From 16a13104442b84b46d07d31dd482e62c829ebee6 Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Thu, 18 Apr 2024 16:42:31 +0100
Subject: [PATCH 01/11] Ensuring at least one <spikeThresh> on all
 <membraneProperties> elements

---
 examples/NML2_FullCell.nml            |  2 ++
 examples/NML2_FullNeuroML.nml         | 11 ++---------
 examples/NML2_InhomogeneousParams.nml |  2 ++
 3 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/examples/NML2_FullCell.nml b/examples/NML2_FullCell.nml
index a80c073..cc6fc5b 100644
--- a/examples/NML2_FullCell.nml
+++ b/examples/NML2_FullCell.nml
@@ -88,6 +88,8 @@
 
                 <channelDensity id="naChansSoma" ionChannel="NaConductance" segmentGroup="soma_group" condDensity="120.0 mS_per_cm2" erev="50mV" ion="na"/>
 
+                <spikeThresh value="0mV"/>
+
                 <specificCapacitance segmentGroup="soma_group" value="1.0 uF_per_cm2"/>
 
                 <specificCapacitance segmentGroup="dendrite_group" value="2.0 uF_per_cm2"/>
diff --git a/examples/NML2_FullNeuroML.nml b/examples/NML2_FullNeuroML.nml
index a824e3e..99957b4 100644
--- a/examples/NML2_FullNeuroML.nml
+++ b/examples/NML2_FullNeuroML.nml
@@ -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 -->
 
@@ -63,20 +62,14 @@
                             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"/>
 
-            <!-- more needed -->
         </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>
diff --git a/examples/NML2_InhomogeneousParams.nml b/examples/NML2_InhomogeneousParams.nml
index 3172cd6..7afc806 100644
--- a/examples/NML2_InhomogeneousParams.nml
+++ b/examples/NML2_InhomogeneousParams.nml
@@ -71,6 +71,8 @@
                     </variableParameter>
                 </channelDensityNonUniform>
 
+                <spikeThresh value="0mV"/>
+
                 <specificCapacitance segmentGroup="soma_group" value="1.0 uF_per_cm2"/>
             </membraneProperties>
 

From 9ff64acb72efbbaa26d4a9908e6afbd6e0a8b285 Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Fri, 19 Apr 2024 10:23:47 +0100
Subject: [PATCH 02/11] Update eden spike times to 0.2.3 behaviour

---
 LEMSexamples/test/.test.ex0.jnmleden.omt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/LEMSexamples/test/.test.ex0.jnmleden.omt b/LEMSexamples/test/.test.ex0.jnmleden.omt
index 51a8777..db1942b 100644
--- a/LEMSexamples/test/.test.ex0.jnmleden.omt
+++ b/LEMSexamples/test/.test.ex0.jnmleden.omt
@@ -25,7 +25,7 @@ experiments:
         spike detection:
           method: threshold
           threshold: -55.1
-        tolerance: 0.00010867391304343428
+        tolerance: 0.00010869565217381418
   iafPop0:
     observables:
       spike times:
@@ -36,7 +36,7 @@ experiments:
         spike detection:
           method: threshold
           threshold: -55.1
-        tolerance: 0.00014932775619959672
+        tolerance: 0.00014938751120392748
   iafRefPop0:
     observables:
       spike times:

From 5c2e0d930916d872758b100d93d074ae6d9d5df1 Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Wed, 24 Apr 2024 14:22:15 +0100
Subject: [PATCH 03/11] Update GHA versions

---
 .github/workflows/ci.yml     | 2 +-
 .github/workflows/omv-ci.yml | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index cfb639f..eb68408 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -16,7 +16,7 @@ jobs:
         java: [ '8', '11', '16', '17', '19' ]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up JDK ${{ matrix.java }}
       uses: actions/setup-java@v3
diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml
index bec4a7c..8510691 100644
--- a/.github/workflows/omv-ci.yml
+++ b/.github/workflows/omv-ci.yml
@@ -25,10 +25,10 @@ jobs:
           - PyLEMS_NeuroML2
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     
     - name: Set up Python  ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version:  ${{ matrix.python-version }}
 

From 8c5b64433c93da478da083d9fe428aefa311d7c2 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Mon, 29 Apr 2024 14:38:51 +0100
Subject: [PATCH 04/11] feat(core-types): add annotation component types

