Adding slo1 channel

openworm · May 21, 2024 · 728364e · 728364e
1 parent 656be08
commit 728364e
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Showing 8 changed files with 728 additions and 12 deletions.
diff --git a/NeuroML2/AWCon.cell.nml b/NeuroML2/AWCon.cell.nml
@@ -9,6 +9,7 @@
     <include href="AWCon_egl19.channel.nml"/>
     <include href="AWCon_cca.channel.nml"/>
     <include href="AWCon_bk.channel.nml"/>
+    <include href="AWCon_slo1.channel.nml"/>
     <include href="AWCon_slo2.channel.nml"/>
     <include href="AWCon_sk.channel.nml"/>
     <include href="CaDynamics.nml"/>
@@ -39,6 +40,7 @@
                 <channelDensity id="egl19_chans" ionChannel="AWCon_egl19" condDensity="122.36248894130962 S_per_m2" erev="60.0mV" ion="ca"/>
                 <channelDensity id="cca_chans" ionChannel="AWCon_cca" condDensity="55.26047887672047 S_per_m2" erev="60.0mV" ion="ca"/>
                 <channelDensity id="bk_chans" ionChannel="AWCon_bk" condDensity="8.68378953777036 S_per_m2" erev="-80.0mV" ion="k"/>
+                <channelDensity id="slo1_chans" ionChannel="AWCon_slo1" condDensity="8.68378953777036 S_per_m2" erev="-80.0mV" ion="k"/>
                 <channelDensity id="slo2_chans" ionChannel="AWCon_slo2" condDensity="7.8943541252457825 S_per_m2" erev="-80.0mV" ion="k"/>
                 <channelDensity id="sk_chans" ionChannel="AWCon_sk" condDensity="4.736612475147469 S_per_m2" erev="-80.0mV" ion="k"/>
                 <spikeThresh value="0mV"/>

diff --git a/NeuroML2/AWCon_slo1.channel.nml b/NeuroML2/AWCon_slo1.channel.nml
diff --git a/NeuroML2/GenerateNeuroML.py b/NeuroML2/GenerateNeuroML.py
@@ -738,6 +738,93 @@ def create_cells(channels_to_include, duration=700, stim_delay=310, stim_duratio
                 ),
             )
 
+        # SLO1-EGL19 COMPLEX
+        if "slo1" in channels_to_include:
+            chan_id = "slo1"
+            ion = "k"
+            g_param = "gslo1"
+            gates = {
+                "m": [1, "minf_slo1", "tm_slo1"],
+                "h": [1, "hinf_egl19", "ths_egl19"],
+            }
+            extra_params = [
+                "backgr",
+                "cac_nano",
+                "wom",
+                "wyx",
+                "kyx",
+                "nyx",
+                "wop",
+                "wxy",
+                "kxy",
+                "nxy",
+                "stm19",
+                "sth19",
+                "pdg1",
+                "pdg2",
+                "pdg3",
+                "pdg4",
+                "pdg5",
+                "pdg6",
+                "pdg7",
+                "stau19",
+                "pds1",
+                "pds2",
+                "pds3",
+                "pds4",
+                "pds5",
+                "pds6",
+                "pds7",
+                "pds8",
+                "pds9",
+                "pds10",
+                "pds11",
+                "shiftdps",
+                "tm_egl19",
+                "pi",
+                "r",
+                "d",
+                "F",
+                "kb",
+                "b",
+                "gsc",
+                "eca",
+                "cao_nano",
+                "kcm2",
+                "kom2",
+                "kop2",
+                "kop",
+                "minf_egl19",
+                "alpha1",
+                "beta1",
+                "stm2",
+                "m_egl19",
+            ]
+            for p in xpps[cell_id]["parameters"]:
+                if "egl19" in p:
+                    extra_params.append(p)
+
+            xpps[cell_id]["parameters"]["pi"] = 3.14159265359
+
+            cell.add_channel_density(
+                cell_doc,
+                cd_id="%s_chans" % chan_id,
+                cond_density="%s S_per_m2"
+                % (float(xpps[cell_id]["parameters"][g_param]) * density_factor),
+                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,
+                    add_all=True,
+                ),
+            )
+
         # SLO2-UNC2 COMPLEX
         if "slo2" in channels_to_include:
             chan_id = "slo2"
@@ -906,6 +993,7 @@ def create_cells(channels_to_include, duration=700, stim_delay=310, stim_duratio
     channels_to_include = ["leak", "unc2"]
     channels_to_include = ["leak", "unc2", "slo2"]
     channels_to_include = ["leak", "unc2", "bk"]
+    channels_to_include = ["leak", "egl19", "slo1"]
     channels_to_include = [
         "leak",
         "nca",
@@ -918,6 +1006,7 @@ def create_cells(channels_to_include, duration=700, stim_delay=310, stim_duratio
         "egl19",
         "ca",
         "bk",
+        "slo1",
         "slo2",
     ]
 

