Defining component types

Defining component types#

Schema against which LEMS based on these should be valid: LEMS_v0.7.6.xsd. Generated on 18/06/24 from this commit. Please file any issues or questions at the issue tracker here.

ComponentType#

Root element for defining LEMS Component Types.

Properties

name	String	The name of the component type. This can be uses as an XML element name in the shorthand form whendefining components.
eXtends	String	The component type that this type inherits field definitions for, if any

can contain these elements

parameters	Parameter
indexParameters	IndexParameter
derivedParameters	DerivedParameter
pathParameters	PathParameter
requirements	Requirement
componentRequirements	ComponentRequirement
instanceRequirements	InstanceRequirement
exposures	Exposure
childs	Child
childrens	Children
links	Link
componentReferences	ComponentReference
componentTypeReferences	ComponentTypeReference
locations	Location
propertys	Property
dynamicses	Dynamics
structures	Structure
simulations	Simulation
equilibriums	Equilibrium
procedures	Procedure
geometrys	Geometry
fixeds	Fixed
constants	Constant
attachmentses	Attachments
eventPorts	EventPort
paths	Path
texts	Text
collections	Collection
pairCollections	PairCollection
abouts	About
metas	Meta

Schema

<xs:complexType name="ComponentType">
  <xs:sequence>
    <xs:element name="Property" type="Property" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="Parameter" type="Parameter" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="DerivedParameter" type="DerivedParameter" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="IndexParameter" type="IndexParameter" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="Constant" type="Constant" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="Child" type="Child" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="Children" type="Children" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="Fixed" type="Fixed" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="Link" type="Link" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="ComponentReference" type="ComponentReference" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="Attachments" type="Attachments" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="EventPort" type="EventPort" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="Exposure" type="Exposure" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="Requirement" type="Requirement" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="ComponentRequirement" type="ComponentRequirement" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="InstanceRequirement" type="InstanceRequirement" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="Path" type="Path" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="Text" type="Text" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="Dynamics" type="Dynamics" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="Structure" type="Structure" minOccurs="0" maxOccurs="1"/>
    <xs:element name="Simulation" type="Simulation" minOccurs="0" maxOccurs="1"/>
  </xs:sequence>
  <xs:attribute name="name" type="xs:string" use="required"/>
  <xs:attribute name="extends" type="xs:string" use="optional"/>
  <xs:attribute name="description" type="xs:string" use="optional"/>
</xs:complexType>

Usage: XML

<ComponentType name="Population">
    <ComponentReference name="component" type="Component"/>
    <Parameter name="size" dimension="none"/>
    <Structure>
        <MultiInstantiate number="size" component="component"/>
    </Structure>
</ComponentType>

<ComponentType name="EventConnectivity">
    <Link name="source" type="Population"/>
    <Link name="target" type="Population"/>
    <Child name="Connections" type="ConnectionPattern"/>
</ComponentType>

<ComponentType name="Network">
    <Children name="populations" type="Population"/>
    <Children name="connectivities" type="EventConnectivity"/>
</ComponentType>

<ComponentType name="AllAll" extends="ConnectionPattern">
    <Structure>
        <ForEach instances="../source" as="a">
            <ForEach instances="../target" as="b">
                <EventConnection from="a" to="b"/>
            </ForEach>
        </ForEach>
    </Structure>
</ComponentType>

<ComponentType name="ConnectionPattern"/>

Parameter#

A quantity, defined by name and dimension, that must be supplied when a Component of the enclosing ComponentType is defined

Properties

name	String	The name of the parameter. This is the name of the attribute to be used when the parameter is supplied in a component definition
dimension	String	The dimension, or ‘none’. This should be the name of an already defined dimension element
description	String	An optional description of the parameter

Schema

<xs:complexType name="Parameter">
  <xs:complexContent>
    <xs:extension base="NamedDimensionalType"/>
  </xs:complexContent>
</xs:complexType>

Usage: XML

<Parameter name="size" dimension="none"/>

<Parameter name="xmin" dimension="none"/>

<Parameter name="xmax" dimension="none"/>

<Parameter name="ymin" dimension="none"/>

<Parameter name="ymax" dimension="none"/>

PathParameter#

A parameter of which the value is a path expression. When a ComponentType declares a PathParameter, a corresponding Component definition should have an attibute with that name whose value is a path expression that evaluates within the instance tree of the built model. This is used, for example, in the definition of a group component class, where the coresponding component specifies a path over the instance tree which selectesthe items that should go in the group.

