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Fix EDEN 0.2.3 spiketimes; update GHA versions; tweaks to examples #223

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Fix EDEN 0.2.3 spiketimes; update GHA versions; tweaks to examples #223

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16a1310
Ensuring at least one <spikeThresh> on all <membraneProperties> elements
pgleeson Apr 18, 2024
9ff64ac
Update eden spike times to 0.2.3 behaviour
pgleeson Apr 19, 2024
1a7f1e6
Merge branch 'development' into experimental
pgleeson Apr 24, 2024
5c2e0d9
Update GHA versions
pgleeson Apr 24, 2024
8c5b644
feat(core-types): add annotation component types
sanjayankur31 Apr 29, 2024
76e8b56
Merge branch 'development' into experimental
pgleeson May 1, 2024
98d2ffd
Test on java 21
pgleeson May 1, 2024
23fabbe
feat(annotations): update keywords
sanjayankur31 May 3, 2024
09f066d
feat(annotations): update combine specifications URL
sanjayankur31 May 3, 2024
ff2587f
feat(annotations): add remaining FOAF bits
sanjayankur31 May 3, 2024
1d248b3
Merge branch 'development' into feat/annotations
sanjayankur31 May 7, 2024
0895147
feat(annotations): use Child instead of Children
sanjayankur31 May 7, 2024
caa8dd9
Merge branch 'development' into experimental
pgleeson May 29, 2024
c989b81
Merge branch 'development' into feat/annotations
pgleeson May 29, 2024
9044162
Merge branch 'feat/annotations' into experimental
pgleeson May 29, 2024
ed7b92b
Add soma_group, as it's referred to in channelDensity
pgleeson May 29, 2024
fe3aa27
Make membraneProperties require at least one each of specificCapacita…
pgleeson May 31, 2024
f33c671
Merge branch 'development' into experimental
pgleeson Jun 11, 2024
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169 changes: 143 additions & 26 deletions NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -36,12 +36,37 @@
<ComponentType name="rdf_RDF" description="Structured block in an _annotation_ based on RDF. See https://github.com/OpenSourceBrain/OSB_API/blob/master/python/examples/grancelllayer.xml">
<Child name="rdf:Description" type="rdf_Description"/>
<Text name="xmlns:rdf"/>
<Text name="xmlns:rdfs"/>
<Text name="xmlns:dcterms"/>
<Text name="xmlns:dc"/>
<Text name="xmlns:prism"/>
<Text name="xmlns:bqbiol"/>
<Text name="xmlns:bqmodel"/>
<Text name="xmlns:scoro"/>
<Text name="xmlns:collex"/>
<Dynamics/>
</ComponentType>


<ComponentType name="rdf_Description" description="Structured block in an _annotation_ based on RDF.">

<Child name="dc:title" type="dc_title"/>
<Child name="dc:description" type="dc_description"/>
<Child name="dcterms:abstract" type="dcterms_abstract"/>
<Child name="dcterms:license" type="dcterms_license"/>
<Child name="dcterms:created" type="dcterms_created"/>

<!-- for people info from FOAF: not complete -->
<Child name="foaf:name" type="foaf_name"/>
<Child name="foaf:homepage" type="foaf_homepage"/>
<Child name="foaf:account" type="foaf_account"/>
<Child name="foaf:fundedBy" type="foaf_fundedBy"/>
<Child name="foaf:mbox" type="foaf_mbox"/>
<Child name="foaf:weblog" type="foaf_weblog"/>
<Child name="foaf:thumbnail" type="foaf_thumbnail"/>
<Child name="foaf:publications" type="foaf_publications"/>
<Child name="orcid:id" type="orcid_id"/>

<Child name="bqbiol:encodes" type="bqbiol_encodes"/>
<Child name="bqbiol:hasPart" type="bqbiol_hasPart"/>
<Child name="bqbiol:hasProperty" type="bqbiol_hasProperty"/>
Expand All @@ -58,65 +83,157 @@
<Child name="bqmodel:is" type="bqmodel_is"/>
<Child name="bqmodel:isDescribedBy" type="bqmodel_isDescribedBy"/>
<Child name="bqmodel:isDerivedFrom" type="bqmodel_isDerivedFrom"/>
<Child name="bqmodel:isIntanceOf" type="bqmodel_isInstanceOf"/>
<Child name="bqmodel:hasInstance" type="bqmodel_hasInstance"/>
<Child name="prism:keyword" type="prism_keyword"/>
<Child name="collex:thumbnail" type="collex_thumbnail"/>
<Child name="scoro:successor" type="scoro_successor"/>
<Child name="rdfs:seeAlso" type="rdfs_seeAlso"/>
<Child name="dcterms:references" type="dcterms_references"/>
<Child name="dc:creator" type="dc_creator"/>
<Child name="dc:contributor" type="dc_contributor"/>
<Child name="dc:source" type="dc_source"/>
<Child name="scoro:funder" type="scoro_funder"/>
<Child name="dcterms:modified" type="dcterms_modified"/>
<Text name="rdf:about"/>
<Dynamics/>
</ComponentType>


