Different form of <gate> to ensure valid neuroml

openworm · Apr 25, 2024 · 3b0a781 · 3b0a781
1 parent 8e001f9
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Showing 15 changed files with 82 additions and 44 deletions.
diff --git a/.gitignore b/.gitignore
@@ -17,3 +17,4 @@ report.*.txt
 /NeuroML2/LEMS_Test_RMD_cca.xml
 /NeuroML2/LEMS_Test_RMD_shak.xml
 /NeuroML2/LEMS_Test_*.xml
+/RMD_2.ode
diff --git a/NeuroML2/AWCon_cca.channel.nml b/NeuroML2/AWCon_cca.channel.nml
@@ -2,14 +2,14 @@
     <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">
+        <gate id="m" instances="2" type="gateHHtauInf">
             <timeCourse type="cca_m_tau"/>
             <steadyState type="cca_m_inf"/>
-        </gateHHtauInf>
-        <gateHHtauInf id="h" instances="1">
+        </gate>
+        <gate id="h" instances="1" type="gateHHtauInf">
             <timeCourse type="cca_h_tau"/>
             <steadyState type="cca_h_inf"/>
-        </gateHHtauInf>
+        </gate>
     </ionChannelHH>
     <ComponentType name="cca_m_inf" extends="baseVoltageDepVariable">
         <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>

diff --git a/NeuroML2/AWCon_kir.channel.nml b/NeuroML2/AWCon_kir.channel.nml
@@ -2,10 +2,10 @@
     <notes>An ion channel from cell AWCon from Nicoletti et al. 2019</notes>
     <ionChannelHH id="AWCon_kir" species="k" conductance="10pS">
         <notes>AWCon_kir channel from Nicoletti et al. 2019</notes>
-        <gateHHtauInf id="m" instances="1">
+        <gate id="m" instances="1" type="gateHHtauInf">
             <timeCourse type="kir_m_tau"/>
             <steadyState type="kir_m_inf"/>
-        </gateHHtauInf>
+        </gate>
     </ionChannelHH>
     <ComponentType name="kir_m_inf" extends="baseVoltageDepVariable">
         <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>

diff --git a/NeuroML2/AWCon_shak.channel.nml b/NeuroML2/AWCon_shak.channel.nml
@@ -2,14 +2,14 @@
     <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">
+        <gate id="m" instances="1" type="gateHHtauInf">
             <timeCourse type="shak_m_tau"/>
             <steadyState type="shak_m_inf"/>
-        </gateHHtauInf>
-        <gateHHtauInf id="h" instances="1">
+        </gate>
+        <gate id="h" instances="1" type="gateHHtauInf">
             <timeCourse type="shak_h_tau"/>
             <steadyState type="shak_h_inf"/>
-        </gateHHtauInf>
+        </gate>
     </ionChannelHH>
     <ComponentType name="shak_m_inf" extends="baseVoltageDepVariable">
         <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>

diff --git a/NeuroML2/AWCon_shal.channel.nml b/NeuroML2/AWCon_shal.channel.nml
@@ -2,11 +2,11 @@
     <notes>An ion channel from cell AWCon from Nicoletti et al. 2019</notes>
     <ionChannelHH id="AWCon_shal" species="k" conductance="10pS">
         <notes>AWCon_shal channel from Nicoletti et al. 2019</notes>
-        <gateHHtauInf id="m" instances="3">
+        <gate id="m" instances="3" type="gateHHtauInf">
             <timeCourse type="shal_m_tau"/>
             <steadyState type="shal_m_inf"/>
-        </gateHHtauInf>
-        <gateFractional id="h" instances="1">
+        </gate>
+        <gate id="h" instances="1" type="gateFractional">
             <subGate id="hf" fractionalConductance="0.7">
                 <steadyState type="shal_h_hf_inf"/>
                 <timeCourse type="shal_h_hf_tau"/>
@@ -15,7 +15,7 @@
                 <steadyState type="shal_h_hs_inf"/>
                 <timeCourse type="shal_h_hs_tau"/>
             </subGate>
-        </gateFractional>
+        </gate>
     </ionChannelHH>
     <ComponentType name="shal_m_inf" extends="baseVoltageDepVariable">
         <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>

diff --git a/NeuroML2/AWCon_unc2.channel.nml b/NeuroML2/AWCon_unc2.channel.nml
@@ -2,14 +2,14 @@
     <notes>An ion channel from cell AWCon from Nicoletti et al. 2019</notes>
     <ionChannelHH id="AWCon_unc2" species="ca" conductance="10pS">
         <notes>AWCon_unc2 channel from Nicoletti et al. 2019</notes>
-        <gateHHtauInf id="m" instances="1">
+        <gate id="m" instances="1" type="gateHHtauInf">
             <timeCourse type="unc2_m_tau"/>
             <steadyState type="unc2_m_inf"/>
-        </gateHHtauInf>
-        <gateHHtauInf id="h" instances="1">
+        </gate>
+        <gate id="h" instances="1" type="gateHHtauInf">
             <timeCourse type="unc2_h_tau"/>
             <steadyState type="unc2_h_inf"/>
-        </gateHHtauInf>
+        </gate>
     </ionChannelHH>
     <ComponentType name="unc2_m_inf" extends="baseVoltageDepVariable">
         <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>

diff --git a/NeuroML2/GenerateNeuroML.py b/NeuroML2/GenerateNeuroML.py
@@ -34,6 +34,8 @@ def _add_tc_ss(chan_id_in_cell, gate_id, inf_expr_param, tau_expr_param, chan_do
     inf_expr = xpp["derived_variables"][inf_expr_param]
     tau_expr = xpp["derived_variables"][tau_expr_param]
 