Properties

name

String

Name of the parameter

Property#

An property on an instance of a component. Unlike a Parameter, a Property can very from instance to instance. It should be set with an Assign element within the build specification.

Properties

name	String
dimension	String
defaultValue	String	The defaultValue for the property must be a plain number (no units) giving the SI magnitude of the quantity.

Schema

<xs:complexType name="Property">
  <xs:attribute name="name" type="xs:string" use="required"/>
  <xs:attribute name="dimension" type="xs:string" use="optional" default="none"/>
  <xs:attribute name="description" type="xs:string" use="optional"/>
  <xs:attribute name="defaultValue" type="xs:double" use="optional"/>
</xs:complexType>

DerivedParameter#

A parameter that is a function of the Component’s Parameters, which does not change with time. Its value can be supplied either with the ‘value’ attribute that evaluates within the scope of the definition, or with the ‘select’ attribute which gives a path to ‘primary’ version of the parameter. For example, setting select=‘//MembranePotential[species=channel/species]/reversal’ within the appropriate context allows a channel’s reversal potential to taken from a single global setting according to its permeant ion, rather than explicitly supplied locally.

Properties

name	String	The name of the derived parameter
dimension	String	The dimension, or ‘none’. This should be the name of an already defined dimension element
description	String	An optional description of the derived parameter
select	String	Path to the parameter that supplies the value. Exactly one of ‘select’ and ‘value’ is required.
value	String	A string defining the value of the element

Schema

<xs:complexType name="DerivedParameter">
  <xs:attribute name="name" type="xs:string" use="required"/>
  <xs:attribute name="dimension" type="xs:string" use="optional" default="none"/>
  <xs:attribute name="value" type="xs:string" use="required"/>
  <xs:attribute name="description" type="xs:string" use="optional"/>
</xs:complexType>

Usage: XML

<DerivedParameter name="erev" dimension="voltage" select="//MembranePotential[species=channel/species]/reversal"/>

Fixed#

Fixes the value of a parameter in the parent class, so that it does not have to be supplied separately in component definitions.

Properties

parameter	String
value	String

Schema

<xs:complexType name="Fixed">
  <xs:attribute name="parameter" type="xs:string" use="required"/>
  <xs:attribute name="value" type="PhysicalQuantity" use="required"/>
  <xs:attribute name="description" type="xs:string" use="optional"/>
</xs:complexType>

Usage: XML

<Fixed parameter="threshold" value="-45mV"/>

<Fixed parameter="relativeConductance" value="0"/>

<Fixed parameter="relativeConductance" value="1"/>

<Fixed parameter="relativeConductance" value="0"/>

<Fixed parameter="relativeConductance" value="1"/>

Requirement#

A Requirement gives the name and dimension of a quantity (parameter or variable) that should be accessible within the scope of a model component. This is only applicable for elements that can be included as children of other elements, where the scope comprises its own parameters and those in the scope of its enclosing element. Once a requirement has been declared, then the quantity can be used within the Dynamics definition of the component. It is the responsibility of an implementation to check that the component is only used in a context in which the requirement is met. A typical example is in defining membrand bound components which require access to the membrane potential but where the variable that holds the potential itself is defined in the top level component.

Properties

name	String	name
dimension	String	The dimension, or ‘none’. This should be the name of an already defined dimension element
description	String	An optional description of the requirement

Schema

<xs:complexType name="Requirement">
  <xs:complexContent>
    <xs:extension base="NamedDimensionalType"/>
  </xs:complexContent>
</xs:complexType>

Usage: XML

<Requirement name="v" dimension="voltage"/>

<Requirement name="v" dimension="voltage"/>

<Requirement name="v" dimension="voltage"/>

<Requirement name="v" dimension="voltage"/>

<Requirement name="v" dimension="voltage"/>

ComponentRequirement#

The name of a component or component reference that must exist in the component hierarchy

