# 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=<
| hhcell (cell) |
| null (0) |
| morphology (morphology) |
| soma (id = 0) |
| null (1) |
| x = 0, y = 0, z = 0, diameter = 17.841242, radius = 8.920621E-6 m, xLength = 0 m, yLength = 0 m, zLength = 0 m |
| null (2) |
| x = 0, y = 0, z = 0, diameter = 17.841242, radius = 8.920621E-6 m, xLength = 0 m, yLength = 0 m, zLength = 0 m |
| soma_group (segmentGroup) |
| null (3) |
| bioPhys1 (biophysicalProperties) |
| null (4) |
| null (5) |
| value = -0.02 V |
| null (6) |
| value = -0.065 V |
| leak (channelDensity) |
| erev = -0.054387000000000005 V, condDensity = 3 kg^-1 m^-4 s^3 A^2 |
| passiveChan (ionChannelPassive) |
| conductance = 1.0E-11 S |
| null (7) |
| naChans (channelDensity) |
| erev = 0.05 V, condDensity = 1200 kg^-1 m^-4 s^3 A^2 |
| naChan (ionChannelHH) |
| conductance = 1.0E-11 S |
| null (8) |
| m (gateHHrates) |
| instances = 3 |
| null (9) |
| rate = 1000 s^-1, midpoint = -0.04 V, scale = 0.01 V |
| null (10) |
| rate = 4000 s^-1, midpoint = -0.065 V, scale = -0.018000000000000002 V |
| h (gateHHrates) |
| instances = 1 |
| null (11) |
| rate = 70 s^-1, midpoint = -0.065 V, scale = -0.02 V |
| null (12) |
| rate = 1000 s^-1, midpoint = -0.035 V, scale = 0.01 V |
| kChans (channelDensity) |
| erev = -0.077 V, condDensity = 360 kg^-1 m^-4 s^3 A^2 |
| kChan (ionChannelHH) |
| conductance = 1.0E-11 S |
| null (13) |
| n (gateHHrates) |
| instances = 4 |
| null (14) |
| rate = 100 s^-1, midpoint = -0.055 V, scale = 0.01 V |
| null (15) |
| rate = 125 s^-1, midpoint = -0.065 V, scale = -0.08 V |
| null (16) |
| value = 0.01 kg^-1 m^-4 s^4 A^2 |
| null (17) |
| null (18) |
| value = 0.3 kg^2 m^2 s^-3 A^-2 |
| cell |
| neuroLexId |
| State vars: v (voltage), spiking |
| initMembPot = biophysicalProperties/membraneProperties/initMembPotential/value |
| thresh = biophysicalProperties/membraneProperties/spikeThresh/value |
| surfaceArea = SUM OF: morphology/segments[*]/surfaceArea |
| totSpecCap = biophysicalProperties/totSpecCap |
| totCap = totSpecCap * surfaceArea |
| iChannels = biophysicalProperties/membraneProperties/totChanCurrent |
| iSyn = SUM OF: synapses[*]/i |
| iCa = biophysicalProperties/membraneProperties/iCa |
| caConc = biophysicalProperties/intracellularProperties/caConc |
| caConcExt = biophysicalProperties/intracellularProperties/caConcExt |
| v' = (iChannels + iSyn) / totCap |
| IF v .gt. thresh AND spiking .lt. 0.5 THEN |
| (spiking = 1) AND (EVENT: spike) |
| IF v .lt. thresh THEN |
| (spiking = 0) |
| Exposures: spiking, iChannels (current), iSyn (current), totSpecCap (specificCapacitance), surfaceArea (area), iCa (current), caConc (concentration), caConcExt (concentration), v (voltage) |
| baseCellMembPot |
| Exposures: v (voltage) |
| baseSpikingCell |
| baseCell |
| baseStandalone |
| notes |
| morphology |
| segment |
| Consts: LEN = 1 m |
| name |
| radDist = distal/radius |
| dx = distal/xLength |
| dy = distal/yLength |
| dz = distal/zLength |
| px = proximal/xLength |
| py = proximal/yLength |
| pz = proximal/zLength |
| length = sqrt(((dx - px) * (dx - px) + (dy - py) * (dy - py) + (dz - pz) * (dz - pz))/(LEN * LEN)) * LEN |
| Exposures: surfaceArea (area), radDist (length), length (length) |
| proximal |
| Consts: MICRON = 1.0E-6 m |
| point3DWithDiam |
| Params: x, y, z, diameter |
| Consts: MICRON = 1.0E-6 m |
| distal |
| Consts: MICRON = 1.0E-6 m |
| point3DWithDiam |
| Params: x, y, z, diameter |
| Consts: MICRON = 1.0E-6 m |
| segmentGroup |
| neuroLexId |
| member |
| segment |
| biophysicalProperties |
| totSpecCap = membraneProperties/totSpecCap |
| Exposures: totSpecCap (specificCapacitance) |
| membraneProperties |
| REQUIRES: surfaceArea (area) |
| totSpecCap = SUM OF: specificCapacitances[*]/specCap |
