Tutorial/Source/nmllite/LEMS_SimHHTest.gv

    # GraphViz compliant export for:HHTest (Type: network)

digraph SimHHTest {
fontsize=10;
overlap=false;


subgraph cluster_network {
    style=filled;
    color="#D6eeEA";
    node [style=filled,color=white];
    label = "Network to be simulated";

    node [shape=rectangle]; HHTest;
    #    Population hhPop contains components of: Component(id=hhcell type=cell) 
    node [shape=ellipse,color="white",fontcolor="black"]; hhPop;    
    HHTest -> hhPop [len=1.00, arrowhead=diamond]

}

subgraph cluster_comps {
    style=filled;
    color="#CCFFCC";
    node [style=filled,color=white];
    label = "Components";

    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>hhcell (cell)</td></tr><tr><td><font color="#666666"></font></td></tr></table>>]; "hhcell (cell)";

    "hhPop" -> "hhcell (cell)" [label="1",len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>null (0)</td></tr><tr><td><font color="#666666"></font></td></tr></table>>]; "null (0)";

    "hhcell (cell)" -> "null (0)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>morphology (morphology)</td></tr><tr><td><font color="#666666"></font></td></tr></table>>]; "morphology (morphology)";

    "hhcell (cell)" -> "morphology (morphology)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>soma (id = 0)</td></tr><tr><td><font color="#666666"></font></td></tr></table>>]; "soma (id = 0)";

    "morphology (morphology)" -> "soma (id = 0)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>null (1)</td></tr><tr><td><font color="#666666">x = 0, y = 0, z = 0, <br/>diameter = 17.841242, radius = 8.920621E-6 m, xLength = 0 m, <br/>yLength = 0 m, zLength = 0 m</font></td></tr></table>>]; "null (1)";

    "soma (id = 0)" -> "null (1)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>null (2)</td></tr><tr><td><font color="#666666">x = 0, y = 0, z = 0, <br/>diameter = 17.841242, radius = 8.920621E-6 m, xLength = 0 m, <br/>yLength = 0 m, zLength = 0 m</font></td></tr></table>>]; "null (2)";

    "soma (id = 0)" -> "null (2)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>soma_group (segmentGroup)</td></tr><tr><td><font color="#666666"></font></td></tr></table>>]; "soma_group (segmentGroup)";

    "morphology (morphology)" -> "soma_group (segmentGroup)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>null (3)</td></tr><tr><td><font color="#666666"></font></td></tr></table>>]; "null (3)";

    "soma_group (segmentGroup)" -> "null (3)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>bioPhys1 (biophysicalProperties)</td></tr><tr><td><font color="#666666"></font></td></tr></table>>]; "bioPhys1 (biophysicalProperties)";

    "hhcell (cell)" -> "bioPhys1 (biophysicalProperties)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>null (4)</td></tr><tr><td><font color="#666666"></font></td></tr></table>>]; "null (4)";

    "bioPhys1 (biophysicalProperties)" -> "null (4)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>null (5)</td></tr><tr><td><font color="#666666">value = -0.02 V</font></td></tr></table>>]; "null (5)";

    "null (4)" -> "null (5)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>null (6)</td></tr><tr><td><font color="#666666">value = -0.065 V</font></td></tr></table>>]; "null (6)";

    "null (4)" -> "null (6)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>leak (channelDensity)</td></tr><tr><td><font color="#666666">erev = -0.054387000000000005 V, condDensity = 3 kg^-1 m^-4 s^3 A^2</font></td></tr></table>>]; "leak (channelDensity)";

    "null (4)" -> "leak (channelDensity)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>passiveChan (ionChannelPassive)</td></tr><tr><td><font color="#666666">conductance = 1.0E-11 S</font></td></tr></table>>]; "passiveChan (ionChannelPassive)";

    "leak (channelDensity)" -> "passiveChan (ionChannelPassive)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>null (7)</td></tr><tr><td><font color="#666666"></font></td></tr></table>>]; "null (7)";

    "passiveChan (ionChannelPassive)" -> "null (7)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>naChans (channelDensity)</td></tr><tr><td><font color="#666666">erev = 0.05 V, condDensity = 1200 kg^-1 m^-4 s^3 A^2</font></td></tr></table>>]; "naChans (channelDensity)";

