NOTE: the latest version of this documentation can be found on docs.neuroml.org!

For more information on NeuroML 2 and LEMS see here.
Note: these descriptions have been updated to the latest NeuroML v2.2 definitions, using the latest version of LEMS!

Channels

NeuroML2 ComponentType definitions from Channels.xml

Original LEMS ComponentType definitions: Channels.xml
Schema against which NeuroML based on these should be valid: NeuroML_v2.2.xsd

baseVoltageDepRate
Base ComponentType for voltage dependent rate. Produces a time varying rate r which depends on v.
Exposures	r	per_time
Requirements	v	voltage

baseVoltageConcDepRate extends baseVoltageDepRate
Base ComponentType for voltage and concentration dependent rate. Produces a time varying rate r which depends on v and caConc.
Exposures	r (from baseVoltageDepRate)	per_time
Requirements	caConc	concentration
	v (from baseVoltageDepRate)	voltage

baseHHRate extends baseVoltageDepRate
Base ComponentType for rate which follow one of the typical forms for rate equations in the standard HH formalism, using the parameters rate, midpoint and scale
Parameters	midpoint	voltage
	rate	per_time
	scale	voltage
Exposures	r (from baseVoltageDepRate)	per_time
Requirements	v (from baseVoltageDepRate)	voltage

HHExpRate extends baseHHRate
Exponential form for rate equation (Q: Should these be renamed hhExpRate, etc?)
Parameters	midpoint (from baseHHRate)	voltage
	rate (from baseHHRate)	per_time
	scale (from baseHHRate)	voltage
Exposures	r (from baseVoltageDepRate)	per_time
Requirements	v (from baseVoltageDepRate)	voltage
Dynamics	Derived Variables r = rate * exp((v - midpoint)/scale) (exposed as r)

HHSigmoidRate extends baseHHRate
Sigmoidal form for rate equation
Parameters	midpoint (from baseHHRate)	voltage
	rate (from baseHHRate)	per_time
	scale (from baseHHRate)	voltage
Exposures	r (from baseVoltageDepRate)	per_time
Requirements	v (from baseVoltageDepRate)	voltage
Dynamics	Derived Variables r = rate / (1 + exp(0 - (v - midpoint)/scale)) (exposed as r)

HHExpLinearRate extends baseHHRate
Exponential linear form for rate equation. Linear for large positive v, exponentially decays for large negative v.
Parameters	midpoint (from baseHHRate)	voltage
	rate (from baseHHRate)	per_time
	scale (from baseHHRate)	voltage
Exposures	r (from baseVoltageDepRate)	per_time
Requirements	v (from baseVoltageDepRate)	voltage
Dynamics	Derived Variables x = (v - midpoint) / scale Conditional Derived Variables IF x != 0 THEN r = rate * x / (1 - exp(0 - x)) (exposed as r) IF x = 0 THEN r = rate (exposed as r)

baseVoltageDepVariable
Base ComponentType for voltage dependent variable x, which depends on v. Can be used for inf/steady state of rate variable.
Exposures	x	Dimensionless
Requirements	v	voltage

baseVoltageConcDepVariable extends baseVoltageDepVariable
Base ComponentType for voltage and calcium concentration dependent variable x, which depends on v and caConc.
Exposures	x (from baseVoltageDepVariable)	Dimensionless
Requirements	caConc	concentration
	v (from baseVoltageDepVariable)	voltage

baseHHVariable extends baseVoltageDepVariable
Base ComponentType for voltage dependent dimensionless variable which follow one of the typical forms for variable equations in the standard HH formalism, using the parameters rate, midpoint, scale
Parameters	midpoint	voltage
	rate	Dimensionless
	scale	voltage
Exposures	x (from baseVoltageDepVariable)	Dimensionless
Requirements	v (from baseVoltageDepVariable)	voltage

