Networks.xml

<Lems xmlns="http://www.neuroml.org/lems/0.7.1"
      xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
      xsi:schemaLocation="http://www.neuroml.org/lems/0.7.1 ../../LEMS/Schemas/LEMS/LEMS_v0.7.1.xsd"
      description="Network descriptions in NeuroML 2. Describes _network_ elements containing _population_s ">

    <!-- A number of network elements for use in NeuroML 2 documents  -->
    
    <Include file="NeuroMLCoreDimensions.xml"/>
    <Include file="Synapses.xml"/>


    <ComponentType name="network" description="Network containing _population_s, _projection_s and lists of _explicitConnection_s (either directly between components of the populations or via synapses)">

        <Children name="regions" type="region"/>
        <Children name="populations" type="basePopulation"/>
        
        <Children name="projections" type="projection"/>
        <Children name="synapticConnections" type="explicitConnection"/>  <!-- Connection either directly between cells or to synapse attachment on post cell-->

        <Children name="explicitInputs" type="explicitInput"/>
        <Children name="inputs" type="inputList"/>

    </ComponentType>
    
    
    <ComponentType name="networkWithTemperature" description="Network containing _population_s, _projection_s and lists of _explicitConnection_s (either directly between components of the populations or via synapses), and an explicit temperature" extends="network">

        <Parameter name="temperature" dimension="temperature"/>

    </ComponentType>


    <ComponentType name="basePopulation" description="A population of cells (anything which extends _baseCell_)">        
        <Child name="notes" type="notes"/>
        <Child name="annotation" type="annotation"/>
        <ComponentReference name="component" type="baseCell"/>
    </ComponentType>


    <ComponentType name="population" extends="basePopulation" description="A population of components, with just one parameter for the _size">
        <Parameter name="size" dimension="none" description="Number of instances of this Component to create when the population is instantiated"/>
        <ComponentReference name="component" type="Component"/>
        <Structure>
            <MultiInstantiate number="size" component="component"/>
        </Structure>
    </ComponentType>


    <ComponentType name="populationList" extends="basePopulation" description="An explicit list of the cells in the population. Work in progress...">
        <Children name="instances" type="instance"/>
    
        <ComponentReference name="component" type="baseCell"/>
    </ComponentType>


    <ComponentType name="instance" description="Initial attempt to specify instances in populations. Work in progress...">
        <Child name="location" type="location"/>
        <Structure>
            <ChildInstance component="../component"/>
        </Structure>

    </ComponentType>


    <ComponentType name="location" description="Initial attempt to specify instances in populations. Work in progress...">
        <Parameter name="x" dimension="none"/>
        <Parameter name="y" dimension="none"/>
        <Parameter name="z" dimension="none"/>
    </ComponentType>
    

    <ComponentType name="region" description="Initial attempt to specify 3D region for placing cells. Work in progress...">
        <Child name="rectangularExtent" type="rectangularExtent"/>
    </ComponentType>


    <ComponentType name="rectangularExtent" description="For defining a 3D rectangular box">
        <Parameter name="xStart" dimension="none"/>
        <Parameter name="yStart" dimension="none"/>
        <Parameter name="zStart" dimension="none"/>
        <Parameter name="xLength" dimension="none"/>
        <Parameter name="yLength" dimension="none"/>
        <Parameter name="zLength" dimension="none"/>
    </ComponentType>


    <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...">
        <!--TODO: allow more than one...-->
        <Child name="synapseComponent" type="synapseComponent"/>
        <Children name="connections" type="connection"/>
        <ComponentReference name="synapse" type="baseSynapse"/>
        <Path name="presynapticPopulation"/>
        <Path name="postsynapticPopulation"/>
    </ComponentType>


    <ComponentType name="synapseComponent" description="Work in progress...">
        <ComponentReference name="component" type="baseSynapse"/>
    </ComponentType>


    <ComponentType name="connection"
        description="Explicit event connection directly between named components, which gets processed via a new instance of a _synapse component which is created on the target component. Normally contained inside a _projection_ element.">

        <Path name="preCellId"/>
        <Path name="postCellId"/>
        <Text name="destination"/>

        <Structure>
            <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"
        extends="explicitConnection">

        <ComponentReference name="synapse" type="baseSynapse"/>
        <Path name="from"/>
        <Path name="to"/>
        <Text name="destination"/>

        <Structure>
            <With instance="from" as="a"/>
            <With instance="to" as="b"/>
            <EventConnection from="a" to="b" receiver="synapse" receiverContainer="destination" sourcePort="sourcePort" targetPort="targetPort"/>
            <!--<EventConnection from="a" to="b" receiver="synapse"/>-->
        </Structure>
    </ComponentType>


    <ComponentType name="synapticConnectionWD"
                   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, includes setting of _weight and _delay for the synaptic connection"
                   extends="synapticConnection">

        <Parameter name="weight" dimension="none"/>
        <Parameter name="delay" dimension="time"/>
        <Path name="from"/>
        <Path name="to"/>

        <Structure>
            <With instance="from" as="a"/>
            <With instance="to" as="b"/>
            <!--<EventConnection from="a" to="b" receiver="synapse" receiverContainer="destination" sourcePort="sourcePort" targetPort="targetPort" delay="delay">-->
            <EventConnection from="a" to="b" receiver="synapse" delay="delay">
                <!--TODO: put back in! -->
                <Assign property="weight" value="weight"/>
            </EventConnection>
        </Structure>

    </ComponentType>


    <!--   Not yet stable...

    <Component Type name="EventConnectivity">
        <Child name="Connections" type="ConnectionPattern"/>
        <Link name="source" type="population"/>
        <Link name="target" type="population"/>
    </ComponentType>

    <Component Type name="ConnectionPattern">
    </ComponentType>
    
    <Component Type name="AllAll" extends="ConnectionPattern">
        <Dynamics>
            <Build>
                <ForEach instances="../source" as="a">
                     <ForEach instances="../target" as="b">
                          <EventConnection from="a" to="b"/>
                     </ForEach>
                </ForEach>
            </Build>
        </Dynamics>
    </ComponentType>-->


    <ComponentType name="explicitInput" description="An explicit input (anything which extends _basePointCurrent_) to a target cell in a population">

        <ComponentReference name="input" type="basePointCurrent"/>

        <Path name="target"/>

        <Text name="destination"/>
        <Text name="sourcePort"/>
        <Text name="targetPort"/>

        <Structure>
            <With instance="target" as="a"/>
            <With instance="target" as="b"/>

            <EventConnection from="a" to="b" receiver="input" receiverContainer="destination"/>
        </Structure>
    </ComponentType>


    <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>

            <With instance="target" as="a"/>
            <With instance="target" as="b"/>

            <EventConnection from="a" to="b" receiver="../component" receiverContainer="destination"/>
        </Structure>

    </ComponentType>

</Lems>