Improved channel parsing

openworm · Apr 19, 2024 · b6a97c0 · b6a97c0
1 parent 6358caf
commit b6a97c0
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Showing 6 changed files with 51 additions and 12 deletions.
diff --git a/.gitignore b/.gitignore
@@ -9,3 +9,4 @@ report.*.txt
 /NeuroML2/IClamp_AWCon.net.nml
 /NeuroML2/LEMS_Sim_IClamp_AWCon.xml
 /NicollettiEtAl2019.pdf
+/NeuroML2/LEMS_Test_RMD_kir.xml
diff --git a/NeuroML2/AWCon_kir.channel.nml b/NeuroML2/AWCon_kir.channel.nml
@@ -1,13 +1,14 @@
 <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_kir">
     <notes>An ion channel from cell AWCon from Nicoletti et al. 2019</notes>
-    <ionChannelHH id="AWCon_kir" conductance="10pS">
+    <ionChannelHH id="AWCon_kir" species="k" conductance="10pS">
         <notes>AWCon_kir channel from Nicoletti et al. 2019</notes>
         <gateHHtauInf id="m" instances="1">
             <timeCourse type="kir_m_tau"/>
             <steadyState type="kir_m_inf"/>
         </gateHHtauInf>
     </ionChannelHH>
     <ComponentType name="kir_m_inf" extends="baseVoltageDepVariable">
+        <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"/>
@@ -17,10 +18,13 @@
         <Constant name="p5tmkir" dimension="none" value="11.1691"/>
         <Constant name="p6tmkir" dimension="none" value="3.8329"/>
         <Dynamics>
-            <DerivedVariable name="x" dimension="none" exposure="x" value="1/(1+exp((v-va_kir+30)/ka_kir))"/>
+            <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)"/>
         </Dynamics>
     </ComponentType>
     <ComponentType name="kir_m_tau" extends="baseVoltageDepTime">
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+        <Constant name="TIME_SCALE" dimension="time" value="1 s"/>
         <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"/>
@@ -30,7 +34,8 @@
         <Constant name="p5tmkir" dimension="none" value="11.1691"/>
         <Constant name="p6tmkir" dimension="none" value="3.8329"/>
         <Dynamics>
-            <DerivedVariable name="t" dimension="time" exposure="t" value="p1tmkir/(exp(-(v-p2tmkir)/p3tmkir)+exp((v-p4tmkir)/p5tmkir))+p6tmkir"/>
+            <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"/>
         </Dynamics>
     </ComponentType>
 </neuroml>
diff --git a/NeuroML2/AWCon_leak.channel.nml b/NeuroML2/AWCon_leak.channel.nml
@@ -1,6 +1,6 @@
 <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_leak">
     <notes>An ion channel from cell AWCon from Nicoletti et al. 2019</notes>
-    <ionChannelHH id="AWCon_leak" conductance="10pS">
+    <ionChannelHH id="AWCon_leak" species="non_specific" conductance="10pS">
         <notes>AWCon_leak channel from Nicoletti et al. 2019</notes>
     </ionChannelHH>
 </neuroml>
diff --git a/NeuroML2/GenerateNeuroML.py b/NeuroML2/GenerateNeuroML.py
@@ -15,7 +15,7 @@
 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, gates={}, parameters={}):
+def create_channel_file(chan_id_in_cell, cell_id, xpp, species, gates={}, parameters={}):
     chan_id = "%s_%s" % (cell_id, chan_id_in_cell)
     chan_doc = NeuroMLDocument(
         id=chan_id,
@@ -28,6 +28,7 @@ def create_channel_file(chan_id_in_cell, cell_id, xpp, gates={}, parameters={}):
         "IonChannelHH",
         id=chan_id,
         conductance="10pS",
+        species=species,
         notes="%s channel from Nicoletti et al. 2019" % chan_id,
     )
 
@@ -44,6 +45,14 @@ def create_channel_file(chan_id_in_cell, cell_id, xpp, gates={}, parameters={}):
         chan_doc.add(ssct)
         chan_doc.add(tcct)
 
