Transforming XML file: NeuroMLFiles/Schemata/v1.8.1/Level2/Biophysics_v1.8.1.xsd using XSL file: NeuroMLFiles/Schemata/XSD_Readable.xsl

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Converting the file: Biophysics_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 **

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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 the biophysical properties of cells. These elements are linked with those in MorphML.xsd and from the ChannelML spec by the NeuroML.xsd file


Schema info

Information on the namespaces, etc.

targetNamespacehttp://morphml.org/biophysics/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


Elements biophysics  
Simple Types ConcentrationValue   ConductanceDensityValue   ConductanceValue   CurrentValue   FrequencyValue   InvTimeConstantValue   LengthValue   MechanismType   SynapticDelayValue   TemperatureValue   TimeConstantValue   TimeConstantValueIncZero   TimeValue   VoltageValue  
Complex Types Biophysics   InhomogeneousValue   InitialMembPotential   IonProperties   Mechanism   NamedParameter   SpecAxialResistance   SpecCapacitance   UnnamedParameter   VariableNamedParameter   VariableParameter  

Elements

Element: biophysics
The root element. All other complex/simple elements will be children of this.
Type: Biophysics


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Simple Types

Simple Type: MechanismType

Specifies the type of cellular mechanism. Note could be used for any type of electrophysiological property of a section of a cell

Restriction: Base: xs:string
Allowed values:
Channel Mechanism (Voltage and/or conductance dependent membrane conductance)
Ion Concentration (Mechanism which alters the oncentration of a specific ion)

MechanismType used by: Mechanism (xs:complexType)

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



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Simple Type: SynapticDelayValue

Units of a delay associated with a synaptic connection
Units in SI: s
Typical value: 0.005 s

Restriction: Base: xs:double

Minimum value inclusive: 0


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Simple Type: TimeConstantValue

Units of any time constant, greater than zero
Units in SI: s
Typical value: 0.005 s

Restriction: Base: xs:double

Minimum value exclusive: 0


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Simple Type: InvTimeConstantValue

Units of the inverse of a time constant
Units in SI: s-1
Typical value: 100 s-1

Restriction: Base: xs:double

Minimum value inclusive: 0


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Simple Type: TimeConstantValueIncZero

Units of any time constant which can have value zero
Units in SI: s
Typical value: 0.005 s

Restriction: Base: xs:double

Minimum value inclusive: 0


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Simple Type: TimeValue

Units of any time value, zero or greater
Units in SI: s
Typical value: 0.005 s

Restriction: Base: xs:double

Minimum value inclusive: 0


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Simple Type: FrequencyValue

Units of any frequency, zero or greater
Units in SI: Hz
Typical value: 50 Hz

Restriction: Base: xs:double

Minimum value inclusive: 0


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Simple Type: ConductanceValue

Units of conductance
Units in SI: S
Typical value: 1e-8 S

Restriction: Base: xs:double

Minimum value inclusive: 0


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Simple Type: ConductanceDensityValue

Units of conductance density
Units in SI: S m-2
Typical value: 100 S m-2

Restriction: Base: xs:double

Minimum value inclusive: 0


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Simple Type: LengthValue

Units of length
Units in SI: m
Typical value: 1e-6 m

Restriction: Base: xs:double


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Simple Type: CurrentValue

Units of current
Units in SI: A
Typical value: 1e-11 A

Restriction: Base: xs:double


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Simple Type: ConcentrationValue

Units of concentration
Units in SI: mM
Typical value: 1e-5 mM

Restriction: Base: xs:double

Minimum value inclusive: 0


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Simple Type: VoltageValue

Units of voltage
Units in SI: V
Typical value: -0.07 V

Restriction: Base: xs:double


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Simple Type: TemperatureValue

Units of temperature
Units in SI: deg C
Typical value: 32 deg C

Restriction: Base: xs:double

Minimum value exclusive: 0


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Complex Types

Complex Type: Biophysics

Description of biophysical properties of a cell.

The following elements must appear in the sequence outlined here.
mechanism
Definition of placement of a single electrophysiological mechanism (e.g. channel mechanism) on a group of cables of a cell. Note there should be at least one of these to specify the passive membrane conductance. Note: elements spec_capacitance, spec_axial_resistance, ion_props etc. should be used in preference to specificCapacitance etc!
Type : Mechanism
Occurances: 1 ... unbounded
Only one of the following SUB elements may appear.
specificCapacitance
Type : SpecCapacitance
spec_capacitance
Type : SpecCapacitance
Only one of the following SUB elements may appear.
specificAxialResistance
Type : SpecAxialResistance
spec_axial_resistance
Type : SpecAxialResistance
Only one of the following SUB elements may appear.
initialMembPotential
Type : InitialMembPotential
Occurances: 0 ... 1
init_memb_potential
Type : InitialMembPotential
Occurances: 0 ... 1
Only one of the following SUB elements may appear.
ionProperties
Type : IonProperties
Occurances: 0 ... 1
ion_props
Type : IonProperties
Occurances: 0 ... unbounded
Attributes
units
Unit system of all quantities.
Type: meta:Units , Use: required

Biophysics used by: biophysics (xs:element)

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



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Complex Type: Mechanism

Definition of placement of a single electrophysiological mechanism (e.g. channel mechanism) on a group of cables of a cell