HHExpVariable extends baseHHVariable
Exponential form for variable equation
Parameters	midpoint (from baseHHVariable)	voltage
	rate (from baseHHVariable)	Dimensionless
	scale (from baseHHVariable)	voltage
Exposures	x (from baseVoltageDepVariable)	Dimensionless
Requirements	v (from baseVoltageDepVariable)	voltage
Dynamics	Derived Variables x = rate * exp((v - midpoint)/scale) (exposed as x)

HHSigmoidVariable extends baseHHVariable
Sigmoidal form for variable equation
Parameters	midpoint (from baseHHVariable)	voltage
	rate (from baseHHVariable)	Dimensionless
	scale (from baseHHVariable)	voltage
Exposures	x (from baseVoltageDepVariable)	Dimensionless
Requirements	v (from baseVoltageDepVariable)	voltage
Dynamics	Derived Variables x = rate / (1 + exp(0 - (v - midpoint)/scale)) (exposed as x)

HHExpLinearVariable extends baseHHVariable
Exponential linear form for variable equation. Linear for large positive v, exponentially decays for large negative v.
Parameters	midpoint (from baseHHVariable)	voltage
	rate (from baseHHVariable)	Dimensionless
	scale (from baseHHVariable)	voltage
Exposures	x (from baseVoltageDepVariable)	Dimensionless
Requirements	v (from baseVoltageDepVariable)	voltage
Dynamics	Derived Variables a = (v - midpoint) / scale x = rate * a / (1 - exp(0 - a)) (exposed as x)

baseVoltageDepTime
Base ComponentType for voltage dependent ComponentType producing value t with dimension time (e.g. for time course of rate variable). Note: time course would not normally be fit to exp/sigmoid etc.
Exposures	t	time
Requirements	v	voltage

baseVoltageConcDepTime extends baseVoltageDepTime
Base type for voltage and calcium concentration dependent ComponentType producing value t with dimension time (e.g. for time course of rate variable).
Exposures	t (from baseVoltageDepTime)	time
Requirements	caConc	concentration
	v (from baseVoltageDepTime)	voltage

fixedTimeCourse extends baseVoltageDepTime
Time course of a fixed magnitude tau* which can be used for the time course in gateHHtauInf, gateHHratesTau or gateHHratesTauInf*
Parameters	tau	time
Exposures	t (from baseVoltageDepTime)	time
Requirements	v (from baseVoltageDepTime)	voltage
Dynamics	Derived Variables t = tau (exposed as t)

baseQ10Settings
Base ComponentType for a scaling to apply to gating variable time course, usually temperature dependent
Exposures	q10	Dimensionless
Requirements	temperature	temperature

q10Fixed extends baseQ10Settings
A fixed value, fixedQ10,* for the scaling of the time course of the gating variable*
Parameters	fixedQ10	Dimensionless
Exposures	q10 (from baseQ10Settings)	Dimensionless
Requirements	temperature (from baseQ10Settings)	temperature
Dynamics	Derived Variables q10 = fixedQ10 (exposed as q10)

q10ExpTemp extends baseQ10Settings
A value for the Q10 scaling which varies as a standard function of the difference between the current temperature, temperature, and the temperature at which the gating variable equations were determined, experimentalTemp
Parameters	experimentalTemp	temperature
Parameters	q10Factor	Dimensionless
Constants	TENDEGREES = 10K	temperature
Exposures	q10 (from baseQ10Settings)	Dimensionless
Requirements	temperature (from baseQ10Settings)	temperature
Dynamics	Derived Variables q10 = q10Factor^((temperature - experimentalTemp)/TENDEGREES) (exposed as q10)

baseConductanceScaling
Base ComponentType for a scaling to apply to a gate's conductance, e.g. temperature dependent scaling
Exposures	factor	Dimensionless
Requirements	temperature	temperature