+        vscale = component_factory("Constant", name='VOLT_SCALE',  dimension="voltage", value="1 mV")
+        ssct.add(vscale)
+        tcct.add(vscale)
+        tscale = component_factory("Constant", name='TIME_SCALE',  dimension="time", value="1 s")
+        tcct.add(tscale)
+
+
+
         for p in parameters:
             const = component_factory(
                 "Constant", name=p, dimension="none", value=str(xpp["parameters"][p])
@@ -54,12 +63,30 @@ def create_channel_file(chan_id_in_cell, cell_id, xpp, gates={}, parameters={}):
 
         d = component_factory("Dynamics")
         ssct.add(d)
-        dv = component_factory("DerivedVariable", name="x", exposure="x", dimension="none", value=xpp["derived_variables"][gates[g][1]])
+        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 = s_expr.subs(v,V)
+
+        dv = component_factory("DerivedVariable", name="x", exposure="x", dimension="none", value=s_expr)
         d.add(dv)
 
         d = component_factory("Dynamics")
         tcct.add(d)
-        dv = component_factory("DerivedVariable", name="t", exposure="t", dimension="time", value=xpp["derived_variables"][gates[g][2]])
+        d.add(dvv)
+
+        expr = xpp["derived_variables"][gates[g][2]]
+        s_expr = parse_expr(expr, evaluate=False)
+        s_expr = s_expr.subs(v,V)
+
+        dv = component_factory("DerivedVariable", name="t", exposure="t", dimension="time", value=s_expr)
         d.add(dv)
 
 
@@ -159,7 +186,7 @@ def create_cells():
             erev="%smV" % xpps[cell_id]["parameters"]["eleak"],
             ion="non_specific",
             ion_channel="%s_leak" % cell_id,
-            ion_chan_def_file=create_channel_file("leak", cell_id, xpps[cell_id]),
+            ion_chan_def_file=create_channel_file("leak", cell_id, xpps[cell_id], species='non_specific'),
         )
 
         # IRK channel
@@ -174,6 +201,7 @@ def create_cells():
                 "kir",
                 cell_id,
                 xpps[cell_id],
+                species='k',
                 gates={'m':[1,'minf_kir','tm_kir']},
                 parameters=[
                     "va_kir",

diff --git a/NeuroML2/RMD_kir.channel.nml b/NeuroML2/RMD_kir.channel.nml
@@ -1,13 +1,14 @@
 <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_kir">
     <notes>An ion channel from cell RMD from Nicoletti et al. 2019</notes>
-    <ionChannelHH id="RMD_kir" conductance="10pS">
+    <ionChannelHH id="RMD_kir" species="k" conductance="10pS">
         <notes>RMD_kir channel from Nicoletti et al. 2019</notes>
         <gateHHtauInf id="m" instances="1">
             <timeCourse type="kir_m_tau"/>
             <steadyState type="kir_m_inf"/>
         </gateHHtauInf>
     </ionChannelHH>
     <ComponentType name="kir_m_inf" extends="baseVoltageDepVariable">
+        <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"/>
@@ -17,10 +18,13 @@
         <Constant name="p5tmkir" dimension="none" value="11.1691"/>
         <Constant name="p6tmkir" dimension="none" value="3.8329"/>
         <Dynamics>
-            <DerivedVariable name="x" dimension="none" exposure="x" value="1/(1+exp((v-va_kir+30)/ka_kir))"/>
+            <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)"/>
         </Dynamics>
     </ComponentType>
     <ComponentType name="kir_m_tau" extends="baseVoltageDepTime">
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+        <Constant name="TIME_SCALE" dimension="time" value="1 s"/>
         <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"/>
@@ -30,7 +34,8 @@
         <Constant name="p5tmkir" dimension="none" value="11.1691"/>
         <Constant name="p6tmkir" dimension="none" value="3.8329"/>
         <Dynamics>
-            <DerivedVariable name="t" dimension="time" exposure="t" value="p1tmkir/(exp(-(v-p2tmkir)/p3tmkir)+exp((v-p4tmkir)/p5tmkir))+p6tmkir"/>
+            <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"/>
         </Dynamics>
     </ComponentType>
 </neuroml>
diff --git a/NeuroML2/RMD_leak.channel.nml b/NeuroML2/RMD_leak.channel.nml
@@ -1,6 +1,6 @@
 <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_leak">
     <notes>An ion channel from cell RMD from Nicoletti et al. 2019</notes>
-    <ionChannelHH id="RMD_leak" conductance="10pS">
+    <ionChannelHH id="RMD_leak" species="non_specific" conductance="10pS">
         <notes>RMD_leak channel from Nicoletti et al. 2019</notes>
     </ionChannelHH>
 </neuroml>