More tests xpp vs nml2

openworm · Apr 19, 2024 · 9faa191 · 9faa191
1 parent b6a97c0
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Showing 13 changed files with 91 additions and 64 deletions.
diff --git a/.gitignore b/.gitignore
@@ -10,3 +10,7 @@ report.*.txt
 /NeuroML2/LEMS_Sim_IClamp_AWCon.xml
 /NicollettiEtAl2019.pdf
 /NeuroML2/LEMS_Test_RMD_kir.xml
+/NeuroML2/LEMS_RMD.xml
+/NeuroML2/Test_RMD.ode
+/NeuroML2/report.txt
+/RMD.model.xml
diff --git a/NeuroML2/AWCon.cell.nml b/NeuroML2/AWCon.cell.nml
@@ -6,8 +6,8 @@
         <notes>AWCon cell from Nicoletti et al. 2019</notes>
         <morphology id="morphology">
             <segment id="0" name="soma">
-                <proximal x="0.0" y="0.0" z="0.0" diameter="10.0"/>
-                <distal x="0.0" y="0.0" z="0.0" diameter="10.0"/>
+                <proximal x="0.0" y="0.0" z="0.0" diameter="17.841242"/>
+                <distal x="0.0" y="0.0" z="0.0" diameter="17.841242"/>
             </segment>
             <segmentGroup id="soma_group" neuroLexId="GO:0043025">
                 <notes>Default soma segment group for the cell</notes>
@@ -23,8 +23,8 @@
                 <channelDensity id="leak_chans" ionChannel="AWCon_leak" condDensity="0.27 S_per_m2" erev="-80.0mV" ion="non_specific"/>
                 <channelDensity id="kir_chans" ionChannel="AWCon_kir" condDensity="0.65 S_per_m2" erev="-80.0mV" ion="k"/>
                 <spikeThresh value="0mV"/>
-                <specificCapacitance value="1.2 uF_per_cm2"/>
-                <initMembPotential value="-75mV"/>
+                <specificCapacitance value="0.0031000000000000003 F_per_m2"/>
+                <initMembPotential value="-70mV"/>
             </membraneProperties>
             <intracellularProperties>
                 <resistivity value="0.1 kohm_cm"/>

diff --git a/NeuroML2/AWCon_kir.channel.nml b/NeuroML2/AWCon_kir.channel.nml
@@ -24,7 +24,7 @@
     </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="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"/>

diff --git a/NeuroML2/GenerateNeuroML.py b/NeuroML2/GenerateNeuroML.py
@@ -9,7 +9,6 @@
 
 xpps = {"RMD": parse_script("../RMD.ode"), "AWCon": parse_script("../AWC.ode")}
 
-c = 1.2
 
 
 colors = {"AWCon": "0 0 0.8", "RMD": "0 0.8 0", "GenericMuscleCell": "0.8 0 0"}
@@ -48,7 +47,7 @@ def create_channel_file(chan_id_in_cell, cell_id, xpp, species, gates={}, parame
         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")
+        tscale = component_factory("Constant", name='TIME_SCALE',  dimension="time", value="1 ms")
         tcct.add(tscale)
 
 
@@ -122,7 +121,7 @@ def generate_nmllite(cell, duration=700, config="IClamp", parameters=None):
         input_source = InputSource(
             id="iclamp_0",
             neuroml2_input="PulseGenerator",
-            parameters={"amplitude": "stim_amp", "delay": "100ms", "duration": "500ms"},
+            parameters={"amplitude": "stim_amp", "delay": "310ms", "duration": "500ms"},
         )
 
     else:
@@ -156,7 +155,7 @@ def generate_nmllite(cell, duration=700, config="IClamp", parameters=None):
     return sim, net
 
 
-def create_cells():
+def create_cells(channels_to_include):
     for cell_id in ["AWCon", "RMD"]:
         # Create the nml file and add the ion channels
         cell_doc = NeuroMLDocument(
@@ -168,7 +167,7 @@ def create_cells():
         cell = cell_doc.add(
             "Cell", id=cell_id, notes="%s cell from Nicoletti et al. 2019" % cell_id
         )
-        diam = 10
+        diam = 17.841242  # Gives a convenient surface area of 1000.0 um^2
         cell.add_segment(
             prox=[0, 0, 0, diam],
             dist=[0, 0, 0, diam],
@@ -178,49 +177,52 @@ def create_cells():
             seg_type="soma",
         )
 
