LEMS_Figure2A.xml

<Lems>


    <!-- Specify which component to run -->
    <Target component="sim1"/>

    <!-- Include core NeuroML2 ComponentType definitions -->
    <Include file="Cells.xml"/>
    <Include file="Networks.xml"/>
    <Include file="Simulation.xml"/>

    <Include file="Leak.channel.nml"/>
    <Include file="k_slow.channel.nml"/>
    <Include file="k_fast.channel.nml"/>
    <Include file="ca_boyle.channel.nml"/>
    <Include file="CaPool.nml"/>
    <Include file="SingleCompMuscle.cell.nml"/>


    <Include file="Figure2A.net.nml"/>



    <Simulation id="sim1" length="45ms" step="0.01ms" target="net1">

        <Display id="d1" title="Voltage responses at 100pA to 700 pA (mV)" timeScale="1ms" xmin="0" xmax="50" ymin="-80" ymax="40">
            <Line id="cell_100pA" quantity="mc1/0/SingleCompMuscleCell/v" scale="1mV"  color="#ffffff" timeScale="1ms"/>
            <Line id="cell_200pA" quantity="mc1/1/SingleCompMuscleCell/v" scale="1mV"  color="#ffffdd" timeScale="1ms"/>
            <Line id="cell_300pA" quantity="mc1/2/SingleCompMuscleCell/v" scale="1mV"  color="#ffffbb" timeScale="1ms"/>
            <Line id="cell_400pA" quantity="mc1/3/SingleCompMuscleCell/v" scale="1mV"  color="#ffddbb" timeScale="1ms"/>
            <Line id="cell_500pA" quantity="mc1/4/SingleCompMuscleCell/v" scale="1mV"  color="#ffbbbb" timeScale="1ms"/>
            <Line id="cell_600pA" quantity="mc1/5/SingleCompMuscleCell/v" scale="1mV"  color="#ddffbb" timeScale="1ms"/>
            <Line id="cell_700pA" quantity="mc1/6/SingleCompMuscleCell/v" scale="1mV"  color="#bbffbb" timeScale="1ms"/>
        </Display>

        <Display id="d2" title="Rate variables at 700 pA (dimensionless)" timeScale="1ms" xmin="0" xmax="50" ymin="-0.1" ymax="1.1">

            <Line id="k_slow/n" quantity="mc1/6/SingleCompMuscleCell/biophys/membraneProperties/k_slow_all/k_slow/n/q" scale="1"  color="#000000" timeScale="1ms"/>
            <Line id="k_fast/p" quantity="mc1/6/SingleCompMuscleCell/biophys/membraneProperties/k_fast_all/k_fast/p/q" scale="1"  color="#0000ff" timeScale="1ms"/>
            <Line id="k_fast/q" quantity="mc1/6/SingleCompMuscleCell/biophys/membraneProperties/k_fast_all/k_fast/q/q" scale="1"  color="#00ffff" timeScale="1ms"/>
            <Line id="ca_boyle/e" quantity="mc1/6/SingleCompMuscleCell/biophys/membraneProperties/ca_boyle_all/ca_boyle/e/q" scale="1"  color="#ff00ff" timeScale="1ms"/>
            <Line id="ca_boyle/f" quantity="mc1/6/SingleCompMuscleCell/biophys/membraneProperties/ca_boyle_all/ca_boyle/f/q" scale="1"  color="#ffff00" timeScale="1ms"/>
            <Line id="ca_boyle/h" quantity="mc1/6/SingleCompMuscleCell/biophys/membraneProperties/ca_boyle_all/ca_boyle/h/q" scale="1"  color="#ff0000" timeScale="1ms"/>
        </Display>
   

        <Display id="d4" title="Current densities at 700 pA (uA/cm2)" timeScale="1ms" xmin="0" xmax="50" ymin="-20" ymax="7">
            <Line id="Leak" quantity="mc1/6/SingleCompMuscleCell/biophys/membraneProperties/Leak_all/iDensity" scale="1uA_per_cm2"  color="#550000" timeScale="1ms"/>
            <Line id="k_slow" quantity="mc1/6/SingleCompMuscleCell/biophys/membraneProperties/k_slow_all/iDensity" scale="1uA_per_cm2"  color="#005500" timeScale="1ms"/>
            <Line id="k_fast" quantity="mc1/6/SingleCompMuscleCell/biophys/membraneProperties/k_fast_all/iDensity" scale="1uA_per_cm2"  color="#000055" timeScale="1ms"/>
            <Line id="ca_boyle" quantity="mc1/6/SingleCompMuscleCell/biophys/membraneProperties/ca_boyle_all/iDensity" scale="1uA_per_cm2"  color="#fff555" timeScale="1ms"/>
       
        </Display>
    
        <Display id="d5" title="Ca concentration (mM)" xmin="0" xmax="50" ymin="-1e-8" ymax="9e-8" timeScale="1ms">
            <Line id="Ca concentration" timeScale="1ms" quantity="mc1/6/SingleCompMuscleCell/caConc" scale="1 mM" color="#000000"/>
        </Display>

    </Simulation>


</Lems>