Inputs.xml

<Lems xmlns="http://www.neuroml.org/lems/0.7.1"
      xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
      xsi:schemaLocation="http://www.neuroml.org/lems/0.7.1 ../../LEMS/Schemas/LEMS/LEMS_v0.7.1.xsd"
      description="A number of ComponentTypes for providing spiking and current inputs to other ComponentTypes">

    <Include file="NeuroMLCoreDimensions.xml"/>

    
    <ComponentType name="basePointCurrent"
                   description="Base type for all ComponentTypes which produce a current _i (with dimension current)">

        <Exposure name="i" dimension="current" description="The total (time varying) current produced by this ComponentType"/>

    </ComponentType>


    <ComponentType name="baseVoltageDepPointCurrent"
                   extends="basePointCurrent"
                   description="Base type for all ComponentTypes which produce a current _i (with dimension current) and require a membrane potential _v exposed on the parent Component">

        <Requirement name="v" dimension="voltage" description="The current may vary with the voltage exposed by the ComponentType on which this is placed"/>

    </ComponentType>


    <ComponentType name="basePointCurrentDL"
                   description="Base type for all ComponentTypes which produce a dimensionless current _I. There will eventually be dimensionless equivalents of all the core current producing ComponentTypes such as _pulseGenerator_, _sineGenerator_ and _rampGenerator_">

        <Exposure name="I" dimension="none" description="The total (time varying) current produced by this ComponentType"/>

    </ComponentType>


    <ComponentType name="baseVoltageDepPointCurrentDL"
                   extends="basePointCurrentDL"
                   description="Base type for all ComponentTypes which produce a dimensionless current _I and require a dimensionless membrane potential _V exposed on the parent Component">

        <Requirement name="V" dimension="none" description="The current may vary with the voltage exposed by the ComponentType on which this is placed"/>

    </ComponentType>


    <ComponentType name="baseSpikeSource"
                   description="Base for any ComponentType whose main purpose is to emit spikes. The exposed variable _tsince can be used for plotting the time since the Component has spiked last">

        <EventPort name="spike"
                   direction="out"
                   description="Port on which spikes are emitted"/>

        <Exposure name="tsince"
                  dimension="time"
                  description="Time since the last spike was emitted"/>

    </ComponentType>


    <ComponentType name="spikeGenerator"
                   extends="baseSpikeSource"
                   description="Simple generator of spikes at a regular interval set by _period.">

        <Parameter name="period" dimension="time" description="Time between spikes. First spike will be emitted after this time."/>
        <Dynamics>
            <StateVariable name="tsince" dimension="time" exposure="tsince"/>

            <TimeDerivative variable="tsince" value="1"/>

            <OnStart>
                <StateAssignment variable="tsince" value="0"/>
            </OnStart>

            <OnCondition test="tsince .gt. period">
                <StateAssignment variable="tsince" value="0"/>
                <EventOut port="spike"/>
            </OnCondition>

        </Dynamics>

    </ComponentType>


    <ComponentType name="spikeGeneratorRandom" extends="baseSpikeSource"
                   description="Generator of spikes with a random interspike interval of at least _minISI and at most _maxISI">

        <Parameter name="maxISI" dimension="time" description="Maximum interspike interval"/>
        <Parameter name="minISI" dimension="time" description="Minimum interspike interval"/>

        <Constant name="MSEC" dimension="time" value="1ms"/>

        <Exposure name="isi" dimension="time" description="The interval until the next spike"/>

        <Dynamics>
            <StateVariable name="tsince" dimension="time" exposure="tsince"/>

            <StateVariable name="isi" dimension="time" exposure="isi"/>

            <TimeDerivative variable="tsince" value="1"/>

            <OnStart>
                <StateAssignment variable="tsince" value="0"/>
                <StateAssignment variable="isi" value="minISI + MSEC * random((maxISI - minISI) / MSEC)"/>
            </OnStart>


