LEMS_HH_Simulation.xml

<Lems>

    <!-- Example with Simple Hodgkin-Huxley cell specifying segment details-->

    <!-- 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,
         imports in "pure" NeuroML 2 and contains some LEMS elements for running
         a simulation -->


    <Target component="sim1"/>

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


    <Include file="HHCellNetwork.net.nml"/>
    <Include file="hhcell.cell.nml"/>
    <Include file="passiveChan.channel.nml"/>
    <Include file="naChan.channel.nml"/>
    <Include file="kChan.channel.nml"/>


    <Simulation id="sim1" length="450ms" step="0.01ms" target="HHCellNetwork">

        <Display id="d1" title="Hodgkin-Huxley Neuron: V (mV)" timeScale="1ms" xmin="-20" xmax="470" ymin="-90" ymax="50">
            <Line id="V" quantity="hhpop[0]/v" scale="1mV" color="#000000" timeScale="1ms"/>
        </Display>

        <Display id="d2" title="Hodgkin-Huxley Neuron: Gating Variables" timeScale="1ms" xmin="-20" xmax="470" ymin="-0.1" ymax="1.1">
            <Line id="m" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/m/q" scale="1"  color="#ff0000" timeScale="1ms"/>
            <Line id="h" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/h/q" scale="1"  color="#00dd00" timeScale="1ms"/>
            <Line id="n" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/kChan/n/q" scale="1"  color="#0000ff" timeScale="1ms"/>
        </Display>

        <Display id="d3" title="Hodgkin-Huxley Neuron: Current" timeScale="1ms" xmin="-20" xmax="470" ymin="-10" ymax="10">
            <Line id="I_na" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/iDensity" scale="1"  color="#00ffff" timeScale="1ms"/>
            <Line id="I_k" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/iDensity" scale="1"  color="#ffff00" timeScale="1ms"/>
            <Line id="I_l" quantity="hhpop[0]/bioPhys1/membraneProperties/leak/iDensity" scale="1"  color="#ff00ff" timeScale="1ms"/>
        </Display>

        <Display id="d4" title="Hodgkin-Huxley Neuron: I_inj (nA)" timeScale="1ms" xmin="-20" xmax="470" ymin="-0.01" ymax="0.4">
            <Line id="I_inj1" quantity="hhpop[0]/pulseGen1/i" scale="1nA"  color="#ffffff" timeScale="1ms"/>
            <Line id="I_inj2" quantity="hhpop[0]/pulseGen2/i" scale="1nA"  color="#000000" timeScale="1ms"/>
        </Display>

        <!-- Saved the membrane potential to file: hh_v.dat -->
        <OutputFile id="of0" fileName="hh_v.dat">
            <OutputColumn id="v" quantity="hhpop[0]/v"/>
        </OutputFile>

        <!-- for plotting results in JupyterNotebook -->
        <OutputFile id="of1" fileName="hh_forJupyterNotebook.dat">
            <OutputColumn id="v" quantity="hhpop[0]/v"/>
            <OutputColumn id="m" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/m/q"/>
            <OutputColumn id="h" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/h/q"/> 
            <OutputColumn id="n" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/kChan/n/q"/>
            <OutputColumn id="I_na" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/iDensity"/>
            <OutputColumn id="I_k"  quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/iDensity"/>
            <OutputColumn id="I_l"  quantity="hhpop[0]/bioPhys1/membraneProperties/leak/iDensity"/>
            <OutputColumn id="I_inj1" quantity="hhpop[0]/pulseGen1/i"/>
            <OutputColumn id="I_inj2" quantity="hhpop[0]/pulseGen2/i"/>
        </OutputFile>

    </Simulation>


</Lems>