LEMS_NeuronMuscle.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="NeuronMuscle.net.nml"/>


    <Simulation id="sim1" length="400ms" step="0.025ms" target="net1">

        <Display id="d1" title="Voltage response neuron (mV)" timeScale="1ms" xmin="-40" xmax="440" ymin="-80" ymax="0">
            <Line id="neuron_v" quantity="neuron/0/generic_iaf_cell/v" scale="1mV"  color="#bbffbb" timeScale="1ms"/>
            <Line id="muscle_v" quantity="muscle/0/SingleCompMuscleCell/v" scale="1mV"  color="#ff0000" timeScale="1ms"/>
        </Display>
        
        
        <Display id="d5" title="Ca concentration muscle (mM)" xmin="-40" xmax="440" ymin="-1e-9" ymax="2e-8" timeScale="1ms">
            <Line id="Ca concentration" timeScale="1ms" quantity="muscle/0/SingleCompMuscleCell/caConc" scale="1 mM" color="#000000"/>
        </Display>
        
        <Display id="d4" title="Current densities in muscle" timeScale="1ms" xmin="-40" xmax="440" ymin="-2" ymax="2">
            <Line id="Leak" quantity="muscle/0/SingleCompMuscleCell/biophys/membraneProperties/Leak_all/iDensity" scale="1uA_per_cm2"  color="#550000" timeScale="1ms"/>
            <Line id="k_slow" quantity="muscle/0/SingleCompMuscleCell/biophys/membraneProperties/k_slow_all/iDensity" scale="1uA_per_cm2"  color="#005500" timeScale="1ms"/>
            <Line id="k_fast" quantity="muscle/0/SingleCompMuscleCell/biophys/membraneProperties/k_fast_all/iDensity" scale="1uA_per_cm2"  color="#000055" timeScale="1ms"/>
            <Line id="ca_boyle" quantity="muscle/0/SingleCompMuscleCell/biophys/membraneProperties/ca_boyle_all/iDensity" scale="1uA_per_cm2"  color="#fff555" timeScale="1ms"/>
       
        </Display>
        
        <OutputFile id="voltage" fileName="nm_v.dat">
            <OutputColumn id="neuron_v" quantity="neuron/0/generic_iaf_cell/v"/>
            <OutputColumn id="muscle_v" quantity="muscle/0/SingleCompMuscleCell/v"/>
        </OutputFile>
        
        <OutputFile id="CaConcentration" fileName="nm_conc.dat">
            <OutputColumn id="muscle_ca_conc" quantity="muscle/0/SingleCompMuscleCell/caConc"/>
        </OutputFile>
    

    </Simulation>


</Lems>