q10ConductanceScaling extends baseConductanceScaling
A value for the conductance scaling which varies as a standard function of the difference between the current temperature, temperature, and the temperature at which the conductance was originally determined, experimentalTemp
Parameters	experimentalTemp	temperature
Parameters	q10Factor	Dimensionless
Constants	TENDEGREES = 10K	temperature
Exposures	factor (from baseConductanceScaling)	Dimensionless
Requirements	temperature (from baseConductanceScaling)	temperature
Dynamics	Derived Variables factor = q10Factor^((temperature - experimentalTemp)/TENDEGREES) (exposed as factor)

baseConductanceScalingCaDependent extends baseConductanceScaling
Base ComponentType for a scaling to apply to a gate's conductance which depends on Ca concentration. Usually a generic expression of caConc* (so no standard, non-base form here).*
Exposures	factor (from baseConductanceScaling)	Dimensionless
Requirements	caConc	concentration
	temperature (from baseConductanceScaling)	temperature

baseGate
Base ComponentType for a voltage and/or concentration dependent gate
Parameters	instances	Dimensionless
Child elements	notes	notes
Exposures	fcond	Dimensionless
Exposures	q	Dimensionless

gate extends baseGate
Conveniently named baseGate
Parameters	instances (from baseGate)	Dimensionless
Exposures	fcond (from baseGate)	Dimensionless
	q (from baseGate)	Dimensionless

gateHHrates extends gate
Gate which follows the general Hodgkin Huxley formalism
Parameters	instances (from baseGate)	Dimensionless
Child elements	forwardRate	baseVoltageDepRate
Child elements	reverseRate	baseVoltageDepRate
Children elements	q10Settings	baseQ10Settings
Exposures	alpha	per_time
	beta	per_time
	fcond (from baseGate)	Dimensionless
	inf	Dimensionless
	q (from baseGate)	Dimensionless
	rateScale	Dimensionless
	tau	time
Dynamics	State Variables q Dimensionless (exposed as q) On Start q = inf Derived Variables rateScale = q10Settings[]->q10 (reduce method: multiply) (exposed as rateScale) alpha* = forwardRate->r (exposed as alpha) beta = reverseRate->r (exposed as beta) fcond = q^instances (exposed as fcond) inf = alpha/(alpha+beta) (exposed as inf) tau = 1/((alpha+beta) * rateScale) (exposed as tau) Time Derivatives d q /dt = (inf - q) / tau

gateHHtauInf extends gate
Gate which follows the general Hodgkin Huxley formalism
Parameters	instances (from baseGate)	Dimensionless
Child elements	timeCourse	baseVoltageDepTime
Child elements	steadyState	baseVoltageDepVariable
Children elements	q10Settings	baseQ10Settings
Exposures	fcond (from baseGate)	Dimensionless
	inf	Dimensionless
	q (from baseGate)	Dimensionless
	rateScale	Dimensionless
	tau	time
Dynamics	State Variables q Dimensionless (exposed as q) On Start q = inf Derived Variables rateScale = q10Settings[]->q10 (reduce method: multiply) (exposed as rateScale) fcond* = q^instances (exposed as fcond) inf = steadyState->x (exposed as inf) tauUnscaled = timeCourse->t tau = tauUnscaled / rateScale (exposed as tau) Time Derivatives d q /dt = (inf - q) / tau

gateHHInstantaneous extends gate
Gate which follows the general Hodgkin Huxley formalism but is instantaneous, so tau = 0 and gate follows exactly inf value
Parameters	instances (from baseGate)	Dimensionless
Child elements	steadyState	baseVoltageDepVariable
Constants	SEC = 1 s	time
Exposures	fcond (from baseGate)	Dimensionless
	inf	Dimensionless
	q (from baseGate)	Dimensionless
	tau	time
Dynamics	Derived Variables inf = steadyState->x (exposed as inf) tau = 0 * SEC (exposed as tau) q = inf (exposed as q) fcond = q^instances (exposed as fcond)

