2 more channels added

openworm · Apr 22, 2024 · 113b1a1 · 113b1a1
1 parent 9faa191
commit 113b1a1
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Showing 16 changed files with 333 additions and 45 deletions.
diff --git a/.gitignore b/.gitignore
@@ -14,3 +14,5 @@ report.*.txt
 /NeuroML2/Test_RMD.ode
 /NeuroML2/report.txt
 /RMD.model.xml
+/NeuroML2/LEMS_Test_RMD_cca.xml
+/NeuroML2/LEMS_Test_RMD_shak.xml
diff --git a/NeuroML2/AWCon.cell.nml b/NeuroML2/AWCon.cell.nml
@@ -1,7 +1,9 @@
 <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.xsd" id="AWCon">
     <notes>A cell from Nicoletti et al. 2019</notes>
     <include href="AWCon_leak.channel.nml"/>
+    <include href="AWCon_shak.channel.nml"/>
     <include href="AWCon_kir.channel.nml"/>
+    <include href="AWCon_cca.channel.nml"/>
     <cell id="AWCon">
         <notes>AWCon cell from Nicoletti et al. 2019</notes>
         <morphology id="morphology">
@@ -21,7 +23,9 @@
         <biophysicalProperties id="biophys">
             <membraneProperties>
                 <channelDensity id="leak_chans" ionChannel="AWCon_leak" condDensity="0.27 S_per_m2" erev="-80.0mV" ion="non_specific"/>
+                <channelDensity id="shak_chans" ionChannel="AWCon_shak" condDensity="0.1 S_per_m2" erev="-80.0mV" ion="k"/>
                 <channelDensity id="kir_chans" ionChannel="AWCon_kir" condDensity="0.65 S_per_m2" erev="-80.0mV" ion="k"/>
+                <channelDensity id="cca_chans" ionChannel="AWCon_cca" condDensity="0.7 S_per_m2" erev="60.0mV" ion="ca"/>
                 <spikeThresh value="0mV"/>
                 <specificCapacitance value="0.0031000000000000003 F_per_m2"/>
                 <initMembPotential value="-70mV"/>

