Add NeuroML1 dir

NeuroML1/GranuleCell/Granule98.py

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+## Aditya Gilra, NCBS, Bangalore, 2012
+
+"""
+Inside the .../moose-examples/GranuleCell/ directory supplied with MOOSE, run
+python testNeuroML_Gran98.py
+(other channels and morph xml files are already present in this same directory).
+The soma name below is hard coded for gran98, else any other file can be used by modifying this script.
+"""
+import os
+os.environ['NUMPTHREADS'] = '1'
+import sys
+#sys.path.append('../../../python')
+import moose
+from moose.utils import setupTable, resetSim
+
+from moose.neuroml.NeuroML import NeuroML
+
+
+simdt = 1e-6 # s
+plotdt = 10e-6 # s
+runtime = 0.7 # s
+
+def loadGran98NeuroML_L123(filename, nogui=False):
+    neuromlR = NeuroML()
+    populationDict, projectionDict = \
+        neuromlR.readNeuroMLFromFile(filename)
+    soma_path = populationDict['Gran'][1][0].path+'/Soma_0'
+    somaVm = setupTable('somaVm',moose.Compartment(soma_path),'Vm')
+    somaCa = setupTable('somaCa',moose.CaConc(soma_path+'/Gran_CaPool_98'),'Ca')
+    somaIKCa = setupTable('somaIKCa',moose.element(soma_path+'/Gran_KCa_98'),'Gk')
+    #KDrX = setupTable('ChanX',moose.element(soma_path+'/Gran_KDr_98'),'X')
+    soma = moose.Compartment(soma_path)
+    print("Reinit MOOSE ... ")
+    resetSim(['/elec','/cells'],simdt,plotdt,simmethod='ee') # from moose.utils
+    print("Running ... ")
+    moose.start(runtime)
+    print("Finished simulation of %s seconds"%runtime)
+
+    if not nogui:
+        import pylab
+        import numpy as np
+        tvec = np.arange(0.0,runtime,plotdt)
+        pylab.plot(tvec,somaVm.vector[1:])
+        pylab.title('Soma Vm')
+        pylab.xlabel('time (s)')
+        pylab.ylabel('Voltage (V)')
+        pylab.figure()
+        pylab.plot(tvec,somaCa.vector[1:])
+        pylab.title('Soma Ca')
+        pylab.xlabel('time (s)')
+        pylab.ylabel('Ca conc (mol/m^3)')
+        pylab.figure()
+        pylab.plot(tvec,somaIKCa.vector[1:])
+        pylab.title('KCa current (A)')
+        pylab.xlabel('time (s)')
+        pylab.ylabel('')
+        print("Showing plots ...")
+        pylab.show()
+
+filename = "GranuleCell.net.xml"
+
+if __name__ == "__main__":
+    nogui = False
+    if '-nogui' in sys.argv:
+        nogui = True
+        sys.argv.remove('-nogui')
+
+    if len(sys.argv)<2:
+        filename = "GranuleCell.net.xml"
+    else:
+        filename = sys.argv[1]
+
+    loadGran98NeuroML_L123(filename, nogui)

