Merge pull request #10 from OpenSourceBrain/development

Latest development to master - fixes for nml validation
OpenSourceBrain · Aug 20, 2024 · 0379682 · 0379682
2 parents 42cf61b + a88d6ad
commit 0379682
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Showing 5 changed files with 56 additions and 53 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,6 @@
+arm64
+__pycache__
+*.log
 *.dat
 x86_64/
 channels/*dat

diff --git a/NeuroML2/.test.validate.omt b/NeuroML2/.test.validate.omt
@@ -1,7 +1,5 @@
 # Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation 
-# Still in development, subject to change without notice!!
 
-
-# This test will validate MOST all of the NeuroML 2 files in the current directory
-target: "*.c*.nml"
+# This test will validate all of the NeuroML 2 files in the current directory using: jnml -validate *.nml
+target: "*.nml"
 engine: jNeuroML_validate
diff --git a/NeuroML2/GGN.cell.nml b/NeuroML2/GGN.cell.nml
@@ -1,4 +1,4 @@
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" 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_v2.3.xsd" id="NeuroML2_file_exported_from_NEURON">
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" 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_v2.3.1.xsd" id="NeuroML2_file_exported_from_NEURON">
     <notes> NeuroML 2 file generated from ModelView by: NEURON -- VERSION 8.2.4+ HEAD (1d87d5d39+) 2024-02-09
           Authors: Michael Hines, Sushil Kambampati and Padraig Gleeson,
           Yale University and UCL 
@@ -9,52 +9,52 @@
         <annotation>
 
             <rdf:RDF
+              xmlns:orcid="https://orcid.org/"
+              xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
               xmlns:dc="http://purl.org/dc/elements/1.1/"
               xmlns:dcterms="http://purl.org/dc/terms/"
-              xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
               xmlns:bqmodel="http://biomodels.net/model-qualifiers/"
+              xmlns:foaf="http://xmlns.com/foaf/0.1/"
             >
               <rdf:Description rdf:about="GGN">
                 <dc:title>Giant GABAergic Neuron model</dc:title>
                 <dc:description>Subhasis Ray, Zane N Aldworth, Mark A Stopfer (2020) Feedback inhibition and its control in an insect olfactory circuit eLife 9:e53281.</dc:description>
                 <dc:source>
-                  <rdf:Bag rdf:nodeID="N0f08af6f211344f29b04cb3d3175c192">
-                    <rdf:_1 rdf:resource="https://modeldb.science/262670"/>
-                  </rdf:Bag>
-                </dc:source>
-                <dc:source>
-                  <rdf:Bag rdf:nodeID="N19161119d1f64f4c85fcb0288a1327a8">
-                    <rdf:_1 rdf:resource="https://github.com/OpenSourceBrain/262670"/>
-                  </rdf:Bag>
-                </dc:source>
-                <dc:source>
-                  <rdf:Bag rdf:nodeID="N8ce8cb74c0a44bfc9943bd92fa055577">
-                    <rdf:_1 rdf:resource="https://v1.opensourcebrain.org/projects/locust-mushroom-body"/>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://modeldb.science/262670"/>
+                    <rdf:li rdf:resource="https://github.com/OpenSourceBrain/262670"/>
+                    <rdf:li rdf:resource="https://v1.opensourcebrain.org/projects/locust-mushroom-body"/>
                   </rdf:Bag>
                 </dc:source>
                 <bqmodel:isDescribedBy>
-                  <rdf:Bag rdf:nodeID="N7d8930ba1e9546d6b602231ee8f9634b">
-                    <rdf:_1 rdf:resource="https://doi.org/10.7554/eLife.53281"/>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://doi.org/10.7554/eLife.53281"/>
                   </rdf:Bag>
                 </bqmodel:isDescribedBy>
                 <dc:creator>
-                  <rdf:Bag rdf:nodeID="N2039210e1f7f4ffc97970ed011e0e937">
-                    <rdf:_1>Subhasis Ray</rdf:_1>
-                    <rdf:_2>https://orcid.org/0000-0003-2566-7146</rdf:_2>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="#Subhasis_Ray"/>
                   </rdf:Bag>
                 </dc:creator>
                 <dc:contributor>
-                  <rdf:Bag rdf:nodeID="N7d06673bf9de4e1293ebcff99aab56d9">
-                    <rdf:_1>Ankur Sinha</rdf:_1>
-                    <rdf:_2>https://orcid.org/0000-0001-7568-7167</rdf:_2>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="#Ankur_Sinha"/>
                   </rdf:Bag>
                 </dc:contributor>
                 <dcterms:created>
-                  <rdf:Description rdf:nodeID="N76d82b5ef0b94239a6530a5cd976a7ac">
+                  <rdf:Description>
                     <dcterms:W3CDTF>2024-04-25</dcterms:W3CDTF>
                   </rdf:Description>
                 </dcterms:created>
               </rdf:Description>
+              <rdf:Description rdf:about="#Ankur_Sinha">
+                <foaf:name>Ankur Sinha</foaf:name>
+                <orcid:id rdf:resource="https://orcid.org/0000-0001-7568-7167"/>
+              </rdf:Description>
+              <rdf:Description rdf:about="#Subhasis_Ray">
+                <foaf:name>Subhasis Ray</foaf:name>
+                <orcid:id rdf:resource="https://orcid.org/0000-0003-2566-7146"/>
+              </rdf:Description>
             </rdf:RDF>
 