+    print("For channel %s, gate %s, inf = [%s], tau = [%s]"%(chan_id_in_cell, gate_id, inf_expr, tau_expr))
+
     potential_parameters = []
     for p in xpp["parameters"]:
         if chan_id_in_cell in p:
@@ -101,12 +103,12 @@ def create_channel_file(chan_id_in_cell, cell_id, xpp, species, gates={}, extra_
         if type(gates[gate_id]) == list:
             ss, tc = _add_tc_ss(chan_id_in_cell, gate_id, gates[gate_id][1], gates[gate_id][2], chan_doc, xpp, extra_params)
 
-            gc = component_factory("GateHHTauInf", id=gate_id, instances=gates[gate_id][0], steady_state=ss, time_course=tc, validate=True) 
+            gc = component_factory("GateHHUndetermined", type="gateHHtauInf", id=gate_id, instances=gates[gate_id][0], steady_state=ss, time_course=tc, validate=True) 
             channel.add(gc)        
 
         elif type(gates[gate_id]) == dict:
 
-            gc = component_factory("GateFractional", id=gate_id, instances=1, validate=False) 
+            gc = component_factory("GateHHUndetermined", type="gateFractional", id=gate_id, instances=1, validate=False) 
 
             for sub_gate in gates[gate_id]:
                 # gates={'m':[3,'minf_shal','tm_shal'],'h':{'hf': [0.7,'hinf_shal','thf_shal'],'hs': [0.3,'hinf_shal','ths_shal']} } 
@@ -343,6 +345,31 @@ def create_cells(channels_to_include):
                 ),
             )
 
+        # EGL-19 CHANNELS
+        if 'egl19' in channels_to_include:
+            chan_id = 'egl19'
+            ion = 'ca'
+            g_param = 'gegl19'
+            gates={'m':[1,'minf_egl19','tm_egl19'],'h':[1,'hinf_egl19','th_egl19']}
+            extra_params = []
+
+            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
+                ),
+            )
+
         # CCA-1 channels
         if 'cca' in channels_to_include:
             chan_id = 'cca'
@@ -400,5 +427,6 @@ def create_cells(channels_to_include):
     channels_to_include = ['leak','kir','shak','cca']
     channels_to_include = ['leak','shal','kir','shak','cca']
     channels_to_include = ['leak','shal','egl36','kir','shak','cca']
+    channels_to_include = ['leak','shal','egl36','kir','shak','cca','unc2','egl19']
     channels_to_include = ['leak','shal','egl36','kir','shak','cca','unc2']
     create_cells(channels_to_include)
diff --git a/NeuroML2/RMD_cca.channel.nml b/NeuroML2/RMD_cca.channel.nml
@@ -2,14 +2,14 @@
     <notes>An ion channel from cell RMD from Nicoletti et al. 2019</notes>
     <ionChannelHH id="RMD_cca" species="ca" conductance="10pS">
         <notes>RMD_cca channel from Nicoletti et al. 2019</notes>
-        <gateHHtauInf id="m" instances="2">
+        <gate id="m" instances="2" type="gateHHtauInf">
             <timeCourse type="cca_m_tau"/>
             <steadyState type="cca_m_inf"/>
-        </gateHHtauInf>
-        <gateHHtauInf id="h" instances="1">
+        </gate>
+        <gate id="h" instances="1" type="gateHHtauInf">
             <timeCourse type="cca_h_tau"/>
             <steadyState type="cca_h_inf"/>
-        </gateHHtauInf>
+        </gate>
     </ionChannelHH>
     <ComponentType name="cca_m_inf" extends="baseVoltageDepVariable">
         <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>

diff --git a/NeuroML2/RMD_egl36.channel.nml b/NeuroML2/RMD_egl36.channel.nml
@@ -2,7 +2,7 @@
     <notes>An ion channel from cell RMD from Nicoletti et al. 2019</notes>
     <ionChannelHH id="RMD_egl36" species="k" conductance="10pS">
         <notes>RMD_egl36 channel from Nicoletti et al. 2019</notes>
-        <gateFractional id="m" instances="1">
+        <gate id="m" instances="1" type="gateFractional">
             <subGate id="m1" fractionalConductance="0.31">
                 <steadyState type="egl36_m_m1_inf"/>
                 <timeCourse type="egl36_m_m1_tau"/>
@@ -15,7 +15,7 @@
                 <steadyState type="egl36_m_m3_inf"/>
                 <timeCourse type="egl36_m_m3_tau"/>
             </subGate>
-        </gateFractional>
+        </gate>
     </ionChannelHH>
     <ComponentType name="egl36_m_m1_inf" extends="baseVoltageDepVariable">
         <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>

