Merge branch 'test_neuron' into test_pg

openworm · Feb 27, 2025 · 79a9e0a · 79a9e0a
2 parents 8264495 + b2e73bb
commit 79a9e0a
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Showing 7 changed files with 337 additions and 47 deletions.
diff --git a/NeuroML/AIY.cell.nml b/NeuroML/AIY.cell.nml
@@ -1,6 +1,10 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="AIY">
     <notes>A cell from Nicoletti et al. 2024</notes>
     <include href="leak.channel.nml"/>
+    <include href="egl19.channel.nml"/>  
+    <!-- <include href="kqt1.channel.nml"/> -->
+    <!-- <include href="slo1iso.channel.nml"/> --> 
+    <include href="CaDynamics.nml"/>
     <cell id="AIY">
         <notes>AIY cell from Nicoletti et al. 2024</notes>
         <morphology id="morphology">
@@ -19,12 +23,17 @@
         </morphology>
         <biophysicalProperties id="biophys">
             <membraneProperties>
-                <channelDensity id="leak_chans" ionChannel="leak" condDensity="0.00021247533768401888 S_per_cm2" erev="-89.57mV" ion="non_specific"/>
+                <channelDensity id="leak_chans" ionChannel="leak" condDensity="2.12475338e-04 S_per_cm2" erev="-89.57mV" ion="non_specific"/>
+                <channelDensityNernst id="egl19_chans" ionChannel="egl19" condDensity="1.51768098e-04 S_per_cm2" ion="ca"/> 
+             <!--   <channelDensity id="kqt1_chans" ionChannel="kqt1" condDensity="3.03536197e-04 S_per_cm2" erev="-80mV"  ion="k"/> -->
+              <!--  <channelDensity id="slo1iso_chans" ionChannel="slo1iso" condDensity="1.51768098e-03 S_per_cm2" erev="-80mV"  ion="k"/> -->
+
                 <spikeThresh value="0mV"/>
                 <specificCapacitance value="1.6 uF_per_cm2"/>
                 <initMembPotential value="-55.2mV"/>
             </membraneProperties>
             <intracellularProperties>
+                <species id="ca" concentrationModel="CaDynamics_VA5" ion="ca" initialConcentration=".0001 mM" initialExtConcentration="2 mM"/>
                 <resistivity value="0.1 kohm_cm"/>
             </intracellularProperties>
         </biophysicalProperties>

diff --git a/NeuroML/AIY_comparison.ipynb b/NeuroML/AIY_comparison.ipynb
diff --git a/NeuroML/LEMS_Sim_IClamp_VB6.xml b/NeuroML/LEMS_Sim_IClamp_VB6.xml
@@ -19,6 +19,33 @@
     <Include file="VB6.cell.nml"/>
 
     <Simulation id="Sim_IClamp_VB6" length="11000.0ms" step="0.025ms" target="IClamp_VB6" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
+
+      <!--  <Display id="pop_VB6_0_biophys/membraneProperties/egl19_chans/egl19/m/q" title="Plots of pop_VB6_0_biophys/membraneProperties/egl19_chans/egl19/m/q" timeScale="1ms" xmin="-240.0" xmax="2640.0" ymin="-1" ymax="1">
+            <Line id="pop_VB6_0_VB6_biophys_membraneProperties_egl19_chans_VB6_egl19_m_q" quantity="pop_VB6/0/VB6/biophys/membraneProperties/egl19_chans/egl19/m/q" scale="1" color="#0534e4" timeScale="1ms"/>
+            <Line id="pop_VB6_0_VB6_biophys_membraneProperties_slo1egl19_chans_VB6_slo1egl19_m_q" quantity="pop_VB6/0/VB6/biophys/membraneProperties/slo1egl19_chans/slo1egl19/slo1_m_inf_instance/q" scale="1" color="#0534e4" timeScale="1ms"/>
+        </Display> 
+        
+
+        <Display id="pop_VB6_0_biophys/membraneProperties/egl19_chans/gDensity" title="Plots of pop_VB6_0_biophys/membraneProperties/egl19_chans/gDensity" timeScale="1ms" xmin="-240.0" xmax="2640.0" ymin="-1" ymax="1">
+            <Line id="pop_VB6_0_VB6_biophys_membraneProperties_egl19_chans_gDensity" quantity="pop_VB6/0/VB6/biophys/membraneProperties/egl19_chans/gDensity" scale="1" color="#98e752" timeScale="1ms"/>
+        </Display>
+
