A project to illustrate how models and data from the Blue Brain Project can be converted to NeuroML and PyNN
Home Page: http://opensourcebrain.org/projects/blue-brain-project-showcase
License: Other
Hi @pgleeson, is there an issue with the opensourcebrain website ? The link from this page to OSB doesn't work anymore, it give a java null pointer execption:
The majority of the cell models in the BBP circuit are fully deterministic, but there are some (stuttering cells) which include stochastic ion channels, which introduces random fluctuations into the voltage traces. The NEURON mechanism for this channel (StochKv) is here.
A deterministic version of this ion channel is used in the NeuroML2 models. A comparison of the stochastic and deterministic mod files can be found here.
A NeuroML2/LEMS version of the stochastic StochKv channel model needs to be created. Initial test will be created here.
When opening the Open Source Brain 3D explorer link in the README, and then click on 'Channels' in the explorer I get the error below. Similar issue for the 'Cell Info' button.
Houston, we have a problem
Error populating the model tree for cADpyr232_L5_TTPC1_0fb1ca4724_0_0.electrical
Details
org.geppetto.core.common.GeppettoExecutionException: org.geppetto.core.common.GeppettoExecutionException: org.geppetto.core.model.ModelInterpreterException: org.geppetto.core.model.ModelInterpreterException: org.geppetto.core.model.ModelInterpreterException: org.geppetto.core.model.ModelInterpreterException: Cannot find the method setCondDensityin the NeuroML object Channel Density Nernst - axonal_gCa_HVAbar_Ca_HVA[[Ion Channel[[org.geppetto.core.model.runtime.TextMetadataNode@55a4a7e0, Anotation[[Description[[isDescribedBy[[org.geppetto.core.model.runtime.TextMetadataNode@2d098f0d, org.geppetto.core.model.runtime.TextMetadataNode@4e8eb594]], isVersionOf[[org.geppetto.core.model.runtime.TextMetadataNode@7b332fd6, org.geppetto.core.model.runtime.TextMetadataNode@5d89c9ca]]]]]], org.geppetto.core.model.runtime.TextMetadataNode@11f1cc0, Gate - m[[org.geppetto.core.model.runtime.TextMetadataNode@219881d3, Forward Rate[[HHExpLinearRate[[Dynamics[[org.geppetto.core.model.runtime.FunctionNode@237354e0]]]], org.geppetto.core.model.runtime.ParameterSpecificationNode@5ff92617, org.geppetto.core.model.runtime.ParameterSpecificationNode@5e33e13a, org.geppetto.core.model.runtime.ParameterSpecificationNode@2007d727]], Backward Rate[[HHExpRate[[Dynamics[[org.geppetto.core.model.runtime.FunctionNode@68c9504e]]]], org.geppetto.core.model.runtime.ParameterSpecificationNode@62be51de, org.geppetto.core.model.runtime.ParameterSpecificationNode@3cf0f877, org.geppetto.core.model.runtime.ParameterSpecificationNode@70486be2]], org.geppetto.core.model.runtime.TextMetadataNode@78b766a0, Type[[Dynamics[[org.geppetto.core.model.runtime.FunctionNode@50b2d04a, org.geppetto.core.model.runtime.FunctionNode@b88d3aa, org.geppetto.core.model.runtime.FunctionNode@440043d0]]]]]], Gate - h[[org.geppetto.core.model.runtime.TextMetadataNode@6d642f90, Forward Rate[[HHExpRate[[Dynamics[[org.geppetto.core.model.runtime.FunctionNode@4c6ecf0b]]]], org.geppetto.core.model.runtime.ParameterSpecificationNode@22a2fc05, org.geppetto.core.model.runtime.ParameterSpecificationNode@7a4fbe06, org.geppetto.core.model.runtime.ParameterSpecificationNode@944baa6]], Backward Rate[[HHSigmoidRate[[Dynamics[[org.geppetto.core.model.runtime.FunctionNode@7edb0260]]]], org.geppetto.core.model.runtime.ParameterSpecificationNode@7f39ed0a, org.geppetto.core.model.runtime.ParameterSpecificationNode@33f96cc7, org.geppetto.core.model.runtime.ParameterSpecificationNode@3c549779]], org.geppetto.core.model.runtime.TextMetadataNode@5c792db0, Type[[Dynamics[[org.geppetto.core.model.runtime.FunctionNode@17a6ad3e, org.geppetto.core.model.runtime.FunctionNode@3fb7cd93, org.geppetto.core.model.runtime.FunctionNode@3c198e93]]]]]], org.geppetto.core.model.runtime.ParameterSpecificationNode@31df73b8, org.geppetto.core.model.runtime.TextMetadataNode@45264e9c, IonChannelDynamics[[Dynamics[[org.geppetto.core.model.runtime.FunctionNode@55f3073b, org.geppetto.core.model.runtime.FunctionNode@465fde92]]]]]], org.geppetto.core.model.runtime.ParameterSpecificationNode@400d6756]]
Just to ensure we have an updated version of the citation on zenodo.
