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Description
Description of the Schema taken from the XSD file
Definition of the elements needed for specifying electrophysiological cellular mechanisms. Voltage/concentration dependent channels can be specified, but also activity dependent ion concentrations (e.g. decaying calcium pools) and synaptic mechanisms. The mechanisms which can be specified by this schema can be mapped on into the scripting languages of a number of common simulation platforms, e.g. NEURON, GENESIS. This mapping can be done a number of XML based ways, but XSL mappings are included with the NeuroMLValidator code. The elements outlined below are linked together with with those in MorphML.xsd and Biophysics.xsd in the NeuroML.xsd file to make Level 2 compliant NeuroML files


Schema info

Information on the namespaces, etc.

targetNamespacehttp://morphml.org/channelml/schema
elementFormDefaultqualified
attributeFormDefaultunqualified


Imported Schemas

Other schemas used by this file, with different target namespaces

Namespace: http://morphml.org/metadata/schemaLocation: ../Level1/Metadata_v1.8.1.xsd
Namespace: http://morphml.org/biophysics/schemaLocation: Biophysics_v1.8.1.xsd


Elements channelml  
Simple Types ConductanceLaw   CoreEquationType   Deprecated_CoreEquationType   Deprecated_IonRole  
Groups Deprecated_AlphaBetaForm   Deprecated_AlphaBetaFormVoltConcDep   Deprecated_ExtraRateExpressions  
Attribute Groups from_to   generic_expr_params   SecondDecay   standard_expr_params   ThirdDecay  
Complex Types Block   BlockingSynapse   ChannelML   ChannelType   ClosedState   ConcDependence   ConcFactor   CurrentVoltageRelation   DecayingPoolModel   Deprecated_AkdEquation   Deprecated_GenericEquation   Deprecated_HHGate   Deprecated_Ion   Deprecated_KSGate   Deprecated_KSState   Deprecated_Ohmic   Deprecated_Parameter   Deprecated_RateConstantEqn   Deprecated_RateConstantEqnChoice   Deprecated_RateConstVoltConcDep   Deprecated_Transition   Deprecated_VoltageConcGate   Deprecated_VoltageGate   DoubleExponentialSynapse   ElectricalSynapse   FacDep   FacDepSynapse   FixedPoolInfo   Gate   GatingComplex   ImplementationPrefs   Initialisation   IntegrateAndFire   IonConcentration   IonSpecies   MultiDecaySynapse   Offset   OpenState   Parameter   Parameters   PoolVolumeInfo   Q10Settings   RateAdjustments   StdpDep   StdpSynapse   SteadyState   SynapseType   TimeCourse   Transition  

Elements

Element: channelml
The root element of any ChannelML file. Note this element will only be present in a standalone ChannelML file. For files covering many levels, neuroml will be the root element
Type: ChannelML


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Simple Types

Simple Type: ConductanceLaw

Introduced in v1.7.3 for new format ChannelML. Specifies which type of conductance law to use: ohmic, etc.

Restriction: Base: xs:string
Allowed values:
ohmic (Current is given by membrane potential times conductance (Ohm's law))
integrate_and_fire (Signifies a current which will cause the cell to behave like an integrate and fire neuron.)

ConductanceLaw used by: CurrentVoltageRelation (xs:complexType)

Instances of this element which are used by other elements in this document



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Simple Type: Deprecated_IonRole

Role ion plays in cellular mechanism, e.g. ion passes through the channel (Na, K), or the concentration of the ion is a factor in the rate equations of gating, or the mechanism alters the concentration of this ion. This greatly simplifies the number of roles an ion can play in the channel, but these options cover the majority of cases currently being modelled. Note: the term subtance is used as this formalism can also be used for other chemicals which may be transmitted, modulate channels, etc.

Restriction: Base: xs:string
Allowed values:
PermeatedSubstance (Ion passes through the channel, e.g. Na ions permeate through an "Na Channel")
PermeatedSubstanceFixedRevPot (WARNING: Ion passes through the channel, but the reversal potential of the ion isn't altered. This case is to cope with existing models which (rightly or wrongly) have calcium channels which lead to a calcium current, but which have a fixed reversal potential (Traub et. al 2003 CaL, Maex, De Schutter 1998 CaHVA). Be sure that this is the correct intended behaviour of the channel before using this IonRole.)
ModulatingSubstance (Concentration of ion/substance modulates dynamics/rate equations of channel, e.g. Ca dependent K channel, K permeates, but the rate is dependent on concentration of internal Ca)
SignallingSubstance (Ion/substance is involved in internal signalling in the cell and the mechanism can alter its concentration, e.g. exponentially decaying Ca pool)

Deprecated_IonRole used by: Deprecated_Ion (xs:complexType)

Instances of this element which are used by other elements in this document



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Simple Type: CoreEquationType

Enumeration of core equation types, used from v1.7.3: exp_linear, sigmoidal, exponential

Restriction: Base: xs:string
Allowed values:
exponential (Of the form: A * exp((v-V1/2)/B))
sigmoid (Of the form: A / (1 + exp((v-V1/2)/B)))
exp_linear (Of the form: A * ((v-V1/2)/B) / (1 - exp(-((v-V1/2)/B))))
generic (A generic expression for the rates. etc. in the expr attribute. If possible the expression should be fit into one of the standard forms above (e.g. exponential, etc.))