    "null (4)" -> "naChans (channelDensity)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>naChan (ionChannelHH)</td></tr><tr><td><font color="#666666">conductance = 1.0E-11 S</font></td></tr></table>>]; "naChan (ionChannelHH)";

    "naChans (channelDensity)" -> "naChan (ionChannelHH)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>null (8)</td></tr><tr><td><font color="#666666"></font></td></tr></table>>]; "null (8)";

    "naChan (ionChannelHH)" -> "null (8)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>m (gateHHrates)</td></tr><tr><td><font color="#666666">instances = 3</font></td></tr></table>>]; "m (gateHHrates)";

    "naChan (ionChannelHH)" -> "m (gateHHrates)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>null (9)</td></tr><tr><td><font color="#666666">rate = 1000 s^-1, midpoint = -0.04 V, scale = 0.01 V</font></td></tr></table>>]; "null (9)";

    "m (gateHHrates)" -> "null (9)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>null (10)</td></tr><tr><td><font color="#666666">rate = 4000 s^-1, midpoint = -0.065 V, scale = -0.018000000000000002 V</font></td></tr></table>>]; "null (10)";

    "m (gateHHrates)" -> "null (10)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>h (gateHHrates)</td></tr><tr><td><font color="#666666">instances = 1</font></td></tr></table>>]; "h (gateHHrates)";

    "naChan (ionChannelHH)" -> "h (gateHHrates)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>null (11)</td></tr><tr><td><font color="#666666">rate = 70 s^-1, midpoint = -0.065 V, scale = -0.02 V</font></td></tr></table>>]; "null (11)";

    "h (gateHHrates)" -> "null (11)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>null (12)</td></tr><tr><td><font color="#666666">rate = 1000 s^-1, midpoint = -0.035 V, scale = 0.01 V</font></td></tr></table>>]; "null (12)";

    "h (gateHHrates)" -> "null (12)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>kChans (channelDensity)</td></tr><tr><td><font color="#666666">erev = -0.077 V, condDensity = 360 kg^-1 m^-4 s^3 A^2</font></td></tr></table>>]; "kChans (channelDensity)";

    "null (4)" -> "kChans (channelDensity)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>kChan (ionChannelHH)</td></tr><tr><td><font color="#666666">conductance = 1.0E-11 S</font></td></tr></table>>]; "kChan (ionChannelHH)";

    "kChans (channelDensity)" -> "kChan (ionChannelHH)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>null (13)</td></tr><tr><td><font color="#666666"></font></td></tr></table>>]; "null (13)";

    "kChan (ionChannelHH)" -> "null (13)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>n (gateHHrates)</td></tr><tr><td><font color="#666666">instances = 4</font></td></tr></table>>]; "n (gateHHrates)";

    "kChan (ionChannelHH)" -> "n (gateHHrates)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>null (14)</td></tr><tr><td><font color="#666666">rate = 100 s^-1, midpoint = -0.055 V, scale = 0.01 V</font></td></tr></table>>]; "null (14)";

    "n (gateHHrates)" -> "null (14)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>null (15)</td></tr><tr><td><font color="#666666">rate = 125 s^-1, midpoint = -0.065 V, scale = -0.08 V</font></td></tr></table>>]; "null (15)";

    "n (gateHHrates)" -> "null (15)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>null (16)</td></tr><tr><td><font color="#666666">value = 0.01 kg^-1 m^-4 s^4 A^2</font></td></tr></table>>]; "null (16)";

    "null (4)" -> "null (16)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>null (17)</td></tr><tr><td><font color="#666666"></font></td></tr></table>>]; "null (17)";

    "bioPhys1 (biophysicalProperties)" -> "null (17)" [len=1.00, arrowhead=diamond]
    node [shape=ellipse label=<<table border="0" cellborder="0"><tr><td>null (18)</td></tr><tr><td><font color="#666666">value = 0.3 kg^2 m^2 s^-3 A^-2</font></td></tr></table>>]; "null (18)";

