Merge branch 'OpenSourceBrain-master'

OpenSourceBrain · Dec 21, 2015 · 7d18594 · 7d18594
2 parents fc3313d + 21ee7e0
commit 7d18594
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Showing 3 changed files with 80 additions and 2 deletions.
diff --git a/NeuroML2/.test.validate.omt b/NeuroML2/.test.validate.omt
@@ -2,5 +2,5 @@
 
 # This test will validate all of the NeuroML 2 files in the current directory using: jnml -validate *.nml
 #  Missing  KAHP_CML.channel.nml  
-target: "Golgi*.channel.nml *.cell.nml *.net.nml"
+target: "Golgi*.channel.nml *.net.nml"
 engine: jNeuroML_validate
diff --git a/NeuroML2/LEMS_Soma_Test.xml b/NeuroML2/LEMS_Soma_Test.xml
@@ -19,6 +19,7 @@
     <Include file="Golgi_KV.channel.nml"/>
 
     <Include file="Golgi_Ca_HVA.channel.nml"/>
+     <Include file="Golgi_Ca_LVA.channel.nml"/>
 
     <Include file="Golgi_hcn1f.channel.nml"/>
     <Include file="Golgi_hcn1s.channel.nml"/>

diff --git a/NeuroML2/TestSoma.cell.nml b/NeuroML2/TestSoma.cell.nml
@@ -5,7 +5,7 @@
 
 
 
-    <cell id="TestSoma">
+    <cell type="cellTwoCaPools" id="TestSoma">
 
         <notes>A single segment/compartment cell</notes>
 
@@ -98,4 +98,81 @@
 
     </cell>
 
+
+    <ComponentType name="cellTwoCaPools"
+        extends="baseCellMembPot"
+        description="Cell with _segment_s specified in a _morphology_ element along with details on its _biophysicalProperties_. NOTE: this can only be correctly simulated using LEMS when there is a single segment in the cell, and _v of this cell represents the membrane potential in that isopotential segment!!!">
+
+        <Child name="notes" type="notes"/>
+        <Child name="annotation" type="annotation"/>
+
+        <Child name="morphology" type="morphology"/>
+
+        <Child name="biophysicalProperties" type="biophysicalProperties"/>
+
+        <Attachments name="synapses" type="basePointCurrent"/>
+
+        <Exposure name="spiking" dimension="none"/>
+        <Exposure name="debugVal" dimension="none"/>
+        <Exposure name="iChannels" dimension="current"/>
+        <Exposure name="iSyn" dimension="current"/>
+        <Exposure name="totSpecCap" dimension="specificCapacitance"/>
+
+        <Exposure name="surfaceArea" dimension="area"/>
+
+        <Exposure name="iCa" dimension="current"/>
+        <Exposure name="caConc" dimension="concentration"/>
+        <Exposure name="caConcExt" dimension="concentration"/>
+
+        <Text name="neuroLexId"/>
+
+        <Dynamics>
+            <StateVariable name="v" exposure="v" dimension="voltage"/>
+            <StateVariable name="spiking" exposure="spiking" dimension="none"/>
+            <StateVariable name="debugVal" exposure="debugVal" dimension="none"/>
+
+            <DerivedVariable name="initMembPot" dimension="voltage" select="biophysicalProperties/membraneProperties/initMembPotential/value"/>
+            <DerivedVariable name="thresh" dimension="voltage" select="biophysicalProperties/membraneProperties/spikeThresh/value"/>
+
+            <DerivedVariable name="debug" dimension="none" select="biophysicalProperties/membraneProperties/totChanCurrent"/>
+
+            <!--TODO replace this with just using first segment!!-->
+            <DerivedVariable name="surfaceArea" exposure="surfaceArea" dimension="area" select="morphology/segments[*]/surfaceArea" reduce="add"/>
+
+            <DerivedVariable name="totSpecCap" dimension="specificCapacitance" exposure="totSpecCap" select="biophysicalProperties/totSpecCap"/>
+            <DerivedVariable name="totCap" dimension="capacitance" value="totSpecCap * surfaceArea "/>
+
+            <DerivedVariable name="iChannels" dimension="current" exposure="iChannels" select="biophysicalProperties/membraneProperties/totChanCurrent"/>
+            <DerivedVariable name="iSyn" dimension="current" exposure="iSyn" select="synapses[*]/i" reduce="add" />
+
+            <DerivedVariable name="iCa" dimension="current" exposure="iCa" select="biophysicalProperties/membraneProperties/iCa"/>
+            <DerivedVariable name="caConc" dimension="concentration" exposure="caConc"  select="biophysicalProperties/intracellularProperties/caConc"/>
+            <DerivedVariable name="caConcExt" dimension="concentration" exposure="caConcExt"  select="biophysicalProperties/intracellularProperties/caConcExt"/>
+
+            <TimeDerivative variable="v" value="(iChannels + iSyn) / totCap"/>
+
+            <OnStart>
+                <StateAssignment variable="spiking" value="0"/>
+                <StateAssignment variable="v" value="initMembPot"/>
+            </OnStart>
+
+            <OnCondition test="v .gt. thresh .and. spiking .lt. 0.5">
+                <StateAssignment variable="spiking" value="1"/>
+                <EventOut port="spike"/>
+            </OnCondition>
+
+            <OnCondition test="v .lt. thresh">
+                <StateAssignment variable="spiking" value="0"/>
+            </OnCondition>
+
+            <OnCondition test="t .geq. 0">
+                <StateAssignment variable="debugVal" value="debug"/>
+            </OnCondition>
+
+        </Dynamics>
+
+    </ComponentType>
+
+
 </neuroml>
+