CoreEquationType used by: Transition (xs:complexType) TimeCourse (xs:complexType) SteadyState (xs:complexType)

Instances of this element which are used by other elements in this document



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Simple Type: Deprecated_CoreEquationType

Core equation types prior to v1.7.3, linoidal, sigmoidal, exponential

Restriction: Base: xs:string
Allowed values:
exponential (Of the form: A * exp(k * (v-d)))
sigmoid (Of the form: A / (1 + exp(k * (v-d))))
linoid (Of the form: A * (k * (v-d)) / (1 - exp(-(k * (v-d)))))

Deprecated_CoreEquationType used by: Deprecated_AkdEquation (xs:complexType)

Instances of this element which are used by other elements in this document



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Groups

Group: Deprecated_AlphaBetaForm

alpha, beta form of rate equations. These will always be together if present. Deprecated! Will be removed in v2.0

The following elements must appear in the sequence outlined here.
alpha
Type : Deprecated_RateConstantEqnChoice
beta
Type : Deprecated_RateConstantEqnChoice


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Group: Deprecated_ExtraRateExpressions

Two more rate variables, which may be needed for calculating a non standard tau, inf, e.g. Kdr in the Purkinje cell model. tau and inf will be calculated as normal unless otherwise specified.

The following elements must appear in the sequence outlined here.
gamma
Type : Deprecated_RateConstantEqnChoice
zeta
Type : Deprecated_RateConstantEqnChoice
Occurances: 0 ... 1


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Group: Deprecated_AlphaBetaFormVoltConcDep

alpha, beta form of rate equations of voltage and conc dependent channels. These will always be together if present

The following elements must appear in the sequence outlined here.
alpha
Type : Deprecated_RateConstVoltConcDep
beta
Type : Deprecated_RateConstVoltConcDep


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Attribute Groups

Attribute Group: SecondDecay

The maximum conductance and decay constant of the 2nd (normally slower) component of the synaptic conductance. Note that either both attributes or neither should be present. Unfortunately attributeGroups can't be made optional...

Attributes
max_conductance_2Type: bio:ConductanceValue , Use: optional
decay_time_2Type: bio:TimeConstantValue , Use: optional


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Attribute Group: ThirdDecay

The maximum conductance and decay constant of the 3nd (normally slower) component of the synaptic conductance. Note that either both attributes or neither should be present. Unfortunately attributeGroups can't be made optional...

Attributes
max_conductance_3Type: bio:ConductanceValue , Use: optional
decay_time_3Type: bio:TimeConstantValue , Use: optional


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Attribute Group: from_to
Attributes
from
Source state of the transition in kinetic scheme.
Type: xs:string , Use: required
to
Target state of the transition in kinetic scheme.
Type: xs:string , Use: required


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Attribute Group: standard_expr_params

Note: the following 3 attributes should always be used when using the exponential/exp_linear/sigmoidal form of expression. These are only optional here, as whole attributeGroups can't be set as optional or required.

Attributes
rateType: xs:string , Use: optional
scaleType: xs:string , Use: optional
midpointType: xs:string , Use: optional


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Attribute Group: generic_expr_params

Note: the following attribute should be used when using the generic form of expression. This is optional here, as whole attributeGroups can't be set as optional or required.

Attributes
exprType: xs:string , Use: optional


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Complex Types

Complex Type: ChannelML

Root element containing the ions used in the mechanism, the unit system of the file (as attribute), and information on channels and/or ion concentration dynamics. Normally only the ion element and one of channel_type, synapse_type or ion_concentration should be present.

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
ion
One or more ions which play some role in the mechanism, e.g. transmitted by the channel, alters the rate, etc. Note: deprecated since v1.7.3
Type : Deprecated_Ion
Occurances: 0 ... unbounded
channel_type
Specification of a voltage or ligand gated membrane conductance mechanism
Type : ChannelType
Occurances: 0 ... unbounded
synapse_type
Specification of a synaptic conductance, triggered by a presynaptic event
Type : SynapseType
Occurances: 0 ... unbounded
ion_concentration
Specification of how an ion concentration alters with time, e.g. calcium dynamics. This may influence other channels (e.g. Ca dependent K channels), and other mechanisms may have a contribution to the concentration of the ion specified here (e.g. a channel transmitting calcium).
Type : IonConcentration
Occurances: 0 ... unbounded
Attributes
units
Unit system of all quantities. Only SI or Physiological units are allowed!
Type: meta:Units , Use: required

ChannelML used by: channelml (xs:element)

Instances of this element which are used by other elements in this document



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Complex Type: Parameters

Fixed value parameters which can be used in generic expressions

The following elements must appear in the sequence outlined here.
parameter
Type : Parameter
Occurances: 1 ... unbounded

Parameters used by: ChannelType (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Parameter

A single parameter which can be used in generic expressions

Attributes
name
A unique name for the parameter
Type: xs:string , Use: required
value
The default value for the parameter
Type: xs:double , Use: required

Parameter used by: Parameters (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: ChannelType