            <OnCondition test="tsince .geq. isi">
                <StateAssignment variable="isi" value="minISI + MSEC * random((maxISI - minISI) / MSEC)"/>
                <StateAssignment variable="tsince" value="0"/>
                <EventOut port="spike"/>
            </OnCondition>

        </Dynamics>
    </ComponentType>


    <ComponentType name="spikeGeneratorPoisson" extends="baseSpikeSource"
                   description="Generator of spikes whose ISI is distributed according to an exponential pdf with scale 1/_averageRate">
        <Parameter name="averageRate" dimension="per_time"/>
        <DerivedParameter name="averageIsi" dimension="time" value="1 / averageRate"/>
        <Dynamics>
            <StateVariable name="tsince" dimension="time" exposure="tsince"/>
            <StateVariable name="isi" dimension="time"/>

            <TimeDerivative variable="tsince" value="1"/>

            <OnStart>
                <StateAssignment variable="tsince" value="0"/>
                <StateAssignment variable="isi" value="- averageIsi * log(1 - random(1))"/>
            </OnStart>

            <OnCondition test="tsince .geq. isi">
                <StateAssignment variable="tsince" value="0"/>
                <StateAssignment variable="isi" value="- averageIsi * log(1 - random(1))"/>
                <EventOut port="spike"/>
            </OnCondition>
        </Dynamics>
    </ComponentType>


    <ComponentType name="pulseGenerator" extends="basePointCurrent"
                   description="Generates a constant current pulse of a certain _amplitude for a specified _duration after a _delay"> <!-- Note: a synpase also extends basePointCurrent -->

        <Parameter name="delay" dimension="time" description="Delay before change in current. Current is zero  prior to this."/>
        <Parameter name="duration" dimension="time" description="Duration for holding current at amplitude. Current is zero after delay + duration."/>
        <Parameter name="amplitude" dimension="current" description="Amplitude of current pulse"/>

        <!--TODO: remove! Only required as EventConnection is used in explicitInput to
        connect inputs to cells. Events aren't passed! ... -->
        <EventPort name="in" direction="in" description="Note this is not used here. Will be removed in future"/>

        <Dynamics>

            <StateVariable name="i" exposure="i" dimension="current"/>

            <OnEvent port="in"><!--TODO: remove, see above...
            <StateAssignment variable="i" value="0"/>-->
            </OnEvent>

            <OnCondition test="t .lt. delay">
                <StateAssignment variable="i" value="0"/>
            </OnCondition>

            <OnCondition test="t .geq. delay .and. t .lt. duration + delay">
                <StateAssignment variable="i" value="amplitude"/>
            </OnCondition>

            <OnCondition test="t .geq. duration + delay">
                <StateAssignment variable="i" value="0"/>
            </OnCondition>

        </Dynamics>
    </ComponentType>


    <ComponentType name="pulseGeneratorDL" extends="basePointCurrentDL"
                   description="Dimensionless equivalent of _pulseGenerator_. Generates a constant current pulse of a certain _amplitude for a specified _duration after a _delay"> <!-- Note: a synpase also extends basePointCurrent -->

        <Parameter name="delay" dimension="time" description="Delay before change in current. Current is zero  prior to this."/>
        <Parameter name="duration" dimension="time" description="Duration for holding current at amplitude. Current is zero after delay + duration."/>
        <Parameter name="amplitude" dimension="none" description="Amplitude of current pulse"/>

        <!--TODO: remove! Only required as EventConnection is used in explicitInput to
        connect inputs to cells. Events aren't passed! ... -->
        <EventPort name="in" direction="in" description="Note this is not used here. Will be removed in future"/>

        <Dynamics>

            <StateVariable name="I" exposure="I" dimension="none"/>

            <OnEvent port="in"><!--TODO: remove, see above...-->
            </OnEvent>

            <OnCondition test="t .lt. delay">
                <StateAssignment variable="I" value="0"/>
            </OnCondition>

            <OnCondition test="t .geq. delay .and. t .lt. duration + delay">
                <StateAssignment variable="I" value="amplitude"/>
            </OnCondition>

