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‎examples/neuroml2/NeuroML2.md

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<table>
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<tr>
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<td><b>izhikevich2007Cells</b></td>
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<td><a href="#izhikevich2007cell">Izhikevich2007Cell</a></td>
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<td><a href="#list">List</a></td>
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<td><i></i></td>
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</tr>
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<tr>
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<td><b>pulseGenerators</b></td>
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<td><a href="#pulsegenerator">PulseGenerator</a></td>
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<td><a href="#list">List</a></td>
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<td><i></i></td>
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</tr>
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<tr>
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<td><b>networks</b></td>
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<td><a href="#network">Network</a></td>
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<td><a href="#list">List</a></td>
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<td><i>The networks present</i></td>
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</tr>
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<table>
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<tr>
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<td><b>populations</b></td>
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<td><a href="#population">Population</a></td>
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<td><a href="#list">List</a></td>
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<td><i>the pops in the net</i></td>
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</tr>
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<tr>
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<td><b>explicitInputs</b></td>
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<td><a href="#explicitinput">ExplicitInput</a></td>
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<td><a href="#list">List</a></td>
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<td><i></i></td>
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</tr>
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‎examples/neuroml2/NeuroML2.rst

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@@ -14,13 +14,13 @@ Allowed field Data Type Description
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**Allowed children**
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======================= ============================================ ====================
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Allowed child Data Type Description
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======================= ============================================ ====================
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**izhikevich2007Cells** `Izhikevich2007Cell <#izhikevich2007cell>`__
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**pulseGenerators** `PulseGenerator <#pulsegenerator>`__
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**networks** `Network <#network>`__ The networks present
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======================= ============================================ ====================
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======================= ================ ====================
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Allowed child Data Type Description
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======================= ================ ====================
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**izhikevich2007Cells** `List <#list>`__
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**pulseGenerators** `List <#list>`__
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**networks** `List <#list>`__ The networks present
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======================= ================ ====================
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==================
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Izhikevich2007Cell
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**Allowed children**
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================== ================================== ===================
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Allowed child Data Type Description
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================== ================================== ===================
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**populations** `Population <#population>`__ the pops in the net
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**explicitInputs** `ExplicitInput <#explicitinput>`__
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================== ================================== ===================
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================== ================ ===================
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Allowed child Data Type Description
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================== ================ ===================
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**populations** `List <#list>`__ the pops in the net
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**explicitInputs** `List <#list>`__
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================== ================ ===================
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==========
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Population

‎examples/neuroml2/NeuroML2.specification.json

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},
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"allowed_children": {
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"izhikevich2007Cells": {
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"type": "Izhikevich2007Cell",
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"type": "List",
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"description": ""
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},
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"pulseGenerators": {
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"type": "PulseGenerator",
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"type": "List",
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"description": ""
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},
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"networks": {
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"type": "Network",
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"type": "List",
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"description": "The networks present"
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}
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}
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},
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"allowed_children": {
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"populations": {
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"type": "Population",
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"type": "List",
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"description": "the pops in the net"
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},
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"explicitInputs": {
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"type": "ExplicitInput",
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"type": "List",
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"description": ""
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}
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}

