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Revert "Revert "add annotations""
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‎NeuroML2/channels/cal_mig.channel.nml‎

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<?xml version="1.0" encoding="ISO-8859-1"?>
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<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">
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<notes>NeuroML file containing a single Channel description</notes>
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<ionChannel id="cal" conductance="10pS" type="ionChannelHH" species="ca">
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<notes>L-calcium channel
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: L-type calcium channel with [Ca]i inactivation
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: from Jaffe, D. B., Ross, W. N., Lisman, J. E., Laser-Ross, N., Miyakawa, H., and Johnston, D. A. A model for dendritic Ca2
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: accumulation in hippocampal pyramidal neurons based on fluorescence imaging measurements. J. Neurophysiol. 71:1O65-1077 1994.
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: conduction density estimate of 50-200 pS/mu2; 0.0025 S/cm2 (5-20 channels of 10 each)
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: M. Migliore, E. Cook, D.B. Jaffe, D.A. Turner and D. Johnston, Computer simulations of morphologically reconstructed CA3
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: hippocampal neurons, J. Neurophysiol. 73, 1157-1168 (1995).
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: adapted from http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=3263&file=\ca3_db\cal2.mod
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: this version from https://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=148094&file=\kv72-R213QW-mutations\cal2.mod
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: Miceli F, Soldovieri MV, Ambrosino P, Barrese V, Migliore M, Cilio MR, Taglialatela M (2013) Genotype-phenotype
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: correlations in neonatal epilepsies caused by mutations in the voltage sensor of Kv7.2 potassium channel subunits. PNAS 110:4386-4391
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</notes>
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<annotation>
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<rdf:RDF
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xmlns:dcterms="http://purl.org/dc/terms/"
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xmlns:dc="http://purl.org/dc/elements/1.1/"
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xmlns:foaf="http://xmlns.com/foaf/0.1/"
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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
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xmlns:bqmodel="http://biomodels.net/model-qualifiers/"
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>
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<rdf:Description rdf:about="cal">
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<dc:title>NeuroML conversion of cal channel from Macaque_auditory_thalamocortical_model</dc:title>
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<dc:description>L-type calcium channel with [Ca]i inactivation</dc:description>
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<dc:source>
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<rdf:Bag>
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<rdf:li rdf:resource="https://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=148094&amp;file=\kv72-R213QW-mutations\cal2.mod"/>
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</rdf:Bag>
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</dc:source>
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<bqmodel:isDerivedFrom>
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<rdf:Bag>
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<rdf:li rdf:resource="http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=3263&amp;file=\ca3_db\cal2.mod"/>
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</rdf:Bag>
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</bqmodel:isDerivedFrom>
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<bqmodel:isDescribedBy>
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<rdf:Bag>
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<rdf:li rdf:resource="https://www.pnas.org/doi/10.1073/pnas.1216867110"/>
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</rdf:Bag>
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</bqmodel:isDescribedBy>
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<dc:contributor>
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<rdf:Bag>
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<rdf:li rdf:resource="#Hengye_Zhu"/>
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</rdf:Bag>
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</dc:contributor>
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<dcterms:created>
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<rdf:Description>
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<dcterms:W3CDTF>2025-07-24</dcterms:W3CDTF>
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</rdf:Description>
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</dcterms:created>
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</rdf:Description>
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<rdf:Description rdf:about="#Hengye_Zhu">
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<foaf:name>Hengye Zhu</foaf:name>
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<dc:identifier>gluciferd at gmail.com</dc:identifier>
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</rdf:Description>
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</rdf:RDF>
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</annotation>
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<ConductanceScalingCaDependent type="cal_scale"/>
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<gate id="m" type="gateHHratesTau" instances="2">