NeuroML1/GranuleCell/GranuleCell.net.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<networkml xmlns="http://morphml.org/networkml/schema" xmlns:meta="http://morphml.org/metadata/schema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://morphml.org/networkml/schema  http://www.neuroml.org/NeuroMLValidator/NeuroMLFiles/Schemata/v1.8.1/Level3/NetworkML_v1.8.1.xsd" lengthUnits="micrometer">
+
+<meta:notes>
+
+Network structure (NeuroML 1.x) for project: GranuleCell saved with neuroConstruct v1.5.1 on: 14:34:18, 15-Nov-11
+
+Cell Group: Gran contains 1 cells
+
+
+</meta:notes>
+
+<meta:properties>
+    <meta:property tag="neuroConstruct_random_seed" value="-1533157804"/>
+
+    <meta:property tag="neuroConstruct_sim_config" value="Default Simulation Configuration"/>
+</meta:properties>
+
+        <populations>
+    <population name="Gran" cell_type="Granule_98">
+        <meta:properties>
+            <meta:property tag="color" value="0.69921875 0.5703125 0.96484375"/>
+
+        </meta:properties>
+        <instances size="1">
+            <instance id="0">
+                <location x="18.7105" y="50.0" z="0.0"/>
+            </instance>
+        </instances>
+    </population>
+</populations>
+
+
+
+            <!--There are no synaptic connections present in the network-->
+
+
+        <inputs units="Physiological Units">
+    <input name="Gran_10pA">
+        <!--<pulse_input delay="100.0" duration="500.0" amplitude="1.0E-5"/>-->
+        <!-- injecting directly into soma.inject in the cell's MorphML -->
+        <pulse_input delay="100.0" duration="500.0" amplitude="1.0E-5"/>
+        <target population="Gran">
+            <sites size="1">
+                <site cell_id="0" segment_id="0" fraction_along="0.5"/>
+            </sites>
+        </target>
+    </input>
+</inputs>
+
+</networkml>

NeuroML1/GranuleCell/README.md

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+This is an altered version of the MOOSE example from https://github.com/BhallaLab/moose-examples/tree/master/neuroml/GranuleCell
+
+

NeuroML1/GranuleCell/cells_channels/GranPassiveCond.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+
+<channelml xmlns="http://morphml.org/channelml/schema" 
+   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
+   xmlns:meta="http://morphml.org/metadata/schema" 
+   xsi:schemaLocation="http://morphml.org/channelml/schema  http://www.neuroml.org/NeuroMLValidator/NeuroMLFiles/Schemata/v1.8.1/Level2/ChannelML_v1.8.1.xsd"
+   units="Physiological Units">
+
+    <meta:notes>ChannelML file containing a single Channel description</meta:notes>
+
+
+    <channel_type name="GranPassiveCond">
+
+        <status value="stable">
+            <meta:contributor>
+                <meta:name>Padraig Gleeson</meta:name>
+            </meta:contributor>
+        </status>
+
+        <meta:notes>Simple leak conductance for Granule cell</meta:notes>
+
+        <meta:publication>
+            <meta:fullTitle>Maex, R and De Schutter, E. 
+            Synchronization of Golgi and Granule Cell Firing in a Detailed Network Model of the 
+            cerebellar Granule Cell Layer. J Neurophysiol, Nov 1998; 80: 2521 - 2537</meta:fullTitle>
+            <meta:pubmedRef>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=9819260&amp;dopt=Abstract</meta:pubmedRef>
+        </meta:publication>
+
+        <current_voltage_relation cond_law="ohmic" ion="non_specific" default_gmax="3.30033e-2" default_erev="-65"/>    <!-- gmax units: mS/cm2-->
+
+    </channel_type>
+
+</channelml>