Fixes #224
---
 NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml | 106 ++++++++++++++++-----
 1 file changed, 83 insertions(+), 23 deletions(-)

diff --git a/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml b/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml
index 5bac908..0a59cff 100644
--- a/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml
+++ b/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml
@@ -36,38 +36,75 @@
     <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="bqbiol:encodes" type="bqbiol_encodes"/>
-        <Child name="bqbiol:hasPart" type="bqbiol_hasPart"/>
-        <Child name="bqbiol:hasProperty" type="bqbiol_hasProperty"/>
-        <Child name="bqbiol:hasVersion" type="bqbiol_hasVersion"/>
-        <Child name="bqbiol:is" type="bqbiol_is"/>
-        <Child name="bqbiol:isDescribedBy" type="bqbiol_isDescribedBy"/>
-        <Child name="bqbiol:isEncodedBy" type="bqbiol_isEncodedBy"/>
-        <Child name="bqbiol:isHomologTo" type="bqbiol_isHomologTo"/>
-        <Child name="bqbiol:isPartOf" type="bqbiol_isPartOf"/>
-        <Child name="bqbiol:isPropertyOf" type="bqbiol_isPropertyOf"/>
-        <Child name="bqbiol:isVersionOf" type="bqbiol_isVersionOf"/>
-        <Child name="bqbiol:occursIn" type="bqbiol_occursIn"/>
-        <Child name="bqbiol:hasTaxon" type="bqbiol_hasTaxon"/>
-        <Child name="bqmodel:is" type="bqmodel_is"/>
-        <Child name="bqmodel:isDescribedBy" type="bqmodel_isDescribedBy"/>
-        <Child name="bqmodel:isDerivedFrom" type="bqmodel_isDerivedFrom"/>
+        <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"/>
+        <Children name="bqbiol:encodes" type="bqbiol_encodes"/>
+        <Children name="bqbiol:hasPart" type="bqbiol_hasPart"/>
+        <Children name="bqbiol:hasProperty" type="bqbiol_hasProperty"/>
+        <Children name="bqbiol:hasVersion" type="bqbiol_hasVersion"/>
+        <Children name="bqbiol:is" type="bqbiol_is"/>
+        <Children name="bqbiol:isDescribedBy" type="bqbiol_isDescribedBy"/>
+        <Children name="bqbiol:isEncodedBy" type="bqbiol_isEncodedBy"/>
+        <Children name="bqbiol:isHomologTo" type="bqbiol_isHomologTo"/>
+        <Children name="bqbiol:isPartOf" type="bqbiol_isPartOf"/>
+        <Children name="bqbiol:isPropertyOf" type="bqbiol_isPropertyOf"/>
+        <Children name="bqbiol:isVersionOf" type="bqbiol_isVersionOf"/>
+        <Children name="bqbiol:occursIn" type="bqbiol_occursIn"/>
+        <Children name="bqbiol:hasTaxon" type="bqbiol_hasTaxon"/>
+        <Children name="bqmodel:is" type="bqmodel_is"/>
+        <Children name="bqmodel:isDescribedBy" type="bqmodel_isDescribedBy"/>
+        <Children name="bqmodel:isDerivedFrom" type="bqmodel_isDerivedFrom"/>
+        <Children name="bqmodel:isIntanceOf" type="bqmodel_isInstanceOf"/>
+        <Children name="bqmodel:hasInstance" type="bqmodel_hasInstance"/>
+        <Children name="prism:keyword" type="prism_keyword"/>
+        <Children name="collex:thumbnail" type="collex_thumbnail"/>
+        <Children name="scoro:successor" type="scoro_successor"/>
+        <Children name="rdfs:seeAlso" type="rdfs_seeAlso"/>
+        <Children name="dcterms:references" type="dcterms_references"/>
+        <Children name="dc:creator" type="dc_creator"/>
+        <Children name="dc:contributor" type="dc_contributor"/>
+        <Children name="scoro:funder" type="scoro_funder"/>
+        <Children name="dcterms:modified" type="dcterms_modified"/>
         <Text name="rdf:about"/>
+        <!-- for dates -->
+        <Text name="dcterms:W3CDTF"/>
         <Dynamics/>
     </ComponentType>
 
