NOTE: the latest version of this documentation can be found on docs.neuroml.org!
Cells |
| NeuroML2 ComponentType definitions from Cells.xml |
| Original LEMS ComponentType definitions: Cells.xml Schema against which NeuroML based on these should be valid: NeuroML_v2.2.xsd |
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baseCell
extends baseStandalone |
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| Base type of any cell (either abstract like izhikevich2007Cell or morphologically detailed like cell) which can be used in a population |
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baseSpikingCell
extends baseCell |
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| Base type of any cell which can emit spike events. | ||
| Event Ports | spike Spike event |
Direction: out |
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baseCellMembPot
extends baseSpikingCell |
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| Any spiking cell which has a membrane potential v with voltage units. | ||
| Exposures | v Membrane potential |
voltage |
| Event Ports | spike (from baseSpikingCell) | Direction: out |
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baseCellMembPotDL
extends baseSpikingCell |
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| Any spiking cell which has a dimensioness membrane potential, V. | ||
| Exposures | V Membrane potential |
Dimensionless |
| Event Ports | spike (from baseSpikingCell) | Direction: out |
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baseChannelPopulation
extends baseVoltageDepPointCurrent |
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| Base type for any current producing population of channels, all of type ionChannel | ||
| Component References | ionChannel | baseIonChannel |
| Exposures | i (from basePointCurrent) | current |
| Requirements | v (from baseVoltageDepPointCurrent) | voltage |
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channelPopulation
extends baseChannelPopulation |
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| Population of number ohmic ion channels. These each produce a conductance channelg across a reversal potential erev, giving a total current i. | ||
| Parameters | erev | voltage | number | Dimensionless |
| Text fields | ion | |
| Constants | vShift = 0mV | voltage |
| Exposures | i (from basePointCurrent) | current |
| Requirements | v (from baseVoltageDepPointCurrent) | voltage |
| Dynamics |
Structure CHILD INSTANCE: ionChannel Derived Variables channelg = ionChannel->g geff = channelg * number i = geff * (erev - v) (exposed as i) |
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channelPopulationNernst
extends baseChannelPopulation |
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| Population of channels with a time varying reversal potential erev determined by Nernst equation. Hard coded for Ca only! | ||
| Parameters | number | Dimensionless |
| Text fields | ion | |
| Constants | R = 8.3144621 J_per_K_per_mol | idealGasConstantDims | zCa = 2 | Dimensionless | F = 96485.3 C_per_mol | charge_per_mole | vShift = 0mV | voltage |
| Exposures | erev | voltage | i (from basePointCurrent) | current |
| Requirements | caConc | concentration | caConcExt | concentration | temperature | temperature | v (from baseVoltageDepPointCurrent) | voltage |
| Dynamics |
Structure CHILD INSTANCE: ionChannel Derived Variables singleChannelConductance = ionChannel->g totalConductance = singleChannelConductance * number erev = (R * temperature / (zCa * F)) * log(caConcExt / caConc) (exposed as erev) i = totalConductance * (erev - v) (exposed as i) |
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| baseChannelDensity | ||
| Base type for current distributed on an area of a cell | ||
| Component References | ionChannel | baseIonChannel |
| Exposures | iDensity | currentDensity |
| Requirements | v | voltage |
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baseChannelDensityCond
extends baseChannelDensity |
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| Base type for distributed conductances on an area of a cell producing a (not necessarily ohmic) current | ||
| Parameters | condDensity | conductanceDensity |
| Exposures | gDensity | conductanceDensity | iDensity (from baseChannelDensity) | currentDensity |
| Requirements | v (from baseChannelDensity) | voltage |
| variableParameter | ||
| Specifies a parameter which can vary its value across a segmentGroup | ||
| Text fields | parameter | segmentGroup |
| Child elements | inhomogeneousValue | inhomogeneousValue |
| inhomogeneousValue | ||
| Specifies the value of a variableParameter | ||
| Text fields | inhomogeneousParameter | value |
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channelDensityNonUniform
extends baseChannelDensity |
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| Specifies a time varying ohmic conductance density, which is distributed on a region of the cell. The conductance density of the channel is not uniform, but is set using the variableParameter. Note, there is no dynamical description of this in LEMS yet, as this type only makes sense for multicompartmental cells. A ComponentType for this needs to be present to enable export of NeuroML 2 multicompartmental cells via LEMS/jNeuroML to NEURON | ||
| Parameters | erev | voltage |
| Text fields | segmentGroup | ion |
| Child elements | variableParameter | variableParameter |
| Constants | ZERO_CURR_DENS = 0 A_per_m2 | currentDensity |
| Exposures | iDensity (from baseChannelDensity) | currentDensity |
| Requirements | v (from baseChannelDensity) | voltage |
| Dynamics |
Structure CHILD INSTANCE: ionChannel Derived Variables iDensity = ZERO_CURR_DENS (exposed as iDensity) |
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channelDensityNonUniformNernst
extends baseChannelDensity |
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| Specifies a time varying conductance density, which is distributed on a region of the cell, and whose reversal potential is calculated from the Nernst equation. Hard coded for Ca only!. The conductance density of the channel is not uniform, but is set using the variableParameter. Note, there is no dynamical description of this in LEMS yet, as this type only makes sense for multicompartmental cells. A ComponentType for this needs to be present to enable export of NeuroML 2 multicompartmental cells via LEMS/jNeuroML to NEURON | ||
| Text fields | segmentGroup | ion |
| Child elements | variableParameter | variableParameter |
| Constants | ZERO_CURR_DENS = 0 A_per_m2 | currentDensity |
| Exposures | iDensity (from baseChannelDensity) | currentDensity |