<ComponentType name="baseBqbiol" description="Structured block in an _annotation_ based on RDF.">
<!-- base RDF types -->
<ComponentType name="baseAnnotation_without_ns" description="Structured block in an _annotation_ based on RDF.">
<Child name="rdf:Bag" type="rdf_Bag"/>
<Dynamics/>
</ComponentType>

<ComponentType name="baseBqbiol" description="Structured block in an _annotation_ based on RDF." extends="baseAnnotation_without_ns">
<Text name="xmlns:bqbiol"/>
<Dynamics/>
</ComponentType>

<ComponentType name="baseBqmodel" description="Structured block in an _annotation_ based on RDF." extends="baseAnnotation_without_ns">
<Text name="xmlns:bqmodel"/>
<Dynamics/>
</ComponentType>

<ComponentType name="rdf_Bag" description="Structured block in an _annotation_ based on RDF.">
<Child name="rdf:li" type="rdf_li"/>
<Dynamics/>
</ComponentType>

<ComponentType name="rdf_li" description="Structured block in an _annotation_ based on RDF.">
<Text name="rdf:resource"/>
<Dynamics/>
</ComponentType>

<ComponentType name="bqbiol_encodes" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>

<ComponentType name="bqbiol_hasPart" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_encodes" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqbiol_hasProperty" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_hasPart" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqbiol_hasVersion" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_hasProperty" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqbiol_is" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_hasVersion" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqbiol_isDescribedBy" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_is" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqbiol_isEncodedBy" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_isDescribedBy" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqbiol_isHomologTo" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_isEncodedBy" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqbiol_isPartOf" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_isHomologTo" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqbiol_isPropertyOf" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_isPartOf" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqbiol_isVersionOf" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol">
<Text name="xmlns:bqbiol"/>
</ComponentType>
<ComponentType name="bqbiol_isPropertyOf" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqbiol_occursIn" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_isVersionOf" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol" />

<ComponentType name="bqbiol_hasTaxon" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_occursIn" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqmodel_is" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="bqbiol_hasTaxon" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>

<ComponentType name="bqmodel_isDescribedBy" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol">
<Text name="xmlns:bqmodel"/>
<ComponentType name="bqmodel_is" description="See https://github.com/combine-org/combine-specifications" extends="baseBqmodel"/>

<ComponentType name="bqmodel_isDescribedBy" description="See https://github.com/combine-org/combine-specifications" extends="baseBqmodel" />

<ComponentType name="bqmodel_isDerivedFrom" description="See https://github.com/combine-org/combine-specifications" extends="baseBqmodel"/>

<ComponentType name="bqmodel_isInstanceOf" description="See https://github.com/combine-org/combine-specifications" extends="baseBqmodel"/>

<ComponentType name="bqmodel_hasInstance" description="See https://github.com/combine-org/combine-specifications" extends="baseBqmodel"/>

<ComponentType name="dc_title" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" />

<ComponentType name="dc_description" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/"/>

<ComponentType name="dcterms_abstract" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/"/>

<ComponentType name="dcterms_license" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/"/>

<ComponentType name="dcterms_created" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/">
<Child name="rdf:Description" type="dcterms_created_description"/>
</ComponentType>

<ComponentType name="bqmodel_isDerivedFrom" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
<ComponentType name="dcterms_created_description" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/">
<Child name="dcterms:W3CDTF" type="dcterms_date" />
</ComponentType>

<ComponentType name="dcterms_date" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" />

<ComponentType name="rdf_Bag" description="Structured block in an _annotation_ based on RDF.">
<Children name="rdf:li" type="rdf:li"/>
<Dynamics/>
<ComponentType name="dcterms_modified" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/">
<Child name="rdf:Description" type="dcterms_modified_description"/>
</ComponentType>

<ComponentType name="dcterms_modified_description" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/">
<Child name="dcterms:W3CDTF" type="dcterms_date_list" />
</ComponentType>

<ComponentType name="dcterms_date_list" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseAnnotation_without_ns"/>
<ComponentType name="dc_source" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseAnnotation_without_ns"/>

<ComponentType name="prism_keyword" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseAnnotation_without_ns"/>

<ComponentType name="collex_thumbnail" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseAnnotation_without_ns"/>

<ComponentType name="scoro_successor" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseAnnotation_without_ns"/>

<ComponentType name="rdf:li" description="Structured block in an _annotation_ based on RDF.">
<ComponentType name="rdfs_seeAlso" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseAnnotation_without_ns"/>

<ComponentType name="dcterms_references" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseAnnotation_without_ns"/>
<ComponentType name="dc_creator" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseAnnotation_without_ns"/>

<ComponentType name="dc_contributor" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseAnnotation_without_ns"/>

<ComponentType name="scoro_funder" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseAnnotation_without_ns"/>