 
+    <!-- base RDF types -->
     <ComponentType name="baseBqbiol" description="Structured block in an _annotation_ based on RDF.">
         <Child name="rdf:Bag" type="rdf_Bag"/>
         <Dynamics/>
     </ComponentType>
 
+    <ComponentType name="rdf_Bag" description="Structured block in an _annotation_ based on RDF.">
+        <Children 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"/>
 
@@ -105,18 +142,41 @@
 
     <ComponentType name="bqmodel_isDerivedFrom" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
 
+    <ComponentType name="bqmodel_isInstanceOf" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
 
-    <ComponentType name="rdf_Bag" description="Structured block in an _annotation_ based on RDF.">
-        <Children name="rdf:li" type="rdf:li"/>
-        <Dynamics/>
-    </ComponentType>
+    <ComponentType name="bqmodel_hasInstance" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
 
+    <ComponentType name="dc_title" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" />
 
-    <ComponentType name="rdf:li" description="Structured block in an _annotation_ based on RDF.">
-        <Text name="rdf:resource"/>
-        <Dynamics/>
+    <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="rdf_Description"/>
+    </ComponentType>
+
+    <ComponentType name="dcterms_modified" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/">
+        <Child name="rdf:Description" type="rdf_Description"/>
     </ComponentType>
 
+    <ComponentType name="prism_keyword" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" />
+
+    <ComponentType name="collex_thumbnail" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseBqbiol"/>
+
+    <ComponentType name="scoro_successor" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseBqbiol"/>
+
+    <ComponentType name="rdfs_seeAlso" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseBqbiol"/>
+
+    <ComponentType name="dcterms_references" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseBqbiol"/>
+    <ComponentType name="dc_creator" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseBqbiol"/>
+
+    <ComponentType name="dc_contributor" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseBqbiol"/>
+
+    <ComponentType name="scoro_funder" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseBqbiol"/>
+
 
     <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.">

From 98d2ffdac9ed5efc1ee6802b9c2012507ec82295 Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Wed, 1 May 2024 16:42:51 +0100
Subject: [PATCH 05/11] Test on java 21

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index eb68408..86b5668 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -13,13 +13,13 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        java: [ '8', '11', '16', '17', '19' ]
+        java: [ '8', '11', '16', '17', '19', '21' ]
 
     steps:
     - uses: actions/checkout@v4
 
     - name: Set up JDK ${{ matrix.java }}
-      uses: actions/setup-java@v3
+      uses: actions/setup-java@v4
       with:
         java-version: ${{ matrix.java }}
         java-package: jdk

From 23fabbed1e1f181665c1e837129bd3d7c523c69c Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Fri, 3 May 2024 21:33:49 +0100
Subject: [PATCH 06/11] feat(annotations): update keywords

---
 NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml b/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml
index 0a59cff..f47983d 100644
--- a/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml
+++ b/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml
@@ -162,7 +162,7 @@
         <Child name="rdf:Description" type="rdf_Description"/>
     </ComponentType>
 
-    <ComponentType name="prism_keyword" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" />
+    <ComponentType name="prism_keyword" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseBqbiol"/>
 
     <ComponentType name="collex_thumbnail" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseBqbiol"/>
 

From 09f066d601f63e13e8b7c073f099ab823209f61a Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Fri, 3 May 2024 21:37:09 +0100
Subject: [PATCH 07/11] feat(annotations): update combine specifications URL

---
 NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml | 36 +++++++++++-----------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml b/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml
index f47983d..581bb85 100644
--- a/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml
+++ b/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml
@@ -106,45 +106,45 @@
     </ComponentType>
 
 
-    <ComponentType name="bqbiol_encodes" 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_hasPart" 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_hasProperty" 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_hasVersion" 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_is" 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_isDescribedBy" 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_isEncodedBy" 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_isHomologTo" 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_isPartOf" 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_isPropertyOf" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
+    <ComponentType name="bqbiol_isPropertyOf" 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">
+    <ComponentType name="bqbiol_isVersionOf" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol">
         <Text name="xmlns:bqbiol"/>
     </ComponentType>
 
-    <ComponentType name="bqbiol_occursIn" 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="bqbiol_hasTaxon" 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_is" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
+    <ComponentType name="bqmodel_is" 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">
+    <ComponentType name="bqmodel_isDescribedBy" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol">
         <Text name="xmlns:bqmodel"/>
     </ComponentType>
 