            <OnCondition test="t .geq. duration + delay">
                <StateAssignment variable="I" value="0"/>
            </OnCondition>

        </Dynamics>
    </ComponentType>


    <ComponentType name="sineGenerator" extends="basePointCurrent"
                   description="Generates a sinusoidally varying current after a time _delay, for a fixed _duration. The _period and maximum _amplitude of the current can be set as well as the _phase at which to start.">

        <Parameter name="phase" dimension="none"/>
        <Parameter name="delay" dimension="time"/>
        <Parameter name="duration" dimension="time"/>
        <Parameter name="amplitude" dimension="current"/>
        <Parameter name="period" dimension="time"/>

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

        <Dynamics>

            <StateVariable name="i" exposure="i" dimension="current"/>

            <OnEvent port="in"><!--TODO: remove-->
            </OnEvent>

            <OnCondition test="t .lt. delay">
                <StateAssignment variable="i" value="0"/>
            </OnCondition>

            <OnCondition test="t .geq. delay .and. t .lt. duration+delay">
                <StateAssignment variable="i" value="amplitude * sin(phase + (2 * 3.14159265 * (t-delay)/period) )"/>
            </OnCondition>

            <OnCondition test="t .geq. duration+delay">
                <StateAssignment variable="i" value="0"/>
            </OnCondition>

        </Dynamics>
    </ComponentType>


    <ComponentType name="rampGenerator" extends="basePointCurrent"
                   description="Generates a ramping current after a time _delay, for a fixed _duration. During this time the current steadily changes from _startAmplitude to _finishAmplitude.">

        <Parameter name="delay" dimension="time"/>
        <Parameter name="duration" dimension="time"/>
        <Parameter name="startAmplitude" dimension="current"/>
        <Parameter name="finishAmplitude" dimension="current"/>
        <Parameter name="baselineAmplitude" dimension="current"/>

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

        <Dynamics>

            <StateVariable name="i" exposure="i" dimension="current"/>

            <OnStart>
                <StateAssignment variable="i" value="baselineAmplitude"/>
            </OnStart>

            <OnEvent port="in"><!--TODO: remove-->
            </OnEvent>

            <OnCondition test="t .lt. delay">
                <StateAssignment variable="i" value="baselineAmplitude"/>
            </OnCondition>

            <OnCondition test="t .geq. delay .and. t .lt. duration+delay">
                <StateAssignment variable="i" value="startAmplitude + (finishAmplitude - startAmplitude) * (t - delay) / (duration)"/>
            </OnCondition>

            <OnCondition test="t .geq. duration+delay">
                <StateAssignment variable="i" value="baselineAmplitude"/>
            </OnCondition>

        </Dynamics>
    </ComponentType>


    <ComponentType name="rampGeneratorDL" extends="basePointCurrentDL"
                   description="Generates a ramping current after a time _delay, for a fixed _duration. During this time the dimensionless current steadily changes from _startAmplitude to _finishAmplitude.">

        <Parameter name="delay" dimension="time"/>
        <Parameter name="duration" dimension="time"/>
        <Parameter name="startAmplitude" dimension="none"/>
        <Parameter name="finishAmplitude" dimension="none"/>
        <Parameter name="baselineAmplitude" dimension="none"/>

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

        <Dynamics>

            <StateVariable name="I" exposure="I" dimension="none"/>

            <OnStart>
                <StateAssignment variable="I" value="baselineAmplitude"/>
            </OnStart>

            <OnEvent port="in"><!--TODO: remove-->
            </OnEvent>

            <OnCondition test="t .lt. delay">
                <StateAssignment variable="I" value="baselineAmplitude"/>
            </OnCondition>

            <OnCondition test="t .geq. delay .and. t .lt. duration+delay">
                <StateAssignment variable="I" value="startAmplitude + (finishAmplitude - startAmplitude) * (t - delay) / (duration)"/>
            </OnCondition>