gateHHratesTau extends gate
Gate which follows the general Hodgkin Huxley formalism
Parameters	instances (from baseGate)	Dimensionless
Child elements	forwardRate	baseVoltageDepRate
	reverseRate	baseVoltageDepRate
	timeCourse	baseVoltageDepTime
Children elements	q10Settings	baseQ10Settings
Exposures	alpha	per_time
	beta	per_time
	fcond (from baseGate)	Dimensionless
	inf	Dimensionless
	q (from baseGate)	Dimensionless
	rateScale	Dimensionless
	tau	time
Dynamics	State Variables q Dimensionless (exposed as q) On Start q = inf Derived Variables rateScale = q10Settings[]->q10 (reduce method: multiply) (exposed as rateScale) alpha* = forwardRate->r (exposed as alpha) beta = reverseRate->r (exposed as beta) fcond = q^instances (exposed as fcond) inf = alpha/(alpha+beta) (exposed as inf) tauUnscaled = timeCourse->t tau = tauUnscaled / rateScale (exposed as tau) Time Derivatives d q /dt = (inf - q) / tau

gateHHratesInf extends gate
Gate which follows the general Hodgkin Huxley formalism
Parameters	instances (from baseGate)	Dimensionless
Child elements	forwardRate	baseVoltageDepRate
	reverseRate	baseVoltageDepRate
	steadyState	baseVoltageDepVariable
Children elements	q10Settings	baseQ10Settings
Exposures	alpha	per_time
	beta	per_time
	fcond (from baseGate)	Dimensionless
	inf	Dimensionless
	q (from baseGate)	Dimensionless
	rateScale	Dimensionless
	tau	time
Dynamics	State Variables q Dimensionless (exposed as q) On Start q = inf Derived Variables rateScale = q10Settings[]->q10 (reduce method: multiply) (exposed as rateScale) alpha* = forwardRate->r (exposed as alpha) beta = reverseRate->r (exposed as beta) fcond = q^instances (exposed as fcond) inf = steadyState->x (exposed as inf) tau = 1/((alpha+beta) * rateScale) (exposed as tau) Time Derivatives d q /dt = (inf - q) / tau

gateHHratesTauInf extends gate
Gate which follows the general Hodgkin Huxley formalism
Parameters	instances (from baseGate)	Dimensionless
Child elements	forwardRate	baseVoltageDepRate
	reverseRate	baseVoltageDepRate
	timeCourse	baseVoltageDepTime
	steadyState	baseVoltageDepVariable
Children elements	q10Settings	baseQ10Settings
Exposures	alpha	per_time
	beta	per_time
	fcond (from baseGate)	Dimensionless
	inf	Dimensionless
	q (from baseGate)	Dimensionless
	rateScale	Dimensionless
	tau	time
Dynamics	State Variables q Dimensionless (exposed as q) On Start q = inf Derived Variables rateScale = q10Settings[]->q10 (reduce method: multiply) (exposed as rateScale) alpha* = forwardRate->r (exposed as alpha) beta = reverseRate->r (exposed as beta) inf = steadyState->x (exposed as inf) tauUnscaled = timeCourse->t tau = tauUnscaled / rateScale (exposed as tau) fcond = q^instances (exposed as fcond) Time Derivatives d q /dt = (inf - q) / tau

gateFractional extends gate
Gate composed of subgates contributing with fractional conductance
Parameters	instances (from baseGate)	Dimensionless
Children elements	q10Settings	baseQ10Settings
Children elements	subGate	subGate
Exposures	fcond (from baseGate)	Dimensionless
	q (from baseGate)	Dimensionless
	rateScale	Dimensionless
Dynamics	Derived Variables q = subGate[]->qfrac (reduce method: add) (exposed as q) fcond* = q^instances (exposed as fcond) rateScale = q10Settings[]->q10 (reduce method: multiply) (exposed as rateScale*)