| Requirements | v (from baseChannelDensity) | voltage |
| Dynamics |
Structure CHILD INSTANCE: ionChannel Derived Variables iDensity = ZERO_CURR_DENS (exposed as iDensity) |
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channelDensityNonUniformGHK
extends baseChannelDensity |
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| Specifies a time varying conductance density, which is distributed on a region of the cell, and whose current is calculated from the Goldman-Hodgkin-Katz equation. Hard coded for Ca only!. The conductance density of the channel is not uniform, but is set using the variableParameter. Note, there is no dynamical description of this in LEMS yet, as this type only makes sense for multicompartmental cells. A ComponentType for this needs to be present to enable export of NeuroML 2 multicompartmental cells via LEMS/jNeuroML to NEURON | ||
| Text fields | segmentGroup | ion |
| Child elements | variableParameter | variableParameter |
| Constants | ZERO_CURR_DENS = 0 A_per_m2 | currentDensity |
| Exposures | iDensity (from baseChannelDensity) | currentDensity |
| Requirements | v (from baseChannelDensity) | voltage |
| Dynamics |
Structure CHILD INSTANCE: ionChannel Derived Variables iDensity = ZERO_CURR_DENS (exposed as iDensity) |
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channelDensity
extends baseChannelDensityCond |
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| Specifies a time varying ohmic conductance density, gDensity, which is distributed on an area of the cell with fixed reversal potential erev producing a current density iDensity | ||
| Parameters | condDensity (from baseChannelDensityCond) | conductanceDensity | erev | voltage |
| Text fields | segmentGroup | ion |
| Constants | vShift = 0mV | voltage |
| Exposures | gDensity (from baseChannelDensityCond) | conductanceDensity | iDensity (from baseChannelDensity) | currentDensity |
| Requirements | v (from baseChannelDensity) | voltage |
| Dynamics |
Structure CHILD INSTANCE: ionChannel Derived Variables channelf = ionChannel->fopen gDensity = condDensity * channelf (exposed as gDensity) iDensity = gDensity * (erev - v) (exposed as iDensity) |
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channelDensityVShift
extends channelDensity |
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| Same as channelDensity, but with a vShift parameter to change voltage activation of gates. The exact usage of vShift in expressions for rates is determined by the individual gates. | ||
| Parameters | condDensity (from baseChannelDensityCond) | conductanceDensity | erev (from channelDensity) | voltage | vShift | voltage |
| Text fields | segmentGroup | ion |
| Exposures | gDensity (from baseChannelDensityCond) | conductanceDensity | iDensity (from baseChannelDensity) | currentDensity |
| Requirements | v (from baseChannelDensity) | voltage |
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channelDensityNernst
extends baseChannelDensityCond |
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| Specifies a time varying conductance density, gDensity, which is distributed on an area of the cell, producing a current density iDensity and whose reversal potential is calculated from the Nernst equation. Hard coded for Ca only! See https://github.com/OpenSourceBrain/ghk-nernst. | ||
| Parameters | condDensity (from baseChannelDensityCond) | conductanceDensity |
| Text fields | segmentGroup | ion |
| Constants | R = 8.3144621 J_per_K_per_mol | idealGasConstantDims | zCa = 2 | Dimensionless | F = 96485.3 C_per_mol | charge_per_mole |
| Exposures | erev | voltage | gDensity (from baseChannelDensityCond) | conductanceDensity | iDensity (from baseChannelDensity) | currentDensity |
| Requirements | caConc | concentration | caConcExt | concentration | temperature | temperature | v (from baseChannelDensity) | voltage |
| Dynamics |
Structure CHILD INSTANCE: ionChannel Derived Variables channelf = ionChannel->fopen Conditional Derived Variables IF caConcExt > 0 THEN gDensity = condDensity * channelf (exposed as gDensity) IF caConcExt <= 0 THEN gDensity = 0 (exposed as gDensity) IF caConcExt > 0 THEN erev = (R * temperature / (zCa * F)) * log(caConcExt / caConc) (exposed as erev) IF caConcExt <= 0 THEN erev = 0 (exposed as erev) IF caConcExt > 0 THEN iDensity = gDensity * (erev - v) (exposed as iDensity) IF caConcExt <= 0 THEN iDensity = 0 (exposed as iDensity) |
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channelDensityNernstCa2
extends baseChannelDensityCond |
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| This component is similar to the original component type channelDensityNernst but it is changed in order to have a reversal potential that depends on a second independent Ca++ pool (ca2). See https://github.com/OpenSourceBrain/ghk-nernst. | ||
| Parameters | condDensity (from baseChannelDensityCond) | conductanceDensity |
| Text fields | segmentGroup | ion |
| Constants | R = 8.3144621 J_per_K_per_mol | idealGasConstantDims | zCa = 2 | Dimensionless | F = 96485.3 C_per_mol | charge_per_mole |
| Exposures | erev | voltage | gDensity (from baseChannelDensityCond) | conductanceDensity | iDensity (from baseChannelDensity) | currentDensity |
| Requirements | caConc2 | concentration | caConcExt2 | concentration | temperature | temperature | v (from baseChannelDensity) | voltage |
| Dynamics |
Structure CHILD INSTANCE: ionChannel Derived Variables channelf = ionChannel->fopen Conditional Derived Variables IF caConcExt2 > 0 THEN gDensity = condDensity * channelf (exposed as gDensity) IF caConcExt2 <= 0 THEN gDensity = 0 (exposed as gDensity) IF caConcExt2 > 0 THEN erev = (R * temperature / (zCa * F)) * log(caConcExt2 / caConc2) (exposed as erev) IF caConcExt2 <= 0 THEN erev = 0 (exposed as erev) IF caConcExt2 > 0 THEN iDensity = gDensity * (erev - v) (exposed as iDensity) IF caConcExt2 <= 0 THEN iDensity = 0 (exposed as iDensity) |
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channelDensityGHK
extends baseChannelDensity |
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| Specifies a time varying conductance density, gDensity, which is distributed on an area of the cell, producing a current density iDensity and whose reversal potential is calculated from the Goldman Hodgkin Katz equation. Hard coded for Ca only! See https://github.com/OpenSourceBrain/ghk-nernst. | ||
| Parameters | permeability | permeability |
| Text fields | segmentGroup | ion |
| Constants | R = 8.3144621 J_per_K_per_mol | idealGasConstantDims | zCa = 2 | Dimensionless | F = 96485.3 C_per_mol | charge_per_mole |