diff --git a/NeuroML2/AWCon_cca.channel.nml b/NeuroML2/AWCon_cca.channel.nml
@@ -0,0 +1,66 @@
+<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.xsd" id="AWCon_cca">
+    <notes>An ion channel from cell AWCon from Nicoletti et al. 2019</notes>
+    <ionChannelHH id="AWCon_cca" species="ca" conductance="10pS">
+        <notes>AWCon_cca channel from Nicoletti et al. 2019</notes>
+        <gateHHtauInf id="m" instances="2">
+            <timeCourse type="cca_m_tau"/>
+            <steadyState type="cca_m_inf"/>
+        </gateHHtauInf>
+        <gateHHtauInf id="h" instances="1">
+            <timeCourse type="cca_h_tau"/>
+            <steadyState type="cca_h_inf"/>
+        </gateHHtauInf>
+    </ionChannelHH>
+    <ComponentType name="cca_m_inf" extends="baseVoltageDepVariable">
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+        <Constant name="va_cca1" dimension="none" value="-42.65"/>
+        <Constant name="ka_cca1" dimension="none" value="1.7"/>
+        <Constant name="sscca1" dimension="none" value="15.0"/>
+        <Constant name="fcca" dimension="none" value="1.4"/>
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
+            <DerivedVariable name="x" dimension="none" exposure="x" value="1/(exp((1/(fcca*ka_cca1))*(-V - sscca1 + va_cca1)) + 1)"/>
+        </Dynamics>
+    </ComponentType>
+    <ComponentType name="cca_m_tau" extends="baseVoltageDepTime">
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+        <Constant name="stmcca1" dimension="none" value="30.0"/>
+        <Constant name="constmcca1" dimension="none" value="0.5"/>
+        <Constant name="p1tmcca1" dimension="none" value="40.0"/>
+        <Constant name="p2tmcca1" dimension="none" value="-62.5393"/>
+        <Constant name="p3tmcca1" dimension="none" value="-12.4758"/>
+        <Constant name="p4tmcca1" dimension="none" value="0.6947"/>
+        <Constant name="f3ca" dimension="none" value="1.7"/>
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
+            <DerivedVariable name="t" dimension="time" exposure="t" value="(constmcca1*(p1tmcca1/(exp((1/(f3ca*p3tmcca1))*(-V + p2tmcca1 - stmcca1)) + 1) + p4tmcca1))/1000"/>
+        </Dynamics>
+    </ComponentType>
+    <ComponentType name="cca_h_inf" extends="baseVoltageDepVariable">
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+        <Constant name="sshcca1" dimension="none" value="15.0"/>
+        <Constant name="f2cca1" dimension="none" value="1.15"/>
+        <Constant name="vi_cca1" dimension="none" value="-58.0"/>
+        <Constant name="ki_cca1" dimension="none" value="7.0"/>
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
+            <DerivedVariable name="x" dimension="none" exposure="x" value="1/(exp((1/(f2cca1*ki_cca1))*(V + sshcca1 - vi_cca1)) + 1)"/>
+        </Dynamics>
+    </ComponentType>
+    <ComponentType name="cca_h_tau" extends="baseVoltageDepTime">
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+        <Constant name="sthcca1" dimension="none" value="15.0"/>
+        <Constant name="consthcca1" dimension="none" value="0.08"/>
+        <Constant name="p1thcca1" dimension="none" value="280.0"/>
+        <Constant name="p2thcca1" dimension="none" value="-60.7312"/>
+        <Constant name="p3thcca1" dimension="none" value="8.5224"/>
+        <Constant name="p4thcca1" dimension="none" value="19.7456"/>
+        <Constant name="f4ca" dimension="none" value="1.1"/>
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
+            <DerivedVariable name="t" dimension="time" exposure="t" value="(consthcca1*(p1thcca1/(exp((1/(f4ca*p3thcca1))*(V - p2thcca1 + sthcca1)) + 1) + p4thcca1))/1000"/>
+        </Dynamics>
+    </ComponentType>
+</neuroml>
diff --git a/NeuroML2/AWCon_kir.channel.nml b/NeuroML2/AWCon_kir.channel.nml
@@ -11,12 +11,6 @@
         <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
         <Constant name="va_kir" dimension="none" value="-52.0"/>
         <Constant name="ka_kir" dimension="none" value="13.0"/>
-        <Constant name="p1tmkir" dimension="none" value="17.0752"/>
-        <Constant name="p2tmkir" dimension="none" value="-17.8258"/>
-        <Constant name="p3tmkir" dimension="none" value="20.3154"/>
-        <Constant name="p4tmkir" dimension="none" value="-43.4414"/>
-        <Constant name="p5tmkir" dimension="none" value="11.1691"/>
-        <Constant name="p6tmkir" dimension="none" value="3.8329"/>
         <Dynamics>
             <DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