Definition of a voltage/concentration dependent cell membrane conductance

The following elements must appear in the sequence outlined here.
Group
Some metadata (notes, etc.) to describe the conductance.
Ref: meta:metadata
Group
A group of elements to include with this element
Ref: meta:referencedata
status
Status of the channel specification: stable, in progress, etc.
Type : meta:Status
Occurances: 0 ... 1
parameters
Fixed value parameters which can be used in generic expressions
Type : Parameters
Occurances: 0 ... 1
current_voltage_relation
The specification of how the current flow etc. into the cell relates to the membrane potential difference (e.g. Ohmic relationship)
Type : CurrentVoltageRelation
hh_gate
Channel specification based on the Hodgkin Huxley formalism. Deprecated! Will be removed in v2.0
Type : Deprecated_HHGate
Occurances: 0 ... unbounded
ks_gate
Channel specification based on a kinetic scheme formalism. Deprecated! Will be removed in v2.0
Type : Deprecated_KSGate
Occurances: 0 ... unbounded
impl_prefs
Optional recommended values, e.g. for size of tables, when creating an implementation of the channel mechanism on a specific simulator
Type : ImplementationPrefs
Occurances: 0 ... 1
Attributes
name
A unique name for the channel mechanism
Type: xs:string , Use: required
density
Is this a specification of conductance per unit area? Note: almost all channel mechanisms to far have been density mechanisms. This attribute is subject to change when use of ChannelML for single channel conductances is supported.
Type: meta:YesNo , Use: optional, default: yes

ChannelType used by: ChannelML (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: SynapseType

Definition of a synaptic mechanism

The following elements must appear in the sequence outlined here.
Group
Some metadata (notes, etc.) to describe the synapse.
Ref: meta:metadata
Group
A group of elements to include with this element
Ref: meta:referencedata
status
Status of the synapse specification: stable, in progress, etc.
Type : meta:Status
Occurances: 0 ... 1
Only one of the following SUB elements may appear.
electrical_syn
Electrical synaptic coupling as at a gap junction
Type : ElectricalSynapse
doub_exp_syn
Synaptic conductance with rise time and decay time
Type : DoubleExponentialSynapse
blocking_syn
For example NMDA receptor synapses
Type : BlockingSynapse
multi_decay_syn
An extension incorporating multiple decay time courses
Type : MultiDecaySynapse
fac_dep_syn
A facilitating and depressing synaptic mechanism
Type : FacDepSynapse
stdp_syn
A synaptic mechanism implementing basic Spike Timing Dependent Plasticity based on Song and Abbott, 2001
Type : StdpSynapse
Attributes
nameType: xs:string , Use: required

SynapseType used by: ChannelML (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: ElectricalSynapse

Electrical synaptic coupling as at a gap junction. A simple model with just a parameter for the (2 way) conductance

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
Attributes
conductance
The conductance of the electrical connection
Type: bio:ConductanceValue , Use: required

ElectricalSynapse used by: SynapseType (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: DoubleExponentialSynapse

A basic synaptic mechanism with a double exponential conductance time course. This mechanism maps easily on to mechanisms in both NEURON (Exp2Syn) and GENESIS (synchan)

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
Attributes
max_conductance
The maximum conductance of the channel
Type: bio:ConductanceValue , Use: required
rise_time
The characteristic rise time of the conductance waveform
Type: bio:TimeConstantValueIncZero , Use: required
decay_time
The characteristic decay time of the conductance waveform
Type: bio:TimeConstantValue , Use: required
reversal_potential
The reversal potential of the synapse, which (along with the membrane potential) will determine the current passing through the synapse when the conductance is non zero
Units in SI: V
Type: bio:VoltageValue , Use: required

DoubleExponentialSynapse used by: SynapseType (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: BlockingSynapse

A synaptic mechanism whose conductance can be blocked by the presence of a specific species (ion/molecule). Based on the mechanism for blocking of an NMDA receptor by Mg as outlined in Gabbiani et al, 1994, Maex DeSchutter 1998

Extension:
The child elements and attributes of the base element will be required in this element too.
Base: DoubleExponentialSynapse
The following elements must appear in the sequence outlined here.
block
Type : Block

BlockingSynapse used by: SynapseType (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Block

Specification for the influence of a blocking species on the conductance of a BlockingSynapse. Based on the mechanism for blocking of an NMDA receptor by Mg as outlined in Gabbiani et al, 1994, Maex DeSchutter 1998

Attributes
species
Name of species. For ions use lowercase, e.g. mg
Type: xs:string , Use: required
conc
Concentration of species. Multiplicative factor for total conductance: 1/(1 + eta * [conc] * exp(-1* gamma * V))
Type: bio:ConcentrationValue , Use: required
eta
Used in multiplicative factor for total conductance: 1/(1 + eta * [conc] * exp(-1* gamma * V))
Units in SI: mM^-1
Type: xs:double , Use: required
gamma
Used in multiplicative factor for total conductance: 1/(1 + eta * [conc] * exp(-1* gamma * V))
Units in SI: V^-1
Type: xs:double , Use: required

Block used by: BlockingSynapse (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: MultiDecaySynapse

A more complex synaptic mechanism featuring up to 4 exponential components (1 rise and 3 decay). Currently there is only an implementation of this in a NEURON mod file. Attributed added can be gmax_2, tau_decay_2, gmax_3 and tau_decay_3. The overall conductance is effectively a linear sum of 3 independent conductances, all with the same rise time and different decays. Note that the gmaxes are specific for each conductance and scaling is calculated for each individually, so the maximum total conductance (gmax + gmax_2 + gmax_3) will only be reached when tau_decay = tau_decay_2 = tau_decay_3, otherwise peaks will not overlap.

Extension:
The child elements and attributes of the base element will be required in this element too.
Base: DoubleExponentialSynapse
Attribute Group
The maximum conductance and decay constant of the 2nd (normally slower) component of the synaptic conductance
Ref: SecondDecay
Attribute Group
The maximum conductance and decay constant of the 3nd (normally slower) component of the synaptic conductance. Note that either both attributes or neither should be present. Unfortunately attributeGroups can't be made optional...
Ref: ThirdDecay

MultiDecaySynapse used by: SynapseType (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: FacDepSynapse

A synaptic type with facilitating and depressing amplitude.