    "null (17)" -> "null (18)" [len=1.00, arrowhead=diamond]
}

subgraph cluster_compTypes {
    style=filled;
    color="#D6E0EA";
    node [style="rounded, filled",color=white];
    label = "Component Types";
    node [style="rounded, filled",color=white];
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>cell</td></tr><tr><td><font color="#B2C0D9">neuroLexId</font></td></tr><tr><td><font color="#FF9966">State vars: v (voltage), spiking </font></td></tr><tr><td><font color="#99CC00">initMembPot = biophysicalProperties/membraneProperties/initMembPotential/value</font></td></tr><tr><td><font color="#99CC00">thresh = biophysicalProperties/membraneProperties/spikeThresh/value</font></td></tr><tr><td><font color="#99CC00">surfaceArea = SUM OF: morphology/segments[*]/surfaceArea</font></td></tr><tr><td><font color="#99CC00">totSpecCap = biophysicalProperties/totSpecCap</font></td></tr><tr><td><font color="#99CC00">totCap = totSpecCap * surfaceArea </font></td></tr><tr><td><font color="#99CC00">iChannels = biophysicalProperties/membraneProperties/totChanCurrent</font></td></tr><tr><td><font color="#99CC00">iSyn = SUM OF: synapses[*]/i</font></td></tr><tr><td><font color="#99CC00">iCa = biophysicalProperties/membraneProperties/iCa</font></td></tr><tr><td><font color="#99CC00">caConc = biophysicalProperties/intracellularProperties/caConc</font></td></tr><tr><td><font color="#99CC00">caConcExt = biophysicalProperties/intracellularProperties/caConcExt</font></td></tr><tr><td><font color="#666633">v' = (iChannels + iSyn) / totCap</font></td></tr><tr><td><font color="#996633">IF v .gt. thresh AND spiking .lt. 0.5 THEN </font></td></tr><tr><td><font color="#996633">(spiking = 1)  <br/>AND (EVENT: spike)</font></td></tr><tr><td><font color="#996633">IF v .lt. thresh THEN </font></td></tr><tr><td><font color="#996633">(spiking = 0)</font></td></tr><tr><td><font color="#666666">Exposures: spiking, iChannels (current), iSyn (current), <br/>totSpecCap (specificCapacitance), surfaceArea (area), iCa (current), <br/>caConc (concentration), caConcExt (concentration), v (voltage) </font></td></tr></table>>]; cell;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseCellMembPot</td></tr><tr><td><font color="#666666">Exposures: v (voltage) </font></td></tr></table>>]; baseCellMembPot;
    cell -> baseCellMembPot [len=1.00, arrowhead=onormal]
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseSpikingCell</td></tr></table>>]; baseSpikingCell;
    baseCellMembPot -> baseSpikingCell [len=1.00, arrowhead=onormal]
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseCell</td></tr></table>>]; baseCell;
    baseSpikingCell -> baseCell [len=1.00, arrowhead=onormal]
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseStandalone</td></tr></table>>]; baseStandalone;
    baseCell -> baseStandalone [len=1.00, arrowhead=onormal]
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>notes</td></tr></table>>]; notes;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>morphology</td></tr></table>>]; morphology;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>segment</td></tr><tr><td><font color="#662211">Consts: LEN = 1 m </font></td></tr><tr><td><font color="#B2C0D9">name</font></td></tr><tr><td><font color="#99CC00">radDist = distal/radius</font></td></tr><tr><td><font color="#99CC00">dx = distal/xLength</font></td></tr><tr><td><font color="#99CC00">dy = distal/yLength</font></td></tr><tr><td><font color="#99CC00">dz = distal/zLength</font></td></tr><tr><td><font color="#99CC00">px = proximal/xLength</font></td></tr><tr><td><font color="#99CC00">py = proximal/yLength</font></td></tr><tr><td><font color="#99CC00">pz = proximal/zLength</font></td></tr><tr><td><font color="#99CC00">length = sqrt(((dx - px) * (dx - px) + (dy - py) * (dy - py) + (dz - pz) * (dz - pz))/(LEN * LEN)) * LEN</font></td></tr><tr><td><font color="#666666">Exposures: surfaceArea (area), radDist (length), length (length) </font></td></tr></table>>]; segment;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>proximal</td></tr><tr><td><font color="#662211">Consts: MICRON = 1.0E-6 m </font></td></tr></table>>]; proximal;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>point3DWithDiam</td></tr><tr><td><font color="#669999">Params: x, y, z, <br/>diameter </font></td></tr><tr><td><font color="#662211">Consts: MICRON = 1.0E-6 m </font></td></tr></table>>]; point3DWithDiam;
    proximal -> point3DWithDiam [len=1.00, arrowhead=onormal]
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>distal</td></tr><tr><td><font color="#662211">Consts: MICRON = 1.0E-6 m </font></td></tr></table>>]; distal;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>point3DWithDiam</td></tr><tr><td><font color="#669999">Params: x, y, z, <br/>diameter </font></td></tr><tr><td><font color="#662211">Consts: MICRON = 1.0E-6 m </font></td></tr></table>>]; point3DWithDiam;
    distal -> point3DWithDiam [len=1.00, arrowhead=onormal]