diff --git a/NeuroML2/LEMS_Sim_IClamp_RMD.xml b/NeuroML2/LEMS_Sim_IClamp_RMD.xml
@@ -139,44 +139,60 @@
             <Line id="pop_RMD_0_RMD_biophys_membraneProperties_sk_chans_iDensity" quantity="pop_RMD/0/RMD/biophys/membraneProperties/sk_chans/iDensity" scale="1" color="#01c4cd" timeScale="1ms"/>
         </Display>
 
+        <Display id="pop_RMD_0_biophys/membraneProperties/slo1_chans/RMD_slo1/h/q" title="Plots of pop_RMD_0_biophys/membraneProperties/slo1_chans/RMD_slo1/h/q" timeScale="1ms" xmin="-180.0" xmax="1980.0000000000002" ymin="-1" ymax="1">
+            <Line id="pop_RMD_0_RMD_biophys_membraneProperties_slo1_chans_RMD_slo1_h_q" quantity="pop_RMD/0/RMD/biophys/membraneProperties/slo1_chans/RMD_slo1/h/q" scale="1" color="#036aae" timeScale="1ms"/>
+        </Display>
+
+        <Display id="pop_RMD_0_biophys/membraneProperties/slo1_chans/RMD_slo1/m/q" title="Plots of pop_RMD_0_biophys/membraneProperties/slo1_chans/RMD_slo1/m/q" timeScale="1ms" xmin="-180.0" xmax="1980.0000000000002" ymin="-1" ymax="1">
+            <Line id="pop_RMD_0_RMD_biophys_membraneProperties_slo1_chans_RMD_slo1_m_q" quantity="pop_RMD/0/RMD/biophys/membraneProperties/slo1_chans/RMD_slo1/m/q" scale="1" color="#53de83" timeScale="1ms"/>
+        </Display>
+
+        <Display id="pop_RMD_0_biophys/membraneProperties/slo1_chans/gDensity" title="Plots of pop_RMD_0_biophys/membraneProperties/slo1_chans/gDensity" timeScale="1ms" xmin="-180.0" xmax="1980.0000000000002" ymin="-1" ymax="1">
+            <Line id="pop_RMD_0_RMD_biophys_membraneProperties_slo1_chans_gDensity" quantity="pop_RMD/0/RMD/biophys/membraneProperties/slo1_chans/gDensity" scale="1" color="#5b9557" timeScale="1ms"/>
+        </Display>
+
+        <Display id="pop_RMD_0_biophys/membraneProperties/slo1_chans/iDensity" title="Plots of pop_RMD_0_biophys/membraneProperties/slo1_chans/iDensity" timeScale="1ms" xmin="-180.0" xmax="1980.0000000000002" ymin="-1" ymax="1">
+            <Line id="pop_RMD_0_RMD_biophys_membraneProperties_slo1_chans_iDensity" quantity="pop_RMD/0/RMD/biophys/membraneProperties/slo1_chans/iDensity" scale="1" color="#92b9f4" timeScale="1ms"/>
+        </Display>
+
         <Display id="pop_RMD_0_biophys/membraneProperties/slo2_chans/RMD_slo2/h/q" title="Plots of pop_RMD_0_biophys/membraneProperties/slo2_chans/RMD_slo2/h/q" timeScale="1ms" xmin="-180.0" xmax="1980.0000000000002" ymin="-1" ymax="1">
-            <Line id="pop_RMD_0_RMD_biophys_membraneProperties_slo2_chans_RMD_slo2_h_q" quantity="pop_RMD/0/RMD/biophys/membraneProperties/slo2_chans/RMD_slo2/h/q" scale="1" color="#036aae" timeScale="1ms"/>
+            <Line id="pop_RMD_0_RMD_biophys_membraneProperties_slo2_chans_RMD_slo2_h_q" quantity="pop_RMD/0/RMD/biophys/membraneProperties/slo2_chans/RMD_slo2/h/q" scale="1" color="#32f19d" timeScale="1ms"/>
         </Display>
 