Extension:
The child elements and attributes of the base element will be required in this element too.
Base: MultiDecaySynapse
The following elements must appear in the sequence outlined here.
plasticity
Type : FacDep

FacDepSynapse used by: SynapseType (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: StdpSynapse

A synaptic mechanism implementing basic Spike Timing Dependent Plasticity based on Song and Abbott, 2001

Extension:
The child elements and attributes of the base element will be required in this element too.
Base: MultiDecaySynapse
The following elements must appear in the sequence outlined here.
spike_time_dep
Type : StdpDep

StdpSynapse used by: SynapseType (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: FacDep

Facilitating and depressing synaptic parameters. See mapping to NEURON mod file for implementation details.

Attributes
init_release_probType: xs:double , Use: required
tau_recType: bio:TimeConstantValueIncZero , Use: required
tau_facType: bio:TimeConstantValueIncZero , Use: required

FacDep used by: FacDepSynapse (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: StdpDep

A synaptic mechanism implementing basic Spike Timing Dependent Plasticity based on Song and Abbott, 2001. See mapping to NEURON mod file for implementation details.

Attributes
tau_ltpType: bio:TimeConstantValue , Use: required
del_weight_ltpType: xs:double , Use: required
tau_ltdType: bio:TimeConstantValue , Use: required
del_weight_ltdType: xs:double , Use: required
max_syn_weightType: xs:double , Use: required
post_spike_threshType: bio:VoltageValue , Use: required

StdpDep used by: StdpSynapse (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: CurrentVoltageRelation

How the current through the channel depends on the conductance of the channel. Only ohmic and integrate_and_fire supported at the moment

The following elements must appear in the sequence outlined here.
ohmic
Deprecated since v1.7.3. Use attribute cond_law and gate elements below this element instead.
Type : Deprecated_Ohmic
Occurances: 0 ... 1
integrate_and_fire
Note: use attribute cond_law="integrate_and_fire" and no other attributes here when using this. Signifies a current which will cause the cell to behave like an integrate and fire neuron
Type : IntegrateAndFire
Occurances: 0 ... 1
conc_dependence
Preferred location of conc_dependence since v1.7.3.
Type : ConcDependence
Occurances: 0 ... 1
conc_factor
Preferred location of conc_factor since v1.7.3.
Type : ConcFactor
Occurances: 0 ... 1
q10_settings
Preferred location of Q10 information since v1.7.3.
Type : Q10Settings
Occurances: 0 ... unbounded
offset
Preferred location of offset information since v1.7.3.
Type : Offset
Occurances: 0 ... 1
gate
Preferred way of expressing gating complexes since v1.7.3.
Type : GatingComplex
Occurances: 0 ... unbounded
Attributes
cond_law
Introduced in v1.7.3 for new format ChannelML. Specifies which type of conductance law to use: ohmic, etc.
Type: ConductanceLaw, Use: optional
ion
Introduced in v1.7.3 for new format ChannelML. The ion which will flow due to the conductance. Note this should be already declared in an Ion element at the beginning of the file.
Type: xs:string , Use: optional
default_gmax
Introduced in v1.7.3 for new format ChannelML. Maximum conductance density of channel. Note this will normally be reset when the channel mechanism is placed on a cell, but it it useful to have a default value here.
Type: bio:ConductanceDensityValue , Use: optional
default_erev
Most implementations of these channel mechanisms (e.g. a mod file) will need a value for the reversal potential for the ion which flows through the channel. However, this is a property of the cell, as opposed to the channel. For convenience though, a typical value can be used here, so a pretty self contained script can be produced, but when used in a real cell the actual value for erev must be calculated
Type: bio:VoltageValue , Use: optional
charge
Electrical charge of the ion in question
Type: xs:positiveInteger , Use: optional
fixed_erev
Flags whether the reversal potential can be influenced from outside the channel (value = no; default) as is normally the case (e.g. a Ca channel whose reversal potential is influenced by a decaying calcium pool), or whether the rev pot remains fixed (just for this channel) at default_erev (value = yes)
Type: meta:YesNo , Use: optional, default: no

CurrentVoltageRelation used by: ChannelType (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: IntegrateAndFire

Signifies a current which will cause the cell to behave like an integrate and fire neuron. There are many ways to describe an Integrate and Fire mechanism, this one is based on the implementation in NEURON of the COBA IandF cell as described in Brette et al (2007)

Attributes
threshold
Voltage at which the mechanism causes the segment/cell to fire, i.e. membrane potential will be reset to v_reset
Type: bio:VoltageValue , Use: required
t_refrac
Time after a spike during which the segment will be clamped to v_reset (clamping current given by i = g_refrac*(v - v_reset))
Type: bio:TimeValue , Use: required
v_reset
Membrane potential is reset to this after spiking
Type: bio:VoltageValue , Use: required
g_refrac
Conductance during the period t_refrac after a spike, when the current due to this mechanism is given by i = g_refrac*(v - v_reset), therefore a high value for g_refrac, e.g. 100 microsiemens, will effectively clamp the cell at v_reset
Type: bio:ConductanceValue , Use: required

IntegrateAndFire used by: CurrentVoltageRelation (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Deprecated_Ohmic

Signifies an ohmic relation; the current is proportional to the potential difference across the channel. Deprecated! Will be removed in v2.0

The following elements must appear in the sequence outlined here.
conductance
Description of the conductance including maximum conductance density and possible (voltage and/or concentration dependent) gating mechanisms
Type : conductance
Attributes
ion
The ion which will flow due to the conductance. Note this should be already declared in an Ion element at the beginning of the file.
Type: xs:string , Use: optional