‎examples/neuroml2/NeuroML2.specification.xml

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<?xml version="1.0" ?>
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<modelspec>
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<NeuroML>
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<definition>Some description...</definition>
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<allowed_parameters>
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<id>
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<type>str</type>
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<description>The id of the NeuroML 2 document</description>
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</id>
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<version>
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<type>str</type>
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<description>NeuroML version used</description>
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</version>
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</allowed_parameters>
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<allowed_children>
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<izhikevich2007Cells>
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<type>Izhikevich2007Cell</type>
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<description/>
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</izhikevich2007Cells>
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<pulseGenerators>
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<type>PulseGenerator</type>
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<description/>
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</pulseGenerators>
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<networks>
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<type>Network</type>
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<description>The networks present</description>
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</networks>
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</allowed_children>
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</NeuroML>
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<Izhikevich2007Cell>
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<definition>Some description...</definition>
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<allowed_parameters>
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<id>
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<type>str</type>
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<description>The id of the cell...</description>
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</id>
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<C>
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<type>str</type>
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<description/>
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</C>
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<v0>
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<type>str</type>
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<description/>
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</v0>
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<k>
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<type>str</type>
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<description/>
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</k>
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<vr>
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<type>str</type>
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<description/>
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</vr>
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<vt>
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<type>str</type>
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<description/>
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</vt>
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<vpeak>
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<type>str</type>
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<description/>
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</vpeak>
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<a>
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<type>str</type>
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<description/>
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</a>
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<b>
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<type>str</type>
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<description/>
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</b>
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<c>
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<type>str</type>
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<description/>
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</c>
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<d>
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<type>str</type>
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<description/>
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</d>
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</allowed_parameters>
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</Izhikevich2007Cell>
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<PulseGenerator>
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<definition>Some description...</definition>
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<allowed_parameters>
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<id>
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<type>str</type>
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<description>The id of the pulseGenerator</description>
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</id>
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<delay>
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<type>str</type>
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<description>the delay</description>
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</delay>
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<duration>
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<type>str</type>
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<description>the duration</description>
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</duration>
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<amplitude>
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<type>str</type>
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<description>the amplitude</description>
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</amplitude>
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</allowed_parameters>
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</PulseGenerator>
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<Network>
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<definition>Some description...</definition>
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<allowed_parameters>
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<id>
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<type>str</type>
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<description>The id of the network</description>
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</id>
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</allowed_parameters>
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<allowed_children>
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<populations>
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<type>Population</type>
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<description>the pops in the net</description>
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</populations>
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<explicitInputs>
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<type>ExplicitInput</type>
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<description/>
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</explicitInputs>
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</allowed_children>
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<NeuroML id="TestNeuroML" version="NeuroML_v2.3">
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<Izhikevich2007Cell id="izh2007RS0" C="100pF" v0="-60mV" k="0.7nS_per_mV" vr="-60mV" vt="-40mV" vpeak="35mV" a="0.03per_ms" b="-2nS" c="-50.0mV" d="100pA"/>
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<PulseGenerator id="pulseGen_0" delay="100ms" duration="800ms" amplitude="0.07 nA"/>
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<Network id="IzNet">
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<Population id="IzhPop0" component="izh2007RS0" size="1"/>
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<ExplicitInput target="IzhPop0[0]" input="pulseGen_0"/>
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</Network>
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<Population>
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<definition>Some description...</definition>
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<allowed_parameters>
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<id>
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<type>str</type>
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<description>The id of the population</description>
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</id>
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<component>
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<type>str</type>
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<description>the component to use in the population</description>
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</component>
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<size>
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<type>int</type>
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<description>the size of the population</description>
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</size>
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</allowed_parameters>
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</Population>
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<ExplicitInput>
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<definition>Some description...</definition>
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<allowed_parameters>
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<target>
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<type>str</type>
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<description>the target of the input</description>
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</target>
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<input>
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<type>str</type>
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<description>the input, e.g. pulseGenerator</description>
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</input>
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</allowed_parameters>
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</ExplicitInput>
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</modelspec>
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</NeuroML>

‎examples/neuroml2/NeuroML2.specification.yaml

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description: NeuroML version used
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allowed_children:
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izhikevich2007Cells:
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type: Izhikevich2007Cell
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type: List
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description: ''
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pulseGenerators:
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type: PulseGenerator
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type: List
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description: ''
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networks:
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type: Network
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type: List
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description: The networks present
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Izhikevich2007Cell:
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definition: Some description...
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description: The id of the network
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allowed_children:
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populations:
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type: Population
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type: List
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description: the pops in the net
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explicitInputs:
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type: ExplicitInput
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type: List
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description: ''
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Population:
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definition: Some description...

‎examples/neuroml2/TestNeuroML.xml

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<?xml version="1.0" ?>
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<modelspec>
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<TestNeuroML>
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<version>NeuroML_v2.3</version>
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<izhikevich2007Cells>
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<izh2007RS0>
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<C>100pF</C>
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<v0>-60mV</v0>
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<k>0.7nS_per_mV</k>
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<vr>-60mV</vr>
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<vt>-40mV</vt>
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<vpeak>35mV</vpeak>
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<a>0.03per_ms</a>
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<b>-2nS</b>
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<c>-50.0mV</c>
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<d>100pA</d>
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</izh2007RS0>
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</izhikevich2007Cells>
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<pulseGenerators>
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<pulseGen_0>
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<delay>100ms</delay>
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<duration>800ms</duration>
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<amplitude>0.07 nA</amplitude>
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</pulseGen_0>
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</pulseGenerators>
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<networks>
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<IzNet>
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<populations>
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<IzhPop0>
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<component>izh2007RS0</component>
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<size>1</size>
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</IzhPop0>
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</populations>
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<explicitInputs>
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<target>IzhPop0[0]</target>
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<input>pulseGen_0</input>
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</explicitInputs>
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</IzNet>
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</networks>
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</TestNeuroML>
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</modelspec>
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<NeuroML id="TestNeuroML" version="NeuroML_v2.3">
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<Izhikevich2007Cell id="izh2007RS0" C="100pF" v0="-60mV" k="0.7nS_per_mV" vr="-60mV" vt="-40mV" vpeak="35mV" a="0.03per_ms" b="-2nS" c="-50.0mV" d="100pA"/>
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<PulseGenerator id="pulseGen_0" delay="100ms" duration="800ms" amplitude="0.07 nA"/>
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<Network id="IzNet">
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<Population id="IzhPop0" component="izh2007RS0" size="1"/>
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<ExplicitInput target="IzhPop0[0]" input="pulseGen_0"/>
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</Network>
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</NeuroML>

‎examples/neuroml2/neuroml2_spec.py

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print(yy)
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d.write(yy)
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save_to_xml_file(doc_dict, "NeuroML2.specification.xml")
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save_to_xml_file(nml_doc, "NeuroML2.specification.xml")

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