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Merge pull request #428 from AurelienJaquier/neuroml-test
Can now write cell as neuroml file
2 parents 3440402 + 7bf509b commit 6fdf07c

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+2343
-6
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‎AUTHORS.txt‎

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@@ -6,3 +6,4 @@ Giuseppe Chindemi @ BBP
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Tanguy Damart @ BBP
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Elisabetta Iavarone @ BBP
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Anil Tuncel @ BBP
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Aurelien Jaquier @ BBP

‎Makefile‎

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@@ -67,8 +67,20 @@ clean:
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rm -rf examples/l5pc/L5PC.py
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rm -rf examples/l5pc/x86_64
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rm -rf examples/stochkv/x86_64
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rm -rf x86_64
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rm -rf .coverage
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rm -rf coverage.xml
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rm -rf channels
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rm -rf LEMS_l5pc.xml
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rm -rf LEMS_l5pc_nrn.py
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rm -rf l5pc.Pop_l5pc_0_0.v.dat
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rm -rf time.dat
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rm -rf l5pc.hoc
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rm -rf l5pc.net.nml
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rm -rf l5pc_0_0.cell.nml
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rm -rf l5pc_0_0.hoc
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rm -rf loadcell.hoc
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rm -rf *.mod
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find . -name "*.pyc" -exec rm -rf {} \;
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l5pc_start: install
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cd examples/l5pc && \

‎bluepyopt/neuroml/NeuroML2_mechanisms/Ca.channel.nml‎

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<?xml version="1.0" encoding="ISO-8859-1"?>
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta3.xsd" id="Ca">
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<notes>NeuroML file containing a single Channel description</notes>
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<ionChannel id="Ca" conductance="10pS" type="ionChannelHH" species="ca">
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<notes>NeuroML file containing a single Channel description
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Note: was called Ca_HVA in Hay et al 2011: http://www.opensourcebrain.org/projects/l5bpyrcellhayetal2011
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</notes>
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<annotation>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="Ca">
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<bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
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<rdf:Bag>
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<rdf:li>Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties,
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Etay Hay, Sean Hill, Felix Schürmann, Henry Markram and Idan Segev, PLoS Comp Biol 2011</rdf:li>
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<rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/21829333"/>
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</rdf:Bag>
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</bqmodel:isDescribedBy>
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<bqbiol:isVersionOf xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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<rdf:Bag>
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<rdf:li>Calcium channels</rdf:li>
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<rdf:li rdf:resource="http://senselab.med.yale.edu/neurondb/channelGene2.aspx#table1"/>
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</rdf:Bag>
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</bqbiol:isVersionOf>
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</rdf:Description>
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</rdf:RDF>
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</annotation>
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<gate id="m" type="gateHHrates" instances="2">
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<forwardRate type="HHExpLinearRate" rate="0.209per_ms" scale="3.8mV" midpoint="-27mV"/>
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<reverseRate type="HHExpRate" rate="0.94per_ms" scale="-17mV" midpoint="-75mV"/>
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</gate>
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<gate id="h" type="gateHHrates" instances="1">
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<forwardRate type="HHExpRate" rate="0.000457per_ms" scale="-50mV" midpoint="-13mV"/>
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<reverseRate type="HHSigmoidRate" rate="0.0065per_ms" scale="28mV" midpoint="-15mV"/>
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</gate>
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</ionChannel>
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</neuroml>

‎bluepyopt/neuroml/NeuroML2_mechanisms/Ca_HVA.channel.nml‎

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<?xml version="1.0" encoding="ISO-8859-1"?>
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="Ca_HVA">
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<notes>NeuroML file containing a single Channel description</notes>
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<ionChannel id="Ca_HVA" conductance="10pS" type="ionChannelHH" species="ca">
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<notes>High voltage activated Ca2+ current.
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Comment from original mod file:
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Reuveni, Friedman, Amitai, and Gutnick, J.Neurosci. 1993</notes>
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<annotation>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="Ca_HVA">
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<bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
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<rdf:Bag>
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<rdf:li>Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties,
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Etay Hay, Sean Hill, Felix Schürmann, Henry Markram and Idan Segev, PLoS Comp Biol 2011</rdf:li>
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<rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/21829333"/>
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</rdf:Bag>
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</bqmodel:isDescribedBy>
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<bqbiol:isVersionOf xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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<rdf:Bag>
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<rdf:li>Calcium channels</rdf:li>
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<rdf:li rdf:resource="http://senselab.med.yale.edu/neurondb/channelGene2.aspx#table1"/>
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</rdf:Bag>
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</bqbiol:isVersionOf>
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</rdf:Description>
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</rdf:RDF>
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</annotation>
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<gate id="m" type="gateHHrates" instances="2">
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<forwardRate type="HHExpLinearRate" rate="0.209per_ms" scale="3.8mV" midpoint="-27mV"/>
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<reverseRate type="HHExpRate" rate="0.94per_ms" scale="-17mV" midpoint="-75mV"/>
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</gate>
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<gate id="h" type="gateHHrates" instances="1">
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<forwardRate type="HHExpRate" rate="0.000457per_ms" scale="-50mV" midpoint="-13mV"/>
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<reverseRate type="HHSigmoidRate" rate="0.0065per_ms" scale="28mV" midpoint="-15mV"/>
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</gate>
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</ionChannel>
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</neuroml>

