Add example with gap junctions

OpenSourceBrain · Mar 12, 2018 · 8c7fa9e · 8c7fa9e
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diff --git a/NeuroML2/pythonScripts/netbuild/TestGap.net.nml b/NeuroML2/pythonScripts/netbuild/TestGap.net.nml
diff --git a/NeuroML2/pythonScripts/netbuild/TestGap.py b/NeuroML2/pythonScripts/netbuild/TestGap.py
@@ -0,0 +1,57 @@
+####################################################################################
+### Author : Rokas Stanislovas & Padraig gleeson
+###
+### GSoC 2016 project: Cortical Networks
+####################################################################################
+
+###########  Main settings  ########################################################
+
+ref =                   "TestGap"
+
+simConfig=              "TempSimConfig"
+
+simDuration =           200 # ms          original duration 1000 ms                      ##
+simDt =                 0.025 # ms
+seed =    134344                                  ##
+
+simulator =             None
+
+defaultSynapticDelay =  0.05 
+
+scaleCortex =             0.02                           ##
+scaleThalamus =           0                                  ##
+
+gabaScaling =             1                               ##
+
+l4ssAmpaScaling =         1                            ##
+
+inNrtTcrNmdaScaling =    0.2
+
+pyrSsNmdaScaling =       2.5
+
+deepBiasCurrent =        -1
+
+from RunColumn import *
+
+RunColumnSimulation(net_id=ref,
+                    nml2_source_dir="../../../neuroConstruct/generatedNeuroML2/",
+                    sim_config=simConfig,
+                    scale_cortex=scaleCortex,
+                    scale_thalamus=scaleThalamus,
+                    default_synaptic_delay=defaultSynapticDelay,
+                    gaba_scaling=gabaScaling,
+                    l4ss_ampa_scaling=l4ssAmpaScaling,
+                    in_nrt_tcr_nmda_scaling=inNrtTcrNmdaScaling,
+                    pyr_ss_nmda_scaling=pyrSsNmdaScaling,
+                    deep_bias_current=deepBiasCurrent,
+                    which_cell_types_to_include=['L23PyrRS'],
+                    include_gap_junctions=True,
+                    backgroundL23Rate=100,
+                    dir_nml2="../../",
+                    duration=simDuration,
+                    dt=simDt,
+                    max_memory='4000M',
+                    seed=seed,
+                    simulator=simulator)
+
+
diff --git a/NeuroML2/pythonScripts/netbuild/TestGap/L23PyrRS.cell.nml b/NeuroML2/pythonScripts/netbuild/TestGap/L23PyrRS.cell.nml
diff --git a/NeuroML2/pythonScripts/netbuild/TestGap/SynForEctStim.synapse.nml b/NeuroML2/pythonScripts/netbuild/TestGap/SynForEctStim.synapse.nml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<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="SynForEctStim">
+
+    <notes>ChannelML file describing a single synaptic mechanism</notes>
+
+    <expTwoSynapse id="SynForEctStim" tauRise="0.1ms" tauDecay="0.2ms" gbase="1.0E-5mS" erev="0mV">
+
+        <notes>Simple example of a synaptic mechanism, which consists of a postsynaptic conductance which changes as 
+        double exponential function of time. Mappings exist for NEURON and GENESIS.</notes>
+
+</expTwoSynapse>
+
+</neuroml>
diff --git a/NeuroML2/pythonScripts/netbuild/TestGap/Syn_AMPA_SupPyr_SupPyr.synapse.nml b/NeuroML2/pythonScripts/netbuild/TestGap/Syn_AMPA_SupPyr_SupPyr.synapse.nml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<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="Syn_AMPA_SupPyr_SupPyr">
+
+    <notes>ChannelML file describing a single synaptic mechanism</notes>
+
+    <alphaSynapse id="Syn_AMPA_SupPyr_SupPyr" tau="2.0ms" gbase="1.83939720586e-07mS" erev="0.0mV">
+
+        <notes>Synapse with syn scaling constant c = 0.25 nS (translating to max cond of 1.8394e-07 mS), time course: 2 ms and reversal potential: 0 mV.