Deprecated_Ohmic used by: CurrentVoltageRelation (xs:complexType)

Instances of this element which are used by other elements in this document



Element: conductance
Description of the conductance including maximum conductance density and possible (voltage and/or concentration dependent) gating mechanisms
 
The following elements must appear in the sequence outlined here. Occurances: 1
Group
A group of elements to include with this element
Ref: meta:metadata
rate_adjustments
Adjustments, e.g. temperature dependence, to apply to the gating mechanisms
Type : RateAdjustments
Occurances: 0 ... 1
conc_factor
Type : ConcFactor
Occurances: 0 ... 1
gate
Voltage/concentration dependent gate
Type : Gate
Occurances: 0 ... unbounded
Attributes
default_gmax
Maximum conductance density of channel
Type: bio:ConductanceDensityValue , Use: required

conductance is used by: Deprecated_Ohmic (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: ImplementationPrefs

These items ideally shouldn't be in a specification which deals with a description of the physiology of the channel. However, some channels won't be properly implemented in the scripting mechanism of given simulator using the standard mappings unless these factors are taken into account, e.g. if the rate equations change rapidly, but the default table size isn't large enough.

The following elements must appear in the sequence outlined here.
comment
Comment element to give explination for the implementation preferences. Having a dedicated element as opposed to a <-- comment --> allows the comment to be repeated in the script file impl.
Type : xs:string
Occurances: 0 ... 1
table_settings
Preferences for the table of values for the rate equations, e.g. used in the TABLE statement in NMODL, or in tabchannel GENESIS objects
Type : table_settings
Occurances: 0 ... 1

ImplementationPrefs used by: ChannelType (xs:complexType)

Instances of this element which are used by other elements in this document



Element: table_settings
Preferences for the table of values for the rate equations, e.g. used in the TABLE statement in NMODL, or in tabchannel GENESIS objects
 
Attributes
max_v
The maximum potential from which to calculate the tables of rate values
Type: xs:double , Use: optional, default: 70
min_v
The minimum potential from which to calculate the tables of rate values
Type: xs:double , Use: optional, default: -100
table_divisions
The number of divisions in the table
Type: xs:positiveInteger , Use: optional, default: 200

table_settings is used by: ImplementationPrefs (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: RateAdjustments

Adjustments necessary to all the rate equations, e.g temperature dependencies, voltage offsets introduced when moving between species, etc. See the XSL mappings for more information on the meaning of these adjustments.

The following elements must appear in the sequence outlined here.
q10_settings
Type : Q10Settings
Occurances: 0 ... unbounded
offset
Type : Offset
Occurances: 0 ... 1

RateAdjustments used by: Deprecated_Ohmic (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Offset
Attributes
value
Offset introduced to alter voltage dependence of rate equations, see NEURON/GENESIS mappings for details
Type: bio:VoltageValue , Use: required

Offset used by: CurrentVoltageRelation (xs:complexType) RateAdjustments (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Q10Settings

Q10 scaling affects the tau in the rate equations. It allows rate equations determined at one temperature to be used at a different temperature. If tauExp is the experimentally measured tau, the rate at temperature T is given by tau(T) = tauExp / q10_factor ^ ((T - experimental_temp)/10). NOTE: if fixed_q10 is specified the expression will be tau(T) = tauExp / fixed_q10, and the experimental_temp can be used to check that a simulation is running at the desired temperature.

Attributes
gate
The gate to which the Q10 adjustment should be applied. If this attribute is not present, assume the adjustment applies at all gates.
Type: xs:string , Use: optional
fixed_q10
Q10 factor if the cell is to be run at a different temp than that at which the alpha and beta were determined. Only one of fixed_q10 or q10_factor should be specified!
Type: xs:double , Use: optional
q10_factor
Q10 factor if the cell is to be run at a different temp than that at which the alpha and beta were determined. Only one of fixed_q10 or q10_factor should be specified!
Type: xs:double , Use: optional
experimental_temp
The experimental temperature at which alpha and beta rate equations were determined were measured
Type: bio:TemperatureValue , Use: required

Q10Settings used by: CurrentVoltageRelation (xs:complexType) RateAdjustments (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Deprecated_Ion

Definition of an ion which is involved in this channel mechanism. Note: deprecated since v1.7.3

Attributes
name
Simple name for the ion. Due to the conventions used in NEURON, it is usually best to use the lower case form of the chemical symbol, e.g. na, ca, k
Type: xs:string , Use: required
default_erev
Most implementations of these channel mechanisms (e.g. a mod file) will need a value for the reversal potential for the ion which flows through the channel. However, this is a property of the cell, as opposed to the channel. For convenience though, a typical value can be used here, so a pretty self contained script can be produced, but when used in a real cell the actual value for erev must be calculated
Type: bio:VoltageValue , Use: optional
charge
Electrical charge of the ion in question
Type: xs:positiveInteger , Use: required
role
What role the ion plays in the dynamics of the channel/cell mechanism
Type: Deprecated_IonRole, Use: optional, default: PermeatedSubstance

Deprecated_Ion used by: ChannelML (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: GatingComplex

Preferred element for defining a gate since v1.7.3. Definition of a single voltage/concentration dependent gate, with explicit definition of open and closed states and information on the transition rates between them.

