Merge pull request #1 from NeuroML/development

Development
NeuroML · Feb 5, 2016 · 4422c96 · 4422c96
2 parents 9bb89f3 + 9cfa7b8
commit 4422c96
Show file tree

Hide file tree

Showing 4 changed files with 190 additions and 14 deletions.
diff --git a/LEMSexamples/LEMS_NML2_Ex16_Inputs.xml b/LEMSexamples/LEMS_NML2_Ex16_Inputs.xml
@@ -29,7 +29,7 @@
 <Include file="../examples/NML2_Inputs.nml"/>
 
 <network id="net1">
-    <population id="izhPop" component="RS" size="9"/>
+    <population id="izhPop" component="RS" size="11"/>
 
     <population id="spikeArrPop" component="spkArr" size="1"/>
     <population id="spikeGenRegularPop" component="spikeGenRegular" size="1"/>
@@ -41,6 +41,8 @@
     <explicitInput target="izhPop[2]" input="rg0" destination="synapses"/>
     <explicitInput target="izhPop[3]" input="vClamp0" destination="synapses"/>
     <explicitInput target="izhPop[8]" input="poissonFiringSyn" destination="synapses"/>
+    <explicitInput target="izhPop[9]" input="ci0" destination="synapses"/>
+    <!--<explicitInput target="izhPop[10]" input="transPoissonFiringSyn" destination="synapses"/>-->
 
     <synapticConnection from="spikeArrPop[0]" to="izhPop[4]" synapse="syn1" destination="synapses"/>
     <synapticConnection from="spikeGenRegularPop[0]" to="izhPop[5]" synapse="syn1" destination="synapses"/>
@@ -77,6 +79,7 @@
         <Line id ="Regular spike gen t since" quantity="spikeGenRegularPop[0]/tsince" scale="1ms"  color="#3fffaa" timeScale="1ms"/>
         <Line id ="Poisson spike gen t since" quantity="spikeGenRandomPop[0]/tsince" scale="1ms"  color="#3ff9999" timeScale="1ms"/>
         <Line id ="Spike array t since" quantity="spikeArrPop[0]/tsince" scale="1ms"  color="#3faa99" timeScale="1ms"/>
+        <!--<Line id ="Transient poisson spike gen" quantity="izhPop[10]/transPoissonFiringSyn/tsince" scale="1ms"  color="#000000" timeScale="1ms"/>-->
     </Display>
 
     <Display id="d4" title="Ex16: Izhikevich cell, spiking inputs" timeScale="1ms" xmin="-20" xmax="320" ymin="-61" ymax="-56">
@@ -88,6 +91,8 @@
 	    color="#01A9DB" timeScale="1ms"/>
       <Line id="poisson spike gen" quantity="izhPop[7]/v" scale="1mV"
 	    color="#8000FF" timeScale="1ms"/>
+      <!--<Line id="transient poisson spike gen" quantity="izhPop[10]/v" scale="1mV"
+	    color="#ff00FF" timeScale="1ms"/>-->
     </Display>
 
     <Display id="d5" title="Ex16: Izhikevich cell, poison firing synapse" timeScale="1ms" xmin="-20" xmax="320" ymin="-80" ymax="45">
@@ -97,6 +102,11 @@
         <Line id ="poison firing synapse time since" quantity="izhPop[8]/poissonFiringSyn/tsince" scale="1ms"  color="#3fffaa" timeScale="1ms"/>
     </Display>
 
+    <!--<Display id="d6" title="Ex16: Izhikevich cell, compound input" timeScale="1ms" xmin="-20" xmax="320" ymin="-110" ymax="45">
+        <Line id ="izh9 v (mV)" quantity="izhPop[9]/v" scale="1mV"  color="#ee40FF" timeScale="1ms"/>
+        <Line id ="compound i (nA)" quantity="izhPop[9]/ci0/i" scale="1nA"  color="#333333" timeScale="1ms"/>
+    </Display>-->
+
 