| Exposures | iDensity (from baseChannelDensity) | currentDensity |
| Requirements | caConc | concentration | caConcExt | concentration | temperature | temperature | v (from baseChannelDensity) | voltage |
| Dynamics |
Structure CHILD INSTANCE: ionChannel Derived Variables K = (zCa * F) / (R * temperature) expKv = exp(-1 * K * v) channelf = ionChannel->fopen Conditional Derived Variables IF caConcExt > 0 THEN iDensity = -1 * channelf * permeability * zCa * F * K * v * ( caConc - (caConcExt * expKv) ) / (1 - expKv) (exposed as iDensity) IF caConcExt <= 0 THEN iDensity = 0 (exposed as iDensity) |
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channelDensityGHK2
extends baseChannelDensityCond |
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| Time varying conductance density, gDensity, which is distributed on an area of the cell, producing a current density iDensity. Modified version of Jaffe et al. 1994 (used also in Lawrence et al. 2006). See https://github.com/OpenSourceBrain/ghk-nernst. | ||
| Parameters | condDensity (from baseChannelDensityCond) | conductanceDensity |
| Text fields | segmentGroup | ion |
| Constants | VOLT_SCALE = 1 mV | voltage | CONC_SCALE = 1 mM | concentration | TEMP_SCALE = 1 K | temperature |
| Exposures | gDensity (from baseChannelDensityCond) | conductanceDensity | iDensity (from baseChannelDensity) | currentDensity |
| Requirements | caConc | concentration | caConcExt | concentration | temperature | temperature | v (from baseChannelDensity) | voltage |
| Dynamics |
Structure CHILD INSTANCE: ionChannel Derived Variables V = v / VOLT_SCALE ca_conc_i = caConc / CONC_SCALE ca_conc_ext = caConcExt / CONC_SCALE T = temperature / TEMP_SCALE channelf = ionChannel->fopen gDensity = condDensity * channelf (exposed as gDensity) tmp = (25 * T) / (293.15 * 2) Conditional Derived Variables IF V/tmp = 0. THEN pOpen = tmp * 1e-3 * (1 - ((ca_conc_i/ca_conc_ext) * exp(V/tmp))) * (1 - (V/tmp)/2) IF V/tmp != 0. THEN pOpen = tmp * 1e-3 * (1 - ((ca_conc_i/ca_conc_ext) * exp(V/tmp))) * ((V/tmp) / (exp(V/tmp) - 1)) IF ca_conc_ext > 0 THEN iDensity = gDensity * pOpen (exposed as iDensity) IF ca_conc_ext <= 0 THEN iDensity = 0 (exposed as iDensity) |
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pointCellCondBased
extends baseCellMembPotCap |
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| Simple model of a conductance based cell, with no separate morphology element, just an absolute capacitance C, and a set of channel populations | ||
| Parameters | C (from baseCellMembPotCap) | capacitance | thresh | voltage | v0 | voltage |
| Children elements | populations | baseChannelPopulation |
| Exposures | iMemb (from baseCellMembPotCap) | current | iSyn (from baseCellMembPotCap) | current | v (from baseCellMembPot) | voltage |
| Event Ports | spike (from baseSpikingCell) | Direction: out |
| Attachments | synapses | basePointCurrent |
| Dynamics |
State Variables v voltage (exposed as v) spiking Dimensionless On Start v = v0 spiking = 0 On Conditions IF v > thresh AND spiking < 0.5 THEN spiking = 1 EVENT OUT on port spike IF v < thresh THEN spiking = 0 Derived Variables iChannels = populations[*]->i (reduce method: add) iSyn = synapses[*]->i (reduce method: add) (exposed as iSyn) iMemb = iChannels + iSyn (exposed as iMemb) Time Derivatives d v /dt = iMemb / C |
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pointCellCondBasedCa
extends baseCellMembPotCap |
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| TEMPORARY: Point cell with conductances and Ca concentration info. Not yet fully tested!!! | ||
| Parameters | C (from baseCellMembPotCap) | capacitance | thresh | voltage | v0 | voltage |
| Children elements | populations | baseChannelPopulation | concentrationModels | concentrationModel |
| Exposures | caConc | concentration | iCa | current | iMemb (from baseCellMembPotCap) | current | iSyn (from baseCellMembPotCap) | current | v (from baseCellMembPot) | voltage |
| Event Ports | spike (from baseSpikingCell) | Direction: out |
| Attachments | synapses | basePointCurrent |
| Dynamics |
State Variables v voltage (exposed as v) spiking Dimensionless On Start v = v0 spiking = 0 On Conditions IF v > thresh AND spiking < 0.5 THEN spiking = 1 EVENT OUT on port spike IF v < thresh THEN spiking = 0 Derived Variables iChannels = populations[*]->i (reduce method: add) iCa = populations[ion='ca']->i (reduce method: add) (exposed as iCa) caConc = concentrationModels[species='ca']->concentration (reduce method: add) (exposed as caConc) iSyn = synapses[*]->i (reduce method: add) (exposed as iSyn) iMemb = iChannels + iSyn (exposed as iMemb) Time Derivatives d v /dt = iMemb / C |
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distal
extends point3DWithDiam |
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| Point furthest from the soma/root in a segment. See also proximal. | ||
| Parameters | diameter (from point3DWithDiam) | Dimensionless | x (from point3DWithDiam) | Dimensionless | y (from point3DWithDiam) | Dimensionless | z (from point3DWithDiam) | Dimensionless |
| Derived Parameters | radius = MICRON * diameter / 2 (from point3DWithDiam) | length | xLength = MICRON * x (from point3DWithDiam) | length | yLength = MICRON * y (from point3DWithDiam) | length | zLength = MICRON * z (from point3DWithDiam) | length |
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proximal
extends point3DWithDiam |
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| Point closest to the soma in a segment. Note: if the proximal point is equal to the distal point of the parent segment, proximal can be omitted. | ||
| Parameters | diameter (from point3DWithDiam) | Dimensionless | x (from point3DWithDiam) | Dimensionless | y (from point3DWithDiam) | Dimensionless | z (from point3DWithDiam) | Dimensionless |
| Derived Parameters | radius = MICRON * diameter / 2 (from point3DWithDiam) | length | xLength = MICRON * x (from point3DWithDiam) | length | yLength = MICRON * y (from point3DWithDiam) | length | zLength = MICRON * z (from point3DWithDiam) | length |
| parent | ||
| Specifies the segment which is this segment's parent. The fractionAlong specifies where it is connected usually 1 (the default value), meaning the distal point of the parent, or 0, meaning the proximal point. If it is between these, a linear interpolation between the 2 points should be used. | ||
| Text fields | segment | fractionAlong |
| segment | ||
