Tutorial2/NeuroML2/LEMS_HHTutorial.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="HHTutorial.net.nml"/>

    <Simulation id="sim1" length="50ms" step="0.001ms" target="HHTutorial">
    
        <Display id="d1" title="Hodgkin-Huxley Neuron: V (mV)" timeScale="1ms" xmin="-5" xmax="55" ymin="-90" ymax="50">
            <Line id="V (mV)" quantity="hhpop/0/hhneuron/v" scale="1mV" color="#000000" timeScale="1ms"/>
        </Display>

        <Display id="d2" title="Hodgkin-Huxley Neuron: Gating Variables" timeScale="1ms" xmin="-5" xmax="55" ymin="-0.1" ymax="1.1">
            <Line id="m" quantity="hhpop/0/hhneuron/biophysics/membraneProperties/naChans/naChan/m/q" scale="1"  color="#ff0000" timeScale="1ms"/>
            <Line id="h" quantity="hhpop/0/hhneuron/biophysics/membraneProperties/naChans/naChan/h/q" scale="1"  color="#00dd00" timeScale="1ms"/>
            <Line id="n" quantity="hhpop/0/hhneuron/biophysics/membraneProperties/kChans/kChan/n/q" scale="1"  color="#0000ff" timeScale="1ms"/>
        </Display>

        <Display id="d3" title="Hodgkin-Huxley Neuron: Current densities" timeScale="1ms" xmin="-5" xmax="55" ymin="-1" ymax="1">
            <Line id="I_na (mA/cm2)" quantity="hhpop/0/hhneuron/biophysics/membraneProperties/naChans/iDensity" scale="1mA_per_cm2"  color="#00ffff" timeScale="1ms"/>
            <Line id="I_k (mA/cm2)" quantity="hhpop/0/hhneuron/biophysics/membraneProperties/kChans/iDensity" scale="1mA_per_cm2"  color="#ffff00" timeScale="1ms"/>
            <Line id="I_l (mA/cm2)" quantity="hhpop/0/hhneuron/biophysics/membraneProperties/leak/iDensity" scale="1mA_per_cm2"  color="#ff00ff" timeScale="1ms"/>
        </Display>
        
        <Display id="d4" title="Hodgkin-Huxley Neuron: Conductances" timeScale="1ms" xmin="-5" xmax="55" ymin="-0.005" ymax="0.035">
            <Line id="g_na (S/cm2)" quantity="hhpop/0/hhneuron/biophysics/membraneProperties/naChans/gDensity" scale="1S_per_cm2"  color="#00ffff" timeScale="1ms"/>
            <Line id="g_k (S/cm2)" quantity="hhpop/0/hhneuron/biophysics/membraneProperties/kChans/gDensity" scale="1S_per_cm2"  color="#ffff00" timeScale="1ms"/>
        </Display>

        <Display id="d5" title="Hodgkin-Huxley Neuron: I_inj (nA)" timeScale="1ms" xmin="-5" xmax="55" ymin="-0.0005" ymax="0.0025">
            <Line id="I_inj (nA)" quantity="hhpop/0/hhneuron/IClamp/i" scale="1nA"  color="#ffffff" timeScale="1ms"/>
        </Display>

        <Display id="d6" title="Hodgkin-Huxley Neuron: VClamp i (nA)" timeScale="1ms" xmin="-5" xmax="55" ymin="-0.0005" ymax="0.0025">
            <Line id="VClamp i (nA)" quantity="hhpop/0/hhneuron/vClamp/i" scale="1nA"  color="#ffffff" timeScale="1ms"/>
        </Display>
        
        <OutputFile id="of0" fileName="hh_tut_v.dat">
            <OutputColumn id="v" quantity="hhpop/0/hhneuron/v"/> 
        </OutputFile>  
        
        <OutputFile id="of1" fileName="hh_tut_g.dat">
            <OutputColumn id="gna" quantity="hhpop/0/hhneuron/biophysics/membraneProperties/naChans/gDensity"/> 
            <OutputColumn id="gk" quantity="hhpop/0/hhneuron/biophysics/membraneProperties/kChans/gDensity"/> 
        </OutputFile>  
    
        <OutputFile id="of2" fileName="hh_tut_ic.dat">
            <OutputColumn id="i" quantity="hhpop/0/hhneuron/IClamp/i"/> 
        </OutputFile>  
        
    </Simulation>


</Lems>