NeuroML1/GranuleCell/cells_channels/Gran_CaHVA_98.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+
+<channelml xmlns="http://morphml.org/channelml/schema" 
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
+    xmlns:meta="http://morphml.org/metadata/schema" 
+    xsi:schemaLocation="http://morphml.org/channelml/schema  http://www.neuroml.org/NeuroMLValidator/NeuroMLFiles/Schemata/v1.8.1/Level2/ChannelML_v1.8.1.xsd"
+    units="SI Units">
+
+    <meta:notes>A channel from Maex, R and De Schutter, E. Synchronization of Golgi and Granule Cell Firing in a 
+    Detailed Network Model of the Cerebellar Granule Cell Layer</meta:notes>
+
+    <channel_type name="Gran_CaHVA_98">
+
+        <status value="stable">
+            <meta:comment>Verified equivalence of NEURON and GENESIS mapping to orig GENESIS impl from www.tnb.ua.ac.be.</meta:comment>
+            <meta:comment>Updated to post v1.7.3 new ChannelML format</meta:comment>
+            <meta:contributor>
+                <meta:name>Padraig Gleeson</meta:name>
+            </meta:contributor>
+        </status>
+
+        <meta:notes>A High Voltage Activated Ca2+ channel</meta:notes>
+
+        <meta:authorList>
+            <meta:modelAuthor>
+                <meta:name>Maex, R.</meta:name>
+            </meta:modelAuthor>
+            <meta:modelAuthor>
+                <meta:name>De Schutter, E.</meta:name>
+            </meta:modelAuthor>
+            <meta:modelTranslator>
+                <meta:name>Padraig Gleeson</meta:name>
+                <meta:institution>UCL</meta:institution>    
+                <meta:email>p.gleeson - at - ucl.ac.uk</meta:email>
+            </meta:modelTranslator>
+        </meta:authorList>
+
+        <meta:publication>
+           <meta:fullTitle>Maex, R and De Schutter, E. 
+           Synchronization of Golgi and Granule Cell Firing in a Detailed Network Model of the 
+           cerebellar Granule Cell Layer. J Neurophysiol, Nov 1998; 80: 2521 - 2537</meta:fullTitle>
+           <meta:pubmedRef>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=9819260&amp;dopt=Abstract</meta:pubmedRef>
+        </meta:publication>
+
+        <meta:neuronDBref>
+           <meta:modelName>Calcium channels</meta:modelName>
+           <meta:uri>http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table1</meta:uri>
+        </meta:neuronDBref>
+
+        <current_voltage_relation cond_law="ohmic" 
+                                  ion="ca" 
+                                  default_gmax="9.084216" 
+                                  default_erev="0.080"
+                                  charge="2"
+                                  fixed_erev="yes">  <!-- In the orig model, [Ca] alterations didn't alter erev for channel from 80mV -->
+
+            <q10_settings q10_factor="3" experimental_temp="17.350264793"/>
+            <offset value="0.010"/>
+
+            <gate name="m" instances="2">
+                <closed_state id="m0"/>
+                <open_state id="m"/>
+
+                <transition name="alpha" from="m0" to="m" expr_form="sigmoid" rate="1600" scale="-0.01388888889" midpoint="0.005" />
+                <transition name="beta" from="m" to="m0" expr_form="exp_linear" rate="100" scale="-0.005" midpoint="-0.0089" />
+
+            </gate>
+
+            <gate name="h" instances="1">
+                <closed_state id="h0"/>
+                <open_state id="h"/>
+
+                <transition name="alpha" from="h0" to="h" expr_form="generic" expr="v  &lt; -0.060 ? 5.0 : 5 * (exp (-50 * (v - (-0.060))))" />
+                <transition name="beta" from="h" to="h0" expr_form="generic" expr="v  &lt; -0.060 ? 0 : 5 - (5 * (exp (-50 * (v - (-0.060)))))" />
+
+            </gate>
+        </current_voltage_relation> 
+
+
+    </channel_type>
+</channelml>
+

NeuroML1/GranuleCell/cells_channels/Gran_CaPool_98.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<channelml xmlns="http://morphml.org/channelml/schema" 
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
+    xmlns:meta="http://morphml.org/metadata/schema" 
+    xsi:schemaLocation="http://morphml.org/channelml/schema   ../../Schemata/v1.7.2/Level2/ChannelML_v1.7.2.xsd" 
+    units="SI Units">
+
+	<meta:notes>A channel from Maex, R and De Schutter, E. Synchronization of Golgi and Granule Cell Firing in a 
+	Detailed Network Model of the Cerebellar Granule Cell Layer</meta:notes>
+
+    <ion name="ca" charge="2" role="SignallingSubstance">  
+        <meta:notes>Signifies that the ion is involved in a process which alters its concentration</meta:notes>
+    </ion>
+
+    <ion_concentration name="Gran_CaPool_98">
+
+        <status value="stable">
+            <meta:comment>This ChannelML file has been updated to reflect the preferred form of elements/attributes which will be required from v2.0.
+            See info on Version 2 Requirements.</meta:comment>
+            <meta:contributor>
+                <meta:name>Padraig Gleeson</meta:name>
+            </meta:contributor>
+        </status>
+
+        <meta:notes>An expontially decaying pool of calcium</meta:notes>
+
+        <meta:publication>
+           <meta:fullTitle>Maex, R and De Schutter, E.
+           Synchronization of Golgi and Granule Cell Firing in a Detailed Network Model of the
+           cerebellar Granule Cell Layer. J Neurophysiol, Nov 1998; 80: 2521 - 2537</meta:fullTitle>
+           <meta:pubmedRef>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=9819260&amp;dopt=Abstract</meta:pubmedRef>
+        </meta:publication>
+
+        <ion_species name="ca"/>
+
+        <decaying_pool_model resting_conc ="7.55e-5" decay_constant="1e-2">
+
+            <pool_volume_info shell_thickness = "8.4e-8"/>
+
+        </decaying_pool_model>
+
+
+    </ion_concentration>
+</channelml>