| A segment defines the smallest unit within a possibly branching structure (morphology), such as a dendrite or axon. The shape is given by the proximal and distal points. If proximal is missing, the proximal point is assumed to be the distal point of the parent. parent specifies the parent segment. The first segment (no parent) usually represents the soma. NOTE: LEMS does not yet support multicompartmental modelling, so the Dynamics here is only appropriate for single compartment modelling. | ||
| Text fields | name | |
| Child elements | parent | parent | distal | distal | proximal | proximal |
| Constants | LEN = 1m | length |
| Exposures | length | length | radDist | length | surfaceArea | area |
| Dynamics |
Derived Variables radDist = distal->radius (exposed as radDist) 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 (exposed as length) Conditional Derived Variables IF length = 0 * LEN THEN surfaceArea = 4 * radDist * radDist * 3.14159265 (exposed as surfaceArea) IF length > 0 * LEN THEN surfaceArea = 2 * radDist * 3.14159265 * length (exposed as surfaceArea) |
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| segmentGroup | ||
| A method to describe a group of segments in a morphology | ||
| Text fields | neuroLexId | |
| Child elements | notes | notes | annotation | annotation | Children elements | property | property | members | member | paths | path | subTrees | subTree | includes | include | inhomogeneousParameter | inhomogeneousParameter |
| member | ||
| A single identified segment which is part of the segmentGroup | ||
| Text fields | segment | |
| from | ||
| Specifies which segment distal from which to calculate the segmentGroup | ||
| Text fields | segment | |
| to | ||
| Specifies which segment up to which to calculate the segmentGroup | ||
| Text fields | segment | |
| include | ||
| Include all members of another segmentGroup in this | ||
| Text fields | href | segmentGroup |
| path | ||
| Include all the segments between those specified by from and to, inclusive | ||
| Child elements | from | from | to | to |
| subTree | ||
| Include all the segments distal to that specified by from in the segmentGroup | ||
| Child elements | from | from |
| inhomogeneousParameter | ||
| An inhomogeneous parameter specified across the segmentGroup | ||
| Text fields | variable | metric |
| Child elements | proximal | proximalProperties | distal | distalProperties |
| proximalProperties | ||
| What to do at the proximal point when creating an inhomogeneous parameter | ||
| Text fields | translationStart | |
| distalProperties | ||
| What to do at the distal point when creating an inhomogeneous parameter | ||
| Text fields | normalizationEnd | |
| morphology | ||
| The collection of segments which specify the 3D structure of the cell, along with a number of segmentGroups | ||
| Children elements | segments | segment | segmentGroups | segmentGroup |
| specificCapacitance | ||
| Capacitance per unit area | ||
| Parameters | value | specificCapacitance |
| Text fields | segmentGroup | |
| Exposures | specCap | specificCapacitance |
| Dynamics |
Derived Variables specCap = value (exposed as specCap) |
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| initMembPotential | ||
| Explicitly set initial membrane potential for the cell | ||
| Parameters | value | voltage |
| spikeThresh | ||
| Membrane potential at which to emit a spiking event. Note, usually the spiking event will not be emitted again until the membrane potential has fallen below this value and rises again to cross it in a positive direction | ||
| Parameters | value | voltage |
| membraneProperties | ||
| Properties specific to the membrane, such as the populations of channels, channelDensities, specificCapacitance, etc. | ||
| Child elements | initMembPotential | initMembPotential | spikeThresh | spikeThresh | Children elements | specificCapacitances | specificCapacitance | populations | baseChannelPopulation | channelDensities | baseChannelDensity |
| Exposures | iCa | current | totChanCurrent | current | totSpecCap | specificCapacitance |
| Requirements | surfaceArea | area |
| Dynamics |
Derived Variables totSpecCap = specificCapacitances[*]->specCap (reduce method: add) (exposed as totSpecCap) totChanPopCurrent = populations[*]->i (reduce method: add) totChanDensCurrentDensity = channelDensities[*]->iDensity (reduce method: add) totChanCurrent = totChanPopCurrent + (totChanDensCurrentDensity * surfaceArea) (exposed as totChanCurrent) totChanPopCurrentCa = populations[ion='ca']->i (reduce method: add) totChanDensCurrentDensityCa = channelDensities[ion='ca']->iDensity (reduce method: add) iCa = totChanPopCurrentCa + (totChanDensCurrentDensityCa * surfaceArea) (exposed as iCa) |
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membraneProperties2CaPools
extends membraneProperties |
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| Variant of membraneProperties with 2 independent Ca pools | ||
| Child elements | initMembPotential | initMembPotential | spikeThresh | spikeThresh | Children elements | specificCapacitances | specificCapacitance | populations | baseChannelPopulation | channelDensities | baseChannelDensity |
| Exposures | iCa (from membraneProperties) | current | iCa2 | current | totChanCurrent (from membraneProperties) | current | totSpecCap (from membraneProperties) | specificCapacitance |
| Requirements | surfaceArea | area | surfaceArea (from membraneProperties) | area |
| Dynamics |
Derived Variables totSpecCap = specificCapacitances[*]->specCap (reduce method: add) (exposed as totSpecCap) totChanPopCurrent = populations[*]->i (reduce method: add) totChanDensCurrentDensity = channelDensities[*]->iDensity (reduce method: add) totChanCurrent = totChanPopCurrent + (totChanDensCurrentDensity * surfaceArea) (exposed as totChanCurrent) totChanPopCurrentCa = populations[ion='ca']->i (reduce method: add) totChanDensCurrentDensityCa = channelDensities[ion='ca']->iDensity (reduce method: add) iCa = totChanPopCurrentCa + (totChanDensCurrentDensityCa * surfaceArea) (exposed as iCa) totChanPopCurrentCa2 = populations[ion='ca2']->i (reduce method: add) totChanDensCurrentDensityCa2 = channelDensities[ion='ca2']->iDensity (reduce method: add) iCa2 = totChanPopCurrentCa2 + (totChanDensCurrentDensityCa2 * surfaceArea) (exposed as iCa2) |
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| biophysicalProperties | ||
| The biophysical properties of the cell, including the membraneProperties and the intracellularProperties | ||
| Child elements | membraneProperties | membraneProperties | intracellularProperties | intracellularProperties |
| Exposures | totSpecCap | specificCapacitance |
| Dynamics |
Derived Variables totSpecCap = membraneProperties->totSpecCap (exposed as totSpecCap) |