When I do:
python $OPENWORM_HOME/BlueBrainProjectShowcase/Channelpedia/NML2ChannelAnalyse.py -temperature 34 -minV -55 -maxV 80 -duration 600 -clampBaseVoltage -55 -clampDuration 580 -stepTargetVoltage 10 -erev -55 k_fast.channel.nml k_fast
with this k_fast.channel.nml, I get this error:
Traceback (most recent call last):
File "/Users/rgerkin/Dropbox/dev/BlueBrainProjectShowcase/Channelpedia/NML2ChannelAnalyse.py", line 226, in <module>
main()
File "/Users/rgerkin/Dropbox/dev/BlueBrainProjectShowcase/Channelpedia/NML2ChannelAnalyse.py", line 191, in main
for c in doc.ion_channel_hhs:
AttributeError: 'NeuroMLDocument' object has no attribute 'ion_channel_hhs'
Inspection of the doc object shows only an 'ion_channels' attribute. Are 'ion_channels_hhs' and 'ion_channel' deprecated in favor of 'ion_channels' or am I missing something?
The example LEMS file for converted Channelpedia channels works with jnml LEMS, but not with NEURON.
$ jnml LEMS_Test_Cav2.1.xml --> OK
$ jnml LEMS_Test_Cav2.1.xml -neuron -run --> ERRORS
The problem seems to be related to NEURON's WATCH statement only allowing a single condition check, whereas the vClampedCell component defined in the LEMS file specifies multiple conditions.
The full output is pasted below:
$ jnml LEMS_Test_Cav2.1.xml -neuron -run
jNeuroML v0.7.5
(INFO) Reading from: /Users/gazelle/Downloads/nrntest/LEMS_Test_Cav2.1.xml
(WARNING) Unused attribute in Component(id=null type=rdf_RDF): XMLAttribute(xmlns:bqmodel, http://biomodels.net/model-qualifiers/) at: org.lemsml.jlems.core.type.Component.resolve(Component.java:538)
(WARNING) Unused attribute in Component(id=null type=rdf_RDF): XMLAttribute(xmlns:bqbiol, http://biomodels.net/biology-qualifiers/) at:
(INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: networkWithTemperature: temperature=305.15 (SI temperature))
(INFO) -- Writing to mod: /Users/gazelle/Downloads/nrntest/holderCell_min60.mod
(INFO) -- Writing to mod: /Users/gazelle/Downloads/nrntest/holderCell_min50.mod
(INFO) -- Writing to mod: /Users/gazelle/Downloads/nrntest/holderCell_min40.mod
(INFO) -- Writing to mod: /Users/gazelle/Downloads/nrntest/holderCell_min30.mod
(INFO) -- Writing to mod: /Users/gazelle/Downloads/nrntest/holderCell_min20.mod
(INFO) -- Writing to mod: /Users/gazelle/Downloads/nrntest/holderCell_min10.mod
(INFO) -- Writing to mod: /Users/gazelle/Downloads/nrntest/holderCell_0.mod
(INFO) -- Writing to mod: /Users/gazelle/Downloads/nrntest/holderCell_10.mod
(INFO) -- Writing to mod: /Users/gazelle/Downloads/nrntest/holderCell_20.mod
(INFO) -- Writing to mod: /Users/gazelle/Downloads/nrntest/holderCell_30.mod
(INFO) -- Writing to mod: /Users/gazelle/Downloads/nrntest/holderCell_40.mod
(INFO) -- Writing to mod: /Users/gazelle/Downloads/nrntest/holderCell_50.mod
(INFO) -- Writing to mod: /Users/gazelle/Downloads/nrntest/holderCell_60.mod
(INFO) -- Writing to mod: /Users/gazelle/Downloads/nrntest/holderCell_70.mod
(INFO) -- Writing to mod: /Users/gazelle/Downloads/nrntest/holderCell_80.mod
(INFO) -- Writing to mod: /Users/gazelle/Downloads/nrntest/holderCell_90.mod
(INFO) -- Writing to mod: /Users/gazelle/Downloads/nrntest/rampCell0.mod
(INFO) Trying to compile mods in: /Users/gazelle/Downloads/nrntest
(INFO) Going to compile the mod files in: /Users/gazelle/Downloads/nrntest, forcing recompile: false
(INFO) Parent dir: /Users/gazelle/Downloads/nrntest
(INFO) Assuming *nix environment...
