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‎tutorials/Rdesigneur/cells/970529c.CNG.swc‎

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‎tutorials/Rdesigneur/cells/CA1.morph.xml‎

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‎tutorials/Rdesigneur/cells/DHC-neuron.CNG.swc‎

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‎tutorials/Rdesigneur/cells/ca1_minimal.p‎

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// genesis
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// cell parameter file for the 1991 Traub CA1 hippocampal cell
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// "phi" parameter reduced by e-3
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*cartesian
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*relative
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*set_global RM 1.0 //ohm*m^2
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*set_global RA 1.0 //ohm*m
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*set_global CM 0.03 //F/m^2
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*set_global EREST_ACT -0.06 // volts
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// The format for each compartment parameter line is :
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// name parent x y z d ch dens ...
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// For channels, "dens" = maximum conductance per unit area of compartment
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dend_3 none 0 220 0 3.84
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dend_5 . 0 220 0 3.84
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dend_6 . 0 220 0 3.84
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dend_8 . 0 110 0 3.84
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soma dend_8 0 125 0 8.46
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apical_10 soma 0 120 0 4.0
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apical_11 apical_10 0 120 0 3
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apical_12 apical_11 0 120 0 3
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apical_13 apical_12 0 120 0 2.6
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apical_14 apical_13 0 120 0 2.6
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apical_15 apical_14 0 120 0 2.6
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apical_16 apical_15 0 120 0 2.6
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apical_17 apical_16 0 120 0 2.6
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apical_18 apical_17 0 120 0 2.6
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apical_19 apical_18 0 120 0 2.6
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apical_11_1 apical_10 -60 60 0 2
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apical_11_2 apical_11_1 -60 60 0 1.8
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apical_11_3 apical_11_2 0 80 0 1.5
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apical_11_4 apical_11_3 0 80 0 1.5
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apical_13_1 apical_12 40 40 0 1.0
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apical_13_2 apical_13_1 40 40 0 1.0
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apical_14_1 apical_13_2 0 10 0 1.0
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apical_14_2 . 0 10 0 1.0
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apical_14_3 . 0 10 0 1.0
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apical_14_4 . 0 10 0 1.0
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apical_14_5 . 0 10 0 1.0
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apical_14_6 . 0 10 0 1.0
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apical_14_7 . 0 10 0 1.0
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apical_14_8 . 0 10 0 1.0
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apical_14_9 . 0 10 0 1.0
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apical_14_10 . 0 10 0 1.0
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apical_14_11 . 0 10 0 1.0
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apical_14_12 . 0 10 0 1.0
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apical_14_13 . 0 10 0 1.0
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apical_15_1 . 0 30 0 1.0
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apical_15_2 . 0 60 0 1.0

‎tutorials/Rdesigneur/chans/CA1.morph.xml‎

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‎tutorials/Rdesigneur/chans/DoubExpSyn.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<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/v1.6/Level2/ChannelML_v1.6.xsd" units="Physiological Units">
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<meta:notes>ChannelML file describing a single synaptic mechanism</meta:notes>
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<synapse_type name="DoubExpSyn">
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<status value="stable"/>
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<meta:notes>Simple example of a synaptic mechanism, which consists of a postsynaptic conductance which changes as
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double exponential function of time. Mappings exist for NEURON and GENESIS.</meta:notes>
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<meta:authorList>
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<meta:modelTranslator>
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<meta:name>Padraig Gleeson</meta:name>
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<meta:institution>UCL</meta:institution>
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<meta:email>p.gleeson - at - ucl.ac.uk</meta:email>
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</meta:modelTranslator>
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</meta:authorList>
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<meta:neuronDBref>
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<meta:modelName>Receptor properties</meta:modelName>
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<meta:uri>http://senselab.med.yale.edu/senselab/NeuronDB/receptors2.asp</meta:uri>
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</meta:neuronDBref>
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<doub_exp_syn max_conductance="1.0E-5" rise_time="1" decay_time="2" reversal_potential="0"/>
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</synapse_type>
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</channelml>

‎tutorials/Rdesigneur/chans/Generated.net.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<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">
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<meta:notes>
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Network structure (NeuroML 1.x) for project: CA1PyramidalCell saved with neuroConstruct v1.7.1 on: 11:29:49, 18-Jul-14
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Cell Group: CA1_CG contains 1 cells
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</meta:notes>
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<meta:properties>
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<meta:property tag="neuroConstruct_random_seed" value="282926701"/>
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<meta:property tag="neuroConstruct_sim_config" value="CA1Cell"/>
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<meta:property tag="neuroConstruct_sim_duration" value="10.0"/>
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<meta:property tag="neuroConstruct_sim_time_step" value="0.002"/>
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<meta:property tag="neuroConstruct_temperature" value="35.0"/>
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</meta:properties>
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<populations>
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<population name="CA1_CG" cell_type="CA1">
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<meta:properties>
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<meta:property tag="color" value="0.8984375 0.8984375 0.8984375"/>
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</meta:properties>
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<instances size="1">
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<instance id="0">
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<location x="0.0" y="0.0" z="0.0"/>
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</instance>
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</instances>
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</population>
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</populations>
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<!--There are no synaptic connections present in the network-->
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<inputs units="SI Units">
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<input name="Input_1">
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<pulse_input delay="0.002" duration="0.005" amplitude="1.8E-9"/>
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<target population="CA1_CG">
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<sites size="1">
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<site cell_id="0" segment_id="0" fraction_along="0.5"/>
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</sites>
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</target>
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</input>
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</inputs>
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</networkml>

