opensourcebrain/HodgkinHuxleyTutorial

1<Lems>2 3    <!-- Example with Simple Hodgkin-Huxley cell specifying segment details-->4 5    <!-- This is a file which can be read and executed by the LEMS Interpreter.6         It imports the LEMS definitions of the core NeuroML 2 Components,7         imports in "pure" NeuroML 2 and contains some LEMS elements for running8         a simulation -->9 10 11    <Target component="sim1"/>12 13    <Include file="Cells.xml"/>14    <Include file="Networks.xml"/>15    <Include file="Simulation.xml"/>16 17 18    <Include file="HHCellNetwork.net.nml"/>19    <Include file="hhcell.cell.nml"/>20    <Include file="passiveChan.channel.nml"/>21    <Include file="naChan.channel.nml"/>22    <Include file="kChan.channel.nml"/>23 24 25    <Simulation id="sim1" length="450ms" step="0.01ms" target="HHCellNetwork">26 27        <Display id="d1" title="Hodgkin-Huxley Neuron: V (mV)" timeScale="1ms" xmin="-20" xmax="470" ymin="-90" ymax="50">28            <Line id="V" quantity="hhpop[0]/v" scale="1mV" color="#000000" timeScale="1ms"/>29        </Display>30 31        <Display id="d2" title="Hodgkin-Huxley Neuron: Gating Variables" timeScale="1ms" xmin="-20" xmax="470" ymin="-0.1" ymax="1.1">32            <Line id="m" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/m/q" scale="1"  color="#ff0000" timeScale="1ms"/>33            <Line id="h" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/h/q" scale="1"  color="#00dd00" timeScale="1ms"/>34            <Line id="n" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/kChan/n/q" scale="1"  color="#0000ff" timeScale="1ms"/>35        </Display>36 37        <Display id="d3" title="Hodgkin-Huxley Neuron: Current" timeScale="1ms" xmin="-20" xmax="470" ymin="-10" ymax="10">38            <Line id="I_na" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/iDensity" scale="1"  color="#00ffff" timeScale="1ms"/>39            <Line id="I_k" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/iDensity" scale="1"  color="#ffff00" timeScale="1ms"/>40            <Line id="I_l" quantity="hhpop[0]/bioPhys1/membraneProperties/leak/iDensity" scale="1"  color="#ff00ff" timeScale="1ms"/>41        </Display>42 43        <Display id="d4" title="Hodgkin-Huxley Neuron: I_inj (nA)" timeScale="1ms" xmin="-20" xmax="470" ymin="-0.01" ymax="0.4">44            <Line id="I_inj1" quantity="hhpop[0]/pulseGen1/i" scale="1nA"  color="#ffffff" timeScale="1ms"/>45            <Line id="I_inj2" quantity="hhpop[0]/pulseGen2/i" scale="1nA"  color="#000000" timeScale="1ms"/>46        </Display>47 48        <!-- Saved the membrane potential to file: hh_v.dat -->49        <OutputFile id="of0" fileName="hh_v.dat">50            <OutputColumn id="v" quantity="hhpop[0]/v"/>51        </OutputFile>52 53        <!-- for plotting results in JupyterNotebook -->54        <OutputFile id="of1" fileName="hh_forJupyterNotebook.dat">55            <OutputColumn id="v" quantity="hhpop[0]/v"/>56            <OutputColumn id="m" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/m/q"/>57            <OutputColumn id="h" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/h/q"/> 58            <OutputColumn id="n" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/kChan/n/q"/>59            <OutputColumn id="I_na" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/iDensity"/>60            <OutputColumn id="I_k"  quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/iDensity"/>61            <OutputColumn id="I_l"  quantity="hhpop[0]/bioPhys1/membraneProperties/leak/iDensity"/>62            <OutputColumn id="I_inj1" quantity="hhpop[0]/pulseGen1/i"/>63            <OutputColumn id="I_inj2" quantity="hhpop[0]/pulseGen2/i"/>64        </OutputFile>65 66    </Simulation>67 68 69</Lems>70