Updating support for instance based network descriptions. Preferred format for NML2 is shown in examples/NML2_InstanceBasedNetwork.nml, with lists of instances in populations, connections in projections and inputs in inputLists.

jLEMS can now read and execute nml files in this format, see NeuroML2CoreTypes/LEMS_NML2_Ex13_Instances.xml.
Schema and other examples updated accordingly.
Note: paths used in selecting cells in connection and input need to be improved!

Author: pgleeson

NeuroML2CoreTypes/LEMS_NML2_Ex13_Instances.xml

@@ -23,9 +23,10 @@
 
     <Simulation id="sim1" length="300ms" step="0.05ms" target="InstanceBasedNetwork">
 
-        <Display id="d1" title="Ex13: Instance Based Network in LEMS" timeScale="1ms" xmin="0" xmax="300" ymin="-75" ymax="-50">
+        <Display id="d1" title="Ex13: Instance Based Network in LEMS" timeScale="1ms" xmin="0" xmax="300" ymin="-65" ymax="-52">
             <Line id ="iaf0" quantity="iafCells/0/iaf/v" scale="1mV"  color="#ee0555" timeScale="1ms"/>
             <Line id ="iaf1" quantity="iafCells/1/iaf/v" scale="1mV"  color="#999255" timeScale="1ms"/>
+            <Line id ="iaf2" quantity="iafCells/2/iaf/v" scale="1mV"  color="#911155" timeScale="1ms"/>
         </Display>
 
 

NeuroML2CoreTypes/Networks.xml

@@ -57,7 +57,7 @@
     </ComponentType>
 
 
-    <ComponentType name="populationList" extends="basePopulation" description="An explicit list of the cells in the population. Not yet stable...">
+    <ComponentType name="populationList" extends="basePopulation" description="An explicit list of the cells in the population. Work in progress...">
 
         <Children name="instances" type="instance"/>
 
@@ -78,14 +78,6 @@
         <Parameter name="y" dimension="none"/>
         <Parameter name="z" dimension="none"/>
     </ComponentType>
-
-    <!--
-    <ComponentType name="networkElementInstance1D"
-        extends="instance"
-        description="Initial attempt to specify instances in 1D populations. Work in progress...">
-        <Parameter name="x" dimension="none"/>
-    </ComponentType>-->
-
 
 
     <ComponentType name="region" description="Initial attempt to specify 3D region for placing cells. Work in progress...">
@@ -106,37 +98,41 @@
 
     <ComponentType name="projection"
         description="Projection from one population to another. Currently it's better to define an explicit list of connections, using _explicitConnection_. Work in progress...">
-        <Children name="synapticConnections" type="synapticConnection"/>
+        <!--TODO: allow more than one...-->
+        <Child name="synapseComponent" type="synapseComponent"/>
         <Children name="connections" type="connection"/>
-        <Path name="from"/>
-        <Path name="to"/>
+        <ComponentReference name="synapse" type="baseSynapse"/>
+        <Path name="presynapticPopulation"/>
+        <Path name="postsynapticPopulation"/>
     </ComponentType>
 
 
-
-    <ComponentType name="explicitConnection"
-        description="Explicit event connection between components">
-        <Path name="from"/>
-        <Path name="to"/>
-        <Text name="targetPort"/>
+    <ComponentType name="synapseComponent" description="Work in progress...">
+        <ComponentReference name="component" type="baseSynapse"/>
     </ComponentType>
 
 
     <ComponentType name="connection"
-        extends="explicitConnection"
         description="Explicit event connection directly between named components">
 
-        <Path name="from"/> <!-- TODO check if these really need to be here if in explicitConnection... -->
-        <Path name="to"/>
+        <Path name="preCellId"/>
+        <Path name="postCellId"/>
 
         <Structure>
-            <With instance="from" as="a"/>
-            <With instance="to" as="b"/>
-            <EventConnection from="a" to="b" targetPort="targetPort"/>
+            <With instance="preCellId" as="a"/>
+            <With instance="postCellId" as="b"/>
+            <EventConnection from="a" to="b" receiver="../synapse" receiverContainer="destination" sourcePort="sourcePort" targetPort="targetPort"/>
         </Structure>
 
     </ComponentType>
 
+    <ComponentType name="explicitConnection"
+        description="Explicit event connection between components">
+        <Path name="from"/>
+        <Path name="to"/>
+        <Text name="targetPort"/>
+    </ComponentType>
+
 
     <ComponentType name="synapticConnection"
         description="Explicit event connection between named components, which gets processed via a new instance of a _synapse component which is created on the target component"
@@ -224,24 +220,23 @@
 
     <ComponentType name="inputList" description="An explicit list of inputs. Not yet stable...">
 
-
         <Children name="inputs" type="input"/>
-
         <ComponentReference name="component" type="basePointCurrent"/>
+        <Text name="population"/>
+
     </ComponentType>
 
 
     <ComponentType name="input" description="Initial attempt to specify input lists. Work in progress...">
 
         <Path name="target"/>
+        <Text name="destination"/>
         <Structure>
-            <ChildInstance component="../component"/>
 
             <With instance="target" as="a"/>
             <With instance="target" as="b"/>
 
-            <!--<EventConnection from="a" to="b" receiver="input" receiverContainer="destination" sourcePort="sourcePort" targetPort="targetPort"/>-->
-            <EventConnection from="a" to="b" receiver="input" receiverContainer="destination"/>
+            <EventConnection from="a" to="b" receiver="../component" receiverContainer="destination"/>
         </Structure>
 
     </ComponentType>