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Converting the file: ChannelML_v1.8.1.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 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_v1.8.1.xsd |
| Namespace: http://morphml.org/biophysics/schema | Location: Biophysics_v1.8.1.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 |
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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 | |
| beta | |
|
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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 | |
| zeta | |
|
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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 | |
| beta | |
|
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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...
|
|
|
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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...
|
|
|
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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.
|
|
|
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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 |
| expr | Type:
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 |
| |
| 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
(e.g. a channel transmitting calcium). |
| |
| 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 | |
|
|
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. |
| |
| parameters |
| Fixed value parameters which can be used in generic expressions |
| |
| 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. Deprecated! Will be removed in v2.0 |
| |
| ks_gate |
| Channel specification based on a kinetic scheme formalism. Deprecated! Will be removed in v2.0 |
| |
| impl_prefs |
| Optional recommended values, e.g. for size of tables, when creating an implementation of the
channel mechanism on a specific simulator |
| |
| 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. |
| |
| Only one of the following SUB elements may appear.
|
| electrical_syn |
| Electrical synaptic coupling as at a gap junction |
| |
| doub_exp_syn |
| Synaptic conductance with rise time and decay time |
| |
| blocking_syn |
| For example NMDA receptor synapses |
| |
| multi_decay_syn |
| An extension incorporating multiple decay time courses |
| |
| fac_dep_syn |
| A facilitating and depressing synaptic mechanism |
| |
| stdp_syn |
| A synaptic mechanism implementing basic Spike Timing Dependent Plasticity based on Song and Abbott, 2001 |
| |
| 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: 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 | |
|
|
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 | |
|
|
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 | |
|
|
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.
|
|
|
|
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.
|
|
|
|
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. |
| |
| 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 |
| |
| conc_dependence |
| Preferred location of conc_dependence since v1.7.3. |
| |
| conc_factor |
| Preferred location of conc_factor since v1.7.3. |
| |
| q10_settings |
| Preferred location of Q10 information since v1.7.3. |
| |
| 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. |
| |
| 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 |
|
|
| 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 |
| |
| conc_factor | |
| 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. |
| |
| 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 | |
| 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 | |
| open_state | |
| initialisation |
| For debugging/testing only! Use with caution!! |
| |
| transition | |
| time_course | |
| steady_state | |
| 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. |
|
|
| 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 |
| 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: Deprecated_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 |
|
|
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 | |
| 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 |
| name | Type:
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_to | Reference: from_to |
| standard_expr_params | Reference: standard_expr_params |
| generic_expr_params | Reference: 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
|
|
|
|
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
|
|
|
|
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 | |
| voltage_conc_gate | |
| 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 |
| value | Type:
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 | |
| tau | |
| inf | |
|
|
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 | |
| conc_dependence | |
| tau | |
| inf | |
|
|
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 |
|
| 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 |
|
| 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_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 |
| |
| generic |
| Note: use generic as opposed to generic_equation_hh. The latter will be removed in v2.0 |
| |
|
|
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 |
| |
| Attributes |
| type | Type:
xs:string
, Use: required |
| expr | Type:
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.
|
|
|
|
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: 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 |
| Which ion is involved in mechanism. |
| |
| 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 |
| 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. |
| |
| 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. |
| |
| 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. |
| |
| inv_decay_constant |
| Reciprocal of exponential decay time constant of pool |
| |
| Only one of the following SUB elements may appear.
|
| pool_volume_info | |
| fixed_pool_info | |
| 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. |
| |
| 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 | |
|
|
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 |
| name | Type:
xs:string
, Use: required |
| value | Type:
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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