The following elements must appear in the sequence outlined here.
closed_state
Type : ClosedState
Occurances: 1 ... unbounded
open_state
Type : OpenState
Occurances: 1 ... unbounded
initialisation
For debugging/testing only! Use with caution!!
Type : Initialisation
Occurances: 0 ... 1
transition
Type : Transition
Occurances: 0 ... unbounded
time_course
Type : TimeCourse
Occurances: 0 ... unbounded
steady_state
Type : SteadyState
Occurances: 0 ... unbounded
Attributes
name
Reference for the gating complex, e.g. m, h, n
Type: xs:string , Use: required
instances
The number of instances of the gate, i.e. the power to which the gating variable is raised in the expression for the total conductance
Type: xs:nonNegativeInteger , Use: required

GatingComplex used by: CurrentVoltageRelation (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: ClosedState

Closed state of a gating complex

Attributes
id
Id to use in transition elements when specifying this as the from or to state of the transition.
Type: xs:string , Use: required

ClosedState used by: GatingComplex (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: OpenState

Open state of a gating complex

Attributes
id
Id to use in transition elements when specifying this as the from or to state of the transition.
Type: xs:string , Use: required
fraction
The fractional conductance of the gate in this state. Has value 1 if not present
Type: meta:ZeroToOne , Use: optional, default: 1

OpenState used by: GatingComplex (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Gate

Definition of a single voltage/concentration dependent gate

The following elements must appear in the sequence outlined here.
state
Internal state of the gate, specifying a name, and possibly a fractional contribution. HHGate or KSGate elements will specify the rate equations, etc. for the gate, referencing this state name.
Type : state
Attributes
power
The power to which the gate is raised in the expression for the total conductance
Type: xs:nonNegativeInteger , Use: required

Gate used by: Deprecated_Ohmic (xs:complexType)

Instances of this element which are used by other elements in this document



Element: state
Internal state of the gate, specifying a name, and possibly a fractional contribution. HHGate or KSGate elements will specify the rate equations, etc. for the gate, referencing this state name.
 
Attributes
nameType: xs:string , Use: required
fractionType: meta:ZeroToOne , Use: optional, default: 1

state is used by: Gate (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Deprecated_HHGate

Gate with Hodgkin Huxley like state transitions

The following elements must appear in the sequence outlined here.
transition
Type : Deprecated_Transition
Attributes
stateType: xs:string , Use: required

Deprecated_HHGate used by: ChannelType (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Deprecated_KSGate

Gate with kinetic scheme transitions

The following elements must appear in the sequence outlined here.
state
Type : Deprecated_KSState
transition
Type : Deprecated_Transition

Deprecated_KSGate used by: ChannelType (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Deprecated_KSState

Single kinetic scheme state. Transitions will happen between these states. Deprecated! Will be removed in v2.0

Attributes
nameType: xs:string , Use: required

Deprecated_KSState used by: Deprecated_KSGate (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Transition

Transition between states in a GatingComplex

Attributes
name
Short name to use to refer to the transition, e.g. alpha, beta for forward, backward rates in HH gates
Type: xs:string , Use: required
expr_form
Form of expression
Type: CoreEquationType, Use: required
Attribute Groups
from_toReference: from_to
standard_expr_paramsReference: standard_expr_params
generic_expr_paramsReference: generic_expr_params

Transition used by: GatingComplex (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: TimeCourse

Time course of the transition between states in a GatingComplex

Attributes
name
Short name to use to refer to the time course e.g. tau
Type: xs:string , Use: required
expr_form
Form of expression
Type: CoreEquationType, Use: required
Attribute Groups
from_toReference: from_to
standard_expr_paramsReference: standard_expr_params
generic_expr_paramsReference: generic_expr_params

TimeCourse used by: GatingComplex (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: SteadyState

Steady state value of the transition between states in a GatingComplex

Attributes
name
Short name to use to refer to the steady state e.g. inf
Type: xs:string , Use: required
expr_form
Form of expression
Type: CoreEquationType, Use: required
Attribute Groups
from_toReference: from_to
standard_expr_paramsReference: standard_expr_params
generic_expr_paramsReference: generic_expr_params

SteadyState used by: GatingComplex (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Deprecated_Transition

Deprecated since v1.7.3. What causes the gate to open and close. A dependence on potential difference, or a voltage and (ion) concentration dependence

Only one of the following elements may appear.
voltage_gate
Type : Deprecated_VoltageGate
voltage_conc_gate
Type : Deprecated_VoltageConcGate
Attributes
source
Source state of the transition if used in kinetic scheme. Must be used with attribute target. Use this in preference to src!!!
Type: xs:string , Use: optional
target
Target state of the transition if used in kinetic scheme. Must be used with attribute src
Type: xs:string , Use: optional

Deprecated_Transition used by: Deprecated_HHGate (xs:complexType) Deprecated_KSGate (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Initialisation

Element added for *testing purposes only*. Used to "incorrectly" initialise a channel when trying to compare it to a mod file implementation (e.g. see Traub et al 2005 channels). Value here will be ignored if option in neuroConstruct "Force correct ChannelML init" is used. Use with caution!!