+        Automatically generated by command:  genSyn.py Syn_AMPA_SupPyr_SupPyr 2 0.25 0 </notes>
+</alphaSynapse>
+
+</neuroml>
diff --git a/NeuroML2/pythonScripts/netbuild/TestGap/Syn_Elect_SupPyr_SupPyr.nml b/NeuroML2/pythonScripts/netbuild/TestGap/Syn_Elect_SupPyr_SupPyr.nml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<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="Syn_Elect_SupPyr_SupPyr">
+
+    <notes>ChannelML file describing a single synaptic mechanism</notes>
+
+    <gapJunction id="Syn_Elect_SupPyr_SupPyr" conductance="3e-06mS"/>
+
+</neuroml>
diff --git a/NeuroML2/pythonScripts/netbuild/TestGap/Syn_NMDA_SupPyr_SupPyr.synapse.nml b/NeuroML2/pythonScripts/netbuild/TestGap/Syn_NMDA_SupPyr_SupPyr.synapse.nml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<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="Syn_NMDA_SupPyr_SupPyr">
+
+    <notes>ChannelML file describing a single synaptic mechanism</notes>
+
+    <blockingPlasticSynapse id="Syn_NMDA_SupPyr_SupPyr" gbase="2.5e-08mS" tauRise="1ms" tauDecay="130.0ms" erev="0.0mV">
+
+        <notes>Synapse with syn scaling constant c = 0.025 nS (translating to max cond of 2.5e-08 mS), time course: 130 ms and reversal potential: 0 mV.
+        Automatically generated by command:  genSyn.py Syn_NMDA_SupPyr_SupPyr 130 0.025 0 </notes>
+
+        <blockMechanism type="voltageConcDepBlockMechanism" species="mg" blockConcentration="1.5e-6mol_per_cm3" scalingConc="0.0000035700005712000914mol_per_cm3" scalingVolt="16.129032258064516mV"/>
+
+    </blockingPlasticSynapse>
+
+</neuroml>
diff --git a/NeuroML2/pythonScripts/netbuild/TestGap/ar__m00_25.channel.nml b/NeuroML2/pythonScripts/netbuild/TestGap/ar__m00_25.channel.nml
@@ -0,0 +1,67 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+
+<!--
+       This file has been generated by neuroConstruct because a cell mechanism (ChannelMLCell Mechanism [InstanceName: ar, channelMLFile: AR_Chan.xml])
+      has a different set of parameters (erev = -35.0, m0 = 0.25) on a group of sections.
+
+      Conversion of the original NML2 file to use the updated parameters is implemented in handleExtraParamsForNml2()
+      in https://github.com/NeuralEnsemble/neuroConstruct/blob/master/src/ucl/physiol/neuroconstruct/neuroml/NeuroMLFileManager.java
+      See that file to check/improve this conversion
+-->
+
+<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="ar__m00_25">
+
+    <notes>ChannelML file based on Traub et al. 2003</notes>
+
+    <ionChannel id="ar__m00_25" conductance="10pS" type="ionChannelHH" species="ar">
+
+        <notes>Anomalous Rectifier conductance, also known as h-conductance (hyperpolarizing). Based on NEURON port of FRB L2/3 model from Traub et al 2003. Same channel used in Traub et al 2005</notes>
+
+        <annotation>
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+                <rdf:Description rdf:about="ar">
+
+                    <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+                        <rdf:Bag>
+                            <rdf:li>Roger D. Traub, Eberhard H. Buhl, Tengis Gloveli, and Miles A. Whittington
+Fast Rhythmic Bursting Can Be Induced in Layer 2/3 Cortical Neurons by Enhancing Persistent Na+ Conductance or by Blocking BK Channels
+J Neurophysiol 89: 909-921, 2003</rdf:li>
+                            <rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=12574468"/>
+                        </rdf:Bag>
+                    </bqmodel:isDescribedBy>
+
+
+                    <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+                        <rdf:Bag>
+                            <rdf:li>Roger D. Traub, Diego Contreras, Mark O. Cunningham, Hilary Murray, Fiona E. N. LeBeau, Anita Roopun, Andrea Bibbig, W. Bryan Wilent, Michael J. Higley, and Miles A. Whittington
+Single-column thalamocortical network model exhibiting gamma oscillations, sleep spindles, and epileptogenic bursts.
+J. Neurophysiol. 93, 2194-2232, 2005</rdf:li>
+                            <rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/15525801?dopt=Abstract"/>
+                        </rdf:Bag>
+                    </bqmodel:isDescribedBy>
+
+                </rdf:Description>
+            </rdf:RDF>
+        </annotation>
+
+        <gate id="m" type="gateHHtauInf" instances="1">
+            <timeCourse type="ar__m00_25_m_tau_tau"/>
+            <steadyState type="HHSigmoidVariable" rate="1" scale="-5.5mV" midpoint="-75mV"/>
+        </gate>
+
+    </ionChannel>
+
+    <ComponentType name="ar__m00_25_m_tau_tau" extends="baseVoltageDepTime">
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+        <!--Note: this parameter (m0) should ideally be defined only once within the ionChannel! Work in progress...-->
+        <Constant name="m0" dimension="none" value="0.25"/>
+
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+            <DerivedVariable name="t" exposure="t" dimension="time" value="(1 /((exp (-14.6 - (0.086 * V) )) + (exp (-1.87 + (0.07 * V))))) * TIME_SCALE"/>
+        </Dynamics>
+
+    </ComponentType>
+
+</neuroml>
diff --git a/NeuroML2/pythonScripts/netbuild/TestGap/cad__beta0_01__phi26000.nml b/NeuroML2/pythonScripts/netbuild/TestGap/cad__beta0_01__phi26000.nml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+
+<!--
+       This file has been generated by neuroConstruct because a cell mechanism (ChannelMLCell Mechanism [InstanceName: cad, channelMLFile: CaD_Conc.xml])
+      has a different set of parameters (beta = 0.01, phi = 26000.0) on a group of sections.