         <Display id="pop_RMD_0_biophys/membraneProperties/slo2_chans/RMD_slo2/m/q" title="Plots of pop_RMD_0_biophys/membraneProperties/slo2_chans/RMD_slo2/m/q" timeScale="1ms" xmin="-180.0" xmax="1980.0000000000002" ymin="-1" ymax="1">
-            <Line id="pop_RMD_0_RMD_biophys_membraneProperties_slo2_chans_RMD_slo2_m_q" quantity="pop_RMD/0/RMD/biophys/membraneProperties/slo2_chans/RMD_slo2/m/q" scale="1" color="#53de83" timeScale="1ms"/>
+            <Line id="pop_RMD_0_RMD_biophys_membraneProperties_slo2_chans_RMD_slo2_m_q" quantity="pop_RMD/0/RMD/biophys/membraneProperties/slo2_chans/RMD_slo2/m/q" scale="1" color="#d43d99" timeScale="1ms"/>
         </Display>
 
         <Display id="pop_RMD_0_biophys/membraneProperties/slo2_chans/gDensity" title="Plots of pop_RMD_0_biophys/membraneProperties/slo2_chans/gDensity" timeScale="1ms" xmin="-180.0" xmax="1980.0000000000002" ymin="-1" ymax="1">
-            <Line id="pop_RMD_0_RMD_biophys_membraneProperties_slo2_chans_gDensity" quantity="pop_RMD/0/RMD/biophys/membraneProperties/slo2_chans/gDensity" scale="1" color="#5b9557" timeScale="1ms"/>
+            <Line id="pop_RMD_0_RMD_biophys_membraneProperties_slo2_chans_gDensity" quantity="pop_RMD/0/RMD/biophys/membraneProperties/slo2_chans/gDensity" scale="1" color="#36379e" timeScale="1ms"/>
         </Display>
 
         <Display id="pop_RMD_0_biophys/membraneProperties/slo2_chans/iDensity" title="Plots of pop_RMD_0_biophys/membraneProperties/slo2_chans/iDensity" timeScale="1ms" xmin="-180.0" xmax="1980.0000000000002" ymin="-1" ymax="1">
-            <Line id="pop_RMD_0_RMD_biophys_membraneProperties_slo2_chans_iDensity" quantity="pop_RMD/0/RMD/biophys/membraneProperties/slo2_chans/iDensity" scale="1" color="#92b9f4" timeScale="1ms"/>
+            <Line id="pop_RMD_0_RMD_biophys_membraneProperties_slo2_chans_iDensity" quantity="pop_RMD/0/RMD/biophys/membraneProperties/slo2_chans/iDensity" scale="1" color="#5d01b7" timeScale="1ms"/>
         </Display>
 
         <Display id="pop_RMD_0_biophys/membraneProperties/unc2_chans/RMD_unc2/h/q" title="Plots of pop_RMD_0_biophys/membraneProperties/unc2_chans/RMD_unc2/h/q" timeScale="1ms" xmin="-180.0" xmax="1980.0000000000002" ymin="-1" ymax="1">
-            <Line id="pop_RMD_0_RMD_biophys_membraneProperties_unc2_chans_RMD_unc2_h_q" quantity="pop_RMD/0/RMD/biophys/membraneProperties/unc2_chans/RMD_unc2/h/q" scale="1" color="#32f19d" timeScale="1ms"/>
+            <Line id="pop_RMD_0_RMD_biophys_membraneProperties_unc2_chans_RMD_unc2_h_q" quantity="pop_RMD/0/RMD/biophys/membraneProperties/unc2_chans/RMD_unc2/h/q" scale="1" color="#c0004f" timeScale="1ms"/>
         </Display>
 