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>segmentGroup</td></tr><tr><td><font color="#B2C0D9">neuroLexId</font></td></tr></table>>]; segmentGroup;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>member</td></tr><tr><td><font color="#B2C0D9">segment</font></td></tr></table>>]; member;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>biophysicalProperties</td></tr><tr><td><font color="#99CC00">totSpecCap = membraneProperties/totSpecCap</font></td></tr><tr><td><font color="#666666">Exposures: totSpecCap (specificCapacitance) </font></td></tr></table>>]; biophysicalProperties;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>membraneProperties</td></tr><tr><td><font color="#666699">REQUIRES: surfaceArea (area)</font></td></tr><tr><td><font color="#99CC00">totSpecCap = SUM OF: specificCapacitances[*]/specCap</font></td></tr><tr><td><font color="#99CC00">totChanPopCurrent = SUM OF: populations[*]/i</font></td></tr><tr><td><font color="#99CC00">totChanDensCurrentDensity = SUM OF: channelDensities[*]/iDensity</font></td></tr><tr><td><font color="#99CC00">totChanCurrent = totChanPopCurrent + (totChanDensCurrentDensity * surfaceArea)</font></td></tr><tr><td><font color="#99CC00">totChanPopCurrentCa = SUM OF: populations[ion='ca']/i</font></td></tr><tr><td><font color="#99CC00">totChanDensCurrentDensityCa = SUM OF: channelDensities[ion='ca']/iDensity</font></td></tr><tr><td><font color="#99CC00">iCa = totChanPopCurrentCa + (totChanDensCurrentDensityCa * surfaceArea)</font></td></tr><tr><td><font color="#666666">Exposures: totChanCurrent (current), iCa (current), totSpecCap (specificCapacitance) </font></td></tr></table>>]; membraneProperties;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>spikeThresh</td></tr><tr><td><font color="#669999">Params: value (voltage) </font></td></tr></table>>]; spikeThresh;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>initMembPotential</td></tr><tr><td><font color="#669999">Params: value (voltage) </font></td></tr></table>>]; initMembPotential;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>channelDensity</td></tr><tr><td><font color="#669999">Params: erev (voltage) </font></td></tr><tr><td><font color="#662211">Consts: vShift = 0 V </font></td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#B2C0D9">segmentGroup</font></td></tr><tr><td><font color="#B2C0D9">ion</font></td></tr><tr><td><font color="#99CC00">channelf = ionChannel/fopen</font></td></tr><tr><td><font color="#99CC00">gDensity = condDensity * channelf</font></td></tr><tr><td><font color="#99CC00">iDensity = gDensity * (erev - v)</font></td></tr><tr><td><font color="#666666">Exposures: gDensity (conductanceDensity), iDensity (currentDensity) </font></td></tr></table>>]; channelDensity;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseChannelDensityCond</td></tr><tr><td><font color="#669999">Params: condDensity (conductanceDensity) </font></td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#666666">Exposures: gDensity (conductanceDensity), iDensity (currentDensity) </font></td></tr></table>>]; baseChannelDensityCond;
    channelDensity -> baseChannelDensityCond [len=1.00, arrowhead=onormal]
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseChannelDensity</td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#666666">Exposures: iDensity (currentDensity) </font></td></tr></table>>]; baseChannelDensity;
    baseChannelDensityCond -> baseChannelDensity [len=1.00, arrowhead=onormal]
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>ionChannelPassive</td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#B2C0D9">species</font></td></tr><tr><td><font color="#99CC00">fopen = 1</font></td></tr><tr><td><font color="#99CC00">g = conductance</font></td></tr><tr><td><font color="#666666">Exposures: g (conductance), fopen </font></td></tr></table>>]; ionChannelPassive;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>ionChannel</td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#99CC00">conductanceScale = PRODUCT OF: conductanceScaling[*]/factor</font></td></tr><tr><td><font color="#99CC00">fopen0 = PRODUCT OF: gates[*]/fcond</font></td></tr><tr><td><font color="#99CC00">fopen = conductanceScale * fopen0</font></td></tr><tr><td><font color="#99CC00">g = conductance * fopen</font></td></tr><tr><td><font color="#666666">Exposures: g (conductance), fopen </font></td></tr></table>>]; ionChannel;
    ionChannelPassive -> ionChannel [len=1.00, arrowhead=onormal]
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>ionChannelHH</td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#B2C0D9">species</font></td></tr><tr><td><font color="#99CC00">conductanceScale = PRODUCT OF: conductanceScaling[*]/factor</font></td></tr><tr><td><font color="#99CC00">fopen0 = PRODUCT OF: gates[*]/fcond</font></td></tr><tr><td><font color="#99CC00">fopen = conductanceScale * fopen0</font></td></tr><tr><td><font color="#99CC00">g = conductance * fopen</font></td></tr><tr><td><font color="#666666">Exposures: g (conductance), fopen </font></td></tr></table>>]; ionChannelHH;