(INFO) Name of file to be created: /Users/gazelle/Downloads/nrntest/i686/libnrnmech.la
(INFO) Backup file to check for success: /Users/gazelle/Downloads/nrntest/umac/libnrnmech.la
(INFO) commandToExecute: /Applications/NEURON-7.3/nrn/x86_64/bin/nrnivmodl
(INFO) Going to check if mods in /Users/gazelle/Downloads/nrntest are newer than null
(INFO) Trying to delete any previous: /Users/gazelle/Downloads/nrntest/i686/libnrnmech.la
(INFO) directoryToExecuteIn: /Users/gazelle/Downloads/nrntest
(INFO) NMODL Compile >> > Creating x86_64 directory for .o files.
(INFO) NMODL Compile >> >
(INFO) Have successfully executed command: /Applications/NEURON-7.3/nrn/x86_64/bin/nrnivmodl
(INFO) NMODL Compile >> > /Users/gazelle/Downloads/nrntest
(INFO) NMODL Compile >> > holderCell_0.mod holderCell_10.mod holderCell_20.mod holderCell_30.mod holderCell_40.mod holderCell_50.mod holderCell_60.mod holderCell_70.mod holderCell_80.mod holderCell_90.mod holderCell_min10.mod holderCell_min20.mod holderCell_min30.mod holderCell_min40.mod holderCell_min50.mod holderCell_min60.mod rampCell0.mod
(INFO) NMODL Compile >> > holderCell_0.mod holderCell_10.mod holderCell_20.mod holderCell_30.mod holderCell_40.mod holderCell_50.mod holderCell_60.mod holderCell_70.mod holderCell_80.mod holderCell_90.mod holderCell_min10.mod holderCell_min20.mod holderCell_min30.mod holderCell_min40.mod holderCell_min50.mod holderCell_min60.mod rampCell0.mod
(INFO) NMODL Compile >> > "/Applications/NEURON-7.3/nrn/x86_64/bin/nocmodl" holderCell_0
(INFO) NMODL Error >> > Translating holderCell_0.mod into holderCell_0.c
(INFO) NMODL Error >> > make: *** [holderCell_0.lo] Abort trap: 6
(INFO) Have successfully executed command: /Applications/NEURON-7.3/nrn/x86_64/bin/nrngui -python /Users/gazelle/Downloads/nrntest/LEMS_Test_Cav2.1_nrn.py
(INFO) NRN Error >>> NEURON -- VERSION 7.4 (1373:f15dcfc7847b) f15dcfc7847b
(INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015
(INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits
(INFO) NRN Error >>>
(INFO) NRN Error >>> /Applications/NEURON-7.3/nrn/x86_64/bin/nrniv: holderCell_min60 is not a template
(INFO) NRN Error >>> near line 1
(INFO) NRN Error >>> holderCellPop_min60[0] { m_holderCell_min60_holderCellPop_min60[0] = new holderCell_min60(0.5) }
(INFO) NRN Error >>> ^
(INFO) NRN Output >>> Population holderCellPop_min60 contains 1 instance(s) of component: holderCell_min60 of type: vClampedCell
(INFO) NRN Error >>> Traceback (most recent call last):
(INFO) NRN Output >>> first instance of n_holderCellPop_min60
(INFO) NRN Error >>> File "/Users/gazelle/Downloads/nrntest/LEMS_Test_Cav2.1_nrn.py", line 65, in <module>
(INFO) NRN Error >>> h.m_holderCell_min60_holderCellPop_min60[i].delay = 1.0
(INFO) NRN Error >>> AttributeError: 'NoneType' object has no attribute 'delay'
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