XML Format

Tag Descriptions

<NineML>

<NineML>

This is the root namespace tag for a NineML file. It can contain <ComponentClass> elements.

Todo

XML namespaces.

<ComponentClass>

<ComponentClass name="">

This tag starts an abstraction layer component definition.

Attributes:

• name [Required]

Child Elements:

• <Parameter> [0+]
• <AnalogPort>[0+]
• <EventPort> [0+]
• <Dynamics> [1]

<Parameter>

<Parameter name="" dimension="">

This tag specifies a parameter in the interface of the component

Attributes:

• name [Required]
• dimension [Required]

Child Elements: None

<AnalogPort>

<AnalogPort name="" mode="" reduce_op="" dimension="" >

This tag specifies an AnalogPort in the interface of the component

Attributes:

• name [Required]
• mode [Required: ‘send’,’recv’ or ‘reduce’]
• reduce_op [Required if mode==’reduce’]
• dimension [Required]

Child Elements: None

<EventPort>

<EventPort name="" mode="">

This tag specifies an EventPort in the interface of the component

Attributes:

• name [Required]
• mode [Required: ‘send’,’recv’]
• dimension [Required]

Child Elements: None

<Dynamics>

<Dynamics>

This tag specifies the dynamics of the component

Attributes: None

Child Elements:

• <StateVariable> [0+]
• <Alias> [0+]
• <Regime> [1+]

<StateVariable>

<StateVariable name='' dimension=''>

This tag declares a state-variable in the component

Attributes:

• name [Required] (The variable name)
• dimension [Required]

Child Elements: None

<Alias>

<Alias name=''>

This tag declares an alias in the component

Attributes:

• name [Required] (The alias name)
• dimension [Required]

Child Elements:

• <MathInline> [Required] (The equation on the right-hand-side of the alias)

<Regime>

<Regime>

This tag declares an regime in the component. There must be exactly on TimeDerivative block for each StateVariable block declared in the enclosing <Dynamics> block, even if it has a RHS of zero.

Attributes:

• name [Required] (The regime name)

Child Elements:

• <TimeDerivative> [0+]
• <OnCondition> [0+] (The transitions from this regime, triggered by conditions)
• <OnEvent> [0+] (The transitions from this regime, triggered by events)

<TimeDerivative>

<TimeDerivative>

This tag defines the differential equation controlling the evolution of a StateVariable while in this regime.

Attributes:

• variable [Required] (The name of the state variable)

Child Elements:

• <MathInline> [1] (The right-hand-side of the differential equation)

<OnCondition>

<OnCondition>

This block specifies a transition from the enclosing Regime, which is triggered by a mathematical function of the Component’s Aliases, StateVariables, Ports and Parameters.

Attributes: None

Child Elements:

• <Trigger> [1] (A <Trigger> block defining the condition that causes this

  transition to occur)

• <StateAssignment> [0+] (The state assignments that should occur when this transition is triggered)

• <EventOut> [0+] (The events that should be sent when this transition is triggered)

<OnEvent>

<OnEvent>

This block specifies a transition from the enclosing Regime, which is triggered by an input event.

Attributes:

• port [Required] The name of the input event port which triggers this transition

Child Elements:

• <StateAssignment> [0+] (The state assignments that should occur when this transition is triggered)
• <EventOut> [0+] (The events that should be sent when this transition is triggered)

<Trigger>

<Trigger>

This block is used by <OnCondition> blocks to define the condition needed for them to be triggered.

Attributes: None

Child Elements:

• <MathInline> [1] (A mathematical expression. This should evaluate to a boolean, for example by invoking a comparison operator :math: (‘>’, ‘<’) )

<StateAssignment>

<StateAssignment>

Used in transitions to assign a value to a state-variable during a transition.

Note

‘In-place’ operations are not supported and should be written out as in full:

Attributes:

• variable [Required] (The name of the variable to be assigned to)

Child Elements:

• <MathInline> [1] (The right-hand-side of the assignment expression)

<EventOut>

<EventOut>

Used in transitions to emit an event.

Attributes:

• port_name [Required] (The name of the EventPort to send an event over)

Child Elements: None

<MathInline>

<MathInline>

A block used to specify mathematical expressions. The expression is expected to be in C style and given as text. In future versions of NineML, we will support <MathML> blocks too.

Attributes: None

Child Elements: None

Example XML

An example model of an Izhikevich model is given:

<?xml version='1.0' encoding='UTF-8'?>
<NineML xmlns="http://nineml.org/9ML/0.1"
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:schemaLocation="http://nineml.org/9ML/0.1 NineML_v0.2.xsd">

  <ComponentClass name="izhikevichCellNew">

    <Parameter name="a" dimension='none'/>
    <Parameter name="c" dimension='none'/>
    <Parameter name="b" dimension='none'/>
    <Parameter name="d" dimension='none'/>
    <Parameter name="theta" dimension='voltage'/>

    <AnalogPort name="iSyn" mode='reduce' reduce_op='+' dimension='current'/>
    <AnalogPort name="U" mode="send" dimension='none'/>
    <AnalogPort name="V" mode="send" dimension='voltage'/>
    <EventPort name="spikeOutput" mode="send"/>


    <Dynamics>

        <StateVariable name="V" dimension="voltage"/>
        <StateVariable name="U" dimension="none"/>

        <Alias name='rv' dimension='none'>
            <MathInline>V*U</MathInline>
        </Alias>

        <Regime name="subthresholdRegime">

          <TimeDerivative variable="U">
            <MathInline>a*(b*V - U)</MathInline>
          </TimeDerivative>

          <TimeDerivative variable="V">
            <MathInline>0.04*V*V + 5*V + 140.0 - U + iSyn</MathInline>
          </TimeDerivative>


          <OnCondition>
            <Trigger>
              <MathInline>V &gt; theta </MathInline>
            </Trigger>

            <StateAssignment variable="V" >
              <MathInline>c</MathInline>
            </StateAssignment>

            <StateAssignment variable="U" >
              <MathInline>U+d</MathInline>
            </StateAssignment>

            <EventOut port="spikeOutput" />

          </OnCondition>

        </Regime>
    </Dynamics>

  </ComponentClass>
</NineML>