-    <ComponentType name="bqmodel_isDerivedFrom" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
+    <ComponentType name="bqmodel_isDerivedFrom" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>
 
-    <ComponentType name="bqmodel_isInstanceOf" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
+    <ComponentType name="bqmodel_isInstanceOf" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>
 
-    <ComponentType name="bqmodel_hasInstance" description="See http://co.mbine.org/standards/qualifiers" extends="baseBqbiol"/>
+    <ComponentType name="bqmodel_hasInstance" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>
 
     <ComponentType name="dc_title" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" />
 

From ff2587f6bbf55e3671b363a4c1b25f36f5688f65 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Fri, 3 May 2024 23:51:45 +0100
Subject: [PATCH 08/11] feat(annotations): add remaining FOAF bits

---
 NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml | 67 ++++++++++++++++++----
 1 file changed, 57 insertions(+), 10 deletions(-)

diff --git a/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml b/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml
index 581bb85..983d5f1 100644
--- a/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml
+++ b/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml
@@ -55,6 +55,18 @@
         <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"/>
+
         <Children name="bqbiol:encodes" type="bqbiol_encodes"/>
         <Children name="bqbiol:hasPart" type="bqbiol_hasPart"/>
         <Children name="bqbiol:hasProperty" type="bqbiol_hasProperty"/>
@@ -80,11 +92,10 @@
         <Children name="dcterms:references" type="dcterms_references"/>
         <Children name="dc:creator" type="dc_creator"/>
         <Children name="dc:contributor" type="dc_contributor"/>
+        <Children name="dc:source" type="dc_source"/>
         <Children name="scoro:funder" type="scoro_funder"/>
         <Children name="dcterms:modified" type="dcterms_modified"/>
         <Text name="rdf:about"/>
-        <!-- for dates -->
-        <Text name="dcterms:W3CDTF"/>
         <Dynamics/>
     </ComponentType>
 
@@ -126,9 +137,7 @@
 
     <ComponentType name="bqbiol_isPropertyOf" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>
 
-    <ComponentType name="bqbiol_isVersionOf" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol">
-        <Text name="xmlns:bqbiol"/>
-    </ComponentType>
+    <ComponentType name="bqbiol_isVersionOf" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol" />
 
     <ComponentType name="bqbiol_occursIn" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>
 
@@ -136,9 +145,7 @@
 
     <ComponentType name="bqmodel_is" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>
 
-    <ComponentType name="bqmodel_isDescribedBy" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol">
-        <Text name="xmlns:bqmodel"/>
-    </ComponentType>
+    <ComponentType name="bqmodel_isDescribedBy" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol" />
 
     <ComponentType name="bqmodel_isDerivedFrom" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>
 
@@ -155,13 +162,26 @@
     <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="rdf_Description"/>
+        <Child name="rdf:Description" type="dcterms_created_description"/>
+    </ComponentType>
+
+    <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="dcterms_modified" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/">
-        <Child name="rdf:Description" type="rdf_Description"/>
+        <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="baseBqbiol"/>
+    <ComponentType name="dc_source" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseBqbiol"/>
+
     <ComponentType name="prism_keyword" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseBqbiol"/>
 
     <ComponentType name="collex_thumbnail" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseBqbiol"/>
@@ -177,6 +197,33 @@
 
     <ComponentType name="scoro_funder" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseBqbiol"/>
 
+    <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"/>
+    </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.">

From 089514713ee047a2d92cb5d9316ae1c7a0053880 Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Tue, 7 May 2024 18:08:42 +0100
Subject: [PATCH 09/11] feat(annotations): use Child instead of Children

Not sure why this is given that Child is meant to mean "one and only
one" and Children mean "one or more". But, using Children causes tests
to fail in org.neuroml.export etc. when building jNeuroML.

This needs looking into.