<ComponentType name="foaf_name" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" >
<Text name="rdf:resource"/>
</ComponentType>
<ComponentType name="foaf_homepage" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" >
<Text name="rdf:resource"/>
</ComponentType>
<ComponentType name="foaf_account" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" >
<Text name="rdf:resource"/>
</ComponentType>
<ComponentType name="foaf_fundedBy" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" >
<Text name="rdf:resource"/>
</ComponentType>
<ComponentType name="foaf_mbox" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" >
<Text name="rdf:resource"/>
</ComponentType>
<ComponentType name="foaf_weblog" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" >
<Text name="rdf:resource"/>
</ComponentType>
<ComponentType name="foaf_thumbnail" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" >
<Text name="rdf:resource"/>
</ComponentType>
<ComponentType name="foaf_publications" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" >
<Text name="rdf:resource"/>
</ComponentType>
<ComponentType name="orcid_id" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" >
<Text name="rdf:resource"/>
<Dynamics/>
</ComponentType>


<ComponentType name="point3DWithDiam"
description="Base type for ComponentTypes which specify an ( _x, _y, _z ) coordinate along with a _diameter. Note: no dimension used in the attributes for these coordinates! These are assumed to have dimension micrometer (10^-6 m). This is due to micrometers being the default option for the majority of neuronal morphology formats, and dimensions are omitted here to facilitate reading and writing of morphologies in NeuroML.">
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4 changes: 2 additions & 2 deletions Schemas/NeuroML2/NeuroML_v2.3.1.xsd
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Expand Up @@ -2118,8 +2118,8 @@
<xs:element name="channelDensityNonUniformNernst" type="ChannelDensityNonUniformNernst" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="channelDensityNonUniformGHK" type="ChannelDensityNonUniformGHK" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="spikeThresh" type="SpikeThresh" minOccurs="1" maxOccurs="unbounded"/>
<xs:element name="specificCapacitance" type="SpecificCapacitance" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="initMembPotential" type="InitMembPotential" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="specificCapacitance" type="SpecificCapacitance" minOccurs="1" maxOccurs="unbounded"/>
<xs:element name="initMembPotential" type="InitMembPotential" minOccurs="1" maxOccurs="unbounded"/>
<!-- Taking this out until confirmation it's needed
<xs:element name="reversalPotential" type="ReversalPotential" minOccurs="0" maxOccurs="unbounded"/>-->
</xs:sequence>
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4 changes: 3 additions & 1 deletion examples/NML2_FullCell.nml
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Expand Up @@ -88,12 +88,14 @@

<channelDensity id="naChansSoma" ionChannel="NaConductance" segmentGroup="soma_group" condDensity="120.0 mS_per_cm2" erev="50mV" ion="na"/>

<spikeThresh value="-10mV" />
<spikeThresh value="0mV"/>

<specificCapacitance segmentGroup="soma_group" value="1.0 uF_per_cm2"/>

<specificCapacitance segmentGroup="dendrite_group" value="2.0 uF_per_cm2"/>

<initMembPotential value="-65mV"/>

</membraneProperties>

<intracellularProperties>
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18 changes: 8 additions & 10 deletions examples/NML2_FullNeuroML.nml
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Expand Up @@ -9,9 +9,8 @@
<!-- Example containing a range of different elements from NeuroML 2 -->



<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
<!-- Strucure of cell neurites -->
<!-- Structure of cell neurites -->

<morphology id="NeuroMorpho_PyrCell123"> <!-- see FullCell.xml for more details -->

Expand All @@ -21,6 +20,10 @@
<distal x="10" y="0" z="0" diameter="10"/>
</segment>

<segmentGroup id="soma_group">
<member segment="0"/>
</segmentGroup>

<!-- more needed -->

</morphology>
Expand Down Expand Up @@ -63,21 +66,16 @@
ion="na"
erev="50mV"/> <!-- Temporarily specifying erev in the channelDensity element-->

<!-- Ions present inside the cell. Note: a fixed reversal potential is specified here
<reversalPotential species="na" value="50mV"/>
<reversalPotential species="k" value="-77mV"/>-->
<spikeThresh value="0mV"/>
<specificCapacitance segmentGroup="soma_group" value="1.0 uF_per_cm2"/>
<initMembPotential value="-65mV"/>

<!-- more needed -->
<spikeThresh value="-10mV" />
</membraneProperties>

<intracellularProperties> <!-- used for bioelectrical properties inside a cell -->

<resistivity value="0.1 kohm_cm"/> <!-- Used for specific axial resistance -->

<!-- REMOVED UNTIL WE CHECK HOW THE USAGE OF LEMS IMPACTS THIS...
<biochemistry reactionScheme="InternalCaDynamics"/> Ref to earlier pathway -->

</intracellularProperties>

</biophysicalProperties>
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5 changes: 4 additions & 1 deletion examples/NML2_InhomogeneousParams.nml
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Expand Up @@ -71,8 +71,11 @@
</variableParameter>
</channelDensityNonUniform>

<spikeThresh value="-10mV" />
<spikeThresh value="0mV"/>

<specificCapacitance segmentGroup="soma_group" value="1.0 uF_per_cm2"/>

<initMembPotential value="-65mV"/>
</membraneProperties>

<intracellularProperties>
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