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| biophysicalProperties2CaPools | ||
| The biophysical properties of the cell, including the membraneProperties2CaPools and the intracellularProperties2CaPools for a cell with two Ca pools | ||
| Child elements | membraneProperties2CaPools | membraneProperties2CaPools | intracellularProperties2CaPools | intracellularProperties2CaPools |
| Exposures | totSpecCap | specificCapacitance |
| Dynamics |
Derived Variables totSpecCap = membraneProperties2CaPools->totSpecCap (exposed as totSpecCap) |
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| intracellularProperties | ||
| Biophysical properties related to the intracellular space within the cell, such as the resistivity and the list of ionic species present. caConc and caConcExt are explicitly exposed here to facilitate accessing these values from other Components, even though caConcExt is clearly not an intracellular property | ||
| Children elements | resistivity | resistivity | speciesList | species |
| Exposures | caConc | concentration | caConcExt | concentration |
| Dynamics |
Derived Variables caConc = speciesList[ion='ca']->concentration (reduce method: add) (exposed as caConc) caConcExt = speciesList[ion='ca']->extConcentration (reduce method: add) (exposed as caConcExt) |
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intracellularProperties2CaPools
extends intracellularProperties |
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| Variant of intracellularProperties with 2 independent Ca pools | ||
| Children elements | speciesList | species | resistivity | resistivity |
| Exposures | caConc (from intracellularProperties) | concentration | caConc2 | concentration | caConcExt (from intracellularProperties) | concentration | caConcExt2 | concentration |
| Dynamics |
Derived Variables caConc2 = speciesList[ion='ca2']->concentration (reduce method: add) (exposed as caConc2) caConcExt2 = speciesList[ion='ca2']->extConcentration (reduce method: add) (exposed as caConcExt2) caConc = speciesList[ion='ca']->concentration (reduce method: add) (exposed as caConc) caConcExt = speciesList[ion='ca']->extConcentration (reduce method: add) (exposed as caConcExt) |
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| resistivity | ||
| The resistivity, or specific axial resistance, of the cytoplasm | ||
| Parameters | value | resistivity |
| Text fields | segmentGroup | |
| concentrationModel | ||
| Base for any model of an ion concentration which changes with time. Internal (_concentration) and external (_extConcentration) values for the concentration of the ion are given. | ||
| Text fields | ion | |
| Exposures | concentration | concentration | extConcentration | concentration |
| Requirements | initialConcentration | concentration | initialExtConcentration | concentration | surfaceArea | area |
| Dynamics |
State Variables concentration concentration (exposed as concentration) extConcentration concentration (exposed as extConcentration) On Start concentration = initialConcentration extConcentration = initialExtConcentration |
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decayingPoolConcentrationModel
extends concentrationModel |
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| Model of an intracellular buffering mechanism for ion (currently hard Coded to be calcium, due to requirement for iCa) which has a baseline level restingConc and tends to this value with time course decayConstant. The ion is assumed to occupy a shell inside the membrane of thickness shellThickness. | ||
| Parameters | decayConstant | time | restingConc | concentration | shellThickness | length |
| Text fields | ion | |
| Constants | Faraday = 96485.3C_per_mol | charge_per_mole | AREA_SCALE = 1m2 | area | LENGTH_SCALE = 1m | length |
| Exposures | concentration (from concentrationModel) | concentration | extConcentration (from concentrationModel) | concentration |
| Requirements | iCa | current | initialConcentration (from concentrationModel) | concentration | initialExtConcentration (from concentrationModel) | concentration | surfaceArea (from concentrationModel) | area |
| Dynamics |
State Variables concentration concentration (exposed as concentration) extConcentration concentration (exposed as extConcentration) On Start concentration = initialConcentration extConcentration = initialExtConcentration On Conditions IF concentration < 0 THEN concentration = 0 Derived Variables effectiveRadius = LENGTH_SCALE * sqrt(surfaceArea/(AREA_SCALE * (4 * 3.14159))) innerRadius = effectiveRadius - shellThickness shellVolume = (4 * (effectiveRadius * effectiveRadius * effectiveRadius) * 3.14159 / 3) - (4 * (innerRadius * innerRadius * innerRadius) * 3.14159 / 3) Time Derivatives d concentration /dt = iCa / (2 * Faraday * shellVolume) - ((concentration - restingConc) / decayConstant) |
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fixedFactorConcentrationModel
extends concentrationModel |
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| Model of buffering of concentration of an ion (currently hard coded to be calcium, due to requirement for iCa) which has a baseline level restingConc and tends to this value with time course decayConstant. A fixed factor rho is used to scale the incoming current independently of the size of the compartment to produce a concentration change. | ||
| Parameters | decayConstant | time | restingConc | concentration | rho | rho_factor |
| Text fields | ion | |
| Exposures | concentration (from concentrationModel) | concentration | extConcentration (from concentrationModel) | concentration |
| Requirements | iCa | current | initialConcentration (from concentrationModel) | concentration | initialExtConcentration (from concentrationModel) | concentration | surfaceArea | area | surfaceArea (from concentrationModel) | area |
| Dynamics |
State Variables concentration concentration (exposed as concentration) extConcentration concentration (exposed as extConcentration) On Start concentration = initialConcentration extConcentration = initialExtConcentration On Conditions IF concentration < 0 THEN concentration = 0 Time Derivatives d concentration /dt = (iCa/surfaceArea) * rho - ((concentration - restingConc) / decayConstant) |
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fixedFactorConcentrationModelTraub
extends concentrationModel |
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| Model of buffering of concentration of an ion (currently hard coded to be calcium, due to requirement for iCa) which has a baseline level restingConc and tends to this value with time course 1 / beta. A fixed factor phi is used to scale the incoming current independently of the size of the compartment to produce a concentration change. Not recommended for use in models other than Traub et al. 2005! | ||
