Maex, R. and De Schutter, E., 1997 (exported from http://www.neuroconstruct.org/). Click on its soma, and See children for its list of channels. Vary the Gbar of these channels to obtain regular firing, adapting and bursty behaviour (may need to increase tau of the Ca pool).

I get

[image: moose-examples/neuroml/GranuleCell/GranuleCell.net.xml] https://user-images.githubusercontent.com/12233689/47804461-2cd59480-dd35-11e8-840e-5fde9cc67d7d.gif

For

Pyloric rhythm generator in the stomatogastric ganglion of lobster File -> Load -> ~/moose/moose-examples/neuroml/pyloric/Generated.net.xml

I get [image: moose-examples/neuroml/pyloric/Generated.net.xml] https://user-images.githubusercontent.com/12233689/47804709-c7ce6e80-dd35-11e8-86ba-4778d3d6cdb6.gif

For

Purkinje cell File -> Load -> ~/moose/moose-examples/neuroml/PurkinjeCell/Purkinje.net.xml This is a purely passive cell, but with extensive morphology [De Schutter, E. and Bower, J. M., 1994] (exported from http://www.neuroconstruct.org/). The channel specifications are in an obsolete ChannelML format which MOOSE does not support.

I get [image: moose-examples/neuroml/PurkinjeCell/Purkinje.net.xml] https://user-images.githubusercontent.com/12233689/47805078-b76ac380-dd36-11e8-8196-f33062f9a97b.gif

For

Olfactory bulb subnetwork File -> Load -> ~/moose/moose-examples/neuroml/OlfactoryBulb/numgloms2_seed100.0_decimated.xml This is a pruned and decimated version of a detailed network model of the Olfactory bulb [Gilra A. and Bhalla U., in preparation] without channels and synaptic connections. We hope to post the ChannelML specifications of the channels and synapses soon.

I get [image: moose-examples/neuroml/OlfactoryBulb/numgloms2_seed100.0_decimated.xml] https://user-images.githubusercontent.com/12233689/47805171-f0a33380-dd36-11e8-8864-bb7a1fdc60d7.gif

For

All channels cell File -> Load -> ~/moose/moose-examples/neuroml/allChannelsCell/allChannelsCell.net.xml This is the Cerebellar granule cell as above, but with loads of channels from various cell types (exported from http://www.neuroconstruct.org/). Play around with the channel properties to see what they do. You can also edit the ChannelML files in ~/moose/moose-examples/neuroml/allChannelsCell/cells_channels/ to experiment further.

I get [image: moose-examples/neuroml/allChannelsCell/allChannelsCell.net.xml] https://user-images.githubusercontent.com/12233689/47805208-0f092f00-dd37-11e8-998d-95f53c0f305d.gif

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Created by: dilawar

@harsha He is using version 3.1.4 on Ubuntu 16.04. It has moogli . You can probably reproduce it with chamcham series.

Created by: hrani

@lungsi When did you download the docker image? I am not able to reproduce the error GranuleCell.net.xml And Yes for Generated.net.xml I am able to reproduce /cells[0]/AB_PD_0[0]/Soma_0/DoubExpSyn_Ach_spikegen' doesn't exist.

Rest all the models are loading.

1.In the Gui we are not displaying the 3D view of the model but the model is loaded into moose, one can see that it loaded by clicking view->DockWidget->python or 2. from python terminal one can load the moose import moose import moose.neuroml moose.neuroml.loadNeuroML_L123('moose-examples/neuroml/GranuleCell/GranuleCell.net.xml')

But now we are using rdesignuer for loading and running the models of these kinds, we will update soon some simple examples in the documentation

Created by: lungsi

@hrani I downloaded the image on 31 Oct 2018 after @dilawar updated the image according to https://github.com/BhallaLab/moose/issues/245