             <DerivedVariable name="x" dimension="none" exposure="x" value="1/(exp((V - va_kir + 30)/ka_kir) + 1)"/>
@@ -25,8 +19,6 @@
     <ComponentType name="kir_m_tau" extends="baseVoltageDepTime">
         <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
         <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
-        <Constant name="va_kir" dimension="none" value="-52.0"/>
-        <Constant name="ka_kir" dimension="none" value="13.0"/>
         <Constant name="p1tmkir" dimension="none" value="17.0752"/>
         <Constant name="p2tmkir" dimension="none" value="-17.8258"/>
         <Constant name="p3tmkir" dimension="none" value="20.3154"/>
@@ -35,7 +27,7 @@
         <Constant name="p6tmkir" dimension="none" value="3.8329"/>
         <Dynamics>
             <DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
-            <DerivedVariable name="t" dimension="time" exposure="t" value="p1tmkir/(exp((-V + p2tmkir)/p3tmkir) + exp((V - p4tmkir)/p5tmkir)) + p6tmkir"/>
+            <DerivedVariable name="t" dimension="time" exposure="t" value="(p1tmkir/(exp((-V + p2tmkir)/p3tmkir) + exp((V - p4tmkir)/p5tmkir)) + p6tmkir)/1000"/>
         </Dynamics>
     </ComponentType>
 </neuroml>
diff --git a/NeuroML2/AWCon_shak.channel.nml b/NeuroML2/AWCon_shak.channel.nml
@@ -0,0 +1,57 @@
+<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.xsd" id="AWCon_shak">
+    <notes>An ion channel from cell AWCon from Nicoletti et al. 2019</notes>
+    <ionChannelHH id="AWCon_shak" species="k" conductance="10pS">
+        <notes>AWCon_shak channel from Nicoletti et al. 2019</notes>
+        <gateHHtauInf id="m" instances="1">
+            <timeCourse type="shak_m_tau"/>
+            <steadyState type="shak_m_inf"/>
+        </gateHHtauInf>
+        <gateHHtauInf id="h" instances="1">
+            <timeCourse type="shak_h_tau"/>
+            <steadyState type="shak_h_inf"/>
+        </gateHHtauInf>
+    </ionChannelHH>
+    <ComponentType name="shak_m_inf" extends="baseVoltageDepVariable">
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+        <Constant name="vashak" dimension="none" value="20.4"/>
+        <Constant name="kashak" dimension="none" value="7.7"/>
+        <Constant name="shiftV05" dimension="none" value="0.0"/>
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
+            <DerivedVariable name="x" dimension="none" exposure="x" value="1/(exp((-V - shiftV05 + vashak)/kashak) + 1)"/>
+        </Dynamics>
+    </ComponentType>
+    <ComponentType name="shak_m_tau" extends="baseVoltageDepTime">
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+        <Constant name="ptmshak1" dimension="none" value="26.571450568169027"/>
+        <Constant name="ptmshak2" dimension="none" value="-33.74161180071613"/>
+        <Constant name="ptmshak3" dimension="none" value="15.757936311607475"/>
+        <Constant name="ptmshak4" dimension="none" value="15.364937728953288"/>
+        <Constant name="ptmshak5" dimension="none" value="1.990037272604829"/>
+        <Constant name="shiftV05" dimension="none" value="0.0"/>
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
+            <DerivedVariable name="t" dimension="time" exposure="t" value="(ptmshak1/(exp((V - (ptmshak2 + shiftV05))/ptmshak3) + exp((-V + ptmshak2 + shiftV05)/ptmshak4)) + ptmshak5)/1000"/>
+        </Dynamics>
+    </ComponentType>
+    <ComponentType name="shak_h_inf" extends="baseVoltageDepVariable">
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+        <Constant name="kishak" dimension="none" value="5.8"/>
+        <Constant name="vishak" dimension="none" value="-6.95"/>
+        <Constant name="shiftV05" dimension="none" value="0.0"/>
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
+            <DerivedVariable name="x" dimension="none" exposure="x" value="1/(exp((V + shiftV05 - vishak)/kishak) + 1)"/>
+        </Dynamics>
+    </ComponentType>
+    <ComponentType name="shak_h_tau" extends="baseVoltageDepTime">
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+        <Constant name="pthshak" dimension="none" value="1400.0"/>
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
+            <DerivedVariable name="t" dimension="time" exposure="t" value="(pthshak)/1000"/>
+        </Dynamics>
+    </ComponentType>
+</neuroml>
diff --git a/NeuroML2/GenerateNeuroML.py b/NeuroML2/GenerateNeuroML.py
@@ -14,7 +14,7 @@
 colors = {"AWCon": "0 0 0.8", "RMD": "0 0.8 0", "GenericMuscleCell": "0.8 0 0"}
 