subGate
Gate composed of subgates contributing with fractional conductance
Parameters	fractionalConductance	Dimensionless
Child elements	notes	notes
	timeCourse	baseVoltageDepTime
	steadyState	baseVoltageDepVariable
Exposures	inf	Dimensionless
	q	Dimensionless
	qfrac	Dimensionless
	tau	time
Requirements	rateScale	Dimensionless
Dynamics	State Variables q Dimensionless (exposed as q) On Start q = inf Derived Variables inf = steadyState->x (exposed as inf) tauUnscaled = timeCourse->t tau = tauUnscaled / rateScale (exposed as tau) qfrac = q * fractionalConductance (exposed as qfrac) Time Derivatives d q /dt = (inf - q) / tau

baseIonChannel
Base for all ion channel ComponentTypes
Parameters	conductance	conductance
Text fields	neuroLexId
Child elements	notes	notes
Child elements	annotation	annotation
Exposures	fopen	Dimensionless
Exposures	g	conductance
Requirements	v	voltage

ionChannelPassive extends ionChannel
Simple passive ion channel where the constant conductance through the channel is equal to conductance
Parameters	conductance (from baseIonChannel)	conductance
Text fields	species
Exposures	fopen (from baseIonChannel)	Dimensionless
Exposures	g (from baseIonChannel)	conductance
Requirements	v (from baseIonChannel)	voltage
Dynamics	Derived Variables fopen = 1 (exposed as fopen) g = conductance (exposed as g)

ionChannelHH extends baseIonChannel
Note ionChannel and ionChannelHH are currently functionally identical. This is needed since many existing examples use ionChannel, some use ionChannelHH. NeuroML v2beta4 should remove one of these, probably ionChannelHH.
Parameters	conductance (from baseIonChannel)	conductance
Text fields	species
Children elements	conductanceScaling	baseConductanceScaling
Children elements	gates	gate
Exposures	fopen (from baseIonChannel)	Dimensionless
Exposures	g (from baseIonChannel)	conductance
Requirements	v (from baseIonChannel)	voltage
Dynamics	Derived Variables conductanceScale = conductanceScaling[]->factor (reduce method: multiply) fopen0* = gates[]->fcond (reduce method: multiply) fopen* = conductanceScale * fopen0 (exposed as fopen) g = conductance * fopen (exposed as g)

ionChannel extends ionChannelHH
Note ionChannel and ionChannelHH are currently functionally identical. This is needed since many existing examples use ionChannel, some use ionChannelHH. NeuroML v2beta4 should remove one of these, probably ionChannelHH.
Parameters	conductance (from baseIonChannel)	conductance
Exposures	fopen (from baseIonChannel)	Dimensionless
Exposures	g (from baseIonChannel)	conductance
Requirements	v (from baseIonChannel)	voltage
Dynamics	Derived Variables conductanceScale = conductanceScaling[]->factor (reduce method: multiply) fopen0* = gates[]->fcond (reduce method: multiply) fopen* = conductanceScale * fopen0 (exposed as fopen) g = conductance * fopen (exposed as g)

ionChannelVShift extends ionChannel
Same as ionChannel, 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	conductance (from baseIonChannel)	conductance
Parameters	vShift	voltage
Text fields	species
Exposures	fopen (from baseIonChannel)	Dimensionless
Exposures	g (from baseIonChannel)	conductance
Requirements	v (from baseIonChannel)	voltage

KSState
One of the states in which a gateKS can be. The rates of transitions between these states are given by KSTransitions
Parameters	relativeConductance	Dimensionless
Exposures	occupancy	Dimensionless
	q	Dimensionless
Dynamics	State Variables occupancy Dimensionless (exposed as occupancy) Derived Variables q = relativeConductance * occupancy (exposed as q)

closedState extends KSState
A KSState with relativeConductance* of 0*
Parameters	relativeConductance (from KSState)	Dimensionless
Exposures	occupancy (from KSState)	Dimensionless
	q (from KSState)	Dimensionless