+
+      Conversion of the original NML2 file to use the updated parameters is implemented in handleExtraParamsForNml2()
+      in https://github.com/NeuralEnsemble/neuroConstruct/blob/master/src/ucl/physiol/neuroconstruct/neuroml/NeuroMLFileManager.java
+      See that file to check/improve this conversion
+-->
+
+<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="cad__beta0_01__phi26000">
+
+    <notes>ChannelML file based on Traub et al. 2003</notes>
+
+    <fixedFactorConcentrationModelTraub id="cad__beta0_01__phi26000" restingConc="0mol_per_cm3" beta="0.01 per_ms" ion="ca" phi="26000.0 mol_per_cm_per_uA_per_ms"/>
+
+</neuroml>
diff --git a/NeuroML2/pythonScripts/netbuild/TestGap/cad__beta0_05__phi52000.nml b/NeuroML2/pythonScripts/netbuild/TestGap/cad__beta0_05__phi52000.nml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+
+<!--
+       This file has been generated by neuroConstruct because a cell mechanism (ChannelMLCell Mechanism [InstanceName: cad, channelMLFile: CaD_Conc.xml])
+      has a different set of parameters (beta = 0.05, phi = 52000.0) on a group of sections.
+
+      Conversion of the original NML2 file to use the updated parameters is implemented in handleExtraParamsForNml2()
+      in https://github.com/NeuralEnsemble/neuroConstruct/blob/master/src/ucl/physiol/neuroconstruct/neuroml/NeuroMLFileManager.java
+      See that file to check/improve this conversion
+-->
+
+<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="cad__beta0_05__phi52000">
+
+    <notes>ChannelML file based on Traub et al. 2003</notes>
+
+    <fixedFactorConcentrationModelTraub id="cad__beta0_05__phi52000" restingConc="0mol_per_cm3" beta="0.05 per_ms" ion="ca" phi="52000.0 mol_per_cm_per_uA_per_ms"/>
+
+</neuroml>
diff --git a/NeuroML2/pythonScripts/netbuild/TestGap/cal.channel.nml b/NeuroML2/pythonScripts/netbuild/TestGap/cal.channel.nml
@@ -0,0 +1,52 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<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="cal">
+
+    <notes>ChannelML file based on Traub et al. 2003</notes>
+
+    <ionChannel id="cal" conductance="10pS" type="ionChannelHH" species="ca">
+
+        <notes>High threshold, long lasting Calcium L-type current. Based on NEURON port of FRB L2/3 model from Traub et al 2003. Same channel used in Traub et al 2005</notes>
+
+        <annotation>
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+                <rdf:Description rdf:about="cal">
+
+                    <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+                        <rdf:Bag>
+                            <rdf:li>Roger D. Traub, Eberhard H. Buhl, Tengis Gloveli, and Miles A. Whittington                
+Fast Rhythmic Bursting Can Be Induced in Layer 2/3 Cortical Neurons by Enhancing Persistent Na+ Conductance or by Blocking BK Channels
+J Neurophysiol 89: 909-921, 2003</rdf:li>
+                            <rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=12574468"/>
+                        </rdf:Bag>
+                    </bqmodel:isDescribedBy>
+
+
+                    <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+                        <rdf:Bag>
+                            <rdf:li>Roger D. Traub, Diego Contreras, Mark O. Cunningham, Hilary Murray, Fiona E. N. LeBeau, Anita Roopun, Andrea Bibbig, W. Bryan Wilent, Michael J. Higley, and Miles A. Whittington
+Single-column thalamocortical network model exhibiting gamma oscillations, sleep spindles, and epileptogenic bursts.