 
-def create_channel_file(chan_id_in_cell, cell_id, xpp, species, gates={}, parameters={}):
+def create_channel_file(chan_id_in_cell, cell_id, xpp, species, gates={},extra_params=[]):
     chan_id = "%s_%s" % (cell_id, chan_id_in_cell)
     chan_doc = NeuroMLDocument(
         id=chan_id,
@@ -51,27 +51,35 @@ def create_channel_file(chan_id_in_cell, cell_id, xpp, species, gates={}, parame
         tcct.add(tscale)
 
 
+        inf_expr = xpp["derived_variables"][gates[g][1]]
+        tau_expr = xpp["derived_variables"][gates[g][2]]
 
-        for p in parameters:
+        potential_parameters = []
+        for p in xpp["parameters"]:
+            if chan_id_in_cell in p:
+                potential_parameters.append(p)
+
+        for p in potential_parameters+extra_params:
             const = component_factory(
                 "Constant", name=p, dimension="none", value=str(xpp["parameters"][p])
             )
-            ssct.add(const)
-            tcct.add(const)
+            if p in inf_expr:
+                ssct.add(const)
+            if p in tau_expr:
+                tcct.add(const)
 
 
         d = component_factory("Dynamics")
         ssct.add(d)
         dvv = component_factory("DerivedVariable", name="V", dimension="none", value="(v) / VOLT_SCALE")
         d.add(dvv)
 
-        expr = xpp["derived_variables"][gates[g][1]]
 
         import sympy
         from sympy.parsing.sympy_parser import parse_expr
         v,V = sympy.symbols('v V')
 
-        s_expr = parse_expr(expr, evaluate=False)
+        s_expr = parse_expr(inf_expr, evaluate=False)
         s_expr = s_expr.subs(v,V)
 
         dv = component_factory("DerivedVariable", name="x", exposure="x", dimension="none", value=s_expr)
@@ -81,11 +89,10 @@ def create_channel_file(chan_id_in_cell, cell_id, xpp, species, gates={}, parame
         tcct.add(d)
         d.add(dvv)
 
-        expr = xpp["derived_variables"][gates[g][2]]
-        s_expr = parse_expr(expr, evaluate=False)
+        s_expr = parse_expr(tau_expr, evaluate=False)
         s_expr = s_expr.subs(v,V)
 
-        dv = component_factory("DerivedVariable", name="t", exposure="t", dimension="time", value=s_expr)
+        dv = component_factory("DerivedVariable", name="t", exposure="t", dimension="time", value='(%s)/1000'%s_expr)
         d.add(dv)
 
 
@@ -177,8 +184,8 @@ def create_cells(channels_to_include):
             seg_type="soma",
         )
 
+        # Leak channel
         if 'leak' in channels_to_include:
-            # Leak channel
             cell.add_channel_density(
                 cell_doc,
                 cd_id="leak_chans",
@@ -189,9 +196,33 @@ def create_cells(channels_to_include):
                 ion_chan_def_file=create_channel_file("leak", cell_id, xpps[cell_id], species='non_specific'),
             )
 
+        # SHK1 CHANNELS
+        if 'shak' in channels_to_include:
+            chan_id = 'shak'
+            ion = 'k'
+            g_param = 'gshak'
+            gates={'m':[1,'minf_shak','tm_shak'],'h':[1,'hinf_shak','th_shak']}
+            extra_params = ['shiftV05']
+
+            cell.add_channel_density(
+                cell_doc,
+                cd_id="%s_chans"%chan_id,
+                cond_density="%s S_per_m2" % xpps[cell_id]["parameters"][g_param],
+                erev="%smV" % xpps[cell_id]["parameters"]["e%s"%ion],
+                ion=ion,
+                ion_channel="%s_%s" % (cell_id,chan_id),
+                ion_chan_def_file=create_channel_file(
+                    chan_id,
+                    cell_id,
+                    xpps[cell_id],
+                    species=ion,
+                    gates=gates,
+                    extra_params = extra_params
+                ),
+            )
 
+        # IRK/Kir channel
         if 'kir' in channels_to_include:
-            # IRK/Kir channel
             cell.add_channel_density(
                 cell_doc,
                 cd_id="kir_chans",
@@ -205,17 +236,28 @@ def create_cells(channels_to_include):
                     xpps[cell_id],
                     species='k',
                     gates={'m':[1,'minf_kir','tm_kir']},
-                    parameters=[
-                        "va_kir",
-                        "ka_kir",
-                        "p1tmkir",
-                        "p2tmkir",
-                        "p3tmkir",
-                        "p4tmkir",
-                        "p5tmkir",
-                        "p6tmkir",
-                    ],
+                ),
+            )
 
+        # CCA-1 channels
+        if 'cca' in channels_to_include:
+            chan_id = 'cca'
+            ion = 'ca'
+
+            cell.add_channel_density(
+                cell_doc,
+                cd_id="%s_chans"%chan_id,
+                cond_density="%s S_per_m2" % xpps[cell_id]["parameters"]["gcca1"],
+                erev="%smV" % xpps[cell_id]["parameters"]["e%s"%ion],
+                ion=ion,
+                ion_channel="%s_%s" % (cell_id,chan_id),
+                ion_chan_def_file=create_channel_file(
+                    chan_id,
+                    cell_id,
+                    xpps[cell_id],
+                    species=ion,
+                    gates={'m':[2,'minf_cca1','tm_cca1'],'h':[1,'hinf_cca1','th_cca1']},
+                    extra_params = ['f3ca','f4ca']
                 ),
             )
 
