|
Converting the file: ChannelML_v1.6.xsd
Note: this representation of the contents of the XSD file is intended as a quick reference only.
** The original *.xsd file should be consulted if there
is any doubt regarding data types **
There is also the option to view this file in Relax NG format.
Note this representation is for
reference only (for those who prefer that format). The XSD should be used for final validation.
Conversion of an XSD file into human readable form
| 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 (eventually) 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.
|
| targetNamespace | http://morphml.org/channelml/schema |
| elementFormDefault | qualified |
| attributeFormDefault | unqualified |
|
Imported Schemas
Other schemas used by this file, with different target namespaces
|
| Namespace: http://morphml.org/metadata/schema | Location: ../Level1/Metadata_v1.6.xsd |
| Namespace: http://morphml.org/biophysics/schema | Location: Biophysics_v1.6.xsd |
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 |
Top
Simple Types
|
Simple Type: 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 three 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")
|
| 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)
|
|
|
IonRole used by:
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, 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)))))
|
|
|
CoreEquationType used by:
AkdEquation (xs:complexType)
Instances of this element which are used by other elements in this document
|
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Groups
|
Group: AlphaBetaForm
alpha, beta form of rate equations. These will always be together if present
|
| The following elements must appear in the sequence outlined here.
|
| alpha | |
| beta | |
|
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|
Group: 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 | |
| zeta | |
|
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|
Group: 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 | |
| beta | |
|
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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, affect the rate, etc. |
| | Type : Ion |
|
Occurances: 0
...
unbounded |
|
| channel_type |
| Specification of a voltage or ligand gated membrane conductance mechanism |
| |
| synapse_type |
| Specification of a synaptic conductance, triggered by a presynaptic event |
| |
| 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. |
| |
| 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: 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. |
| |
| current_voltage_relation |
| The specification of how the current flow etc. into the cell relates to the membrane potential difference (e.g. Ohmic relationship) |
| |
| hh_gate |
| Channel specification based on the Hodgkin Huxley formalism |
| | Type : HHGate |
|
Occurances: 0
...
unbounded |
|
| ks_gate |
| Channel specification based on a kinetic scheme formalism |
| | Type : KSGate |
|
Occurances: 0
...
unbounded |
|
| impl_prefs |
| Optional recommended values when creating implementation of the channel mechanism |
| |
| Attributes |
| name | Type:
xs:string
, Use: required |
| density |
| Is this a specification of conductance per unit area? |
| 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. |
| |
| Only one of the following SUB elements may appear.
|
| doub_exp_syn |
| Synaptic conductance with rise time and decay time |
| |
| blocking_syn |
| For example NMDA receptor synapses |
| |
| Attributes |
| name | Type:
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: 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:TimeConstantValue
, 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 | |
|
|
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: CurrentVoltageRelation
How the current through the channel depends on the conductance of the channel.
Only ohmic and integrate_and_fire supported at the moment
|
| Only one of the following elements may appear.
|
| ohmic |
| Signifies an ohmic relation; the current is proportional to the potential difference across the channel |
| |
| integrate_and_fire |
| Signifies a current which will cause the cell to behave like an integrate and fire neuron |
| |
| Attributes |
| name | Type:
xs:string
, Use: optional |
|
|
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
|
| 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: Ohmic
Signifies an ohmic relation; the current is proportional to the potential difference across the channel
|
| The following elements must appear in the sequence outlined here.
|
| conductance |
| Description of the conductance including maximum conductance density and possible (voltage dependent) gating mechanisms |
|
|
| 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 |
|
|
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 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 |
| |
| 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: 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. |
| |
| 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 |
|
|
|
|
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 |
| 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. |
|
|
| offset | | Type : offset |
|
Occurances: 0
...
1 |
|
|
|
RateAdjustments used by:
Ohmic (xs:complexType)
Instances of this element which are used by other elements in this document
|
| Element: q10_settings |
| 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 |
|
q10_settings is used by: RateAdjustments (xs:complexType)
Instances of this element which are used by other elements in this document
|
| Element: offset | |
| Attributes |
| value |
| Offset introduced to alter voltage dependence of
rate equations, see NEURON/GENESIS mappings for details |
| Type:
bio:VoltageValue
, Use: optional |
|
offset is used by: RateAdjustments (xs:complexType)
Instances of this element which are used by other elements in this document
|
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|
Complex Type: Ion
Definition of an ion which is involved in this channel mechanism
|
| 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: IonRole, Use: optional, default: PermeatedSubstance |
|
|
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: 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. |
|
|
| 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:
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 |
| name | Type:
xs:string
, Use: required |
| fraction | Type:
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: HHGate
Gate with Hodgkin Huxley like state transitions
|
| The following elements must appear in the sequence outlined here.