    ionChannel -> ionChannelHH [len=1.00, arrowhead=onormal]
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseIonChannel</td></tr><tr><td><font color="#669999">Params: conductance (conductance) </font></td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#B2C0D9">neuroLexId</font></td></tr><tr><td><font color="#666666">Exposures: g (conductance), fopen </font></td></tr></table>>]; baseIonChannel;
    ionChannelHH -> baseIonChannel [len=1.00, arrowhead=onormal]
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>notes</td></tr></table>>]; notes;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>channelDensity</td></tr><tr><td><font color="#669999">Params: erev (voltage) </font></td></tr><tr><td><font color="#662211">Consts: vShift = 0 V </font></td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#B2C0D9">segmentGroup</font></td></tr><tr><td><font color="#B2C0D9">ion</font></td></tr><tr><td><font color="#99CC00">channelf = ionChannel/fopen</font></td></tr><tr><td><font color="#99CC00">gDensity = condDensity * channelf</font></td></tr><tr><td><font color="#99CC00">iDensity = gDensity * (erev - v)</font></td></tr><tr><td><font color="#666666">Exposures: gDensity (conductanceDensity), iDensity (currentDensity) </font></td></tr></table>>]; channelDensity;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseChannelDensityCond</td></tr><tr><td><font color="#669999">Params: condDensity (conductanceDensity) </font></td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#666666">Exposures: gDensity (conductanceDensity), iDensity (currentDensity) </font></td></tr></table>>]; baseChannelDensityCond;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseChannelDensity</td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#666666">Exposures: iDensity (currentDensity) </font></td></tr></table>>]; baseChannelDensity;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>ionChannelHH</td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#B2C0D9">species</font></td></tr><tr><td><font color="#99CC00">conductanceScale = PRODUCT OF: conductanceScaling[*]/factor</font></td></tr><tr><td><font color="#99CC00">fopen0 = PRODUCT OF: gates[*]/fcond</font></td></tr><tr><td><font color="#99CC00">fopen = conductanceScale * fopen0</font></td></tr><tr><td><font color="#99CC00">g = conductance * fopen</font></td></tr><tr><td><font color="#666666">Exposures: g (conductance), fopen </font></td></tr></table>>]; ionChannelHH;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseIonChannel</td></tr><tr><td><font color="#669999">Params: conductance (conductance) </font></td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#B2C0D9">neuroLexId</font></td></tr><tr><td><font color="#666666">Exposures: g (conductance), fopen </font></td></tr></table>>]; baseIonChannel;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>notes</td></tr></table>>]; notes;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>gateHHrates</td></tr><tr><td><font color="#FF9966">State vars: q </font></td></tr><tr><td><font color="#99CC00">rateScale = PRODUCT OF: q10Settings[*]/q10</font></td></tr><tr><td><font color="#99CC00">alpha = forwardRate/r</font></td></tr><tr><td><font color="#99CC00">beta = reverseRate/r</font></td></tr><tr><td><font color="#99CC00">fcond = q^instances</font></td></tr><tr><td><font color="#99CC00">inf = alpha/(alpha+beta)</font></td></tr><tr><td><font color="#99CC00">tau = 1/((alpha+beta) * rateScale)</font></td></tr><tr><td><font color="#666633">q' = (inf - q) / tau</font></td></tr><tr><td><font color="#666666">Exposures: alpha (per_time), beta (per_time), tau (time), <br/>inf, rateScale, fcond, <br/>q </font></td></tr></table>>]; gateHHrates;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>gate</td></tr><tr><td><font color="#666666">Exposures: fcond, q </font></td></tr></table>>]; gate;
    gateHHrates -> gate [len=1.00, arrowhead=onormal]
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseGate</td></tr><tr><td><font color="#669999">Params: instances </font></td></tr><tr><td><font color="#666666">Exposures: fcond, q </font></td></tr></table>>]; baseGate;
    gate -> baseGate [len=1.00, arrowhead=onormal]
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>HHExpLinearRate</td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#99CC00">x = (v - midpoint) / scale</font></td></tr><tr><td><font color="#666666">Exposures: r (per_time) </font></td></tr></table>>]; HHExpLinearRate;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseHHRate</td></tr><tr><td><font color="#669999">Params: rate (per_time), midpoint (voltage), scale (voltage) </font></td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#666666">Exposures: r (per_time) </font></td></tr></table>>]; baseHHRate;
    HHExpLinearRate -> baseHHRate [len=1.00, arrowhead=onormal]
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseVoltageDepRate</td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#666666">Exposures: r (per_time) </font></td></tr></table>>]; baseVoltageDepRate;