| Parameters | beta | per_time | phi | rho_factor | restingConc | concentration |
| Text fields | species | |
| Exposures | concentration (from concentrationModel) | concentration | extConcentration (from concentrationModel) | concentration |
| Requirements | iCa | current | initialConcentration (from concentrationModel) | concentration | initialExtConcentration (from concentrationModel) | concentration | surfaceArea | area | surfaceArea (from concentrationModel) | area |
| Dynamics |
State Variables concentration concentration (exposed as concentration) extConcentration concentration (exposed as extConcentration) On Start concentration = initialConcentration extConcentration = initialExtConcentration On Conditions IF concentration < 0 THEN concentration = 0 Time Derivatives d concentration /dt = (iCa/surfaceArea) * 1e-9 * phi - ((concentration - restingConc) * beta) |
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| species | ||
| Description of a chemical species identified by ion, which has internal, concentration, and external, extConcentration values for its concentration | ||
| Parameters | initialConcentration | concentration | initialExtConcentration | concentration |
| Text fields | ion | segmentGroup |
| Component References | concentrationModel | concentrationModel |
| Exposures | concentration | concentration | extConcentration | concentration |
| Dynamics |
Structure CHILD INSTANCE: concentrationModel Derived Variables concentration = concentrationModel->concentration (exposed as concentration) extConcentration = concentrationModel->extConcentration (exposed as extConcentration) |
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cell
extends baseCellMembPot |
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| Cell with segments specified in a morphology element along with details on its biophysicalProperties. NOTE: this can only be correctly simulated using jLEMS when there is a single segment in the cell, and v of this cell represents the membrane potential in that isopotential segment. | ||
| Text fields | neuroLexId | |
| Child elements | morphology | morphology | biophysicalProperties | biophysicalProperties |
| Exposures | caConc | concentration | caConcExt | concentration | iCa | current | iChannels | current | iSyn | current | spiking | Dimensionless | surfaceArea | area | totSpecCap | specificCapacitance | v (from baseCellMembPot) | voltage |
| Event Ports | spike (from baseSpikingCell) | Direction: out |
| Attachments | synapses | basePointCurrent |
| Dynamics |
State Variables v voltage (exposed as v) spiking Dimensionless (exposed as spiking) On Start spiking = 0 v = initMembPot On Conditions IF v > thresh AND spiking < 0.5 THEN spiking = 1 EVENT OUT on port spike IF v < thresh THEN spiking = 0 Derived Variables initMembPot = biophysicalProperties->membraneProperties->initMembPotential->value thresh = biophysicalProperties->membraneProperties->spikeThresh->value surfaceArea = morphology->segments[*]->surfaceArea (reduce method: add) (exposed as surfaceArea) totSpecCap = biophysicalProperties->totSpecCap (exposed as totSpecCap) totCap = totSpecCap * surfaceArea iChannels = biophysicalProperties->membraneProperties->totChanCurrent (exposed as iChannels) iSyn = synapses[*]->i (reduce method: add) (exposed as iSyn) iCa = biophysicalProperties->membraneProperties->iCa (exposed as iCa) caConc = biophysicalProperties->intracellularProperties->caConc (exposed as caConc) caConcExt = biophysicalProperties->intracellularProperties->caConcExt (exposed as caConcExt) Time Derivatives d v /dt = (iChannels + iSyn) / totCap |
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cell2CaPools
extends cell |
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| Variant of cell with two independent Ca2+ pools. Cell with segments specified in a morphology element along with details on its biophysicalProperties. NOTE: this can only be correctly simulated using jLEMS when there is a single segment in the cell, and v of this cell represents the membrane potential in that isopotential segment. | ||
| Text fields | neuroLexId | |
| Child elements | biophysicalProperties2CaPools | biophysicalProperties2CaPools |
| Exposures | caConc (from cell) | concentration | caConc2 | concentration | caConcExt (from cell) | concentration | caConcExt2 | concentration | iCa (from cell) | current | iCa2 | current | iChannels (from cell) | current | iSyn (from cell) | current | spiking (from cell) | Dimensionless | surfaceArea (from cell) | area | totSpecCap (from cell) | specificCapacitance | v (from baseCellMembPot) | voltage |
| Event Ports | spike (from baseSpikingCell) | Direction: out |
| Attachments | synapses | basePointCurrent |
| Dynamics |
State Variables v voltage (exposed as v) spiking Dimensionless (exposed as spiking) On Start spiking = 0 v = initMembPot On Conditions IF v > thresh AND spiking < 0.5 THEN spiking = 1 EVENT OUT on port spike IF v < thresh THEN spiking = 0 Derived Variables initMembPot = biophysicalProperties2CaPools->membraneProperties2CaPools->initMembPotential->value thresh = biophysicalProperties2CaPools->membraneProperties2CaPools->spikeThresh->value surfaceArea = morphology->segments[*]->surfaceArea (reduce method: add) (exposed as surfaceArea) totSpecCap = biophysicalProperties2CaPools->totSpecCap (exposed as totSpecCap) totCap = totSpecCap * surfaceArea iChannels = biophysicalProperties2CaPools->membraneProperties2CaPools->totChanCurrent (exposed as iChannels) iSyn = synapses[*]->i (reduce method: add) (exposed as iSyn) iCa = biophysicalProperties2CaPools->membraneProperties2CaPools->iCa (exposed as iCa) caConc = biophysicalProperties2CaPools->intracellularProperties2CaPools->caConc (exposed as caConc) caConcExt = biophysicalProperties2CaPools->intracellularProperties2CaPools->caConcExt (exposed as caConcExt) iCa2 = biophysicalProperties2CaPools->membraneProperties2CaPools->iCa2 (exposed as iCa2) caConc2 = biophysicalProperties2CaPools->intracellularProperties2CaPools->caConc2 (exposed as caConc2) caConcExt2 = biophysicalProperties2CaPools->intracellularProperties2CaPools->caConcExt2 (exposed as caConcExt2) Time Derivatives d v /dt = (iChannels + iSyn) / totCap |
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baseCellMembPotCap
extends baseCellMembPot |
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| Any cell with a membrane potential v with voltage units and a membrane capacitance C. Also defines exposed value iSyn for current due to external synapses and iMemb for total transmembrane current (usually channel currents plus iSyn) | ||