     <!-- <OutputFile id="of1" fileName="results/ex16_g.dat">
         <OutputColumn id="syn1exp_g" quantity="izhPop[8]/poissonFiringSyn/synInput/g" />
@@ -106,11 +116,13 @@
         <OutputColumn id="v0" quantity="izhPop[0]/v" />
         <OutputColumn id="v1" quantity="izhPop[1]/v" />
         <OutputColumn id="v2" quantity="izhPop[2]/v" />
-        <OutputColumn id="v2" quantity="izhPop[3]/v" />
-        <OutputColumn id="v2" quantity="izhPop[4]/v" />
-        <OutputColumn id="v2" quantity="izhPop[5]/v" />
-        <OutputColumn id="v2" quantity="izhPop[6]/v" />
-        <OutputColumn id="v2" quantity="izhPop[7]/v" />
+        <OutputColumn id="v3" quantity="izhPop[3]/v" />
+        <OutputColumn id="v4" quantity="izhPop[4]/v" />
+        <OutputColumn id="v5" quantity="izhPop[5]/v" />
+        <OutputColumn id="v6" quantity="izhPop[6]/v" />
+        <OutputColumn id="v7" quantity="izhPop[7]/v" />
+        <OutputColumn id="v8" quantity="izhPop[8]/v" />
+        <OutputColumn id="v9" quantity="izhPop[9]/v" />
     </OutputFile>
 
 </Simulation>

diff --git a/NeuroML2CoreTypes/Inputs.xml b/NeuroML2CoreTypes/Inputs.xml
@@ -187,13 +187,13 @@
                 <StateAssignment variable="tsince" value="0"/>
                 <StateAssignment variable="isi" value="- averageIsi * log(1 - random(1))"/>
             </OnStart>
-
-            <OnCondition test="tsince .gt. isi">
-                <StateAssignment variable="tsince" value="0"/>
-                <StateAssignment variable="isi" value="- averageIsi * log(1 - random(1))"/>
-                <EventOut port="spike"/>
-            </OnCondition>
 
+            <OnCondition test="tsince .gt. isi">
+                   <StateAssignment variable="tsince" value="0"/>
+                   <StateAssignment variable="isi" value="- averageIsi * log(1 - random(1))"/>
+                   <EventOut port="spike"/>
+              </OnCondition>
+
         </Dynamics>
         <Structure>
             <ChildInstance component="synapse"/>
@@ -208,8 +208,8 @@
 
 
     <ComponentType name="transientPoissonFiringSynapse"
-                   description="Poisson spike generator with delay and duration connected to single synapse providing an input current
-                              .Similar to ComponentType poissonFiringSynapse."
+                   description="Poisson spike generator with delay and duration connected to single synapse providing an input current. 
+                      Similar to ComponentType poissonFiringSynapse."
                    extends="baseVoltageDepPointCurrentSpiking">
 
         <Parameter name="averageRate" dimension="per_time"/>
@@ -298,6 +298,48 @@
 
         </Dynamics>
     </ComponentType>
+
+
+
+    <ComponentType name="compoundInput" extends="basePointCurrent"
+                   description="Generates a current which is the sum of all its child _basePointCurrent_ elements"> 
+
+        <Children name="currents" type="basePointCurrent"/>
+
+        <!--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>
+
+            <DerivedVariable name="i" dimension="current" exposure="i" select="currents[*]/i" reduce="add"/>
+
+            <OnEvent port="in"><!--TODO: remove, see above... -->
+            </OnEvent>
+
+
+        </Dynamics>
+    </ComponentType>
+
+    <ComponentType name="compoundInputDL" extends="basePointCurrentDL"
+                   description="Generates a current which is the sum of all its child _basePointCurrentDL_ elements"> 
+
+        <Children name="currents" type="basePointCurrentDL"/>
+
+        <!--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>
+
+            <DerivedVariable name="I" dimension="none" exposure="I" select="currents[*]/I" reduce="add"/>
+
+            <OnEvent port="in"><!--TODO: remove, see above... -->
+            </OnEvent>
+
+
+        </Dynamics>
+    </ComponentType>
 