NeuroML1/GranuleCell/cells_channels/Gran_H_98.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+
+<channelml xmlns="http://morphml.org/channelml/schema" 
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
+    xmlns:meta="http://morphml.org/metadata/schema" 
+    xsi:schemaLocation="http://morphml.org/channelml/schema  http://www.neuroml.org/NeuroMLValidator/NeuroMLFiles/Schemata/v1.8.1/Level2/ChannelML_v1.8.1.xsd"
+    units="SI Units">
+
+    <meta:notes>A channel from Maex, R and De Schutter, E. Synchronization of Golgi and Granule Cell Firing in a 
+    Detailed Network Model of the Cerebellar Granule Cell Layer</meta:notes>
+
+    <channel_type name="Gran_H_98">
+
+        <status value="stable">
+            <meta:comment>Verified equivalence of NEURON and GENESIS mapping to orig GENESIS impl from www.tnb.ua.ac.be</meta:comment>
+            <meta:comment>Updated to post v1.7.3 new ChannelML format</meta:comment>
+            <meta:issue>A values don't match table 1 in M and DeS 98</meta:issue>
+            <meta:contributor>
+                <meta:name>Padraig Gleeson</meta:name>
+            </meta:contributor>
+        </status>
+
+        <meta:notes>Anomalous inward rectifying H conductance</meta:notes>
+
+        <meta:authorList>
+            <meta:modelAuthor>
+                <meta:name>Maex, R.</meta:name>
+            </meta:modelAuthor>
+            <meta:modelAuthor>
+                <meta:name>De Schutter, E.</meta:name>
+            </meta:modelAuthor>
+            <meta:modelTranslator>
+                <meta:name>Padraig Gleeson</meta:name>
+                <meta:institution>UCL</meta:institution>    
+                <meta:email>p.gleeson - at - ucl.ac.uk</meta:email>
+            </meta:modelTranslator>
+        </meta:authorList>
+
+        <meta:publication>
+           <meta:fullTitle>Maex, R and De Schutter, E. 
+           Synchronization of Golgi and Granule Cell Firing in a Detailed Network Model of the 
+           cerebellar Granule Cell Layer. J Neurophysiol, Nov 1998; 80: 2521 - 2537</meta:fullTitle>
+           <meta:pubmedRef>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=9819260&amp;dopt=Abstract</meta:pubmedRef>
+        </meta:publication>
+
+        <current_voltage_relation cond_law="ohmic" ion="h" default_gmax="0.30905062" default_erev="-0.042">
+
+            <q10_settings q10_factor="3" experimental_temp="17.350264793"/>
+            <offset value="0.01"/>
+
+            <gate name="n" instances="1">
+                <closed_state id="n0"/>
+                <open_state id="n"/>
+
+                <transition name="alpha" from="n0" to="n" expr_form="exponential" rate="0.8" scale="-0.01100110011" midpoint="-0.075" />
+                <transition name="beta" from="n" to="n0" expr_form="exponential" rate="0.8" scale="0.01100110011" midpoint="-0.075" />
+
+            </gate>
+        </current_voltage_relation>
+
+
+
+    </channel_type>
+</channelml>