‎bluepyopt/neuroml/NeuroML2_mechanisms/Ca_LVAst.channel.nml‎

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<?xml version="1.0" encoding="ISO-8859-1"?>
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="Ca_LVAst">
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<notes>NeuroML file containing a single Channel description</notes>
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<ionChannel id="Ca_LVAst" conductance="10pS" type="ionChannelHH" species="ca">
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<notes>Low voltage activated Ca2+ current
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Comment from original mod file:
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Note: mtau is an approximation from the plots
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:Reference : : Avery and Johnston 1996, tau from Randall 1997
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:Comment: shifted by -10 mv to correct for junction potential
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:Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21</notes>
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<annotation>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="Ca_LVAst">
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<bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
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<rdf:Bag>
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<rdf:li>Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties,
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Etay Hay, Sean Hill, Felix Schürmann, Henry Markram and Idan Segev, PLoS Comp Biol 2011</rdf:li>
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<rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/21829333"/>
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</rdf:Bag>
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</bqmodel:isDescribedBy>
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<bqbiol:isVersionOf xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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<rdf:Bag>
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<rdf:li>Ca channels</rdf:li>
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<rdf:li rdf:resource="http://senselab.med.yale.edu/neurondb/channelGene2.aspx#table1"/>
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</rdf:Bag>
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</bqbiol:isVersionOf>
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</rdf:Description>
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</rdf:RDF>
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</annotation>
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<gate id="m" type="gateHHtauInf" instances="2">
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<q10Settings type="q10Fixed" fixedQ10="2.95288264"/>
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<timeCourse type="Ca_LVAst_m_tau_tau"/>
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<steadyState type="HHSigmoidVariable" rate="1" scale="6mV" midpoint="-40mV"/>
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</gate>
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<gate id="h" type="gateHHtauInf" instances="1">
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<q10Settings type="q10Fixed" fixedQ10="2.95288264"/>
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<timeCourse type="Ca_LVAst_h_tau_tau"/>
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<steadyState type="HHSigmoidVariable" rate="1" scale="-6.4mV" midpoint="-90mV"/>
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</gate>
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</ionChannel>
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<ComponentType name="Ca_LVAst_m_tau_tau" extends="baseVoltageDepTime">
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<Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
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<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
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<Dynamics>
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<DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
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<DerivedVariable name="t" exposure="t" dimension="time" value="(5 + 20 / (1 + (exp ((V+35)/5) ))) * TIME_SCALE"/>
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</Dynamics>
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</ComponentType>
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<ComponentType name="Ca_LVAst_h_tau_tau" extends="baseVoltageDepTime">
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<Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
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<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
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<Dynamics>
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<DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
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<DerivedVariable name="t" exposure="t" dimension="time" value="(20 + 50 / (1 + (exp ((V+50)/7) ))) * TIME_SCALE"/>
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</Dynamics>
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</ComponentType>
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</neuroml>

‎bluepyopt/neuroml/NeuroML2_mechanisms/Ih.channel.nml‎

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<?xml version="1.0" encoding="ISO-8859-1"?>
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="Ih">
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<notes>NeuroML file containing a single Channel description</notes>
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<ionChannel id="Ih" conductance="10pS" type="ionChannelHH" species="hcn">
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<notes>Non-specific cation current
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Comment from original mod file:
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Reference : : Kole,Hallermann,and Stuart, J. Neurosci. 2006</notes>
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<annotation>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="Ih">
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<bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
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<rdf:Bag>
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<rdf:li>Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties,
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Etay Hay, Sean Hill, Felix Schürmann, Henry Markram and Idan Segev, PLoS Comp Biol 2011</rdf:li>
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<rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/21829333"/>
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</rdf:Bag>
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</bqmodel:isDescribedBy>
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</rdf:Description>
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</rdf:RDF>
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</annotation>
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<gate id="m" type="gateHHrates" instances="1">
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<forwardRate type="HHExpLinearRate" rate="0.076517per_ms" scale="-11.9mV" midpoint="-154.9mV"/>
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<reverseRate type="HHExpRate" rate="0.193per_ms" scale="33.1mV" midpoint="0mV"/>
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</gate>
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</ionChannel>
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</neuroml>