See also https://github.com/NeuroML/NeuroML2/issues/54
---
 NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml | 102 +++++++++++----------
 1 file changed, 56 insertions(+), 46 deletions(-)

diff --git a/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml b/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml
index 983d5f1..3255598 100644
--- a/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml
+++ b/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml
@@ -67,51 +67,61 @@
         <Child name="foaf:publications" type="foaf_publications"/>
         <Child name="orcid:id" type="orcid_id"/>
 
-        <Children name="bqbiol:encodes" type="bqbiol_encodes"/>
-        <Children name="bqbiol:hasPart" type="bqbiol_hasPart"/>
-        <Children name="bqbiol:hasProperty" type="bqbiol_hasProperty"/>
-        <Children name="bqbiol:hasVersion" type="bqbiol_hasVersion"/>
-        <Children name="bqbiol:is" type="bqbiol_is"/>
-        <Children name="bqbiol:isDescribedBy" type="bqbiol_isDescribedBy"/>
-        <Children name="bqbiol:isEncodedBy" type="bqbiol_isEncodedBy"/>
-        <Children name="bqbiol:isHomologTo" type="bqbiol_isHomologTo"/>
-        <Children name="bqbiol:isPartOf" type="bqbiol_isPartOf"/>
-        <Children name="bqbiol:isPropertyOf" type="bqbiol_isPropertyOf"/>
-        <Children name="bqbiol:isVersionOf" type="bqbiol_isVersionOf"/>
-        <Children name="bqbiol:occursIn" type="bqbiol_occursIn"/>
-        <Children name="bqbiol:hasTaxon" type="bqbiol_hasTaxon"/>
-        <Children name="bqmodel:is" type="bqmodel_is"/>
-        <Children name="bqmodel:isDescribedBy" type="bqmodel_isDescribedBy"/>
-        <Children name="bqmodel:isDerivedFrom" type="bqmodel_isDerivedFrom"/>
-        <Children name="bqmodel:isIntanceOf" type="bqmodel_isInstanceOf"/>
-        <Children name="bqmodel:hasInstance" type="bqmodel_hasInstance"/>
-        <Children name="prism:keyword" type="prism_keyword"/>
-        <Children name="collex:thumbnail" type="collex_thumbnail"/>
-        <Children name="scoro:successor" type="scoro_successor"/>
-        <Children name="rdfs:seeAlso" type="rdfs_seeAlso"/>
-        <Children name="dcterms:references" type="dcterms_references"/>
-        <Children name="dc:creator" type="dc_creator"/>
-        <Children name="dc:contributor" type="dc_contributor"/>
-        <Children name="dc:source" type="dc_source"/>
-        <Children name="scoro:funder" type="scoro_funder"/>
-        <Children name="dcterms:modified" type="dcterms_modified"/>
+        <Child name="bqbiol:encodes" type="bqbiol_encodes"/>
+        <Child name="bqbiol:hasPart" type="bqbiol_hasPart"/>
+        <Child name="bqbiol:hasProperty" type="bqbiol_hasProperty"/>
+        <Child name="bqbiol:hasVersion" type="bqbiol_hasVersion"/>
+        <Child name="bqbiol:is" type="bqbiol_is"/>
+        <Child name="bqbiol:isDescribedBy" type="bqbiol_isDescribedBy"/>
+        <Child name="bqbiol:isEncodedBy" type="bqbiol_isEncodedBy"/>
+        <Child name="bqbiol:isHomologTo" type="bqbiol_isHomologTo"/>
+        <Child name="bqbiol:isPartOf" type="bqbiol_isPartOf"/>
+        <Child name="bqbiol:isPropertyOf" type="bqbiol_isPropertyOf"/>
+        <Child name="bqbiol:isVersionOf" type="bqbiol_isVersionOf"/>
+        <Child name="bqbiol:occursIn" type="bqbiol_occursIn"/>
+        <Child name="bqbiol:hasTaxon" type="bqbiol_hasTaxon"/>
+        <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>
 
 
     <!-- base RDF types -->
-    <ComponentType name="baseBqbiol" description="Structured block in an _annotation_ based on RDF.">
+    <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.">
-        <Children name="rdf:li" type="rdf:li"/>
+        <Child name="rdf:li" type="rdf_li"/>
         <Dynamics/>
     </ComponentType>
 
-    <ComponentType name="rdf:li" description="Structured block in an _annotation_ based on RDF.">
+    <ComponentType name="rdf_li" description="Structured block in an _annotation_ based on RDF.">
         <Text name="rdf:resource"/>
         <Dynamics/>
     </ComponentType>
@@ -143,15 +153,15 @@
 
     <ComponentType name="bqbiol_hasTaxon" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>
 