         <Display id="pop_RMD_0_biophys/membraneProperties/unc2_chans/RMD_unc2/m/q" title="Plots of pop_RMD_0_biophys/membraneProperties/unc2_chans/RMD_unc2/m/q" timeScale="1ms" xmin="-180.0" xmax="1980.0000000000002" ymin="-1" ymax="1">
-            <Line id="pop_RMD_0_RMD_biophys_membraneProperties_unc2_chans_RMD_unc2_m_q" quantity="pop_RMD/0/RMD/biophys/membraneProperties/unc2_chans/RMD_unc2/m/q" scale="1" color="#d43d99" timeScale="1ms"/>
+            <Line id="pop_RMD_0_RMD_biophys_membraneProperties_unc2_chans_RMD_unc2_m_q" quantity="pop_RMD/0/RMD/biophys/membraneProperties/unc2_chans/RMD_unc2/m/q" scale="1" color="#771a1c" timeScale="1ms"/>
         </Display>
 
         <Display id="pop_RMD_0_biophys/membraneProperties/unc2_chans/gDensity" title="Plots of pop_RMD_0_biophys/membraneProperties/unc2_chans/gDensity" timeScale="1ms" xmin="-180.0" xmax="1980.0000000000002" ymin="-1" ymax="1">
-            <Line id="pop_RMD_0_RMD_biophys_membraneProperties_unc2_chans_gDensity" quantity="pop_RMD/0/RMD/biophys/membraneProperties/unc2_chans/gDensity" scale="1" color="#36379e" timeScale="1ms"/>
+            <Line id="pop_RMD_0_RMD_biophys_membraneProperties_unc2_chans_gDensity" quantity="pop_RMD/0/RMD/biophys/membraneProperties/unc2_chans/gDensity" scale="1" color="#a8e7b4" timeScale="1ms"/>
         </Display>
 
         <Display id="pop_RMD_0_biophys/membraneProperties/unc2_chans/iDensity" title="Plots of pop_RMD_0_biophys/membraneProperties/unc2_chans/iDensity" timeScale="1ms" xmin="-180.0" xmax="1980.0000000000002" ymin="-1" ymax="1">
-            <Line id="pop_RMD_0_RMD_biophys_membraneProperties_unc2_chans_iDensity" quantity="pop_RMD/0/RMD/biophys/membraneProperties/unc2_chans/iDensity" scale="1" color="#5d01b7" timeScale="1ms"/>
+            <Line id="pop_RMD_0_RMD_biophys_membraneProperties_unc2_chans_iDensity" quantity="pop_RMD/0/RMD/biophys/membraneProperties/unc2_chans/iDensity" scale="1" color="#149bc7" timeScale="1ms"/>
         </Display>
 
         <Display id="pop_RMD_0_caConc" title="Plots of pop_RMD_0_caConc" timeScale="1ms" xmin="-180.0" xmax="1980.0000000000002" ymin="-1" ymax="1">
-            <Line id="pop_RMD_0_RMD_caConc" quantity="pop_RMD/0/RMD/caConc" scale="1" color="#c0004f" timeScale="1ms"/>
+            <Line id="pop_RMD_0_RMD_caConc" quantity="pop_RMD/0/RMD/caConc" scale="1" color="#76f116" timeScale="1ms"/>
         </Display>
 
         <Display id="pop_RMD_v" title="Plots of pop_RMD_v" timeScale="1ms" xmin="-180.0" xmax="1980.0000000000002" ymin="-80" ymax="40">
-            <Line id="pop_RMD_0_RMD_v" quantity="pop_RMD/0/RMD/v" scale="1mV" color="#771a1c" timeScale="1ms"/>
+            <Line id="pop_RMD_0_RMD_v" quantity="pop_RMD/0/RMD/v" scale="1mV" color="#3d56b9" timeScale="1ms"/>
         </Display>
 
         <OutputFile id="Sim_IClamp_RMD_pop_RMD_v_dat" fileName="Sim_IClamp_RMD.pop_RMD.v.dat">
@@ -303,6 +319,22 @@
             <OutputColumn id="pop_RMD_0_RMD_biophys_membraneProperties_sk_chans_iDensity" quantity="pop_RMD/0/RMD/biophys/membraneProperties/sk_chans/iDensity"/>
         </OutputFile>
 