Attributes
valueType: xs:string , Use: required

Initialisation used by: GatingComplex (xs:complexType) Deprecated_VoltageGate (xs:complexType) Deprecated_VoltageConcGate (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Deprecated_VoltageGate

Definition of a voltage gate. Normally this will be specified as rate equations for alpha and beta, or for tau and inf. Deprecated! Will be removed in v2.0

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: Deprecated_AlphaBetaForm Occurances: 0 ... 1
Group
A group of elements to include with this element
Ref: Deprecated_ExtraRateExpressions Occurances: 0 ... 1
initialisation
Type : Initialisation
Occurances: 0 ... 1
tau
Type : Deprecated_RateConstantEqnChoice
Occurances: 0 ... 1
inf
Type : Deprecated_RateConstantEqnChoice
Occurances: 0 ... 1

Deprecated_VoltageGate used by: Deprecated_Transition (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Deprecated_VoltageConcGate

Definition of a mechanics of a gate which depends on voltage and concentration (e.g. Calcium conc dependent K channel). Normally this will be specified as rate equations for alpha and beta (in terms of v and conc), or for tau and inf. Deprecated! Will be removed in v2.0

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: Deprecated_AlphaBetaFormVoltConcDep Occurances: 0 ... 1
Group
A group of elements to include with this element
Ref: Deprecated_ExtraRateExpressions Occurances: 0 ... 1
initialisation
Type : Initialisation
Occurances: 0 ... 1
conc_dependence
Type : ConcDependence
tau
Type : Deprecated_RateConstVoltConcDep
Occurances: 0 ... 1
inf
Type : Deprecated_RateConstVoltConcDep
Occurances: 0 ... 1

Deprecated_VoltageConcGate used by: Deprecated_Transition (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: ConcFactor

Specification of the time independent scaling factor for a concentration dependent conductance. This factor will not be used n alpha, beta, etc. but the expression in expr will scale the total conductance at each time step.

Attributes
ion
Name of the ion
Type: xs:string , Use: required
charge
Electrical charge of the ion in question. Assumes charge of 1 if not present
Type: xs:integer , Use: optional, default: 1
variable_name
How the value of conductance will be expressed in the equations
Type: xs:string , Use: required
expr
Expression for the time independent multiplicative factor for the concentration dependence
Type: xs:string , Use: required
min_conc
Minimum expected concentration. May be needed by simulators (e.g. for generating tables)
Type: bio:ConcentrationValue , Use: required
max_conc
Maximum expected concentration. May be needed by simulators (e.g. for generating tables)
Type: bio:ConcentrationValue , Use: required

ConcFactor used by: CurrentVoltageRelation (xs:complexType) Deprecated_Ohmic (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: ConcDependence

Specification of the factor to use in the concentration dependence of the rate expressions of a gate

Attributes
name
Name of substance, just for reference
Type: xs:string , Use: required
ion
Name of the ion
Type: xs:string , Use: required
charge
Electrical charge of the ion in question. Assumes charge of 1 if not present
Type: xs:integer , Use: optional, default: 1
variable_name
How the value of conductance will be expressed in the rate equations
Type: xs:string , Use: required
min_conc
Minimum expected concentration. Quite likely to be needed by simulators (e.g. for generating tables)
Type: bio:ConcentrationValue , Use: required
max_conc
Maximum expected concentration. Quite likely to be needed by simulators (e.g. for generating tables)
Type: bio:ConcentrationValue , Use: required

ConcDependence used by: CurrentVoltageRelation (xs:complexType) Deprecated_VoltageConcGate (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Deprecated_RateConstantEqnChoice

Choice of the various rate constant expressions allowed

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
Only one of the following SUB elements may appear.
parameterised_hh
Type : Deprecated_AkdEquation
generic_equation_hh
Note: use generic as opposed to generic_equation_hh. The latter will be removed in v2.0
Type : Deprecated_GenericEquation
generic
Note: use generic as opposed to generic_equation_hh. The latter will be removed in v2.0
Type : Deprecated_GenericEquation

Deprecated_RateConstantEqnChoice used by: Deprecated_VoltageGate (xs:complexType) Deprecated_VoltageGate (xs:complexType) Deprecated_AlphaBetaForm (xs:group) Deprecated_AlphaBetaForm (xs:group) Deprecated_ExtraRateExpressions (xs:group) Deprecated_ExtraRateExpressions (xs:group)

Instances of this element which are used by other elements in this document



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Complex Type: Deprecated_RateConstVoltConcDep

Rate constant expressions allowed for voltage and conc dependent channels. Note, at this stage no Akd like expression for a generic voltage/conc dep experssion. Time will tell if there's an expression common enough across different models to be expressed in such a way

Only one of the following elements may appear.
generic_equation_hh
Note: use generic as opposed to generic_equation_hh. The latter will be removed in v2.0
Type : Deprecated_GenericEquation
generic
Note: use generic as opposed to generic_equation_hh. The latter will be removed in v2.0
Type : Deprecated_GenericEquation

Deprecated_RateConstVoltConcDep used by: Deprecated_VoltageConcGate (xs:complexType) Deprecated_VoltageConcGate (xs:complexType) Deprecated_AlphaBetaFormVoltConcDep (xs:group) Deprecated_AlphaBetaFormVoltConcDep (xs:group)

Instances of this element which are used by other elements in this document



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Complex Type: Deprecated_RateConstantEqn

Definition of a rate constant equation.

The following elements must appear in the sequence outlined here.
parameter
A parameter which is used in the equation
Type : Deprecated_Parameter
Occurances: 0 ... unbounded
Attributes
typeType: xs:string , Use: required
exprType: xs:string , Use: optional


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Complex Type: Deprecated_AkdEquation

Definition of a type of rate constant equation which takes parameters A, k, d and maps to either exponential, sigmoidal or linoidal.