|
| transition | |
| Attributes |
| state | Type:
xs:string
, Use: required |
|
|
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: KSGate
Gate with kinetic scheme transitions
|
| The following elements must appear in the sequence outlined here.
|
| state | |
| transition | |
|
|
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: KSState
Single kinetic scheme state. Transitions will happen between these states
|
| Attributes |
| name | Type:
xs:string
, Use: required |
|
|
KSState used by:
KSGate (xs:complexType)
Instances of this element which are used by other elements in this document
|
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|
Complex Type: Transition
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 | |
| voltage_conc_gate | |
| Attributes |
| src |
| Source state of the transition if used in kinetic scheme. Must be used with attribute target |
| 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 |
|
|
Transition used by:
HHGate (xs:complexType)
KSGate (xs:complexType)
Instances of this element which are used by other elements in this document
|
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|
Complex Type: VoltageGate
Definition of a voltage gate. Normally this will be specified as rate equations for
alpha and beta, or for tau and inf
|
| The following elements must appear in the sequence outlined here.
|
| Group |
| A group of elements to include with this element |
| Ref: AlphaBetaForm
Occurances: 0
...
1 |
| Group |
| A group of elements to include with this element |
| Ref: ExtraRateExpressions
Occurances: 0
...
1 |
| tau | |
| inf | |
|
|
VoltageGate used by:
Transition (xs:complexType)
Instances of this element which are used by other elements in this document
|
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|
Complex Type: 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
|
| The following elements must appear in the sequence outlined here.
|
| Group |
| A group of elements to include with this element |
| Ref: AlphaBetaFormVoltConcDep
Occurances: 0
...
1 |
| Group |
| A group of elements to include with this element |
| Ref: ExtraRateExpressions
Occurances: 0
...
1 |
| conc_dependence | |
| tau | |
| inf | |
|
|
VoltageConcGate used by:
Transition (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 concentration dependence of a gate
|
| Attributes |
| name |
| Name of substance, just for reference |
| Type:
xs:string
, Use: required |
| ion |
| If the substance is an ion, here is a reference the entry in the ion list at the start of the file |
| Type:
xs:string
, Use: optional |
| 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:
VoltageConcGate (xs:complexType)
Instances of this element which are used by other elements in this document
|
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|
Complex Type: 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 | |
| generic_equation_hh | |
|
|
RateConstantEqnChoice used by:
VoltageGate (xs:complexType)
VoltageGate (xs:complexType)
AlphaBetaForm (xs:group)
AlphaBetaForm (xs:group)
ExtraRateExpressions (xs:group)
ExtraRateExpressions (xs:group)
Instances of this element which are used by other elements in this document
|
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|
Complex Type: 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
accross different models to be expressed in such a way
|
| Only one of the following elements may appear.
|
| generic_equation_hh | |
|
|
RateConstVoltConcDep used by:
VoltageConcGate (xs:complexType)
VoltageConcGate (xs:complexType)
AlphaBetaFormVoltConcDep (xs:group)
AlphaBetaFormVoltConcDep (xs:group)
Instances of this element which are used by other elements in this document
|
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|
Complex Type: 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 |
| |
| Attributes |
| type | Type:
xs:string
, Use: required |
| expr | Type:
xs:string
, Use: optional |
|
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|
Complex Type: AkdEquation
Definition of a type of rate constant equation which takes parameters A, k, d
and maps to either exponential, sigmoidal or linoidal.
|
|
|
|
AkdEquation used by:
RateConstantEqnChoice (xs:complexType)
Instances of this element which are used by other elements in this document
|
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|
Complex Type: 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 |
|
|
GenericEquation used by:
RateConstantEqnChoice (xs:complexType)
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. |
| |
| ion_species | |
| 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 |
| |
| Attributes |
| name |
| The name of the ion, as used in the Ion element. |
| 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: 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 |
| |
| decay_constant |
| Exponential decay time of pool |
| |
| The following SUB elements must appear in the sequence outlined here.
Minimum occurances allowed: Maximum occurances allowed: |
| pool_volume_info | |
|
|
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 | |
|
|
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: 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 |
| name | Type:
xs:string
, Use: required |
| value | Type:
xs:double
, Use: required |
|
|
Parameter used by:
RateConstantEqn (xs:complexType)
AkdEquation (xs:complexType)
Instances of this element which are used by other elements in this document
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