Properties

name

String

name

Schema

<xs:complexType name="ComponentRequirement">
  <xs:attribute name="name" type="xs:string" use="required"/>
</xs:complexType>

InstanceRequirement#

An instance that must be supplied at build time. Expressions can contain references to quantities in the instance

Properties

name

String

name

Schema

<xs:complexType name="InstanceRequirement">
  <xs:attribute name="name" type="xs:string" use="required"/>
  <xs:attribute name="type" type="xs:string" use="required"/>
</xs:complexType>

Exposure#

A quantity that is made available to other components in the simulation. Note that all variables in a Dynamics definition are private. If other components need access to them, then the definition should explicitly link them to an exposure defined in the component class

Properties

name	String	Name of the exposure element
dimension	String	The dimension, or ‘none’. This should be the name of an already defined dimension element
description	String	An optional description of the element

Schema

<xs:complexType name="Exposure">
  <xs:complexContent>
    <xs:extension base="NamedDimensionalType"/>
  </xs:complexContent>
</xs:complexType>

Usage: XML

<Exposure name="v" dimension="voltage"/>

<Exposure name="tsince" dimension="time"/>

<Exposure name="r" dimension="per_time"/>

<Exposure name="fcond" dimension="none"/>

<Exposure name="fcond" dimension="none"/>

Child#

Specifies that a component can have a child of a particular type. The name supplied here can be used in path expressions to access the component. This is useful, for example, where a component can have multiple children of the same type but with different roles, such as the forward and reverse transition rates in a channel.

Properties

name	String	Name of the child
type	String	Reference to a component class, the value should be the name of the target class.
description	String	An optional description of the child

Schema

<xs:complexType name="Child">
  <xs:attribute name="name" type="xs:string" use="required"/>
  <xs:attribute name="type" type="xs:string" use="required"/>
  <xs:attribute name="description" type="xs:string" use="optional"/>
</xs:complexType>

Usage: XML

<Child name="Connections" type="ConnectionPattern"/>

<Child name="Forward" type="HHRate"/>

<Child name="Reverse" type="HHRate"/>

<Child name="Forward" type="HHRate"/>

<Child name="Reverse" type="HHRate"/>

Children#

Specifies that a component can have children of a particular class. The class may refer to an extendedtype, in which case components of any class that extends the specified target class should be valid as child components

Properties

name	String	Name of the children
type	String	The class of component allowed as children.

Schema

<xs:complexType name="Children">
  <xs:attribute name="name" type="xs:string" use="required"/>
  <xs:attribute name="type" type="xs:string" use="optional"/>
  <xs:attribute name="min" type="xs:integer" use="optional"/>
  <xs:attribute name="max" type="xs:integer" use="optional"/>
  <xs:attribute name="description" type="xs:string" use="optional"/>
</xs:complexType>

Usage: XML

<Children name="populations" type="Population"/>

<Children name="connectivities" type="EventConnectivity"/>

<Children name="lines" type="Line"/>

<Children name="outputColumn" type="OutputColumn"/>

<Children name="displays" type="Display"/>

Link#

Like a ComponentRef, but resolved relative to the enclosing object so the target must already be in the model. One or the other should be deprecated. The Link element has the same properties as ComponentRef. The Link element just establishes a connection with the target component, but leaves it in its existing place in the hierarchy. Variables in the target component can be accessed via the name of the link element.

Properties

name	String	A name for the ComponentReference
type	String	The type of the target Component
description	String	An optional description of the ComponentReference

Schema

<xs:complexType name="Link">
  <xs:attribute name="name" type="xs:string" use="required"/>
  <xs:attribute name="type" type="xs:string" use="required"/>
  <xs:attribute name="description" type="xs:string" use="optional"/>
</xs:complexType>

Usage: XML

<Link name="source" type="Population"/>

<Link name="target" type="Population"/>

<Link name="from" type="KSState"/>

<Link name="to" type="KSState"/>

<Link name="from" type="KSState"/>

ComponentReference#

A reference to another component. The target component can be accessed with path expressions in the same way as a child component, but can be defined independently

Properties

name	String	A name for the ComponentReference
type	String	The type of the target Component
description	String	An optional description of the ComponentReference

Schema

<xs:complexType name="ComponentReference">
  <xs:attribute name="name" type="xs:string" use="required"/>
  <xs:attribute name="type" type="xs:string" use="required"/>
  <xs:attribute name="local" type="xs:string" use="optional"/>
  <xs:attribute name="description" type="xs:string" use="optional"/>
</xs:complexType>

Usage: XML

<ComponentReference name="component" type="Component"/>

<ComponentReference name="target" type="Component"/>

<ComponentReference name="channel" type="HHChannel"/>

<ComponentReference name="component" type="Component"/>

<ComponentReference name="synapse" type="Synapse"/>

ComponentTypeReference#

This is used in conjunction with PathParameter elements to specify the target class of selections defined within components operating over the instance tree.