-        # Leak channel
-        cell.add_channel_density(
-            cell_doc,
-            cd_id="leak_chans",
-            cond_density="%s S_per_m2" % xpps[cell_id]["parameters"]["gleak"],
-            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], species='non_specific'),
-        )
+        if 'leak' in channels_to_include:
+            # Leak channel
+            cell.add_channel_density(
+                cell_doc,
+                cd_id="leak_chans",
+                cond_density="%s S_per_m2" % xpps[cell_id]["parameters"]["gleak"],
+                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], species='non_specific'),
+            )
 
-        # IRK channel
-        cell.add_channel_density(
-            cell_doc,
-            cd_id="kir_chans",
-            cond_density="%s S_per_m2" % xpps[cell_id]["parameters"]["gkir"],
-            erev="%smV" % xpps[cell_id]["parameters"]["ek"],
-            ion="k",
-            ion_channel="%s_kir" % cell_id,
-            ion_chan_def_file=create_channel_file(
-                "kir",
-                cell_id,
-                xpps[cell_id],
-                species='k',
-                gates={'m':[1,'minf_kir','tm_kir']},
-                parameters=[
-                    "va_kir",
-                    "ka_kir",
-                    "p1tmkir",
-                    "p2tmkir",
-                    "p3tmkir",
-                    "p4tmkir",
-                    "p5tmkir",
-                    "p6tmkir",
-                ],
-
-            ),
-        )
 
-        cell.set_specific_capacitance("%s uF_per_cm2" % c)
+        if 'kir' in channels_to_include:
+            # IRK/Kir channel
+            cell.add_channel_density(
+                cell_doc,
+                cd_id="kir_chans",
+                cond_density="%s S_per_m2" % xpps[cell_id]["parameters"]["gkir"],
+                erev="%smV" % xpps[cell_id]["parameters"]["ek"],
+                ion="k",
+                ion_channel="%s_kir" % cell_id,
+                ion_chan_def_file=create_channel_file(
+                    "kir",
+                    cell_id,
+                    xpps[cell_id],
+                    species='k',
+                    gates={'m':[1,'minf_kir','tm_kir']},
+                    parameters=[
+                        "va_kir",
+                        "ka_kir",
+                        "p1tmkir",
+                        "p2tmkir",
+                        "p3tmkir",
+                        "p4tmkir",
+                        "p5tmkir",
+                        "p6tmkir",
+                    ],
+
+                ),
+            )
+
+        cell.set_specific_capacitance("%s F_per_m2" % (float(xpps[cell_id]["parameters"]["c"]) * 1e-3))
 
         cell.add_membrane_property("SpikeThresh", value="0mV")
-        cell.set_init_memb_potential("-75mV")
+        cell.set_init_memb_potential("-70mV")
 
         # This value is not really used as it's a single comp cell model
         cell.set_resistivity("0.1 kohm_cm")
@@ -233,7 +235,7 @@ def create_cells():
         )
 
         sim, net = generate_nmllite(
-            cell_id, duration=700, config="IClamp", parameters=None
+            cell_id, duration=400, config="IClamp", parameters=None
         )
 
         ################################################################################
@@ -246,4 +248,7 @@ def create_cells():
 
 
 if __name__ == "__main__":
-    create_cells()
+
+    channels_to_include = ['leak']
+    channels_to_include = ['leak','kir']
+    create_cells(channels_to_include)
diff --git a/NeuroML2/IClamp_AWCon.json b/NeuroML2/IClamp_AWCon.json
@@ -14,7 +14,7 @@
             "iclamp_0": {
                 "parameters": {
                     "amplitude": "stim_amp",
-                    "delay": "100ms",
+                    "delay": "310ms",
                     "duration": "500ms"
                 },
                 "neuroml2_input": "PulseGenerator"

diff --git a/NeuroML2/IClamp_RMD.json b/NeuroML2/IClamp_RMD.json
@@ -14,7 +14,7 @@
             "iclamp_0": {
                 "parameters": {
                     "amplitude": "stim_amp",
-                    "delay": "100ms",
+                    "delay": "310ms",
                     "duration": "500ms"
                 },
                 "neuroml2_input": "PulseGenerator"