‎tutorials/Rdesigneur/chans/HChannel.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<channelml xmlns="http://morphml.org/channelml/schema"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xmlns:meta="http://morphml.org/metadata/schema"
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xsi:schemaLocation="http://morphml.org/channelml/schema http://www.neuroml.org/NeuroMLValidator/NeuroMLFiles/Schemata/v1.8.0/Level2/ChannelML_v1.8.0.xsd"
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units="Physiological Units">
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<meta:notes>ChannelML file containing a single Channel description</meta:notes>
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<channel_type name="hd" density="yes">
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<status value="stable">
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<meta:comment>Agreement of generated NEURON and GENESIS to original NEURON mod. Compared voltage and l traces on single comp with current pulse</meta:comment>
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<meta:contributor>
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<meta:name>Padraig Gleeson</meta:name>
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</meta:contributor>
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</status>
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<meta:notes>H current. Comment from original mod: I-h channel from Magee 1998 for distal dendrites</meta:notes>
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<meta:authorList>
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<meta:modelAuthor>
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<meta:name>Michele Migliore</meta:name>
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<meta:comment>Cited implementer according to ModelDB</meta:comment>
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</meta:modelAuthor>
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<meta:modelTranslator>
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<meta:name>Padraig Gleeson</meta:name>
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<meta:institution>UCL</meta:institution>
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<meta:email>p.gleeson - at - ucl.ac.uk</meta:email>
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</meta:modelTranslator>
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</meta:authorList>
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<meta:publication>
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<meta:fullTitle>Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155</meta:fullTitle>
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<meta:pubmedRef>http://www.ncbi.nlm.nih.gov/pubmed/16293591</meta:pubmedRef>
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</meta:publication>
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<meta:modelDBref>
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<meta:modelName>CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005)</meta:modelName>
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<meta:uri>http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035</meta:uri>
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</meta:modelDBref>
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<parameters>
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<parameter name="vhalfl" value ="-81"/>
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</parameters>
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<current_voltage_relation cond_law="ohmic" ion="hd" default_gmax="0.05" default_erev="-30">
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<q10_settings q10_factor="4.5" experimental_temp="33"/>
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<gate name="l" instances="1">
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<closed_state id="l0"/>
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<open_state id="l" fraction="1"/>
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<!-- As taken from the mod file
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<transition name="alpha" from="l0" to="l" expr_form="exponential" rate="1" scale="12.025" midpoint="-75" />
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<transition name="beta" from="l" to="l0" expr_form="exponential" rate="1" scale="30.06253" midpoint="-75" />
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<time_course name="tau" from="l0" to="l" expr_form="generic" expr="beta/(0.011 * (1 + alpha)) " />-->
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<time_course name="tau" from="l0" to="l" expr_form="generic" expr="(exp (0.033264 * (v - (-75))))/(0.011 * (1 + (exp (0.08316 * (v - (-75)))))) " />
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<steady_state name="inf" from="l0" to="l" expr_form="generic" expr="1/(1 + (exp (- (v-(vhalfl))/ (-8) )) )" />
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</gate>
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</current_voltage_relation>
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<impl_prefs>
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<comment>Suggesting using a large table of precomputed rate equation values since original mod didn't use any table, i.e. used continuous values</comment>
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<table_settings max_v="100" min_v="-100" table_divisions="2000"/>
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</impl_prefs>
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</channel_type>
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</channelml>

‎tutorials/Rdesigneur/chans/pas.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<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/v1.8.0/Level2/ChannelML_v1.8.0.xsd" units="Physiological Units">
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<meta:notes>ChannelML file containing a single Channel description</meta:notes>
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<channel_type name="pas" density="yes">
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<status value="stable"/>
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<meta:notes>Simple example of a leak/passive conductance. Note: for GENESIS cells with a single leak conductance,
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it is better to use the Rm and Em variables for a passive current.</meta:notes>
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<current_voltage_relation cond_law="ohmic" ion="non_specific" default_erev="-58" default_gmax="3.57143e-2 "/>
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</channel_type>
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</channelml>

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