+J. Neurophysiol. 93, 2194-2232, 2005</rdf:li>
+                            <rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/15525801?dopt=Abstract"/>
+                        </rdf:Bag>
+                    </bqmodel:isDescribedBy>
+
+
+                    <bqbiol:isVersionOf xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                        <rdf:Bag>
+                            <rdf:li>Calcium channels</rdf:li>
+                            <rdf:li rdf:resource="http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table1"/>
+                        </rdf:Bag>
+                    </bqbiol:isVersionOf>
+
+                </rdf:Description>
+            </rdf:RDF>
+        </annotation>
+
+        <gate id="m" type="gateHHrates" instances="2">
+            <forwardRate type="HHSigmoidRate" rate="1.6per_ms" scale="13.888889mV" midpoint="5mV"/>
+            <reverseRate type="HHExpLinearRate" rate="0.1per_ms" scale="-5mV" midpoint="-8.9mV"/>
+        </gate>
+
+    </ionChannel>
+
+</neuroml>
diff --git a/NeuroML2/pythonScripts/netbuild/TestGap/cat.channel.nml b/NeuroML2/pythonScripts/netbuild/TestGap/cat.channel.nml
@@ -0,0 +1,82 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<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="cat">
+
+    <notes>ChannelML file based on Traub et al. 2003</notes>
+
+    <ionChannel id="cat" conductance="10pS" type="ionChannelHH" species="cat">
+
+        <notes>Low threshold, inactivating Calcium T-type ("transient") conductance. Based on NEURON port of FRB L2/3 model from Traub et al 2003. Same channel used in Traub et al 2005</notes>
+
+        <annotation>
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+                <rdf:Description rdf:about="cat">
+
+                    <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+                        <rdf:Bag>
+                            <rdf:li>Roger D. Traub, Eberhard H. Buhl, Tengis Gloveli, and Miles A. Whittington                
+Fast Rhythmic Bursting Can Be Induced in Layer 2/3 Cortical Neurons by Enhancing Persistent Na+ Conductance or by Blocking BK Channels
+J Neurophysiol 89: 909-921, 2003</rdf:li>
+                            <rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=12574468"/>
+                        </rdf:Bag>
+                    </bqmodel:isDescribedBy>
+
+
+                    <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+                        <rdf:Bag>
+                            <rdf:li>Roger D. Traub, Diego Contreras, Mark O. Cunningham, Hilary Murray, Fiona E. N. LeBeau, Anita Roopun, Andrea Bibbig, W. Bryan Wilent, Michael J. Higley, and Miles A. Whittington
+Single-column thalamocortical network model exhibiting gamma oscillations, sleep spindles, and epileptogenic bursts.
+J. Neurophysiol. 93, 2194-2232, 2005</rdf:li>
+                            <rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/15525801?dopt=Abstract"/>
+                        </rdf:Bag>
+                    </bqmodel:isDescribedBy>
+
+
+                    <bqbiol:isVersionOf xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                        <rdf:Bag>
+                            <rdf:li>Calcium channels</rdf:li>
+                            <rdf:li rdf:resource="http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table1"/>
+                        </rdf:Bag>
+                    </bqbiol:isVersionOf>
+
+                </rdf:Description>
+            </rdf:RDF>
+        </annotation>
+
+        <gate id="m" type="gateHHtauInf" instances="2">
+            <timeCourse type="cat_m_tau_tau"/>
+            <steadyState type="HHSigmoidVariable" rate="1" scale="6.2mV" midpoint="-56.0mV"/>
+        </gate>
+
+        <gate id="h" type="gateHHtauInf" instances="1">
+            <timeCourse type="cat_h_tau_tau"/>
+            <steadyState type="HHSigmoidVariable" rate="1" scale="-4mV" midpoint="-80mV"/>
+        </gate>
+
+    </ionChannel>
+
+    <ComponentType name="cat_m_tau_tau" extends="baseVoltageDepTime">
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+            <DerivedVariable name="t" exposure="t" dimension="time" value="(0.204 + 0.333 / ( (exp ((15.8 + V) / 18.2 )) + (exp ((- V - 131) / 16.7)) )) * TIME_SCALE"/>
+        </Dynamics>
+
+    </ComponentType>
+
+    <ComponentType name="cat_h_tau_tau" extends="baseVoltageDepTime">
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+            <ConditionalDerivedVariable name="t" exposure="t" dimension="time">
+                <Case condition="V  .lt. ( -81.0 )" value="( 0.333 * (exp (( V + 466 ) / 66.6)) ) * TIME_SCALE"/>
+                <Case value="( 9.32 + 0.333 * (exp (( - V - 21 ) / 10.5))) * TIME_SCALE"/>
+            </ConditionalDerivedVariable>
+        </Dynamics>
+
+    </ComponentType>
+
+</neuroml>