‎NeuroML2/channels/can_mig.channel.nml‎

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<?xml version="1.0" encoding="ISO-8859-1"?>
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<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="can">
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<notes>NeuroML file containing a single Channel description</notes>
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<ionChannel id="can" conductance="10pS" type="ionChannelHH" species="ca">
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<notes>n-calcium channel
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: n-type calcium channel
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: MODELDB 126814 CA3 by Safiulina et al - http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=126814
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: by Michele Migliore
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</notes>
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<annotation>
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<rdf:RDF
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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
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xmlns:foaf="http://xmlns.com/foaf/0.1/"
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xmlns:dc="http://purl.org/dc/elements/1.1/"
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xmlns:dcterms="http://purl.org/dc/terms/"
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>
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<rdf:Description rdf:about="can">
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<dc:title>NeuroML conversion of can channel from Macaque_auditory_thalamocortical_model</dc:title>
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<dc:description>n-calcium channel</dc:description>
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<dc:source>
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<rdf:Bag>
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<rdf:li rdf:resource="http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=126814"/>
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</rdf:Bag>
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</dc:source>
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<dc:creator>
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<rdf:Bag>
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<rdf:li rdf:resource="#Safiulina_et_al"/>
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</rdf:Bag>
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</dc:creator>
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<dc:contributor>
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<rdf:Bag>
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<rdf:li rdf:resource="#Hengye_Zhu"/>
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</rdf:Bag>
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</dc:contributor>
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<dcterms:created>
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<rdf:Description>
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<dcterms:W3CDTF>2025-07-24</dcterms:W3CDTF>
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</rdf:Description>
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</dcterms:created>
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</rdf:Description>
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<rdf:Description rdf:about="#Hengye_Zhu">
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<foaf:name>Hengye Zhu</foaf:name>
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<dc:identifier>gluciferd at gmail.com</dc:identifier>
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</rdf:Description>
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<rdf:Description rdf:about="#Safiulina_et_al">
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<foaf:name>Safiulina et al</foaf:name>
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</rdf:Description>
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</rdf:RDF>
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</annotation>
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<ConductanceScalingCaDependent type="can_scale"/>
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<gate id="m" type="gateHHratesTau" instances="2">

‎NeuroML2/channels/cat_mig.channel.nml‎

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<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">
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<ionChannel id="cat" conductance="10pS" type="ionChannelHH" species="ca">
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<notes>T-calcium channel
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: T-type calcium channel
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: MODELDB 126814 CA3 by Safiulina et al - http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=126814
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: by Michele Migliore
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</notes>
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<annotation>
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<rdf:RDF
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xmlns:foaf="http://xmlns.com/foaf/0.1/"
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xmlns:dc="http://purl.org/dc/elements/1.1/"
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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
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xmlns:dcterms="http://purl.org/dc/terms/"
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>
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<rdf:Description rdf:about="cat">
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<dc:title>NeuroML conversion of cat channel from Macaque_auditory_thalamocortical_model</dc:title>
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<dc:description>T-calcium channel</dc:description>
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<dc:source>
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<rdf:Bag>
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<rdf:li rdf:resource="http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=126814"/>
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</rdf:Bag>
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</dc:source>
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<dc:contributor>
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<rdf:Bag>
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<rdf:li rdf:resource="#Hengye_Zhu"/>
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</rdf:Bag>
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</dc:contributor>
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<dcterms:created>
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<rdf:Description>
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<dcterms:W3CDTF>2025-07-24</dcterms:W3CDTF>
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</rdf:Description>
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</dcterms:created>
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</rdf:Description>
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<rdf:Description rdf:about="#Hengye_Zhu">
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<foaf:name>Hengye Zhu</foaf:name>
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<dc:identifier>gluciferd at gmail.com</dc:identifier>
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</rdf:Description>
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</rdf:RDF>
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</annotation>
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<gate id="m" type="gateHHratesTau" instances="2">
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<q10Settings type="q10ExpTemp" q10Factor="5" experimentalTemp="25degC"/>

‎NeuroML2/channels/create_annotations.py‎

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#!/usr/bin/env python3
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"""
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Script to create annotations for various models.
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File: create_annotations.py
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Copyright 2024 Ankur Sinha
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Author: Ankur Sinha <sanjay DOT ankur AT gmail DOT com>
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"""
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from pyneuroml.annotations import create_annotation
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def annotate_():
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"""Annotation for channel"""
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annotation = create_annotation(
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subject="cat",
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title="NeuroML conversion of cat channel from Macaque_auditory_thalamocortical_model",
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abstract=None,
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serialization_format="pretty-xml",
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annotation_style="miriam",
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indent=12,
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xml_header=False,
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description="T-calcium channel",
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creation_date="2025-07-24",
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#citations={"https://www.pnas.org/doi/10.1073/pnas.1216867110": "PNAS"},
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sources={"http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=126814": "modeldb"},
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#predecessors={"http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=3263&file=\ca3_db\cal2.mod": "Original model"},
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contributors={"Hengye Zhu": {"gluciferd at gmail.com": "email"}}
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)
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print(annotation)
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if __name__ == "__main__":
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annotate_()