Properties

name

String

Collection#

Specifies that instances of components based on this class can containe a named collection of other instances. This provides for containers for oprating on groups of instances with path and filter expressions defined in components to operate over the instance tree.

Properties

name

String

PairCollection#

Defines a named collection of paris of instances, similar to the Collection element.

Properties

name

String

EventPort#

A port on a component that can send or receive events, depending on the direction specified

Properties

name	String	Name of the EventPort
direction	String	‘IN’ or ‘OUT’
description	String	An optional description of the EventPort

Schema

<xs:complexType name="EventPort">
  <xs:attribute name="name" type="xs:string" use="required"/>
  <xs:attribute name="direction" type="xs:string" use="required"/>
  <xs:attribute name="description" type="xs:string" use="optional"/>
</xs:complexType>

Usage: XML

<EventPort name="spikes-in" direction="in"/>

<EventPort name="a" direction="out"/>

<EventPort name="in" direction="in"/>

<EventPort name="out" direction="out"/>

<EventPort name="in" direction="in"/>

Text#

Holds textual information that does not change the model but is needed for other purposes such as labelling graphs.

Properties

name	String	The textual content
description	String	An optional description of the element

Schema

<xs:complexType name="Text">
  <xs:attribute name="name" type="xs:string" use="required"/>
  <xs:attribute name="description" type="xs:string" use="optional"/>
</xs:complexType>

Usage: XML

<Text name="title"/>

<Text name="color"/>

<Text name="path"/>

<Text name="fileName"/>

<Text name="destination"/>

Path#

Duplicates some functionality of PathParameter - the two should be merged.

Properties

name

String

Schema

<xs:complexType name="Path">
  <xs:attribute name="name" type="xs:string" use="required"/>
  <xs:attribute name="description" type="xs:string" use="optional"/>
</xs:complexType>

Usage: XML

<Path name="quantity"/>

<Path name="quantity"/>

<Path name="from"/>

<Path name="to"/>

<Path name="quantity"/>

Attachments#

Specifies that a component can accept attached components of a particular class. Attached components can be added at build time dependent on other events. For scoping and access purposes they are like child components. The cannonical use of attachments is in adding synapses to a cell when a network connection is made.

Properties

name	String	A name for the Attachments
type	String	The type of the Attachments

Schema

<xs:complexType name="Attachments">
  <xs:attribute name="name" type="xs:string" use="required"/>
  <xs:attribute name="type" type="xs:string" use="required"/>
  <xs:attribute name="description" type="xs:string" use="optional"/>
</xs:complexType>

Usage: XML

<Attachments name="synapses" type="Synapse"/>

Insertion#

IntegerParameter#

Properties

name	String	The name of the parameter. This is the name of the attribute to be used when the parameter is supplied in a component definition
dimension	String	The dimension, or ‘none’. This should be the name of an already defined dimension element
description	String	An optional description of the parameter

IndexParameter#

Properties

name	String	The name of the parameter. This is the name of the attribute to be used when the parameter is supplied in a component definition
dimension	String	The dimension, or ‘none’. This should be the name of an already defined dimension element
description	String	An optional description of the parameter

Schema

<xs:complexType name="IndexParameter">
  <xs:attribute name="name" type="xs:string" use="required"/>
</xs:complexType>

About#

Meta#

Meta element to provide arbitrary metadata to LEMS simulations. Note that this is not processed by the LEMS interpreter.

Schema

<xs:complexType name="Meta">
  <xs:sequence>
    <xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax"/>
  </xs:sequence>
  <xs:anyAttribute processContents="skip"/>
</xs:complexType>