The following elements must appear in the sequence outlined here.
parameter
Type : NamedParameter
Occurances: 0 ... unbounded
variableParameter
Note variable_parameter will be the preferred form in v2.0
Type : VariableNamedParameter
Occurances: 0 ... unbounded
variable_parameter
Note variable_parameter will be the preferred form in v2.0
Type : VariableNamedParameter
Occurances: 0 ... unbounded
Attributes
name
Name of the mechanism. Should refer to a named mechanism in a ChannelML file
Type: xs:string , Use: required
type
Specifies the type of cellular mechanism (Channel Mechanism/Ion Concentration). Note could be used for any type of electrophysiological property of a section of a cell
Type: MechanismType, Use: required
passive_conductance
Whether this is a passive/leak conductance. In this case, 2 params, gmax and e should be sufficient to fully specify the mechanism, independent of any implementation. Useful e.g. for mapping to and from inbuilt mechanisms in simulators (e.g. pas in NEURON, Em/Rm in GENESIS). NOTE: this attribute will be required in v2.0!! Don't use passiveConductance anymore. Changed for consistency with ChannelML and NetworkML naming conventions.
Type: xs:boolean , Use: optional, default: false
passiveConductance
Whether this is a passive/leak conductance. NOTE: this attribute will be removed in v2.0!! Use passive_conductance instead. Changed for consistency with ChannelML and NetworkML naming conventions.
Type: xs:boolean , Use: optional, default: false

Mechanism used by: Biophysics (xs:complexType)

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



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Complex Type: SpecCapacitance

Capacitance per unit area of a group of sections
Units in SI: F/m2

The following elements must appear in the sequence outlined here.
parameter
Type : UnnamedParameter
Occurances: 0 ... unbounded
variableParameter
Note variable_parameter will be the preferred form in v2.0
Type : VariableParameter
Occurances: 0 ... unbounded
variable_parameter
Note variable_parameter will be the preferred form in v2.0
Type : VariableParameter
Occurances: 0 ... unbounded

SpecCapacitance used by: Biophysics (xs:complexType) Biophysics (xs:complexType)

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



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Complex Type: SpecAxialResistance

Specific axial resistance of a group of sections
Units in SI: ohm m

The following elements must appear in the sequence outlined here.
parameter
Type : UnnamedParameter
Occurances: 0 ... unbounded
variableParameter
Note variable_parameter will be the preferred form in v2.0
Type : VariableParameter
Occurances: 0 ... unbounded
variable_parameter
Note variable_parameter will be the preferred form in v2.0
Type : VariableParameter
Occurances: 0 ... unbounded

SpecAxialResistance used by: Biophysics (xs:complexType) Biophysics (xs:complexType)

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



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Complex Type: InitialMembPotential

This quantity is often required for computational simulations and specifies the potential difference across the membrane at the start of the simulation. This is an optional field
Units in SI: V

The following elements must appear in the sequence outlined here.
parameter
Type : UnnamedParameter
Occurances: 0 ... unbounded
variableParameter
Type : VariableParameter
Occurances: 0 ... unbounded

InitialMembPotential used by: Biophysics (xs:complexType) Biophysics (xs:complexType)

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



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Complex Type: IonProperties

Some properties accociated with an ion type which takes part in the mechanisms on the cell

The following elements must appear in the sequence outlined here.
parameter
Type : NamedParameter
Occurances: 0 ... unbounded
Attributes
nameType: xs:string , Use: required

IonProperties used by: Biophysics (xs:complexType) Biophysics (xs:complexType)

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



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Complex Type: NamedParameter

Definition of a value for a quantity and the associated groups of cables which have this value. Can have any name, but gmax and e are special...

The following elements must appear in the sequence outlined here.
group
Type : xs:string
Occurances: 1 ... unbounded
Attributes
name
2 names have special meaning: gmax for the maximum conductance density, and e for the reversal potential of a passive channel
Type: xs:string , Use: required
valueType: xs:double , Use: required

NamedParameter used by: Mechanism (xs:complexType) IonProperties (xs:complexType)

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



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Complex Type: VariableParameter

Definition of a value for a quantity which varies over a given group of cables

The following elements must appear in the sequence outlined here.
group
Type : xs:string
inhomogeneous_value
Type : InhomogeneousValue
Attributes
nameType: xs:string , Use: optional

VariableParameter used by: SpecCapacitance (xs:complexType) SpecCapacitance (xs:complexType) SpecAxialResistance (xs:complexType) SpecAxialResistance (xs:complexType) InitialMembPotential (xs:complexType)

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



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Complex Type: VariableNamedParameter

Definition of a value for a quantity which varies over a given group of cables

The following elements must appear in the sequence outlined here.
group
Type : xs:string
inhomogeneous_value
Type : InhomogeneousValue
Attributes
nameType: xs:string , Use: required

VariableNamedParameter used by: Mechanism (xs:complexType) Mechanism (xs:complexType)

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



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Complex Type: InhomogeneousValue

How a value changes over the cable group. Implementation here based on NEURON inhomogeneous parameter specification. See example for usage of this element

Attributes
param_name
Name used in the inhomogeneous_param element in the cable group
Type: xs:string , Use: required
value
Equation showing how parameter changes as function of variable attribute in inhomogeneous_param element
Type: xs:string , Use: required

InhomogeneousValue used by: VariableParameter (xs:complexType) VariableNamedParameter (xs:complexType)

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



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Complex Type: UnnamedParameter

Definition of a value for a quantity and the associated groups of cables which have this value. The quantity referred to will be clear from the usage, e.g. InitialMembPotential

The following elements must appear in the sequence outlined here.
group
Type : xs:string
Attributes
valueType: xs:double , Use: required

UnnamedParameter used by: SpecCapacitance (xs:complexType) SpecAxialResistance (xs:complexType) InitialMembPotential (xs:complexType)

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



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