-    <ComponentType name="bqmodel_is" description="See https://github.com/combine-org/combine-specifications" extends="baseBqbiol"/>
+    <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="baseBqbiol" />
+    <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="baseBqbiol"/>
+    <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="baseBqbiol"/>
+    <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="baseBqbiol"/>
+    <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/" />
 
@@ -179,23 +189,23 @@
         <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="baseBqbiol"/>
-    <ComponentType name="dc_source" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseBqbiol"/>
+    <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="baseBqbiol"/>
+    <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="baseBqbiol"/>
+    <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="baseBqbiol"/>
+    <ComponentType name="scoro_successor" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseAnnotation_without_ns"/>
 
-    <ComponentType name="rdfs_seeAlso" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseBqbiol"/>
+    <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="baseBqbiol"/>
-    <ComponentType name="dc_creator" description="https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/" extends="baseBqbiol"/>
+    <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="baseBqbiol"/>
+    <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="baseBqbiol"/>
+    <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"/>

From ed7b92b91ec075a687d07c8a275c1937f888c745 Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Wed, 29 May 2024 14:27:12 +0100
Subject: [PATCH 10/11] Add soma_group, as it's referred to in channelDensity

---
 examples/NML2_FullNeuroML.nml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/examples/NML2_FullNeuroML.nml b/examples/NML2_FullNeuroML.nml
index 99957b4..b44f4b3 100644
--- a/examples/NML2_FullNeuroML.nml
+++ b/examples/NML2_FullNeuroML.nml
@@ -20,6 +20,10 @@
             <distal x="10" y="0" z="0" diameter="10"/>
         </segment>
 
+        <segmentGroup id="soma_group">   
+            <member segment="0"/>
+        </segmentGroup>
+
         <!-- more needed -->
 
     </morphology>

From fe3aa27d2ed146938be3efa19dfb15ddd8cc3804 Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Fri, 31 May 2024 10:29:46 +0100
Subject: [PATCH 11/11] Make membraneProperties require at least one each of
 specificCapacitance and initMembPotential

---
 Schemas/NeuroML2/NeuroML_v2.3.1.xsd   | 4 ++--
 examples/NML2_FullCell.nml            | 2 ++
 examples/NML2_FullNeuroML.nml         | 2 ++
 examples/NML2_InhomogeneousParams.nml | 2 ++
 4 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/Schemas/NeuroML2/NeuroML_v2.3.1.xsd b/Schemas/NeuroML2/NeuroML_v2.3.1.xsd
index 877edef..741f1e8 100644
--- a/Schemas/NeuroML2/NeuroML_v2.3.1.xsd
+++ b/Schemas/NeuroML2/NeuroML_v2.3.1.xsd
@@ -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>
diff --git a/examples/NML2_FullCell.nml b/examples/NML2_FullCell.nml
index cc6fc5b..51b0288 100644
--- a/examples/NML2_FullCell.nml
+++ b/examples/NML2_FullCell.nml
@@ -94,6 +94,8 @@
 
                 <specificCapacitance segmentGroup="dendrite_group" value="2.0 uF_per_cm2"/>
 
+                <initMembPotential value="-65mV"/>
+
             </membraneProperties>
 
             <intracellularProperties>
diff --git a/examples/NML2_FullNeuroML.nml b/examples/NML2_FullNeuroML.nml
index b44f4b3..32fb42c 100644
--- a/examples/NML2_FullNeuroML.nml
+++ b/examples/NML2_FullNeuroML.nml
@@ -67,6 +67,8 @@
                             erev="50mV"/>  <!-- Temporarily specifying erev in the channelDensity element-->
 
             <spikeThresh value="0mV"/>
+            <specificCapacitance segmentGroup="soma_group" value="1.0 uF_per_cm2"/>
+            <initMembPotential value="-65mV"/>
 
         </membraneProperties>
 
diff --git a/examples/NML2_InhomogeneousParams.nml b/examples/NML2_InhomogeneousParams.nml
index 85f8ac9..5703d38 100644
--- a/examples/NML2_InhomogeneousParams.nml
+++ b/examples/NML2_InhomogeneousParams.nml
@@ -74,6 +74,8 @@
                 <spikeThresh value="0mV"/>
 
                 <specificCapacitance segmentGroup="soma_group" value="1.0 uF_per_cm2"/>
+                
+                <initMembPotential value="-65mV"/>
             </membraneProperties>
 
             <intracellularProperties>