 
     <ComponentType name="pulseGeneratorDL" extends="basePointCurrentDL"
@@ -367,6 +409,39 @@
         </Dynamics>
     </ComponentType>
 
+    <ComponentType name="sineGeneratorDL" extends="basePointCurrentDL"
+                   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="none"/>
+        <Parameter name="period" dimension="time"/>
+
+        <EventPort name="in" direction="in"/>
+
+        <Dynamics>
+
+            <StateVariable name="I" exposure="I" dimension="none"/>
+
+            <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.">

diff --git a/Schemas/NeuroML2/NeuroML_v2beta4.xsd b/Schemas/NeuroML2/NeuroML_v2beta4.xsd
@@ -531,8 +531,16 @@
                     minOccurs="0" maxOccurs="unbounded"/>
             <xs:element name="sineGenerator" type="SineGenerator"
                     minOccurs="0" maxOccurs="unbounded"/>
+            <xs:element name="sineGeneratorDL" type="SineGeneratorDL"
+                    minOccurs="0" maxOccurs="unbounded"/>
             <xs:element name="rampGenerator" type="RampGenerator"
                     minOccurs="0" maxOccurs="unbounded"/>
+            <xs:element name="rampGeneratorDL" type="RampGeneratorDL"
+                    minOccurs="0" maxOccurs="unbounded"/>
+            <xs:element name="compoundInput" type="CompoundInput"
+                    minOccurs="0" maxOccurs="unbounded"/>
+            <xs:element name="compoundInputDL" type="CompoundInputDL"
+                    minOccurs="0" maxOccurs="unbounded"/>
             <xs:element name="voltageClamp" type="VoltageClamp"
                     minOccurs="0" maxOccurs="unbounded"/>
             <xs:element name="spikeArray" type="SpikeArray" minOccurs="0"
@@ -545,6 +553,8 @@
                     minOccurs="0" maxOccurs="unbounded"/>
             <xs:element name="poissonFiringSynapse" type="PoissonFiringSynapse"
                     minOccurs="0" maxOccurs="unbounded"/>
+            <xs:element name="transientPoissonFiringSynapse" type="TransientPoissonFiringSynapse"
+                    minOccurs="0" maxOccurs="unbounded"/>
         </xs:sequence>
     </xs:group>
 
@@ -2025,6 +2035,24 @@
         </xs:complexContent>
     </xs:complexType>
 
+    <xs:complexType name="SineGeneratorDL">
+        <xs:complexContent>
+            <xs:extension base="Standalone">
+                <xs:attribute name="delay" type="Nml2Quantity_time"
+                              use="required"/>
+                <xs:attribute name="phase" type="Nml2Quantity_none"
+                              use="required"/>
+                <xs:attribute name="duration" type="Nml2Quantity_time"
+                              use="required"/>
+                <xs:attribute name="amplitude"
+                              type="Nml2Quantity_none"
+                              use="required"/>
+                <xs:attribute name="period" type="Nml2Quantity_time"
+                              use="required"/>
+            </xs:extension>
+        </xs:complexContent>
+    </xs:complexType>
+
 
     <xs:complexType name="RampGenerator">
         <xs:complexContent>
@@ -2046,6 +2074,58 @@
         </xs:complexContent>
     </xs:complexType>
 