diff --git a/NeuroML2/IClamp_RMD.net.nml b/NeuroML2/IClamp_RMD.net.nml
@@ -5,11 +5,11 @@
     NeuroMLlite parameters: 
         stim_amp = 10pA</notes>
     <include href="RMD.cell.nml"/>
-    <pulseGenerator id="iclamp_0" delay="100ms" duration="500ms" amplitude="10pA"/>
+    <pulseGenerator id="iclamp_0" delay="310ms" duration="500ms" amplitude="10pA"/>
     <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="700.0"/>
+        <property tag="recommended_duration_ms" value="400.0"/>
         <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="700.0ms" 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="-70.0" xmax="770.0000000000001" ymin="-80" ymax="40">
+    <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">
             <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
@@ -6,8 +6,8 @@
         <notes>RMD cell from Nicoletti et al. 2019</notes>
         <morphology id="morphology">
             <segment id="0" name="soma">
-                <proximal x="0.0" y="0.0" z="0.0" diameter="10.0"/>
-                <distal x="0.0" y="0.0" z="0.0" diameter="10.0"/>
+                <proximal x="0.0" y="0.0" z="0.0" diameter="17.841242"/>
+                <distal x="0.0" y="0.0" z="0.0" diameter="17.841242"/>
             </segment>
             <segmentGroup id="soma_group" neuroLexId="GO:0043025">
                 <notes>Default soma segment group for the cell</notes>
@@ -23,8 +23,8 @@
                 <channelDensity id="leak_chans" ionChannel="RMD_leak" condDensity="0.4 S_per_m2" erev="-80.0mV" ion="non_specific"/>
                 <channelDensity id="kir_chans" ionChannel="RMD_kir" condDensity="0.2 S_per_m2" erev="-80.0mV" ion="k"/>
                 <spikeThresh value="0mV"/>
-                <specificCapacitance value="1.2 uF_per_cm2"/>
-                <initMembPotential value="-75mV"/>
+                <specificCapacitance value="0.0012 F_per_m2"/>
+                <initMembPotential value="-70mV"/>
             </membraneProperties>
             <intracellularProperties>
                 <resistivity value="0.1 kohm_cm"/>

diff --git a/NeuroML2/RMD_kir.channel.nml b/NeuroML2/RMD_kir.channel.nml
@@ -24,7 +24,7 @@
     </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="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"/>

diff --git a/NeuroML2/Sim_IClamp_AWCon.json b/NeuroML2/Sim_IClamp_AWCon.json
@@ -2,7 +2,7 @@
     "Sim_IClamp_AWCon": {
         "version": "NeuroMLlite v0.5.9",
         "network": "IClamp_AWCon.json",
-        "duration": 700.0,
+        "duration": 400.0,
         "dt": 0.025,
         "seed": 12345,
         "record_traces": {

diff --git a/NeuroML2/Sim_IClamp_RMD.json b/NeuroML2/Sim_IClamp_RMD.json
@@ -2,7 +2,7 @@
     "Sim_IClamp_RMD": {
         "version": "NeuroMLlite v0.5.9",
         "network": "IClamp_RMD.json",
-        "duration": 700.0,
+        "duration": 400.0,
         "dt": 0.025,
         "seed": 12345,
         "record_traces": {

diff --git a/NeuroML2/TestXPP.py b/NeuroML2/TestXPP.py
@@ -0,0 +1,18 @@
+
+from pyneuroml.xppaut import parse_script, to_lems, to_xpp, run_xpp_file
+
+
+parsed_data = parse_script("../RMD.ode")
+
+all_g = ['gshal','gkir','gshak','gegl36','gunc2','gegl19','gcca1','gslo1','gbk','gbk2','gslo2','gca','gsc','gnca']
+
+all_g.remove('gkir')
+
+for p in all_g:
+    parsed_data['parameters'][p] = 0
+
+new_ode_file = 'Test_RMD.ode'
+new_ode = to_xpp(parsed_data, new_ode_file)
+
+
+run_xpp_file(new_ode_file, plot=True)