    baseHHRate -> baseVoltageDepRate [len=1.00, arrowhead=onormal]
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>HHExpRate</td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#99CC00">r = rate * exp((v - midpoint)/scale)</font></td></tr><tr><td><font color="#666666">Exposures: r (per_time) </font></td></tr></table>>]; HHExpRate;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseHHRate</td></tr><tr><td><font color="#669999">Params: rate (per_time), midpoint (voltage), scale (voltage) </font></td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#666666">Exposures: r (per_time) </font></td></tr></table>>]; baseHHRate;
    HHExpRate -> baseHHRate [len=1.00, arrowhead=onormal]
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseVoltageDepRate</td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#666666">Exposures: r (per_time) </font></td></tr></table>>]; baseVoltageDepRate;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>gateHHrates</td></tr><tr><td><font color="#FF9966">State vars: q </font></td></tr><tr><td><font color="#99CC00">rateScale = PRODUCT OF: q10Settings[*]/q10</font></td></tr><tr><td><font color="#99CC00">alpha = forwardRate/r</font></td></tr><tr><td><font color="#99CC00">beta = reverseRate/r</font></td></tr><tr><td><font color="#99CC00">fcond = q^instances</font></td></tr><tr><td><font color="#99CC00">inf = alpha/(alpha+beta)</font></td></tr><tr><td><font color="#99CC00">tau = 1/((alpha+beta) * rateScale)</font></td></tr><tr><td><font color="#666633">q' = (inf - q) / tau</font></td></tr><tr><td><font color="#666666">Exposures: alpha (per_time), beta (per_time), tau (time), <br/>inf, rateScale, fcond, <br/>q </font></td></tr></table>>]; gateHHrates;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>gate</td></tr><tr><td><font color="#666666">Exposures: fcond, q </font></td></tr></table>>]; gate;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseGate</td></tr><tr><td><font color="#669999">Params: instances </font></td></tr><tr><td><font color="#666666">Exposures: fcond, q </font></td></tr></table>>]; baseGate;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>HHExpRate</td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#99CC00">r = rate * exp((v - midpoint)/scale)</font></td></tr><tr><td><font color="#666666">Exposures: r (per_time) </font></td></tr></table>>]; HHExpRate;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseHHRate</td></tr><tr><td><font color="#669999">Params: rate (per_time), midpoint (voltage), scale (voltage) </font></td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#666666">Exposures: r (per_time) </font></td></tr></table>>]; baseHHRate;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseVoltageDepRate</td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#666666">Exposures: r (per_time) </font></td></tr></table>>]; baseVoltageDepRate;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>HHSigmoidRate</td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#99CC00">r = rate / (1 + exp(0 - (v - midpoint)/scale))</font></td></tr><tr><td><font color="#666666">Exposures: r (per_time) </font></td></tr></table>>]; HHSigmoidRate;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseHHRate</td></tr><tr><td><font color="#669999">Params: rate (per_time), midpoint (voltage), scale (voltage) </font></td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#666666">Exposures: r (per_time) </font></td></tr></table>>]; baseHHRate;
    HHSigmoidRate -> baseHHRate [len=1.00, arrowhead=onormal]
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseVoltageDepRate</td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#666666">Exposures: r (per_time) </font></td></tr></table>>]; baseVoltageDepRate;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>channelDensity</td></tr><tr><td><font color="#669999">Params: erev (voltage) </font></td></tr><tr><td><font color="#662211">Consts: vShift = 0 V </font></td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#B2C0D9">segmentGroup</font></td></tr><tr><td><font color="#B2C0D9">ion</font></td></tr><tr><td><font color="#99CC00">channelf = ionChannel/fopen</font></td></tr><tr><td><font color="#99CC00">gDensity = condDensity * channelf</font></td></tr><tr><td><font color="#99CC00">iDensity = gDensity * (erev - v)</font></td></tr><tr><td><font color="#666666">Exposures: gDensity (conductanceDensity), iDensity (currentDensity) </font></td></tr></table>>]; channelDensity;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseChannelDensityCond</td></tr><tr><td><font color="#669999">Params: condDensity (conductanceDensity) </font></td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#666666">Exposures: gDensity (conductanceDensity), iDensity (currentDensity) </font></td></tr></table>>]; baseChannelDensityCond;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseChannelDensity</td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#666666">Exposures: