File size: 3,792 Bytes
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<!-- 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>
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