         </annotation>
@@ -213258,6 +213258,7 @@
         <biophysicalProperties id="biophys">
             <membraneProperties>
                 <channelDensity id="pas" ionChannel="pas" condDensity="0.00003 S_per_cm2" erev="-51 mV" ion="non_specific"/>
+                <spikeThresh value="-10mV"/>
                 <specificCapacitance value="1 uF_per_cm2"/>
                 <initMembPotential value="-80mV"/>
             </membraneProperties>

diff --git a/NeuroML2/KC.cell.nml b/NeuroML2/KC.cell.nml
@@ -1,4 +1,4 @@
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" 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_v2.3.xsd" id="KC_doc">
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" 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_v2.3.1.xsd" id="KC_doc">
     <include href="channels/pas.channel.nml"/>
     <include href="channels/kv.channel.nml"/>
     <include href="channels/ka.channel.nml"/>
@@ -9,58 +9,58 @@
         <annotation>
 
             <rdf:RDF
+              xmlns:orcid="https://orcid.org/"
+              xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
               xmlns:dc="http://purl.org/dc/elements/1.1/"
-              xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
               xmlns:dcterms="http://purl.org/dc/terms/"
-              xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+              xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
               xmlns:bqmodel="http://biomodels.net/model-qualifiers/"
+              xmlns:foaf="http://xmlns.com/foaf/0.1/"
             >
               <rdf:Description rdf:about="KC">
                 <dc:title>Kenyon cell model</dc:title>
                 <dc:description>Subhasis Ray, Zane N Aldworth, Mark A Stopfer (2020) Feedback inhibition and its control in an insect olfactory circuit eLife 9:e53281.</dc:description>
                 <bqbiol:encodes>
-                  <rdf:Bag rdf:nodeID="Nc00a268a26874598bff06e0876cc57ed">
-                    <rdf:_1 rdf:resource="http://uri.neuinfo.org/nif/nifstd/nlx_147420"/>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://uri.neuinfo.org/nif/nifstd/nlx_147420"/>
                   </rdf:Bag>
                 </bqbiol:encodes>
                 <dc:source>
-                  <rdf:Bag rdf:nodeID="N273df5f0f5134d69aa88c5f4be36205f">
-                    <rdf:_1 rdf:resource="https://modeldb.science/262670"/>
-                  </rdf:Bag>
-                </dc:source>
-                <dc:source>
-                  <rdf:Bag rdf:nodeID="N52bb0f14a2c745b5ad6ad543a175b940">
-                    <rdf:_1 rdf:resource="https://github.com/OpenSourceBrain/262670"/>
-                  </rdf:Bag>
-                </dc:source>
-                <dc:source>
-                  <rdf:Bag rdf:nodeID="N8ba0bc6b71f04e1297a2f41690fb845e">
-                    <rdf:_1 rdf:resource="https://v1.opensourcebrain.org/projects/locust-mushroom-body"/>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://modeldb.science/262670"/>
+                    <rdf:li rdf:resource="https://github.com/OpenSourceBrain/262670"/>
+                    <rdf:li rdf:resource="https://v1.opensourcebrain.org/projects/locust-mushroom-body"/>
                   </rdf:Bag>
                 </dc:source>
                 <bqmodel:isDescribedBy>
-                  <rdf:Bag rdf:nodeID="N32688f93918a4ad38df9061c90c2ab30">
-                    <rdf:_1 rdf:resource="https://doi.org/10.7554/eLife.53281"/>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://doi.org/10.7554/eLife.53281"/>
                   </rdf:Bag>
                 </bqmodel:isDescribedBy>
                 <dc:creator>
-                  <rdf:Bag rdf:nodeID="Ncd61d80f8e2c4b2a945b3daf84437df6">
-                    <rdf:_1>Subhasis Ray</rdf:_1>
-                    <rdf:_2>https://orcid.org/0000-0003-2566-7146</rdf:_2>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="#Subhasis_Ray"/>
                   </rdf:Bag>
                 </dc:creator>
                 <dc:contributor>
-                  <rdf:Bag rdf:nodeID="N8376b6c99c734829a6c8a38eca97b3da">
-                    <rdf:_1>Ankur Sinha</rdf:_1>
-                    <rdf:_2>https://orcid.org/0000-0001-7568-7167</rdf:_2>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="#Ankur_Sinha"/>
                   </rdf:Bag>
                 </dc:contributor>
                 <dcterms:created>
-                  <rdf:Description rdf:nodeID="Ncc1a5b98ec974d12b90db9403e67ef79">
+                  <rdf:Description>
                     <dcterms:W3CDTF>2024-04-25</dcterms:W3CDTF>
                   </rdf:Description>
                 </dcterms:created>
               </rdf:Description>
+              <rdf:Description rdf:about="#Ankur_Sinha">
+                <foaf:name>Ankur Sinha</foaf:name>
+                <orcid:id rdf:resource="https://orcid.org/0000-0001-7568-7167"/>
+              </rdf:Description>
+              <rdf:Description rdf:about="#Subhasis_Ray">
+                <foaf:name>Subhasis Ray</foaf:name>
+                <orcid:id rdf:resource="https://orcid.org/0000-0003-2566-7146"/>
+              </rdf:Description>
             </rdf:RDF>
 
         </annotation>

diff --git a/NeuroML2/postprocess_cells.py b/NeuroML2/postprocess_cells.py
@@ -114,6 +114,7 @@ def postprocess_GGN():
     cell.set_resistivity("0.1 kohm_cm", group_id="all")
     cell.set_specific_capacitance("1 uF_per_cm2", group_id="all")
     cell.set_init_memb_potential("-80mV")
+    cell.set_spike_thresh("-10mV")
 
     # L1 validation
     # cell.validate(recursive=True)