| Parameters | C | capacitance |
| Exposures | iMemb Total current crossing the cell membrane |
current | iSyn Total current due to synaptic inputs |
current | v (from baseCellMembPot) | voltage |
| Event Ports | spike (from baseSpikingCell) | Direction: out |
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baseIaf
extends baseCellMembPot |
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| Base ComponentType for an integrate and fire cell which emits a spiking event at membrane potential thresh and and resets to reset | ||
| Parameters | reset | voltage | thresh | voltage |
| Exposures | v (from baseCellMembPot) | voltage |
| Event Ports | spike (from baseSpikingCell) | Direction: out |
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iafTauCell
extends baseIaf |
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| Integrate and fire cell which returns to its leak reversal potential of leakReversal with a time constant tau | ||
| Parameters | leakReversal | voltage | reset (from baseIaf) | voltage | tau | time | thresh (from baseIaf) | voltage |
| Exposures | v (from baseCellMembPot) | voltage |
| Event Ports | spike (from baseSpikingCell) | Direction: out |
| Dynamics |
State Variables v voltage (exposed as v) On Start v = leakReversal On Conditions IF v > thresh THEN v = reset EVENT OUT on port spike Time Derivatives d v /dt = (leakReversal - v) / tau |
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iafTauRefCell
extends iafTauCell |
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| Integrate and fire cell which returns to its leak reversal potential of leakReversal with a time course tau. It has a refractory period of refract after spiking | ||
| Parameters | leakReversal (from iafTauCell) | voltage | refract | time | reset (from baseIaf) | voltage | tau (from iafTauCell) | time | thresh (from baseIaf) | voltage |
| Exposures | v (from baseCellMembPot) | voltage |
| Event Ports | spike (from baseSpikingCell) | Direction: out |
| Dynamics |
State Variables v voltage (exposed as v) lastSpikeTime time On Start v = leakReversal Regime: refractory (initial) On Entry lastSpikeTime = t v = reset On Conditions IF t > lastSpikeTime + refract THEN TRANSITION to REGIME integrating Regime: integrating (initial) On Conditions IF v > thresh THEN EVENT OUT on port spike TRANSITION to REGIME refractory Time Derivatives d v /dt = (leakReversal - v) / tau |
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baseIafCapCell
extends baseCellMembPotCap |
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| Base Type for all Integrate and Fire cells with a capacitance C, threshold thresh and reset membrane potential reset | ||
| Parameters | C (from baseCellMembPotCap) | capacitance | reset | voltage | thresh | voltage |
| Exposures | iMemb (from baseCellMembPotCap) | current | iSyn (from baseCellMembPotCap) | current | v (from baseCellMembPot) | voltage |
| Event Ports | spike (from baseSpikingCell) | Direction: out |
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iafCell
extends baseIafCapCell |
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| Integrate and fire cell with capacitance C, leakConductance and leakReversal | ||
| Parameters | C (from baseCellMembPotCap) | capacitance | leakConductance | conductance | leakReversal | voltage | reset (from baseIafCapCell) | voltage | thresh (from baseIafCapCell) | voltage |
| Exposures | iMemb (from baseCellMembPotCap) | current | iSyn (from baseCellMembPotCap) | current | v (from baseCellMembPot) | voltage |
| Event Ports | spike (from baseSpikingCell) | Direction: out |
| Attachments | synapses | basePointCurrent |
| Dynamics |
State Variables v voltage (exposed as v) On Start v = leakReversal On Conditions IF v > thresh THEN v = reset EVENT OUT on port spike Derived Variables iSyn = synapses[*]->i (reduce method: add) (exposed as iSyn) iMemb = leakConductance * (leakReversal - v) + iSyn (exposed as iMemb) Time Derivatives d v /dt = iMemb / C |
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iafRefCell
extends iafCell |
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| Integrate and fire cell with capacitance C, leakConductance, leakReversal and refractory period refract | ||
| Parameters | C (from baseCellMembPotCap) | capacitance | leakConductance (from iafCell) | conductance | leakReversal (from iafCell) | voltage | refract | time | reset (from baseIafCapCell) | voltage | thresh (from baseIafCapCell) | voltage |
| Exposures | iMemb (from baseCellMembPotCap) | current | iSyn (from baseCellMembPotCap) | current | v (from baseCellMembPot) | voltage |
| Event Ports | spike (from baseSpikingCell) | Direction: out |
| Attachments | synapses | basePointCurrent |
| Dynamics |
State Variables v voltage (exposed as v) lastSpikeTime time On Start v = leakReversal Derived Variables iSyn = synapses[*]->i (reduce method: add) (exposed as iSyn) iMemb = leakConductance * (leakReversal - v) + iSyn (exposed as iMemb) Regime: refractory (initial) On Entry lastSpikeTime = t v = reset On Conditions IF t > lastSpikeTime + refract THEN TRANSITION to REGIME integrating Regime: integrating (initial) On Conditions IF v > thresh THEN EVENT OUT on port spike TRANSITION to REGIME refractory Time Derivatives d v /dt = iMemb / C |
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izhikevichCell
extends baseCellMembPot |
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| Cell based on the 2003 model of Izhikevich, see http://izhikevich.org/publications/spikes.htm | ||
| Parameters | a | Dimensionless | b | Dimensionless | c | Dimensionless | d | Dimensionless | thresh | voltage | v0 | voltage |
| Constants | MSEC = 1ms | time | MVOLT = 1mV | voltage |
| Exposures | U | Dimensionless | v (from baseCellMembPot) | voltage |
| Event Ports | spike (from baseSpikingCell) | Direction: out |
| Attachments | synapses | basePointCurrentDL |
| Dynamics |
State Variables v voltage (exposed as v) U Dimensionless (exposed as U) On Start v = v0 U = v0 * b / MVOLT On Conditions IF v > thresh THEN v = c * MVOLT U = U + d EVENT OUT on port spike Derived Variables ISyn = synapses[*]->I (reduce method: add) Time Derivatives d v /dt = (0.04 * v^2 / MVOLT + 5 * v + (140.0 - U + ISyn) * MVOLT)/MSEC d U /dt = a * (b * v / MVOLT - U) / MSEC |
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izhikevich2007Cell
extends baseCellMembPotCap |
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| Cell based on the modified Izhikevich model in Izhikevich 2007, Dynamical systems in neuroscience, MIT Press | ||