+        <OutputFile id="pop_RMD_0_biophys_membraneProperties_slo1_chans_RMD_slo1_h_q_dat" fileName="pop_RMD_0.biophys_membraneProperties_slo1_chans_RMD_slo1_h_q.dat">
+            <OutputColumn id="pop_RMD_0_RMD_biophys_membraneProperties_slo1_chans_RMD_slo1_h_q" quantity="pop_RMD/0/RMD/biophys/membraneProperties/slo1_chans/RMD_slo1/h/q"/>
+        </OutputFile>
+
+        <OutputFile id="pop_RMD_0_biophys_membraneProperties_slo1_chans_RMD_slo1_m_q_dat" fileName="pop_RMD_0.biophys_membraneProperties_slo1_chans_RMD_slo1_m_q.dat">
+            <OutputColumn id="pop_RMD_0_RMD_biophys_membraneProperties_slo1_chans_RMD_slo1_m_q" quantity="pop_RMD/0/RMD/biophys/membraneProperties/slo1_chans/RMD_slo1/m/q"/>
+        </OutputFile>
+
+        <OutputFile id="pop_RMD_0_biophys_membraneProperties_slo1_chans_gDensity_dat" fileName="pop_RMD_0.biophys_membraneProperties_slo1_chans_gDensity.dat">
+            <OutputColumn id="pop_RMD_0_RMD_biophys_membraneProperties_slo1_chans_gDensity" quantity="pop_RMD/0/RMD/biophys/membraneProperties/slo1_chans/gDensity"/>
+        </OutputFile>
+
+        <OutputFile id="pop_RMD_0_biophys_membraneProperties_slo1_chans_iDensity_dat" fileName="pop_RMD_0.biophys_membraneProperties_slo1_chans_iDensity.dat">
+            <OutputColumn id="pop_RMD_0_RMD_biophys_membraneProperties_slo1_chans_iDensity" quantity="pop_RMD/0/RMD/biophys/membraneProperties/slo1_chans/iDensity"/>
+        </OutputFile>
+
         <OutputFile id="pop_RMD_0_biophys_membraneProperties_slo2_chans_RMD_slo2_h_q_dat" fileName="pop_RMD_0.biophys_membraneProperties_slo2_chans_RMD_slo2_h_q.dat">
             <OutputColumn id="pop_RMD_0_RMD_biophys_membraneProperties_slo2_chans_RMD_slo2_h_q" quantity="pop_RMD/0/RMD/biophys/membraneProperties/slo2_chans/RMD_slo2/h/q"/>
         </OutputFile>

diff --git a/NeuroML2/RMD.cell.nml b/NeuroML2/RMD.cell.nml
@@ -10,6 +10,7 @@
     <include href="RMD_egl19.channel.nml"/>
     <include href="RMD_cca.channel.nml"/>
     <include href="RMD_bk.channel.nml"/>
+    <include href="RMD_slo1.channel.nml"/>
     <include href="RMD_slo2.channel.nml"/>
     <include href="RMD_sk.channel.nml"/>
     <include href="CaDynamics.nml"/>
@@ -41,6 +42,7 @@
                 <channelDensity id="egl19_chans" ionChannel="RMD_egl19" condDensity="78.15410583993324 S_per_m2" erev="60.0mV" ion="ca"/>
                 <channelDensity id="cca_chans" ionChannel="RMD_cca" condDensity="244.72497788261924 S_per_m2" erev="60.0mV" ion="ca"/>
                 <channelDensity id="bk_chans" ionChannel="RMD_bk" condDensity="23.683062375737347 S_per_m2" erev="-80.0mV" ion="k"/>
+                <channelDensity id="slo1_chans" ionChannel="RMD_slo1" condDensity="23.683062375737347 S_per_m2" erev="-80.0mV" ion="k"/>
                 <channelDensity id="slo2_chans" ionChannel="RMD_slo2" condDensity="23.683062375737347 S_per_m2" erev="-80.0mV" ion="k"/>
                 <channelDensity id="sk_chans" ionChannel="RMD_sk" condDensity="4.736612475147469 S_per_m2" erev="-80.0mV" ion="k"/>
                 <spikeThresh value="0mV"/>