            <OnCondition test="t .geq. duration+delay">
                <StateAssignment variable="I" value="baselineAmplitude"/>
            </OnCondition>

        </Dynamics>
    </ComponentType>


    <ComponentType name="voltageClamp" extends="baseVoltageDepPointCurrent"
                   description="Voltage clamp. Applies a variable current _i to try to keep parent at _targetVoltage. Not yet fully tested!!!">

        <Parameter name="delay" dimension="time" description="Delay before change in current. Current is zero  prior to this."/>
        <Parameter name="duration" dimension="time" description="Duration for attempting to keep parent at targetVoltage. Current is zero after delay + duration."/>
        <Parameter name="targetVoltage" dimension="voltage" description="Current will be applied to try to get parent to this target voltage"/>
        
        <!-- seriesResistance renamed to simpleSeriesResistance & factor of 1e-5 removed from calculation of current. Still being tested... -->
        <Parameter name="simpleSeriesResistance" dimension="resistance" description="Current will be calculated by the difference in voltage between the target and parent, divided by this value"/>

        <!--TODO: remove! Only required as EventConnection is used in explicitInput to
        connect inputs to cells. Events aren't passed! ... -->
        <EventPort name="in" direction="in" description="Note this is not used here. Will be removed in future"/>

        <Dynamics>

            <StateVariable name="i" exposure="i" dimension="current"/>

            <OnEvent port="in"><!--TODO: remove, see above...
            <StateAssignment variable="i" value="0"/>-->
            </OnEvent>

            <OnCondition test="t .lt. delay">
                <StateAssignment variable="i" value="0"/>
            </OnCondition>

            <OnCondition test="t .geq. delay">
                <!-- seriesResistance renamed to simpleSeriesResistance & factor of 1e-5 removed from calculation of current. Still being tested... -->
                <StateAssignment variable="i" value="(targetVoltage - v) / simpleSeriesResistance"/>
            </OnCondition>

            <OnCondition test="t .gt. duration + delay">
                <StateAssignment variable="i" value="0"/>
            </OnCondition>

        </Dynamics>

    </ComponentType>


    <ComponentType name="spikeArray" extends="baseSpikeSource"
                   description="Set of spike ComponentTypes, each emitting one spike at a certain time. Can be used to feed a predetermined spike train into a cell">

        <Children name="spikes" type="spike"/>
        <EventPort name="in" direction="in" description="This will receive events from the children"/>

        <Dynamics>
            <StateVariable name="tsince" dimension="time" exposure="tsince"/>

            <TimeDerivative variable="tsince" value="1"/>

            <OnStart>
                <StateAssignment variable="tsince" value="0"/>
            </OnStart>

            <OnEvent port="in">
                <StateAssignment variable="tsince" value="0"/>
                <EventOut port="spike"/>
            </OnEvent>

        </Dynamics>

    </ComponentType>


    <ComponentType name="spike" extends="baseSpikeSource"
                   description="Emits a single spike at the specified time">

        <Parameter name="time" dimension="time" description="Time at which to emit one spike event"/>
        <Exposure name="spiked" dimension="none" description="0 signals not yet spiked, 1 signals has spiked"/>

        <Dynamics>

            <StateVariable name="tsince" dimension="time" exposure="tsince"/>
            <StateVariable name="spiked" dimension="none" exposure="spiked"/>

            <TimeDerivative variable="tsince" value="1"/>

            <OnStart>
                <StateAssignment variable="tsince" value="0"/>
            </OnStart>

            <OnCondition test="(t .geq. time) .and. (spiked .eq. 0)">
                <StateAssignment variable="spiked" value="1"/>
                <StateAssignment variable="tsince" value="0"/>
                <EventOut port="spike"/>
            </OnCondition>
        </Dynamics>

        <Structure>
            <With instance="this" as="a"/>
            <With instance="parent" as="b"/>
            <EventConnection from="a" to="b"/>
        </Structure>

    </ComponentType>

</Lems>