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Initial nml version
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‎.gitignore‎

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/NeuroML2/.mod
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/NeuroML2/*.dat
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*_nrn.py
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/NeuroML2/x86_64
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*.mod
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/NeuroML2/*.hoc
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*_netpyne.py

‎NeuroML2/.test.l23.jnmlnetpyne.omt‎

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# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
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target: LEMS_L23_PC_cADpyr.xml
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engine: jNeuroML_NetPyNE
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mep: .test.l23.mep
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experiments:
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stepcurrent3_0:
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observables:
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spike times:
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file:
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path: L23_PC_cADpyr.v.dat
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columns: [0,1]
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scaling: [1000, 1000]
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spike detection:
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method: threshold
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threshold: 0
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tolerance: 0.00989843257597

‎NeuroML2/.test.l23.jnmlnrn.omt‎

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# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
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target: LEMS_L23_PC_cADpyr.xml
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engine: jNeuroML_NEURON
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mep: .test.l23.mep
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experiments:
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stepcurrent3_0:
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observables:
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spike times:
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file:
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path: L23_PC_cADpyr.v.dat
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columns: [0,1]
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scaling: [1000, 1000]
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spike detection:
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method: threshold
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threshold: 0
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tolerance: 0.0156742403108

‎NeuroML2/.test.l23.mep‎

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# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
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system: Testing L23
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experiments:
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stepcurrent3_0:
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expected:
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spike times: [748.975, 1103.475, 1548.975, 1986.175, 2419.575]
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‎NeuroML2/.test.validate.omt‎

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# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
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# Still in development, subject to change without notice!!
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# This test will validate MOST all of the NeuroML 2 files in the current directory
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target: "*.cell*.nml pas.channel.nml Na*.nml Ca_*.nml Ca.*.nml K*.nml SK*.nml I*.nml"
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engine: jNeuroML_validate

