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openworm / org.geppetto.model.neuroml

NeuroML Model Bundle for Geppetto
http://www.geppetto.org/
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Extract visual group information from NeuroML documents #30

Closed tarelli closed 10 years ago

tarelli commented 10 years ago
jrmartin commented 10 years ago

@tarelli I've been using the latest development code for model.neuroml and noticed is taking a lot longer for Purkinje to load than it used to. Time for hhcell is alright (~4 seconds), only purkinje is very slow (50 seconds for me).

I get a lot of warning reading the file now too. [2014-10-25 22:00:55.762] INFO http-bio-8080-exec-20 org.geppetto.simulation.SimulationService Initializing simulation [2014-10-25 22:00:56.053] INFO http-bio-8080-exec-20 org.geppetto.simulation.SimulationService Reading configuration file, took 291 ms
[2014-10-25 22:02:32.344] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/Leak.nml [2014-10-25 22:02:33.017] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/KMnew2.nml [2014-10-25 22:02:33.664] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/NaF.nml [2014-10-25 22:02:34.366] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/KA.nml [2014-10-25 22:02:34.993] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/Kdr.nml [2014-10-25 22:02:35.617] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/Kh2.nml [2014-10-25 22:02:36.283] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/NaP.nml [2014-10-25 22:02:36.949] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/CaT.nml [2014-10-25 22:02:37.616] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/KC.nml [2014-10-25 22:02:38.234] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/cad.nml [2014-10-25 22:02:38.895] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/K2.nml [2014-10-25 22:02:39.566] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/CaP.nml [2014-10-25 22:02:40.564] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/Kh1.nml [2014-10-25 22:02:44.701] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/Leak.nml [2014-10-25 22:02:45.255] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/KMnew2.nml [2014-10-25 22:02:45.834] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/NaF.nml [2014-10-25 22:02:46.403] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/KA.nml [2014-10-25 22:02:46.963] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/Kdr.nml [2014-10-25 22:02:47.591] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/Kh2.nml [2014-10-25 22:02:48.183] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/NaP.nml [2014-10-25 22:02:48.771] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/CaT.nml [2014-10-25 22:02:49.472] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/KC.nml [2014-10-25 22:02:50.480] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/cad.nml [2014-10-25 22:02:51.056] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/K2.nml [2014-10-25 22:02:51.691] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/CaP.nml [2014-10-25 22:02:52.287] WARN http-bio-8080-exec-20 org.geppetto.model.neuroml.utils.OptimizedLEMSReader java.io.FileNotFoundException: https://raw.githubusercontent.com/openworm/org.geppetto.samples/master/NeuroML/Purkinje/Kh1.nml [2014-10-25 22:02:52.473] INFO http-bio-8080-exec-20 org.geppetto.simulation.visitor.LoadSimulationVisitor Finished reading model, took 116069 ms

pgleeson commented 10 years ago

Root cause of that is that the ion channels are used in the cell NeuroML 2 file channelDensity elements (since the model has interesting channel distributions for visualising in OSB explorer) but the NeuroML 2 versions of the channels are missing (reason: I simply haven't had time to check this model's channels when converted from original ChannelML form to NeuroML2; the NeuroML 1 version of the model needs to be completely updated/rechecked also; awaiting a Purkinje cell modelling expert volunteer...).

That's why it may be better to concentrate on the simple ACnet2 cells and complex Hay et al Layer 5 cell as outlined here: https://github.com/openworm/org.geppetto/issues/288

These examples will be kept as up to date as possible & fully in NeuroML2. I'll update that list as more full NML2 examples become available.

tarelli commented 10 years ago

Since we are using this sample in Geppetto only for morphology visualization purposes I will remove the channels that are nowhere to be found in the geppetto sample repo until the model is fully in NeuroML and then we can put them back in.