| totChanPopCurrent = SUM OF: populations[*]/i |
| totChanDensCurrentDensity = SUM OF: channelDensities[*]/iDensity |
| totChanCurrent = totChanPopCurrent + (totChanDensCurrentDensity * surfaceArea) |
| totChanPopCurrentCa = SUM OF: populations[ion='ca']/i |
| totChanDensCurrentDensityCa = SUM OF: channelDensities[ion='ca']/iDensity |
| iCa = totChanPopCurrentCa + (totChanDensCurrentDensityCa * surfaceArea) |
| Exposures: totChanCurrent (current), iCa (current), totSpecCap (specificCapacitance) |
| spikeThresh |
| Params: value (voltage) |
| initMembPotential |
| Params: value (voltage) |
| channelDensity |
| Params: erev (voltage) |
| Consts: vShift = 0 V |
| REQUIRES: v (voltage) |
| segmentGroup |
| ion |
| channelf = ionChannel/fopen |
| gDensity = condDensity * channelf |
| iDensity = gDensity * (erev - v) |
| Exposures: gDensity (conductanceDensity), iDensity (currentDensity) |
| baseChannelDensityCond |
| Params: condDensity (conductanceDensity) |
| REQUIRES: v (voltage) |
| Exposures: gDensity (conductanceDensity), iDensity (currentDensity) |
| baseChannelDensity |
| REQUIRES: v (voltage) |
| Exposures: iDensity (currentDensity) |
| ionChannelPassive |
| REQUIRES: v (voltage) |
| species |
| fopen = 1 |
| g = conductance |
| Exposures: g (conductance), fopen |
| ionChannel |
| REQUIRES: v (voltage) |
| conductanceScale = PRODUCT OF: conductanceScaling[*]/factor |
| fopen0 = PRODUCT OF: gates[*]/fcond |
| fopen = conductanceScale * fopen0 |
| g = conductance * fopen |
| Exposures: g (conductance), fopen |
| ionChannelHH |
| REQUIRES: v (voltage) |
| species |
| conductanceScale = PRODUCT OF: conductanceScaling[*]/factor |
| fopen0 = PRODUCT OF: gates[*]/fcond |
| fopen = conductanceScale * fopen0 |
| g = conductance * fopen |
| Exposures: g (conductance), fopen |
| baseIonChannel |
| Params: conductance (conductance) |
| REQUIRES: v (voltage) |
| neuroLexId |
| Exposures: g (conductance), fopen |
| notes |
| channelDensity |
| Params: erev (voltage) |
| Consts: vShift = 0 V |
| REQUIRES: v (voltage) |
| segmentGroup |
| ion |
| channelf = ionChannel/fopen |
| gDensity = condDensity * channelf |
| iDensity = gDensity * (erev - v) |
| Exposures: gDensity (conductanceDensity), iDensity (currentDensity) |
| baseChannelDensityCond |
| Params: condDensity (conductanceDensity) |
| REQUIRES: v (voltage) |
| Exposures: gDensity (conductanceDensity), iDensity (currentDensity) |
| baseChannelDensity |
| REQUIRES: v (voltage) |
| Exposures: iDensity (currentDensity) |
| ionChannelHH |
| REQUIRES: v (voltage) |
| species |
| conductanceScale = PRODUCT OF: conductanceScaling[*]/factor |
| fopen0 = PRODUCT OF: gates[*]/fcond |
| fopen = conductanceScale * fopen0 |
| g = conductance * fopen |
| Exposures: g (conductance), fopen |
| baseIonChannel |
| Params: conductance (conductance) |
| REQUIRES: v (voltage) |
| neuroLexId |
| Exposures: g (conductance), fopen |
| notes |
| gateHHrates |
| State vars: q |
| rateScale = PRODUCT OF: q10Settings[*]/q10 |
| alpha = forwardRate/r |
| beta = reverseRate/r |
| fcond = q^instances |
| inf = alpha/(alpha+beta) |
| tau = 1/((alpha+beta) * rateScale) |
| q' = (inf - q) / tau |
| Exposures: alpha (per_time), beta (per_time), tau (time), inf, rateScale, fcond, q |
| gate |
| Exposures: fcond, q |
| baseGate |
| Params: instances |
| Exposures: fcond, q |
| HHExpLinearRate |
| REQUIRES: v (voltage) |
| x = (v - midpoint) / scale |
| Exposures: r (per_time) |
| baseHHRate |
| Params: rate (per_time), midpoint (voltage), scale (voltage) |
| REQUIRES: v (voltage) |
| Exposures: r (per_time) |
| baseVoltageDepRate |
| REQUIRES: v (voltage) |
| Exposures: r (per_time) |
| HHExpRate |
| REQUIRES: v (voltage) |
| r = rate * exp((v - midpoint)/scale) |