‎NeuroML2/CaDynamics_E2_NML2.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"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta3.xsd"
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id="CaDynamics_E2_NML2">
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<notes>NeuroML 2 implementation of the Ca Pool mechanism</notes>
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<!--<decayingPoolConcentrationModel id="CaDynamics_E2_NML2" restingConc="1e-10mol_per_cm3" decayConstant="80ms" ion="ca" shellThickness="2.787e-4cm"/>-->
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<concentrationModel id="CaDynamics_E2_NML2" type="concentrationModelHayEtAl" minCai="1e-4 mM" decay="80 ms" depth="0.1 um" gamma="0.05" ion="ca"/>
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<concentrationModel id="CaDynamics_E2_NML2__cSTUT_7_axonal" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.010353" decay="64.277990 ms" depth="0.1 um"/> <!-- For group axonal in cSTUT_7-->
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<concentrationModel id="CaDynamics_E2_NML2__cSTUT_7_somatic" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.000511" decay="731.707637 ms" depth="0.1 um"/> <!-- For group somatic in cSTUT_7-->
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<concentrationModel id="CaDynamics_E2_NML2__dNAC_1_axonal" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.010353" decay="64.277990 ms" depth="0.1 um"/> <!-- For group axonal in dNAC_1-->
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<concentrationModel id="CaDynamics_E2_NML2__dNAC_1_somatic" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.000511" decay="731.707637 ms" depth="0.1 um"/> <!-- For group somatic in dNAC_1-->
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<concentrationModel id="CaDynamics_E2_NML2__bNAC_1_axonal" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.001739" decay="468.069681 ms" depth="0.1 um"/> <!-- For group axonal in bNAC_1-->
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<concentrationModel id="CaDynamics_E2_NML2__bNAC_1_somatic" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.000500" decay="645.079741 ms" depth="0.1 um"/> <!-- For group somatic in bNAC_1-->
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<concentrationModel id="CaDynamics_E2_NML2__bSTUT_1_axonal" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.001739" decay="468.069681 ms" depth="0.1 um"/> <!-- For group axonal in bSTUT_1-->
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<concentrationModel id="CaDynamics_E2_NML2__bSTUT_1_somatic" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.000500" decay="645.079741 ms" depth="0.1 um"/> <!-- For group somatic in bSTUT_1-->
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<concentrationModel id="CaDynamics_E2_NML2__cADpyr_229_axonal" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.016713" decay="384.114655 ms" depth="0.1 um"/> <!-- For group axonal in cADpyr_229-->
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<concentrationModel id="CaDynamics_E2_NML2__cADpyr_229_somatic" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.000533" decay="342.544232 ms" depth="0.1 um"/> <!-- For group somatic in cADpyr_229-->
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<concentrationModel id="CaDynamics_E2_NML2__cADpyr_230_axonal" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.000502" decay="179.044149 ms" depth="0.1 um"/> <!-- For group axonal in cADpyr_230-->
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<concentrationModel id="CaDynamics_E2_NML2__cADpyr_230_somatic" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.002253" decay="739.416497 ms" depth="0.1 um"/> <!-- For group somatic in cADpyr_230-->
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<concentrationModel id="CaDynamics_E2_NML2__cADpyr_231_axonal" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.001734" decay="103.091390 ms" depth="0.1 um"/> <!-- For group axonal in cADpyr_231-->
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<concentrationModel id="CaDynamics_E2_NML2__cADpyr_231_somatic" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.000996" decay="873.498863 ms" depth="0.1 um"/> <!-- For group somatic in cADpyr_231-->
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<concentrationModel id="CaDynamics_E2_NML2__cNAC_149_axonal" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.010353" decay="64.277990 ms" depth="0.1 um"/> <!-- For group axonal in cNAC_149-->
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<concentrationModel id="CaDynamics_E2_NML2__cNAC_149_somatic" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.000511" decay="731.707637 ms" depth="0.1 um"/> <!-- For group somatic in cNAC_149-->
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<concentrationModel id="CaDynamics_E2_NML2__cIR_1_axonal" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.000503" decay="573.007045 ms" depth="0.1 um"/> <!-- For group axonal in cIR_1-->
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<concentrationModel id="CaDynamics_E2_NML2__cIR_1_somatic" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.000814" decay="967.678789 ms" depth="0.1 um"/> <!-- For group somatic in cIR_1-->
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<concentrationModel id="CaDynamics_E2_NML2__bIR_1_axonal" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.003923" decay="20.715642 ms" depth="0.1 um"/> <!-- For group axonal in bIR_1-->
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<concentrationModel id="CaDynamics_E2_NML2__bIR_1_somatic" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.000893" decay="605.033222 ms" depth="0.1 um"/> <!-- For group somatic in bIR_1-->
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<concentrationModel id="CaDynamics_E2_NML2__bAC_1_axonal" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.003923" decay="20.715642 ms" depth="0.1 um"/> <!-- For group axonal in bAC_1-->
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<concentrationModel id="CaDynamics_E2_NML2__bAC_1_somatic" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.000893" decay="605.033222 ms" depth="0.1 um"/> <!-- For group somatic in bAC_1-->
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<concentrationModel id="CaDynamics_E2_NML2__cACint_237_axonal" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.000503" decay="573.007045 ms" depth="0.1 um"/> <!-- For group axonal in cACint_237-->
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<concentrationModel id="CaDynamics_E2_NML2__cACint_237_somatic" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.000814" decay="967.678789 ms" depth="0.1 um"/> <!-- For group somatic in cACint_237-->
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<concentrationModel id="CaDynamics_E2_NML2__dSTUT_1_axonal" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.010353" decay="64.277990 ms" depth="0.1 um"/> <!-- For group axonal in dSTUT_1-->
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<concentrationModel id="CaDynamics_E2_NML2__dSTUT_1_somatic" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.000511" decay="731.707637 ms" depth="0.1 um"/> <!-- For group somatic in dSTUT_1-->
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<concentrationModel id="CaDynamics_E2_NML2__cADpyr_232_axonal" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.002910" decay="287.198731 ms" depth="0.1 um"/> <!-- For group axonal in cADpyr_232-->
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<concentrationModel id="CaDynamics_E2_NML2__cADpyr_232_somatic" ion="ca" type="concentrationModelHayEtAl" minCai="1e-4 mM" gamma="0.000609" decay="210.485284 ms" depth="0.1 um"/> <!-- For group somatic in cADpyr_232-->
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<!--
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This is a new, custom ComponentType to handle the calcium mechanism with parameters
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PARAMETER {
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gamma = 0.05 : percent of free calcium (not buffered)
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decay = 80 (ms) : rate of removal of calcium
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depth = 0.1 (um) : depth of shell
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minCai = 1e-4 (mM)
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}
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and derivative mechanism:
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DERIVATIVE states {
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cai' = -(10000)*(ica*gamma/(2*FARADAY*depth)) - (cai - minCai)/decay
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}
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See https://github.com/OpenSourceBrain/L5bPyrCellHayEtAl2011/blob/master/neuroConstruct/cellMechanisms/CaDynamics_E2_init_mod/CaDynamics_E2.mod
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-->
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<ComponentType name="concentrationModelHayEtAl" extends="concentrationModel" description="Model of buffering of concentration of specific to Hay Et Al 2011">
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<Parameter name="gamma" dimension="none"/>
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<Parameter name="minCai" dimension="concentration"/>
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<Parameter name="decay" dimension="time"/>
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<Parameter name="depth" dimension="length"/>
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<Constant name="Faraday" dimension="charge_per_mole" value="96485.3C_per_mol"/>
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<Constant name="AREA_SCALE" dimension="area" value="1m2"/>
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<Constant name="LENGTH_SCALE" dimension="length" value="1m"/>
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<Requirement name="iCa" dimension="current"/>
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<Text name="ion"/>
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<Dynamics>
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<StateVariable name="concentration" exposure="concentration" dimension="concentration"/>
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<StateVariable name="extConcentration" exposure="extConcentration" dimension="concentration"/>
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<DerivedVariable name="currDensCa" dimension="currentDensity" value="iCa / surfaceArea"/>
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<TimeDerivative variable="concentration" value="(currDensCa*gamma/(2*Faraday*depth)) - ((concentration - minCai) / decay)"/>
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<OnStart>
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<StateAssignment variable="concentration" value="initialConcentration"/>
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<StateAssignment variable="extConcentration" value="initialExtConcentration"/>
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</OnStart>
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</Dynamics>
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</ComponentType>
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</neuroml>

‎NeuroML2/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>

‎NeuroML2/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>

‎NeuroML2/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"/>
32+
</gate>
33+
34+
</ionChannel>
35+
36+
</neuroml>

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