+        <Display id="pop_VB6_0_biophys/membraneProperties/egl19_chans/iDensity" title="Plots of pop_VB6_0_biophys/membraneProperties/egl19_chans/iDensity" timeScale="1ms" xmin="-240.0" xmax="2640.0" ymin="-1" ymax="1">
+            <Line id="pop_VB6_0_VB6_biophys_membraneProperties_egl19_chans_iDensity" quantity="pop_VB6/0/VB6/biophys/membraneProperties/egl19_chans/iDensity" scale="1" color="#bca074" timeScale="1ms"/>
+        </Display>
+
+
+
+        <Display id="pop_VB6_0_biophys/membraneProperties/slo1egl19_chans/gDensity" title="Plots of pop_VB6_0_biophys/membraneProperties/slo1egl19_chans/gDensity" timeScale="1ms" xmin="-240.0" xmax="2640.0" ymin="-1" ymax="1">
+            <Line id="pop_VB6_0_VB6_biophys_membraneProperties_slo1egl19_chans_gDensity" quantity="pop_VB6/0/VB6/biophys/membraneProperties/slo1egl19_chans/gDensity" scale="1" color="#98e752" timeScale="1ms"/>
+        </Display>
+
+        <Display id="pop_VB6_0_biophys/membraneProperties/slo1egl19_chans/iDensity" title="Plots of pop_VB6_0_biophys/membraneProperties/slo1egl19_chans/iDensity" timeScale="1ms" xmin="-240.0" xmax="2640.0" ymin="-1" ymax="1">
+            <Line id="pop_VB6_0_VB6_biophys_membraneProperties_slo1egl19_chans_iDensity" quantity="pop_VB6/0/VB6/biophys/membraneProperties/slo1egl19_chans/iDensity" scale="1" color="#bca074" timeScale="1ms"/>
+        </Display>
+
+-->
+       <!--
         <Display id="pop_VB6_0_caConc" title="Plots of pop_VB6_0_caConc" timeScale="1ms" xmin="-1100.0" xmax="12100.000000000002" ymin="-1" ymax="1">
             <Line id="pop_VB6_0_VB6_caConc" quantity="pop_VB6/0/VB6/caConc" scale="1" color="#d54f33" timeScale="1ms"/>
         </Display>
@@ -62,7 +89,7 @@
         <Display id="pop_VB6_9_caConc" title="Plots of pop_VB6_9_caConc" timeScale="1ms" xmin="-1100.0" xmax="12100.000000000002" ymin="-1" ymax="1">
             <Line id="pop_VB6_9_VB6_caConc" quantity="pop_VB6/9/VB6/caConc" scale="1" color="#dda9d2" timeScale="1ms"/>
         </Display> 
-
+        -->
         <Display id="pop_VB6_v" title="Plots of pop_VB6_v" timeScale="1ms" xmin="-1100.0" xmax="12100.000000000002" ymin="-80" ymax="40">
             <Line id="pop_VB6_0_VB6_v" quantity="pop_VB6/0/VB6/v" scale="1mV" color="#85ad96" timeScale="1ms"/>
             <Line id="pop_VB6_1_VB6_v" quantity="pop_VB6/1/VB6/v" scale="1mV" color="#59438f" timeScale="1ms"/>
@@ -90,7 +117,7 @@
             <OutputColumn id="pop_VB6_9_VB6_v" quantity="pop_VB6/9/VB6/v"/>
             <OutputColumn id="pop_VB6_10_VB6_v" quantity="pop_VB6/10/VB6/v"/>
         </OutputFile>
-
+        <!-- 
         <OutputFile id="pop_VB6_0_caConc_dat" fileName="pop_VB6_0.caConc.dat">
             <OutputColumn id="pop_VB6_0_VB6_caConc" quantity="pop_VB6/0/VB6/caConc"/>
         </OutputFile>
@@ -134,7 +161,7 @@
         <OutputFile id="pop_VB6_9_caConc_dat" fileName="pop_VB6_9.caConc.dat">
             <OutputColumn id="pop_VB6_9_VB6_caConc" quantity="pop_VB6/9/VB6/caConc"/>
         </OutputFile>
-
+    --> 
     </Simulation>
 
 </Lems>
diff --git a/NeuroML/VB6.cell.nml b/NeuroML/VB6.cell.nml
@@ -4,7 +4,7 @@
     <include href="leak.channel.nml"/>
 <!--    <include href="unc2.channel.nml"/> -->
 <!--    <include href="slo1unc2.channel.nml"/>   -->
-    <include href="slo1egl19.channel.nml"/> 
+<!--    <include href="slo1egl19.channel.nml"/> -->
  <!--   <include href="slo2egl19.channel.nml"/>  -->
   <!--  <include href="slo2iso.channel.nml"/>  -->
     <include href="CaDynamics.nml"/>
@@ -27,10 +27,10 @@
         <biophysicalProperties id="biophys">
             <membraneProperties>
                 <channelDensity id="leak_chans" ionChannel="leak" condDensity="2.4778896e-05 S_per_cm2" erev="-52mV" ion="non_specific"/>