Restriction: Base: Deprecated_RateConstantEqn

Deprecated_AkdEquation used by: Deprecated_RateConstantEqnChoice (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Deprecated_GenericEquation

Definition of a type of rate constant equation

Attributes
expr
Note: only variable allowed in expression is v (or for an expression for tau or inf, alpha and beta can be used too). Also, liberal use of brackets, e.g. 5.0*(exp (-50*(v +46))) instead of 5.0* exp (-50*(v +46)) is advised, due to GENESIS's handling of exp, abs, etc.
Type: xs:string , Use: required

Deprecated_GenericEquation used by: Deprecated_RateConstantEqnChoice (xs:complexType) Deprecated_RateConstantEqnChoice (xs:complexType) Deprecated_RateConstVoltConcDep (xs:complexType) Deprecated_RateConstVoltConcDep (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: IonConcentration

Specification of how an ion concentration alters with time, e.g. calcium dynamics. This may influence other channels (e.g. Ca dependent K channels), and other mechanisms may have a contribution to the concentration of the ion specified here.

The following elements must appear in the sequence outlined here.
Group
Some metadata to describe the ion concentration
Ref: meta:metadata
Group
A group of elements to include with this element
Ref: meta:referencedata
status
Status of the ion conc mech specification: stable, in progress, etc.
Type : meta:Status
Occurances: 0 ... 1
ion_species
Which ion is involved in mechanism.
Type : IonSpecies
Only one of the following SUB elements may appear.
decaying_pool_model
At present there is only one choice of a model for this process, more can be added later..
Type : DecayingPoolModel
Attributes
name
A unique name for this ion concentration mechanism, as opposed to name of the ion used.
Type: xs:string , Use: required

IonConcentration used by: ChannelML (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: IonSpecies

Which ion is involved in an ion_concentration mechanism. Note in v2.0 the attribute form for defining the name will be required.

IonSpecies used by: IonConcentration (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: DecayingPoolModel

Element for parameters in a decaying pool model of ion concentration (e.g. calcium pool)

The following elements must appear in the sequence outlined here.
resting_conc
Resting concentration of ion. NOTE: In v2.0 this element will be removed. Attribute resting_conc will be used instead.
Type : bio:ConcentrationValue
Occurances: 0 ... 1
ceiling
The maximum concentration which the ion pool should be allowed get to. NOTE: In v2.0 this element will be removed. Attribute ceiling will be used instead.
Type : bio:ConcentrationValue
Occurances: 0 ... 1
Only one of the following SUB elements may appear.
decay_constant
Exponential decay time of pool. NOTE: In v2.0 this element will be removed. Attribute decay_constant will be used instead.
Type : bio:TimeConstantValue
Occurances: 0 ... 1
inv_decay_constant
Reciprocal of exponential decay time constant of pool
Type : bio:InvTimeConstantValue
Only one of the following SUB elements may appear.
pool_volume_info
Type : PoolVolumeInfo
fixed_pool_info
Type : FixedPoolInfo
Attributes
resting_conc
Resting concentration of ion. NOTE: In v2.0 the option for a resting_conc element will be removed. Attribute resting_conc will be required instead.
Type: bio:ConcentrationValue , Use: optional
decay_constant
Exponential decay time of pool. Either decay_constant or inv_decay_constant must be included. NOTE: In v2.0 the option for a decay_constant/inv_decay_constant element will be removed. Attribute decay_constant/inv_decay_constant will be used instead.
Type: bio:TimeConstantValue , Use: optional
inv_decay_constant
Reciprocal of exponential decay time of pool. Either decay_constant or inv_decay_constant must be included. NOTE: In v2.0 the option for a decay_constant/inv_decay_constant element will be removed. Attribute decay_constant/inv_decay_constant will be used instead.
Type: bio:InvTimeConstantValue , Use: optional
ceiling
The maximum concentration which the ion pool should be allowed get to. NOTE: In v2.0 the option for a ceiling element will be removed. Attribute ceiling will be used instead.
Type: bio:ConcentrationValue , Use: optional

DecayingPoolModel used by: IonConcentration (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: PoolVolumeInfo

Information on the volume of the ion pool

The following elements must appear in the sequence outlined here.
shell_thickness
The volume of the pool is calculated from the thickness of the shell inside the membrane. This will have to be multiplied by the surface area of the relevant compartment. NOTE: In v2.0 the option for a shell_thickness element will be removed. Attribute shell_thickness will be used instead.
Type : bio:LengthValue
Occurances: 0 ... 1
Attributes
shell_thickness
The volume of the pool is calculated from the thickness of the shell inside the membrane. This will have to be multiplied by the surface area of the relevant compartment. NOTE: In v2.0 the option for a shell_thickness element will be removed. Attribute shell_thickness will be used instead.
Type: bio:LengthValue , Use: optional

PoolVolumeInfo used by: DecayingPoolModel (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: FixedPoolInfo

(IN PROGRESS, not stable!!!!) In this case the parameter which determines how quickly the internal pool 'fills' is given as a fixed value. Note this is a far from ideal way to express this value, but needed to be included as this was the parameter which was all that was present in a number of models, e.g. Traub et al. 2003 Layer 2/3 cell.

The following elements must appear in the sequence outlined here.
phi
Type : xs:double

FixedPoolInfo used by: DecayingPoolModel (xs:complexType)

Instances of this element which are used by other elements in this document



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Complex Type: Deprecated_Parameter

Generic parameter used in rate equations

The following elements must appear in the sequence outlined here.
Group
A group of elements to include with this element
Ref: meta:metadata
Attributes
nameType: xs:string , Use: required
valueType: xs:double , Use: required

Deprecated_Parameter used by: Deprecated_RateConstantEqn (xs:complexType) Deprecated_AkdEquation (xs:complexType)

Instances of this element which are used by other elements in this document



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