| Exposures: r (per_time) |
| baseHHRate |
| Params: rate (per_time), midpoint (voltage), scale (voltage) |
| REQUIRES: v (voltage) |
| Exposures: r (per_time) |
| baseVoltageDepRate |
| REQUIRES: v (voltage) |
| Exposures: r (per_time) |
| gateHHrates |
| State vars: q |
| rateScale = PRODUCT OF: q10Settings[*]/q10 |
| alpha = forwardRate/r |
| beta = reverseRate/r |
| fcond = q^instances |
| inf = alpha/(alpha+beta) |
| tau = 1/((alpha+beta) * rateScale) |
| q' = (inf - q) / tau |
| Exposures: alpha (per_time), beta (per_time), tau (time), inf, rateScale, fcond, q |
| gate |
| Exposures: fcond, q |
| baseGate |
| Params: instances |
| Exposures: fcond, q |
| HHExpRate |
| REQUIRES: v (voltage) |
| r = rate * exp((v - midpoint)/scale) |
| Exposures: r (per_time) |
| baseHHRate |
| Params: rate (per_time), midpoint (voltage), scale (voltage) |
| REQUIRES: v (voltage) |
| Exposures: r (per_time) |
| baseVoltageDepRate |
| REQUIRES: v (voltage) |
| Exposures: r (per_time) |
| HHSigmoidRate |
| REQUIRES: v (voltage) |
| r = rate / (1 + exp(0 - (v - midpoint)/scale)) |
| Exposures: r (per_time) |
| baseHHRate |
| Params: rate (per_time), midpoint (voltage), scale (voltage) |
| REQUIRES: v (voltage) |
| Exposures: r (per_time) |
| baseVoltageDepRate |
| REQUIRES: v (voltage) |
| Exposures: r (per_time) |
| channelDensity |
| Params: erev (voltage) |
| Consts: vShift = 0 V |
| REQUIRES: v (voltage) |
| segmentGroup |
| ion |
| channelf = ionChannel/fopen |
| gDensity = condDensity * channelf |
| iDensity = gDensity * (erev - v) |
| Exposures: gDensity (conductanceDensity), iDensity (currentDensity) |
| baseChannelDensityCond |
| Params: condDensity (conductanceDensity) |
| REQUIRES: v (voltage) |
| Exposures: gDensity (conductanceDensity), iDensity (currentDensity) |
| baseChannelDensity |
| REQUIRES: v (voltage) |
| Exposures: iDensity (currentDensity) |
| ionChannelHH |
| REQUIRES: v (voltage) |
| species |
| conductanceScale = PRODUCT OF: conductanceScaling[*]/factor |
| fopen0 = PRODUCT OF: gates[*]/fcond |
| fopen = conductanceScale * fopen0 |
| g = conductance * fopen |
| Exposures: g (conductance), fopen |
| baseIonChannel |
| Params: conductance (conductance) |
| REQUIRES: v (voltage) |
| neuroLexId |
| Exposures: g (conductance), fopen |
| notes |
| gateHHrates |
| State vars: q |
| rateScale = PRODUCT OF: q10Settings[*]/q10 |
| alpha = forwardRate/r |
| beta = reverseRate/r |
| fcond = q^instances |
| inf = alpha/(alpha+beta) |
| tau = 1/((alpha+beta) * rateScale) |
| q' = (inf - q) / tau |
| Exposures: alpha (per_time), beta (per_time), tau (time), inf, rateScale, fcond, q |
| gate |
| Exposures: fcond, q |
| baseGate |
| Params: instances |
| Exposures: fcond, q |
| HHExpLinearRate |
| REQUIRES: v (voltage) |
| x = (v - midpoint) / scale |
| Exposures: r (per_time) |
| baseHHRate |
| Params: rate (per_time), midpoint (voltage), scale (voltage) |
| REQUIRES: v (voltage) |
| Exposures: r (per_time) |
| baseVoltageDepRate |
| REQUIRES: v (voltage) |
| Exposures: r (per_time) |
| HHExpRate |
| REQUIRES: v (voltage) |
| r = rate * exp((v - midpoint)/scale) |
| Exposures: r (per_time) |
| baseHHRate |
| Params: rate (per_time), midpoint (voltage), scale (voltage) |
| REQUIRES: v (voltage) |
| Exposures: r (per_time) |
| baseVoltageDepRate |
| REQUIRES: v (voltage) |
| Exposures: r (per_time) |
| specificCapacitance |
| Params: value (specificCapacitance) |
| segmentGroup |
| specCap = value |
| Exposures: specCap (specificCapacitance) |
| intracellularProperties |
| caConc = SUM OF: speciesList[ion='ca']/concentration |
| caConcExt = SUM OF: speciesList[ion='ca']/extConcentration |
| Exposures: caConc (concentration), caConcExt (concentration) |
| resistivity |
| Params: value (resistivity) |
| segmentGroup |