-                <channelDensity id="slo1egl19_chans" ionChannel="slo1egl19" condDensity="3.81213785e-05 S_per_cm2" erev="-80mV"   ion="k"/>
                 <channelDensityNernst id="egl19_chans" ionChannel="egl19" condDensity="1.90606892e-05 S_per_cm2" ion="ca"/> 
              <!--    <channelDensityNernst id="unc2_chans" ionChannel="unc2" condDensity="1.90606892e-05 S_per_cm2"  ion="ca"/> -->
             <!--     <channelDensity id="slo1unc2_chans" ionChannel="slo1unc2" condDensity="1.90606892e-04 S_per_cm2" erev ="-80mV" ion="k"/>  -->
+            <!--    <channelDensity id="slo1egl19_chans" ionChannel="slo1egl19" condDensity="3.81213785e-05 S_per_cm2" erev="-80mV"   ion="k"/> -->
             <!--    <channelDensity id="slo2egl19_chans" ionChannel="slo2egl19" condDensity="7.70613922e-04 S_per_cm2" erev="-80mV"   ion="k"/> -->
             <!--    <channelDensity id="slo2iso_chans" ionChannel="slo2iso" condDensity="7.70613922e-04 S_per_cm2" erev="-80mV"  ion="k"/> -->
 

diff --git a/NeuroML/VB6_comparison.ipynb b/NeuroML/VB6_comparison.ipynb
diff --git a/NeuroML/slo1egl19.channel.nml b/NeuroML/slo1egl19.channel.nml
@@ -2,12 +2,16 @@
     <notes>An ion channel from cell AIY from Nicoletti et al. 2024</notes>
 
     <ionChannelHH id="slo1egl19" species="k" conductance="10 pS">
-
+
+
+
         <gate id="m" instances="1" type="gateHHtauInf">
             <timeCourse type="slo1_m_tau"/>
             <steadyState type="slo1_m_inf"/>
         </gate>
 
+
+
         <gate id="h" instances="1" type="gateHHtauInf">
             <timeCourse type="slo1_h_tau"/>
             <steadyState type="slo1_h_inf"/>

diff --git a/NeuroML/slo2unc2.channel.nml b/NeuroML/slo2unc2.channel.nml
@@ -0,0 +1,144 @@
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="AWCon_slo2">
+    <notes>An ion channel from cell AWCon from Nicoletti et al. 2024</notes>
+    <ionChannelHH id="slo2unc2" species="k" conductance="10pS">
+
+        <gate id="m" instances="1" type="gateHHtauInf">
+            <timeCourse type="slo2_m_tau"/>
+            <steadyState type="slo2_m_inf"/>
+        </gate>
+
+    </ionChannelHH>
+    <ComponentType name="slo2_m_inf" extends="baseVoltageDepVariable">
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+        <Constant name="bkg" dimension="none" value="0.05"/>
+        <Constant name="gbar" dimension="none" value="0.11"/>
+        <Constant name="wom" dimension="none" value="0.896395"/>
+        <Constant name="wyx1" dimension="none" value="0.019405"/>
+        <Constant name="kyx" dimension="none" value="3294.553404"/>
+        <Constant name="nyx" dimension="none" value="0.0000100"/>
+        <Constant name="wop" dimension="none" value="0.026719"/>
+        <Constant name="wxy" dimension="none" value="-0.024123"/>
+        <Constant name="kxy" dimension="none" value="93.449423"/>
+        <Constant name="nxy" dimension="none" value="1.835067"/>
+        <Constant name="r" dimension="none" value="13e-9"/>
+        <Constant name="d" dimension="none" value="250e-12"/>
+        <Constant name="kb" dimension="none" value="500e6"/>
+        <Constant name="b" dimension="none" value="30e-6"/>
+        <Constant name="gsc" dimension="none" value="40e-12"/>
+        <Constant name="pi" dimension="none" value="3.14"/>
+        <Constant name="va_unc2" dimension="none" value="-12.17"/>
+        <Constant name="ka_unc2" dimension="none" value="3.97"/>
+        <Constant name="vi_unc2" dimension="none" value="-52.47"/>
+        <Constant name="ki_unc2" dimension="none" value="5.6"/>