iDensity (currentDensity) </font></td></tr></table>>]; baseChannelDensity;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>ionChannelHH</td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#B2C0D9">species</font></td></tr><tr><td><font color="#99CC00">conductanceScale = PRODUCT OF: conductanceScaling[*]/factor</font></td></tr><tr><td><font color="#99CC00">fopen0 = PRODUCT OF: gates[*]/fcond</font></td></tr><tr><td><font color="#99CC00">fopen = conductanceScale * fopen0</font></td></tr><tr><td><font color="#99CC00">g = conductance * fopen</font></td></tr><tr><td><font color="#666666">Exposures: g (conductance), fopen </font></td></tr></table>>]; ionChannelHH;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseIonChannel</td></tr><tr><td><font color="#669999">Params: conductance (conductance) </font></td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#B2C0D9">neuroLexId</font></td></tr><tr><td><font color="#666666">Exposures: g (conductance), fopen </font></td></tr></table>>]; baseIonChannel;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>notes</td></tr></table>>]; notes;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>gateHHrates</td></tr><tr><td><font color="#FF9966">State vars: q </font></td></tr><tr><td><font color="#99CC00">rateScale = PRODUCT OF: q10Settings[*]/q10</font></td></tr><tr><td><font color="#99CC00">alpha = forwardRate/r</font></td></tr><tr><td><font color="#99CC00">beta = reverseRate/r</font></td></tr><tr><td><font color="#99CC00">fcond = q^instances</font></td></tr><tr><td><font color="#99CC00">inf = alpha/(alpha+beta)</font></td></tr><tr><td><font color="#99CC00">tau = 1/((alpha+beta) * rateScale)</font></td></tr><tr><td><font color="#666633">q' = (inf - q) / tau</font></td></tr><tr><td><font color="#666666">Exposures: alpha (per_time), beta (per_time), tau (time), <br/>inf, rateScale, fcond, <br/>q </font></td></tr></table>>]; gateHHrates;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>gate</td></tr><tr><td><font color="#666666">Exposures: fcond, q </font></td></tr></table>>]; gate;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseGate</td></tr><tr><td><font color="#669999">Params: instances </font></td></tr><tr><td><font color="#666666">Exposures: fcond, q </font></td></tr></table>>]; baseGate;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>HHExpLinearRate</td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#99CC00">x = (v - midpoint) / scale</font></td></tr><tr><td><font color="#666666">Exposures: r (per_time) </font></td></tr></table>>]; HHExpLinearRate;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseHHRate</td></tr><tr><td><font color="#669999">Params: rate (per_time), midpoint (voltage), scale (voltage) </font></td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#666666">Exposures: r (per_time) </font></td></tr></table>>]; baseHHRate;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseVoltageDepRate</td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#666666">Exposures: r (per_time) </font></td></tr></table>>]; baseVoltageDepRate;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>HHExpRate</td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#99CC00">r = rate * exp((v - midpoint)/scale)</font></td></tr><tr><td><font color="#666666">Exposures: r (per_time) </font></td></tr></table>>]; HHExpRate;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseHHRate</td></tr><tr><td><font color="#669999">Params: rate (per_time), midpoint (voltage), scale (voltage) </font></td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#666666">Exposures: r (per_time) </font></td></tr></table>>]; baseHHRate;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>baseVoltageDepRate</td></tr><tr><td><font color="#666699">REQUIRES: v (voltage)</font></td></tr><tr><td><font color="#666666">Exposures: r (per_time) </font></td></tr></table>>]; baseVoltageDepRate;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>specificCapacitance</td></tr><tr><td><font color="#669999">Params: value (specificCapacitance) </font></td></tr><tr><td><font color="#B2C0D9">segmentGroup</font></td></tr><tr><td><font color="#99CC00">specCap = value</font></td></tr><tr><td><font color="#666666">Exposures: specCap (specificCapacitance) </font></td></tr></table>>]; specificCapacitance;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>intracellularProperties</td></tr><tr><td><font color="#99CC00">caConc = SUM OF: speciesList[ion='ca']/concentration</font></td></tr><tr><td><font color="#99CC00">caConcExt = SUM OF: speciesList[ion='ca']/extConcentration</font></td></tr><tr><td><font color="#666666">Exposures: caConc (concentration), caConcExt (concentration) </font></td></tr></table>>]; intracellularProperties;
    node [shape=box label=<<table border="0" cellborder="0"><tr><td>resistivity</td></tr><tr><td><font color="#669999">Params: value (resistivity) </font></td></tr><tr><td><font color="#B2C0D9">segmentGroup</font></td></tr></table>>]; resistivity;
}