openState extends KSState
A KSState with relativeConductance* of 1*
Parameters	relativeConductance (from KSState)	Dimensionless
Exposures	occupancy (from KSState)	Dimensionless
	q (from KSState)	Dimensionless

ionChannelKS extends baseIonChannel
A kinetic scheme based ion channel with multiple gateKSs, each of which consists of multiple KSStates and KSTransitions giving the rates of transition between them
Parameters	conductance (from baseIonChannel)	conductance
Text fields	species
Children elements	conductanceScaling	baseConductanceScaling
Children elements	gates	gateKS
Exposures	fopen (from baseIonChannel)	Dimensionless
Exposures	g (from baseIonChannel)	conductance
Requirements	v (from baseIonChannel)	voltage
Dynamics	Derived Variables fopen = gates[]->fcond (reduce method: multiply) (exposed as fopen) g = fopen conductance (exposed as g)

KSTransition
Specified the forward and reverse rates of transition between two KSStates in a gateKS
Exposures	rf	per_time
	rr	per_time

forwardTransition extends KSTransition
A forward only KSTransition for a gateKS which specifies a rate* (type baseHHRate) which follows one of the standard Hodgkin Huxley forms (e.g. HHExpRate, HHSigmoidRate, HHExpLinearRate*
Child elements	rate	baseHHRate
Constants	SEC = 1s	time
Exposures	rf (from KSTransition)	per_time
Exposures	rr (from KSTransition)	per_time
Dynamics	Derived Variables rf0 = rate->r rf = rf0 (exposed as rf) rr = 0/SEC (exposed as rr)

reverseTransition extends KSTransition
A reverse only KSTransition for a gateKS which specifies a rate* (type baseHHRate) which follows one of the standard Hodgkin Huxley forms (e.g. HHExpRate, HHSigmoidRate, HHExpLinearRate*
Child elements	rate	baseHHRate
Constants	SEC = 1s	time
Exposures	rf (from KSTransition)	per_time
Exposures	rr (from KSTransition)	per_time
Dynamics	Derived Variables rr0 = rate->r rr = rr0 (exposed as rr) rf = 0/SEC (exposed as rf)

vHalfTransition extends KSTransition
Transition which specifies both the forward and reverse rates of transition
Parameters	gamma	Dimensionless
	tau	time
	tauMin	time
	vHalf	voltage
	z	Dimensionless
Constants	kte = 25.3mV	voltage
Exposures	rf (from KSTransition)	per_time
Exposures	rr (from KSTransition)	per_time
Requirements	v	voltage
Dynamics	Derived Variables rf0 = exp(z * gamma * (v - vHalf) / kte) / tau rr0 = exp(-z * (1 - gamma) * (v - vHalf) / kte) / tau rf = 1 / (1/rf0 + tauMin) (exposed as rf) rr = 1 / (1/rr0 + tauMin) (exposed as rr)

tauInfTransition extends KSTransition
KS Transition specified in terms of time constant ??? and steady state ???
Child elements	timeCourse	baseVoltageDepTime
	steadyState	baseVoltageDepVariable
Exposures	rf (from KSTransition)	per_time
	rr (from KSTransition)	per_time
Dynamics	Derived Variables tau = timeCourse->t inf = steadyState->x rf = inf/tau (exposed as rf) rr = (1-inf)/tau (exposed as rr)

gateKS extends baseGate
A gate which consists of multiple KSStates and KSTransitions giving the rates of transition between them
Parameters	instances (from baseGate)	Dimensionless
Children elements	states	KSState
	transitions	KSTransition
	q10Settings	baseQ10Settings
Exposures	fcond (from baseGate)	Dimensionless
	q (from baseGate)	Dimensionless
	rateScale	Dimensionless
Dynamics	Derived Variables rateScale = q10Settings[]->q10 (reduce method: multiply) (exposed as rateScale) q = states[]->q (reduce method: add) (exposed as q) fcond = q^instances (exposed as fcond)