+    <xs:complexType name="RampGeneratorDL">
+        <xs:complexContent>
+            <xs:extension base="Standalone">
+                <xs:attribute name="delay" type="Nml2Quantity_time"
+                              use="required"/>
+                <xs:attribute name="duration" type="Nml2Quantity_time"
+                              use="required"/>
+                <xs:attribute name="startAmplitude"
+                              type="Nml2Quantity_none"
+                              use="required"/>
+                <xs:attribute name="finishAmplitude"
+                              type="Nml2Quantity_none"
+                              use="required"/>
+                <xs:attribute name="baselineAmplitude"
+                              type="Nml2Quantity_none"
+                              use="required"/>
+            </xs:extension>
+        </xs:complexContent>
+    </xs:complexType>
+
+
+    <xs:complexType name="CompoundInput">
+        <xs:complexContent>
+            <xs:extension base="Standalone">
+                <xs:sequence>
+                    <xs:element name="pulseGenerator" type="PulseGenerator"
+                                minOccurs="0" maxOccurs="unbounded"/>
+                    <xs:element name="sineGenerator" type="SineGenerator"
+                        minOccurs="0" maxOccurs="unbounded"/>
+                    <xs:element name="rampGenerator" type="RampGenerator"
+                        minOccurs="0" maxOccurs="unbounded"/>
+                </xs:sequence>
+            </xs:extension>
+        </xs:complexContent>
+    </xs:complexType>
+
+
+    <xs:complexType name="CompoundInputDL">
+        <xs:complexContent>
+            <xs:extension base="Standalone">
+                <xs:sequence>
+                    <xs:element name="pulseGeneratorDL" type="PulseGeneratorDL"
+                                minOccurs="0" maxOccurs="unbounded"/>
+                    <xs:element name="sineGeneratorDL" type="SineGeneratorDL"
+                        minOccurs="0" maxOccurs="unbounded"/>
+                    <xs:element name="rampGeneratorDL" type="RampGeneratorDL"
+                        minOccurs="0" maxOccurs="unbounded"/>
+                </xs:sequence>
+            </xs:extension>
+        </xs:complexContent>
+    </xs:complexType>
+
 
     <xs:complexType name="VoltageClamp">
         <xs:complexContent>

diff --git a/examples/NML2_Inputs.nml b/examples/NML2_Inputs.nml
@@ -8,12 +8,19 @@
     <!-- Some examples of the currently supported input types -->
 
     <expTwoSynapse id="synInput" gbase="8nS" erev="20mV" tauRise="1ms" tauDecay="5ms"/><!-- Will be used below... -->
+    <expTwoSynapse id="synInputFast" gbase="1nS" erev="20mV" tauRise="0.2ms" tauDecay="1ms"/><!-- Will be used below... -->
 
     <pulseGenerator id="pulseGen0" delay="50ms" duration="200ms" amplitude="1 nA" />
 
     <sineGenerator id="sg0" phase="0" delay="50ms" duration="200ms" amplitude="1.4nA" period="50ms"/>
 
     <rampGenerator id="rg0" delay="50ms" duration="200ms" startAmplitude="0.5nA" finishAmplitude="4nA" baselineAmplitude="0nA"/>
+
+    <compoundInput id="ci0">
+        <pulseGenerator id="pg1" delay="50ms" duration="200ms" amplitude="1 nA" />
+        <pulseGenerator id="pg2" delay="100ms" duration="100ms" amplitude="1 nA" />
+        <sineGenerator id="sg0" phase="0" delay="125ms" duration="50ms" amplitude="1nA" period="25ms"/>
+    </compoundInput>
 
     <voltageClamp id="vClamp0" delay="50ms" duration="200ms"
               targetVoltage="-50mV" simpleSeriesResistance="1e6ohm"/>
@@ -34,5 +41,7 @@
     <spikeGeneratorPoisson id="spikeGenPoisson" averageRate="50 Hz"/>
 
     <poissonFiringSynapse id="poissonFiringSyn" averageRate="10 Hz" synapse="synInput" spikeTarget="./synInput"/>
+
+    <transientPoissonFiringSynapse id="transPoissonFiringSyn" delay="50ms" duration="50ms" averageRate="300 Hz" synapse="synInputFast" spikeTarget="./synInputFast"/>
 
 </neuroml>