+        <Constant name="stm2" dimension="none" value="25"/>
+        <Constant name="sth2" dimension="none" value="25"/>
+        <Constant name="p1tmunc2" dimension="none" value="1.4969"/>
+        <Constant name="p2tmunc2" dimension="none" value="-8.1761"/>
+        <Constant name="p3tmunc2" dimension="none" value="9.0753"/>
+        <Constant name="p4tmunc2" dimension="none" value="15.3456"/>
+        <Constant name="p5tmunc2" dimension="none" value="0.1029"/>
+        <Constant name="p1thunc2" dimension="none" value="83.8037"/>
+        <Constant name="p2thunc2" dimension="none" value="52.8997"/>
+        <Constant name="p3thunc2" dimension="none" value="3.4557"/>
+        <Constant name="p4thunc2" dimension="none" value="72.0995"/>
+        <Constant name="p5thunc2" dimension="none" value="23.9009"/>
+        <Constant name="p6thunc2" dimension="none" value="3.5903"/>
+        <Constant name="shifthunc2" dimension="none" value="30"/>
+        <Constant name="shiftmunc2" dimension="none" value="30"/>
+        <Constant name="consthunc2" dimension="none" value="1.7"/>
+        <Constant name="constmunc2" dimension="none" value="3"/>
+        <Constant name="func2" dimension="none" value="1"/>
+        <Constant name="f2unc2" dimension="none" value="1"/>
+        <Constant name="fp3" dimension="none" value="1"/>
+        <Constant name="fp4" dimension="none" value="1"/>
+        <Constant name="fp5" dimension="none" value="1"/>
+        <Constant name="eca" dimension="none" value="60.0"/>
+        <Constant name="F" dimension="none" value="96485.0"/>
+
+
+        <Dynamics>
+            <StateVariable name="munc2_unc2" dimension="none"/>
+            <DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
+            <DerivedVariable name = "minf_unc2" dimension="none" value="1 / (1 + exp(-(V - va_unc2 + 25) / ka_unc2))"/>
+
+            <DerivedVariable name="tm_unc2" dimension="none" 
+                value ="(p1tmunc2/(exp(-(V-p2tmunc2+30)/(p3tmunc2))+exp((V-p2tmunc2+30)/(p4tmunc2)))+p5tmunc2)*3"/>
+            <DerivedVariable name="cao_nano" dimension="none" value="(((abs(gsc*(V - eca))/(8*pi*F*d*r))*exp(-r/(sqrt(d/(b*kb)))))*1e6*1e-3) + bkg"/>
+            <DerivedVariable name = "kop" dimension="none" value="wop*exp(-wxy*V)*(1/(1+((kxy/cao_nano)^nxy)))"/>
+            <DerivedVariable name = "alpha1" dimension="none" value="minf_unc2/tm_unc2"/>
+            <DerivedVariable name = "beta1" dimension="none" value="(1/tm_unc2)-alpha1"/>
+            <DerivedVariable name = "kcm" dimension="none" value="wom*exp(-wyx1*V)*(1/(1+((bkg/kyx)^nyx)))"/>
+            <DerivedVariable name = "kom" dimension="none" value="wom*exp(-wyx1*V)*(1/(1+((cao_nano/kyx)^nyx)))"/>
+            <DerivedVariable name="x" dimension="none" exposure="x"
+                value="(munc2_unc2*kop*(alpha1+beta1+kcm))/((kop+kom)*(kcm+alpha1)+(beta1*kcm))"/>
+
+            <TimeDerivative variable="munc2_unc2" value="((-munc2_unc2 + minf_unc2)/tm_unc2) / TIME_SCALE"/>
+
+
+        </Dynamics>
+    </ComponentType>
+    <ComponentType name="slo2_m_tau" extends="baseVoltageDepTime">
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+        <Constant name="bkg" dimension="none" value="0.05"/>
+        <Constant name="gbar" dimension="none" value="0.11"/>
+        <Constant name="wom" dimension="none" value="0.896395"/>
+        <Constant name="wyx1" dimension="none" value="0.019405"/>
+        <Constant name="kyx" dimension="none" value="3294.553404"/>
+        <Constant name="nyx" dimension="none" value="0.0000100"/>
+        <Constant name="wop" dimension="none" value="0.026719"/>
+        <Constant name="wxy" dimension="none" value="-0.024123"/>