| Parameters | C (from baseCellMembPotCap) | capacitance | a | per_time | b | conductance | c | voltage | d | current | k | conductance_per_voltage | v0 | voltage | vpeak | voltage | vr | voltage | vt | voltage |
| Exposures | iMemb (from baseCellMembPotCap) | current | iSyn (from baseCellMembPotCap) | current | u | current | v (from baseCellMembPot) | voltage |
| Event Ports | spike (from baseSpikingCell) | Direction: out |
| Attachments | synapses | basePointCurrent |
| Dynamics |
State Variables v voltage (exposed as v) u current (exposed as u) On Start v = v0 u = 0 On Conditions IF v > vpeak THEN v = c u = u + d EVENT OUT on port spike Derived Variables iSyn = synapses[*]->i (reduce method: add) (exposed as iSyn) iMemb = k * (v-vr) * (v-vt) + iSyn - u (exposed as iMemb) Time Derivatives d v /dt = iMemb / C d u /dt = a * (b * (v-vr) - u) |
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adExIaFCell
extends baseCellMembPotCap |
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| Model based on Brette R and Gerstner W (2005) Adaptive Exponential Integrate-and-Fire Model as an Effective Description of Neuronal Activity. J Neurophysiol 94:3637-3642 | ||
| Parameters | C (from baseCellMembPotCap) | capacitance | EL | voltage | VT | voltage | a | conductance | b | current | delT | voltage | gL | conductance | refract | time | reset | voltage | tauw | time | thresh | voltage |
| Exposures | iMemb (from baseCellMembPotCap) | current | iSyn (from baseCellMembPotCap) | current | v (from baseCellMembPot) | voltage | w | current |
| Event Ports | spike (from baseSpikingCell) | Direction: out |
| Attachments | synapses | basePointCurrent |
| Dynamics |
State Variables v voltage (exposed as v) w current (exposed as w) lastSpikeTime time On Start v = EL w = 0 Derived Variables iSyn = synapses[*]->i (reduce method: add) (exposed as iSyn) iMemb = -1 * gL * (v - EL) + gL * delT * exp((v - VT) / delT) - w + iSyn (exposed as iMemb) Regime: refractory (initial) On Entry lastSpikeTime = t v = reset w = w + b On Conditions IF t > lastSpikeTime + refract THEN TRANSITION to REGIME integrating Time Derivatives d w /dt = (a * (v - EL) - w) / tauw Regime: integrating (initial) On Conditions IF v > thresh THEN EVENT OUT on port spike TRANSITION to REGIME refractory Time Derivatives d v /dt = iMemb / C d w /dt = (a * (v - EL) - w) / tauw |
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fitzHughNagumoCell
extends baseCellMembPotDL |
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| Simple dimensionless model of spiking cell from FitzHugh and Nagumo. Superseded by fitzHughNagumo1969Cell (See https://github.com/NeuroML/NeuroML2/issues/42) | ||
| Parameters | I | Dimensionless |
| Constants | SEC = 1s | time |
| Exposures | V (from baseCellMembPotDL) | Dimensionless | W | Dimensionless |
| Event Ports | spike (from baseSpikingCell) | Direction: out |
| Dynamics |
State Variables V Dimensionless (exposed as V) W Dimensionless (exposed as W) Time Derivatives d V /dt = ( (V - ((V^3) / 3)) - W + I) / SEC d W /dt = (0.08 * (V + 0.7 - 0.8 * W)) / SEC |
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pinskyRinzelCA3Cell
extends baseCellMembPot |
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| Reduced CA3 cell model from Pinsky and Rinzel 1994. See https://github.com/OpenSourceBrain/PinskyRinzelModel | ||
| Parameters | alphac | Dimensionless | betac | Dimensionless | cm | specificCapacitance | eCa | voltage | eK | voltage | eL | voltage | eNa | voltage | gAmpa | conductanceDensity | gCa | conductanceDensity | gKC | conductanceDensity | gKahp | conductanceDensity | gKdr | conductanceDensity | gLd | conductanceDensity | gLs | conductanceDensity | gNa | conductanceDensity | gNmda | conductanceDensity | gc | conductanceDensity | iDend | currentDensity | iSoma | currentDensity | pp | Dimensionless | qd0 | Dimensionless |
| Constants | MSEC = 1 ms | time | MVOLT = 1 mV | voltage | UAMP_PER_CM2 = 1 uA_per_cm2 | currentDensity | Smax = 125.0 | Dimensionless | Vsyn = 60.0 mV | voltage | betaqd = 0.001 | Dimensionless |
| Exposures | Cad | Dimensionless | ICad | currentDensity | Si | Dimensionless | Vd | voltage | Vs | voltage | Wi | Dimensionless | cd | Dimensionless | hs | Dimensionless | ns | Dimensionless | qd | Dimensionless | sd | Dimensionless | v (from baseCellMembPot) | voltage |
| Event Ports | spike (from baseSpikingCell) | Direction: out |
| Dynamics |
State Variables Vs voltage (exposed as Vs) Vd voltage (exposed as Vd) Cad Dimensionless (exposed as Cad) hs Dimensionless (exposed as hs) ns Dimensionless (exposed as ns) sd Dimensionless (exposed as sd) cd Dimensionless (exposed as cd) qd Dimensionless (exposed as qd) Si Dimensionless (exposed as Si) Wi Dimensionless (exposed as Wi) Sisat Dimensionless On Start Vs = eL Vd = eL qd = qd0 Derived Variables v = Vs (exposed as v) ICad = gCa*sd*sd*(Vd-eCa) (exposed as ICad) alphams_Vs = 0.32*(-46.9-Vs/MVOLT)/(exp((-46.9-Vs/MVOLT)/4.0)-1.0) betams_Vs = 0.28*(Vs/MVOLT+19.9)/(exp((Vs/MVOLT+19.9)/5.0)-1.0) Minfs_Vs = alphams_Vs/(alphams_Vs+betams_Vs) alphans_Vs = 0.016*(-24.9-Vs/MVOLT)/(exp((-24.9-Vs/MVOLT)/5.0)-1.0) betans_Vs = 0.25*exp(-1.0-0.025*Vs/MVOLT) alphahs_Vs = 0.128*exp((-43.0-Vs/MVOLT)/18.0) betahs_Vs = 4.0/(1.0+exp((-20.0-Vs/MVOLT)/5.0)) alphasd_Vd = 1.6/(1.0+exp(-0.072*(Vd/MVOLT-5.0))) betasd_Vd = 0.02*(Vd/MVOLT+8.9)/(exp((Vd/MVOLT+8.9)/5.0)-1.0) Iampa = gAmpa*Wi*(Vd-Vsyn) Inmda = gNmda*Sisat*(Vd-Vsyn)/(1.0+0.28*exp(-0.062*(Vd/MVOLT-60.0))) Isyn = Iampa+Inmda Conditional Derived Variables IF 0.00002*Cad > 0.01 THEN alphaqd = 0.01 OTHERWISE alphaqd = 0.00002*Cad IF Cad/250 > 1 THEN chid = 1 OTHERWISE chid = Cad/250 IF Vd < -10*MVOLT THEN alphacd_Vd = exp((Vd/MVOLT+50.0)/11-(Vd/MVOLT+53.5)/27)/18.975 OTHERWISE alphacd_Vd = 2.0*exp((-53.5-Vd/MVOLT)/27.0) IF Vd < -10*MVOLT THEN betacd_Vd = (2.0*exp((-53.5-Vd/MVOLT)/27.0)-alphacd_Vd) OTHERWISE betacd_Vd = 0 IF Si > Smax THEN Sisat = Smax OTHERWISE Sisat = Si Time Derivatives d Vs /dt = (-gLs*(Vs-eL)-gNa*(Minfs_Vs^2)*hs*(Vs-eNa)-gKdr*ns*(Vs-eK)+(gc/pp)*(Vd-Vs)+iSoma/pp) / cm d Vd /dt = (iDend/(1.0-pp)-Isyn/(1.0-pp)-gLd*(Vd-eL)-ICad-gKahp*qd*(Vd-eK)-gKC*cd*chid*(Vd-eK)+(gc*(Vs-Vd))/(1.0-pp)) / cm d Cad /dt = (-0.13*ICad/UAMP_PER_CM2-0.075*Cad) / MSEC d hs /dt = (alphahs_Vs-(alphahs_Vs+betahs_Vs)*hs) / MSEC d ns /dt = (alphans_Vs-(alphans_Vs+betans_Vs)*ns) / MSEC d sd /dt = (alphasd_Vd-(alphasd_Vd+betasd_Vd)*sd) / MSEC d cd /dt = (alphacd_Vd-(alphacd_Vd+betacd_Vd)*cd) / MSEC d qd /dt = (alphaqd-(alphaqd+betaqd)*qd) / MSEC d Si /dt = -Si/150.0 d Wi /dt = -Wi/2.0 |
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