‎NeuroML2/compare_MC/HTC/HTC_reduced_cell.nml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd"
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id = "NeuroML2_file_exported_from_NEURON">
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<notes> NeuroML 2 file generated from ModelView by: NEURON -- VERSION 8.2.6+ HEAD (078a34a9d+) 2024-07-24
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Authors: Michael Hines, Sushil Kambampati and Padraig Gleeson,
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Yale University and UCL
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</notes>
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<cell id="HTC_reduced_cell_0_0">
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<notes>Cell: HTC_reduced_cell_0_0 exported from NEURON ModelView</notes>
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<morphology id="morphology">
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<!-- Section: HTC_reduced_cell[0].soma (segmentGroup: soma) which has 2 3D points, so 1 segment(s)-->
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<segment id="0" name = "Seg0_soma">
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<proximal x="0" y="0" z="0" diameter="96"/>
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<distal x="0" y="96" z="0" diameter="96"/>
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</segment>
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<!-- Section: HTC_reduced_cell[0].soma (segmentGroup: soma) which has 2 3D points, so 1 segment(s)-->
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<segmentGroup id = "soma" neuroLexId="sao864921383">
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<notes>This group contains an unbranched set of segments, and all of the segmentGroups marked with
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neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
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These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
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<member segment = "0"/>
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</segmentGroup>
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<segmentGroup id="all"> <!-- Replacing subset name ModelViewParmSubset_0 with all, as it contains all sections -->
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<include segmentGroup = "soma"/>
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</segmentGroup>
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<segmentGroup id="OneSecGrp_SectionRef_1"> <!-- Creating a group containing a single section: soma... -->
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<include segmentGroup = "soma"/>
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</segmentGroup>
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</morphology>
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<biophysicalProperties id="biophys">
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<membraneProperties>
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<channelDensityNernst id="cal_all" ionChannel="cal" condDensity="0.001 S_per_cm2" segmentGroup="all" ion="ca"/>
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<channelDensity ionChannel="ia" id="ia_all" segmentGroup="all" ion="k" erev="-95.0 mV" condDensity="0.007 S_per_cm2"/>
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TODO: <channelDensity ionChannel="ittc" id="ittc_all" segmentGroup="all" ion="ca" erev="-104 mV" condDensity="0.002 S_per_cm2"/>
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TODO: htc
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TODO: hh2ad
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<channelDensity ionChannel="kl" id="kl_all" segmentGroup="all" ion="k" erev="-95.0 mV" condDensity="2.3e-05 S_per_cm2"/>
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<channelDensity ionChannel="pas" id="pas_all" segmentGroup="all" ion="non_specific" erev="-50 mV" condDensity="1.8e-05 S_per_cm2"/>
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<spikeThresh value="5mV"/>
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<specificCapacitance segmentGroup="all" value="1.0 uF_per_cm2"/>
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<initMembPotential segmentGroup="all" value="-70 mV"/>
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</membraneProperties>
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<intracellularProperties>
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<species segmentGroup="all" ion="ca" initialExtConcentration="2.0E-6 mol_per_cm3" concentrationModel="cadad_HTC_soma" id="ca" initialConcentration="5.0E-11 mol_per_cm3"/>
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<resistivity value="100 ohm_cm"/>
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</intracellularProperties>
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</biophysicalProperties>
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</cell>
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</neuroml>

‎NeuroML2/compare_MC/HTC/HTC_reduced_cellParams.json‎

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{
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"conds": {
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"cellModel": "HH_reduced",
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"cellType": "HTC",
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"ynorm": [
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1.2,
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1.4
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]
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},
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"globals": {
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"erev_kl": -95.0,
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"q10m_ittc": 3.55,
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"v_init": -70.0
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},
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"secLists": {},
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"secs": {
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"soma": {
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"geom": {
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"L": 96.0,
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"Ra": 100.0,
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"cm": 1.0,
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"diam": 96.0,
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"nseg": 1,
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"pt3d": [
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[
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0,
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0,
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0,
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96.0
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],
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[
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0,
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96.0,
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0,
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96.0
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]
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]
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},
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"ions": {
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"ca": {
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"e": 132.4579341637009,
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"i": 5e-05,
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"o": 2.0
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},
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"k": {
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"e": -95.0,
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"i": 54.4,
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"o": 2.5
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},
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"na": {
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"e": 50.0,
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"i": 10.0,
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"o": 140.0
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}
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},
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"mechs": {
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"cadad": {
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"cainf": 0.00024,
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"depth": 1.0,
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"kd": 0.0,
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"kt": 0.0,
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"taur": 5.0
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},
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"cal": {
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"gcalbar": 0.001
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},
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"hh2ad": {
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"gkbar": 0.012,
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"gnabar": 0.02,
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"vtraub": -63.0
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},
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"htc": {
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"Pc": 0.01,
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"cac": 0.002,
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"exptemp": 36.0,
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"ginc": 2.0,
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"gmax": 1e-06,
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"k2": 0.0004,
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"k4": 0.001,
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"nca": 4.0,
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"nexp": 1.0,
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"shift": 0.0,
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"taum": 20.0
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},
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"ia": {
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"exptemp": 23.5,
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"gmax": 0.007,
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"q10": 3.0
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},
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"ittc": {
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"gmax": 0.002,
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"shift": 3
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},
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"kl": {
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"gmax": 2.3e-05
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},
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"pas": {
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"e": -50,
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"g": 1.8e-05
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}
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},
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"topol": {},
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"vinit": -70.0,
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"weightNorm": [
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0.0020910235715425945
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]
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}
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}
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}

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