+        <Constant name="kxy" dimension="none" value="93.449423"/>
+        <Constant name="nxy" dimension="none" value="1.835067"/>
+        <Constant name="r" dimension="none" value="13e-9"/>
+        <Constant name="d" dimension="none" value="250e-12"/>
+        <Constant name="kb" dimension="none" value="500e6"/>
+        <Constant name="b" dimension="none" value="30e-6"/>
+        <Constant name="gsc" dimension="none" value="40e-12"/>
+        <Constant name="pi" dimension="none" value="3.14"/>
+        <Constant name="va_unc2" dimension="none" value="-12.17"/>
+        <Constant name="ka_unc2" dimension="none" value="3.97"/>
+        <Constant name="vi_unc2" dimension="none" value="-52.47"/>
+        <Constant name="ki_unc2" dimension="none" value="5.6"/>
+        <Constant name="stm2" dimension="none" value="25"/>
+        <Constant name="sth2" dimension="none" value="25"/>
+        <Constant name="p1tmunc2" dimension="none" value="1.4969"/>
+        <Constant name="p2tmunc2" dimension="none" value="-8.1761"/>
+        <Constant name="p3tmunc2" dimension="none" value="9.0753"/>
+        <Constant name="p4tmunc2" dimension="none" value="15.3456"/>
+        <Constant name="p5tmunc2" dimension="none" value="0.1029"/>
+        <Constant name="p1thunc2" dimension="none" value="83.8037"/>
+        <Constant name="p2thunc2" dimension="none" value="52.8997"/>
+        <Constant name="p3thunc2" dimension="none" value="3.4557"/>
+        <Constant name="p4thunc2" dimension="none" value="72.0995"/>
+        <Constant name="p5thunc2" dimension="none" value="23.9009"/>
+        <Constant name="p6thunc2" dimension="none" value="3.5903"/>
+        <Constant name="shifthunc2" dimension="none" value="30"/>
+        <Constant name="shiftmunc2" dimension="none" value="30"/>
+        <Constant name="consthunc2" dimension="none" value="1.7"/>
+        <Constant name="constmunc2" dimension="none" value="3"/>
+        <Constant name="func2" dimension="none" value="1"/>
+        <Constant name="f2unc2" dimension="none" value="1"/>
+        <Constant name="fp3" dimension="none" value="1"/>
+        <Constant name="fp4" dimension="none" value="1"/>
+        <Constant name="fp5" dimension="none" value="1"/>
+        <Constant name="eca" dimension="none" value="60.0"/>
+        <Constant name="F" dimension="none" value="96485.0"/>
+
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
+             <DerivedVariable name="cao_nano" dimension="none" value="(((abs(gsc*(V - eca))/(8*pi*F*d*r))*exp(-r/(sqrt(d/(b*kb)))))*1e6*1e-3) + bkg"/>
+
+            <DerivedVariable name = "minf_unc2" dimension="none" value="1 / (1 + exp(-(V - va_unc2 + 25) / ka_unc2))"/>
+            <DerivedVariable name="tm_unc2" dimension="none" 
+                value ="(p1tmunc2/(exp(-(V-p2tmunc2+shiftmunc2)/(p3tmunc2))+exp((V-p2tmunc2+shiftmunc2)/(p4tmunc2)))+p5tmunc2)*constmunc2"/>
+            <DerivedVariable name = "kop" dimension="none" value="wop*exp(-wxy*V)*(1/(1+((kxy/cao_nano)^nxy)))"/>
+            <DerivedVariable name = "alpha1" dimension="none" value="minf_unc2/tm_unc2"/>
+            <DerivedVariable name = "beta1" dimension="none" value="(1/tm_unc2)-alpha1"/>
+            <DerivedVariable name = "kcm" dimension="none" value="wom*exp(-wyx1*V)*(1/(1+((bkg/kyx)^nyx)))"/>
+            <DerivedVariable name = "kom" dimension="none" value="wom*exp(-wyx1*V)*(1/(1+((cao_nano/kyx)^nyx)))"/>
+            <DerivedVariable name="t" dimension="time" exposure="t" value="((alpha1+beta1+kcm)/((kop)+kom)*(kcm+alpha1)+(beta1*kcm))* TIME_SCALE"/>
+        </Dynamics>
+    </ComponentType>
+</neuroml>