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 running 8         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    <Include file="vclamp.xml"/>18 19 20    <Include file="HHCellVClamp.net.nml"/>21    <Include file="hhcell.cell.nml"/>22    <Include file="passiveChan.channel.nml"/>23    <Include file="naChan.channel.nml"/>24    <Include file="kChan.channel.nml"/>25 26 27    <Simulation id="sim1" length="50ms" step="0.0001ms" target="HHCellNetwork">28    29        <Display id="d1" title="Hodgkin-Huxley Neuron: V (mV)" timeScale="1ms" xmin="-5" xmax="55" ymin="-90" ymax="50">30            <Line id="V" quantity="hhpop[0]/v" scale="1mV" color="#000000" timeScale="1ms"/>31        </Display>32 33        <Display id="d2" title="Hodgkin-Huxley Neuron: Gating Variables" timeScale="1ms" xmin="-5" xmax="55" ymin="-0.1" ymax="1.1">34            <Line id="m" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/m/q" scale="1"  color="#ff0000" timeScale="1ms"/>35            <Line id="h" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/h/q" scale="1"  color="#00dd00" timeScale="1ms"/>36            <Line id="n" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/kChan/n/q" scale="1"  color="#0000ff" timeScale="1ms"/>37        </Display>38 39        <Display id="d3" title="Hodgkin-Huxley Neuron: Current" timeScale="1ms" xmin="-5" xmax="55" ymin="-30" ymax="20">40            <Line id="I_na" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/iDensity" scale="1"  color="#00ffff" timeScale="1ms"/>41            <Line id="I_k" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/iDensity" scale="1"  color="#ffff00" timeScale="1ms"/>42            <Line id="I_l" quantity="hhpop[0]/bioPhys1/membraneProperties/leak/iDensity" scale="1"  color="#ff00ff" timeScale="1ms"/>43        </Display>44 45        <Display id="d4" title="Hodgkin-Huxley Neuron: I_vClamp (nA)" timeScale="1ms" xmin="-5" xmax="55" ymin="-15" ymax="25">46            <Line id="I_vClamp" quantity="hhpop[0]/vClamp/i" scale="1nA"  color="#ffffff" timeScale="1ms"/>47        </Display>48        49        <!-- Saved the membrane potential to file: hh_v.dat -->50        <OutputFile id="of0" fileName="hh_v.dat">51            <OutputColumn id="v" quantity="hhpop[0]/v"/> 52        </OutputFile>  53    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_vClamp" quantity="hhpop[0]/vClamp/i" />63        </OutputFile>    64    </Simulation>65 66 67</Lems>68