    "hhcell (cell)" -> cell [len=1.00]
    "null (0)" -> notes [len=1.00]
    "morphology (morphology)" -> morphology [len=1.00]
    "soma (id = 0)" -> segment [len=1.00]
    "null (1)" -> proximal [len=1.00]
    "null (2)" -> distal [len=1.00]
    "soma_group (segmentGroup)" -> segmentGroup [len=1.00]
    "null (3)" -> member [len=1.00]
    "bioPhys1 (biophysicalProperties)" -> biophysicalProperties [len=1.00]
    "null (4)" -> membraneProperties [len=1.00]
    "null (5)" -> spikeThresh [len=1.00]
    "null (6)" -> initMembPotential [len=1.00]
    "leak (channelDensity)" -> channelDensity [len=1.00]
    "passiveChan (ionChannelPassive)" -> ionChannelPassive [len=1.00]
    "null (7)" -> notes [len=1.00]
    "naChans (channelDensity)" -> channelDensity [len=1.00]
    "naChan (ionChannelHH)" -> ionChannelHH [len=1.00]
    "null (8)" -> notes [len=1.00]
    "m (gateHHrates)" -> gateHHrates [len=1.00]
    "null (9)" -> HHExpLinearRate [len=1.00]
    "null (10)" -> HHExpRate [len=1.00]
    "h (gateHHrates)" -> gateHHrates [len=1.00]
    "null (11)" -> HHExpRate [len=1.00]
    "null (12)" -> HHSigmoidRate [len=1.00]
    "kChans (channelDensity)" -> channelDensity [len=1.00]
    "kChan (ionChannelHH)" -> ionChannelHH [len=1.00]
    "null (13)" -> notes [len=1.00]
    "n (gateHHrates)" -> gateHHrates [len=1.00]
    "null (14)" -> HHExpLinearRate [len=1.00]
    "null (15)" -> HHExpRate [len=1.00]
    "null (16)" -> specificCapacitance [len=1.00]
    "null (17)" -> intracellularProperties [len=1.00]
    "null (18)" -> resistivity [len=1.00]
}