LEMS_NML2_Ex7_STP.xml

<Lems>

    <!-- Example showing Short Term Plasticity synapse -->

    <!-- This is a file which can be read and executed by the LEMS Interpreter.
         It imports the LEMS definitions of the core NeuroML 2 Components, creates
         a model in "pure" NeuroML 2 and contains some LEMS elements for running
         a simulation -->


    <Target component="sim1" reportFile="report.ex7.txt"/>

    <Include file="NeuroMLCoreDimensions.xml"/>
    <Include file="Cells.xml"/>
    <Include file="Networks.xml"/>
    <Include file="Simulation.xml"/>


    <!-- Including file with a <neuroml> root, a "real" NeuroML 2 file -->
    <!-- Note: components defined in this can be reused, but we don't use the network here (net1) for simulation,
         We use the one defined below! -->
    <Include file="../examples/NML2_SingleCompHHCell.nml"/>


    <!-- NeuroML 2 elements... -->

    <spikeGenerator id="spikeGen30ms" period="30ms" />

    <cell id="passiveCell">

        <morphology id="morph1">
            <segment id="0" name="soma">
                <proximal x="0" y="0" z="0" diameter="17.841242"/> <!--Gives a convenient surface area of 1000.0 ?m�-->
                <distal x="0" y="0" z="0" diameter="17.841242"/>
            </segment>

            <segmentGroup id="soma_group">
                <member segment="0"/>
            </segmentGroup>

        </morphology>

        <biophysicalProperties id="bioPhys1">

            <membraneProperties>
                <channelDensity id="leak" ionChannel="passiveChan" condDensity="3.0 S_per_m2" erev="-54.3mV" ion="non_specific"/>
                <spikeThresh value="-20mV"/>
                <specificCapacitance value="1.0 uF_per_cm2"/>
                <initMembPotential value="-65mV"/>
            </membraneProperties>

            <intracellularProperties>
                <resistivity value="0.03 kohm_cm"/>   <!-- Note: not used in single compartment simulations -->
            </intracellularProperties>

        </biophysicalProperties>

    </cell>

    <expTwoSynapse id="noStpSyn" gbase="1nS" erev="0mV" tauRise="0.1ms" tauDecay="40ms"/>

    <blockingPlasticSynapse id="stpSynDep" gbase="1nS" erev="0mV" tauRise="0.1ms" tauDecay="40ms">
            <tsodyksMarkramDepMechanism id="depMech" initReleaseProb = "0.5" tauRec = "300 ms"/>
    </blockingPlasticSynapse>

    <blockingPlasticSynapse id="stpSynDepFac" gbase="1nS" erev="0mV" tauRise="0.1ms" tauDecay="40ms">
            <tsodyksMarkramDepFacMechanism id="depFacMech" initReleaseProb = "0.5" tauFac = "200 ms" tauRec = "300 ms"/>
    </blockingPlasticSynapse>


    <network id="net2">
        <population id="srcPop" component="spikeGen30ms" size="1"/>
        <population id="pasPop" component="passiveCell" size="5"/>
        <synapticConnection from="srcPop[0]" to="pasPop[0]" synapse="noStpSyn" destination="synapses"/>
        <synapticConnection from="srcPop[0]" to="pasPop[1]" synapse="stpSynDep" destination="synapses"/>
        <synapticConnection from="srcPop[0]" to="pasPop[2]" synapse="stpSynDepFac" destination="synapses"/>
    </network>

   <!-- End of NeuroML 2 elements... -->



    <Simulation id="sim1" length="300ms" step="0.01ms" target="net2">
        <Display id="d1" title="Ex7: Cells with STP synapse: voltage" timeScale="1ms" xmin="-20" xmax="320" ymin="-56" ymax="-35">
                <Line id="v_noStp" quantity="pasPop[0]/v" scale="1mV" color="#000000" timeScale="1ms"/>
                <Line id="v_stpSynDep" quantity="pasPop[1]/v" scale="1mV" color="#0000FF" timeScale="1ms"/>
                <Line id="v_stpSynDepFac" quantity="pasPop[2]/v" scale="1mV" color="#ff0000" timeScale="1ms"/>
        </Display>

        <Display id="d2" title="Ex7: Cells with STP synapse: synaptic conductances" timeScale="1ms" xmin="-20" xmax="320" ymin="-0.1" ymax="2.0">
                <Line id ="g_noStp" quantity="pasPop[0]/synapses:noStpSyn:0/g" scale="1nS"  color="#000000" timeScale="1ms"/>
                <Line id ="g_stpSynDep" quantity="pasPop[1]/synapses:stpSynDep:0/g" scale="1nS"  color="#0000FF" timeScale="1ms"/>
                <Line id ="g_stpSynDepFac" quantity="pasPop[2]/synapses:stpSynDepFac:0/g" scale="1nS"  color="#ff0000" timeScale="1ms"/>
        </Display>

        <Display id="d4" title="Ex7: Cells with STP synapse: scaling variables" timeScale="1ms" xmin="-20" xmax="320" ymin="-0.1" ymax="1.1">
                <Line id ="R_Dep" quantity="pasPop[1]/synapses:stpSynDep:0/depMech/R" scale="1"  color="#00ffff" timeScale="1ms"/>
                <Line id ="U_Dep" quantity="pasPop[1]/synapses:stpSynDep:0/depMech/U" scale="1"  color="#ff00ff" timeScale="1ms"/>
                <Line id ="R_DepFac" quantity="pasPop[2]/synapses:stpSynDepFac:0/depFacMech/R" scale="1"  color="#ffffff" timeScale="1ms"/>
                <Line id ="U_DepFac" quantity="pasPop[2]/synapses:stpSynDepFac:0/depFacMech/U" scale="1"  color="#0055ff" timeScale="1ms"/>
        </Display>
        
        <OutputFile id="of0" fileName="results/ex7_v.dat">
            <OutputColumn id="v0" quantity="pasPop[0]/v"/> 
            <OutputColumn id="v1" quantity="pasPop[1]/v"/> 
            <OutputColumn id="2" quantity="pasPop[2]/v"/> 
        </OutputFile>  
        
        <EventOutputFile id="spikes" fileName="results/ex7.spikes" format="ID_TIME">
            <EventSelection id="0" select="srcPop[0]" eventPort="spike"/>
        </EventOutputFile>
        
    </Simulation>


</Lems>