‎bluepyopt/neuroml/NeuroML2_mechanisms/Im.channel.nml‎

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<?xml version="1.0" encoding="ISO-8859-1"?>
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="Im">
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<notes>NeuroML file containing a single Channel description</notes>
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<ionChannel id="Im" conductance="10pS" type="ionChannelHH" species="k">
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<notes>Muscarinic K+ current
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Comment from original mod file:
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:Reference : : Adams et al. 1982 - M-currents and other potassium currents in bullfrog sympathetic neurones
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:Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21</notes>
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<annotation>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="Im">
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<bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
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<rdf:Bag>
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<rdf:li>Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties,
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Etay Hay, Sean Hill, Felix Schürmann, Henry Markram and Idan Segev, PLoS Comp Biol 2011</rdf:li>
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<rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/21829333"/>
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</rdf:Bag>
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</bqmodel:isDescribedBy>
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<bqbiol:isVersionOf xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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<rdf:Bag>
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<rdf:li>K channels</rdf:li>
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<rdf:li rdf:resource="http://senselab.med.yale.edu/neurondb/channelGene2.aspx#table3"/>
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</rdf:Bag>
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</bqbiol:isVersionOf>
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</rdf:Description>
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</rdf:RDF>
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</annotation>
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<gate id="m" type="gateHHrates" instances="1">
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<q10Settings type="q10Fixed" fixedQ10="2.95288264"/>
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<forwardRate type="HHExpRate" rate="0.0033per_ms" scale="10mV" midpoint="-35mV"/>
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<reverseRate type="HHExpRate" rate="0.0033per_ms" scale="-10mV" midpoint="-35mV"/>
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</gate>
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</ionChannel>
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</neuroml>

‎bluepyopt/neuroml/NeuroML2_mechanisms/K_Pst.channel.nml‎

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<?xml version="1.0" encoding="ISO-8859-1"?>
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="K_Pst">
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<notes>NeuroML file containing a single Channel description</notes>
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<ionChannel id="K_Pst" conductance="10pS" type="ionChannelHH" species="k">
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<notes>Slow inactivating K+ current
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Comment from original mod file:
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:Comment : The persistent component of the K current
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:Reference : : Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000
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:Comment : shifted -10 mv to correct for junction potential
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:Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21</notes>
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<annotation>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="K_Pst">
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<bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
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<rdf:Bag>
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<rdf:li>Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties,
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Etay Hay, Sean Hill, Felix Schürmann, Henry Markram and Idan Segev, PLoS Comp Biol 2011</rdf:li>
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<rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/21829333"/>
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</rdf:Bag>
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</bqmodel:isDescribedBy>
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<bqbiol:isVersionOf xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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<rdf:Bag>
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<rdf:li>K channels</rdf:li>
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<rdf:li rdf:resource="http://senselab.med.yale.edu/neurondb/channelGene2.aspx#table3"/>
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</rdf:Bag>
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</bqbiol:isVersionOf>
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</rdf:Description>
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</rdf:RDF>
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</annotation>
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<gate id="m" type="gateHHtauInf" instances="2">
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<q10Settings type="q10Fixed" fixedQ10="2.95288264"/>
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<timeCourse type="K_Pst_m_tau_tau"/>
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<steadyState type="HHSigmoidVariable" rate="1" scale="12mV" midpoint="-11mV"/>
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</gate>
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<gate id="h" type="gateHHtauInf" instances="1">
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<q10Settings type="q10Fixed" fixedQ10="2.95288264"/>
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<timeCourse type="K_Pst_h_tau_tau"/>
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<steadyState type="HHSigmoidVariable" rate="1" scale="-11mV" midpoint="-64mV"/>
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</gate>
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</ionChannel>
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<ComponentType name="K_Pst_m_tau_tau" extends="baseVoltageDepTime">
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<Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
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<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
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<Dynamics>
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<DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
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<ConditionalDerivedVariable name="t" exposure="t" dimension="time">
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<Case condition="V .lt. ( -60 )" value="( (1.25 + 175.03 * (exp ((V+10) * 0.026))) ) * TIME_SCALE"/>
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<Case value="( (1.25 + 13 * (exp ((V+10) * -0.026)))) * TIME_SCALE"/>
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</ConditionalDerivedVariable>
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</Dynamics>
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</ComponentType>
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<ComponentType name="K_Pst_h_tau_tau" extends="baseVoltageDepTime">
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<Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
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<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
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<Dynamics>
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<DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
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<DerivedVariable name="t" exposure="t" dimension="time" value="(360 + (1010 + 24*(V+65)) * (exp (-1 *((V+85)/48)*((V+85)/48)))) * TIME_SCALE"/>
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</Dynamics>
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</ComponentType>
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</neuroml>

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