@@ -235,7 +277,7 @@ def create_cells(channels_to_include):
         )
 
         sim, net = generate_nmllite(
-            cell_id, duration=400, config="IClamp", parameters=None
+            cell_id, duration=1400, config="IClamp", parameters=None
         )
 
         ################################################################################
@@ -251,4 +293,5 @@ def create_cells(channels_to_include):
 
     channels_to_include = ['leak']
     channels_to_include = ['leak','kir']
+    channels_to_include = ['leak','kir','shak','cca']
     create_cells(channels_to_include)
diff --git a/NeuroML2/IClamp_RMD.net.nml b/NeuroML2/IClamp_RMD.net.nml
@@ -9,7 +9,7 @@
     <network id="IClamp_RMD" type="networkWithTemperature" temperature="34.0degC">
         <notes>A network model: IClamp_RMD</notes>
         <property tag="recommended_dt_ms" value="0.025"/>
-        <property tag="recommended_duration_ms" value="400.0"/>
+        <property tag="recommended_duration_ms" value="1400.0"/>
         <population id="pop_RMD" component="RMD" size="1" type="populationList">
             <property tag="color" value="0 0.8 0"/>
             <property tag="region" value="Worm"/>

diff --git a/NeuroML2/LEMS_Sim_IClamp_RMD.xml b/NeuroML2/LEMS_Sim_IClamp_RMD.xml
@@ -18,8 +18,8 @@
     <Include file="IClamp_RMD.net.nml"/>
     <Include file="RMD.cell.nml"/>
 
-    <Simulation id="Sim_IClamp_RMD" length="400.0ms" step="0.025ms" target="IClamp_RMD" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
-        <Display id="pop_RMD_v" title="Plots of pop_RMD_v" timeScale="1ms" xmin="-40.0" xmax="440.00000000000006" ymin="-80" ymax="40">
+    <Simulation id="Sim_IClamp_RMD" length="1400.0ms" step="0.025ms" target="IClamp_RMD" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
+        <Display id="pop_RMD_v" title="Plots of pop_RMD_v" timeScale="1ms" xmin="-140.0" xmax="1540.0000000000002" ymin="-80" ymax="40">
             <Line id="pop_RMD_0_RMD_v" quantity="pop_RMD/0/RMD/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
         </Display>
 

diff --git a/NeuroML2/RMD.cell.nml b/NeuroML2/RMD.cell.nml
@@ -1,7 +1,9 @@
 <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.xsd" id="RMD">
     <notes>A cell from Nicoletti et al. 2019</notes>
     <include href="RMD_leak.channel.nml"/>
+    <include href="RMD_shak.channel.nml"/>
     <include href="RMD_kir.channel.nml"/>
+    <include href="RMD_cca.channel.nml"/>
     <cell id="RMD">
         <notes>RMD cell from Nicoletti et al. 2019</notes>
         <morphology id="morphology">
@@ -21,7 +23,9 @@
         <biophysicalProperties id="biophys">
             <membraneProperties>
                 <channelDensity id="leak_chans" ionChannel="RMD_leak" condDensity="0.4 S_per_m2" erev="-80.0mV" ion="non_specific"/>
+                <channelDensity id="shak_chans" ionChannel="RMD_shak" condDensity="1.1 S_per_m2" erev="-80.0mV" ion="k"/>
                 <channelDensity id="kir_chans" ionChannel="RMD_kir" condDensity="0.2 S_per_m2" erev="-80.0mV" ion="k"/>
+                <channelDensity id="cca_chans" ionChannel="RMD_cca" condDensity="3.1 S_per_m2" erev="60.0mV" ion="ca"/>
                 <spikeThresh value="0mV"/>
                 <specificCapacitance value="0.0012 F_per_m2"/>
                 <initMembPotential value="-70mV"/>