diff --git a/NeuroML2/RMD_kir.channel.nml b/NeuroML2/RMD_kir.channel.nml
@@ -2,10 +2,10 @@
     <notes>An ion channel from cell RMD from Nicoletti et al. 2019</notes>
     <ionChannelHH id="RMD_kir" species="k" conductance="10pS">
         <notes>RMD_kir channel from Nicoletti et al. 2019</notes>
-        <gateHHtauInf id="m" instances="1">
+        <gate id="m" instances="1" type="gateHHtauInf">
             <timeCourse type="kir_m_tau"/>
             <steadyState type="kir_m_inf"/>
-        </gateHHtauInf>
+        </gate>
     </ionChannelHH>
     <ComponentType name="kir_m_inf" extends="baseVoltageDepVariable">
         <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>

diff --git a/NeuroML2/RMD_shak.channel.nml b/NeuroML2/RMD_shak.channel.nml
@@ -2,14 +2,14 @@
     <notes>An ion channel from cell RMD from Nicoletti et al. 2019</notes>
     <ionChannelHH id="RMD_shak" species="k" conductance="10pS">
         <notes>RMD_shak channel from Nicoletti et al. 2019</notes>
-        <gateHHtauInf id="m" instances="1">
+        <gate id="m" instances="1" type="gateHHtauInf">
             <timeCourse type="shak_m_tau"/>
             <steadyState type="shak_m_inf"/>
-        </gateHHtauInf>
-        <gateHHtauInf id="h" instances="1">
+        </gate>
+        <gate id="h" instances="1" type="gateHHtauInf">
             <timeCourse type="shak_h_tau"/>
             <steadyState type="shak_h_inf"/>
-        </gateHHtauInf>
+        </gate>
     </ionChannelHH>
     <ComponentType name="shak_m_inf" extends="baseVoltageDepVariable">
         <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>

diff --git a/NeuroML2/RMD_shal.channel.nml b/NeuroML2/RMD_shal.channel.nml
@@ -2,11 +2,11 @@
     <notes>An ion channel from cell RMD from Nicoletti et al. 2019</notes>
     <ionChannelHH id="RMD_shal" species="k" conductance="10pS">
         <notes>RMD_shal channel from Nicoletti et al. 2019</notes>
-        <gateHHtauInf id="m" instances="3">
+        <gate id="m" instances="3" type="gateHHtauInf">
             <timeCourse type="shal_m_tau"/>
             <steadyState type="shal_m_inf"/>
-        </gateHHtauInf>
-        <gateFractional id="h" instances="1">
+        </gate>
+        <gate id="h" instances="1" type="gateFractional">
             <subGate id="hf" fractionalConductance="0.7">
                 <steadyState type="shal_h_hf_inf"/>
                 <timeCourse type="shal_h_hf_tau"/>
@@ -15,7 +15,7 @@
                 <steadyState type="shal_h_hs_inf"/>
                 <timeCourse type="shal_h_hs_tau"/>
             </subGate>
-        </gateFractional>
+        </gate>
     </ionChannelHH>
     <ComponentType name="shal_m_inf" extends="baseVoltageDepVariable">
         <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>

diff --git a/NeuroML2/RMD_unc2.channel.nml b/NeuroML2/RMD_unc2.channel.nml
@@ -2,14 +2,14 @@
     <notes>An ion channel from cell RMD from Nicoletti et al. 2019</notes>
     <ionChannelHH id="RMD_unc2" species="ca" conductance="10pS">
         <notes>RMD_unc2 channel from Nicoletti et al. 2019</notes>
-        <gateHHtauInf id="m" instances="1">
+        <gate id="m" instances="1" type="gateHHtauInf">
             <timeCourse type="unc2_m_tau"/>
             <steadyState type="unc2_m_inf"/>
-        </gateHHtauInf>
-        <gateHHtauInf id="h" instances="1">
+        </gate>
+        <gate id="h" instances="1" type="gateHHtauInf">
             <timeCourse type="unc2_h_tau"/>
             <steadyState type="unc2_h_inf"/>
-        </gateHHtauInf>
+        </gate>
     </ionChannelHH>
     <ComponentType name="unc2_m_inf" extends="baseVoltageDepVariable">
         <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>

diff --git a/NeuroML2/TestXPP.py b/NeuroML2/TestXPP.py
@@ -1,18 +1,26 @@
 
 from pyneuroml.xppaut import parse_script, to_lems, to_xpp, run_xpp_file
 
-
+from pprint import pprint 
 parsed_data = parse_script("../RMD.ode")
+pprint(parsed_data)
+
+all_g = ['gleak','gshal','gkir','gshak','gegl36','gunc2','gegl19','gcca1','gslo1','gbk','gbk2','gslo2','gca','gsc','gnca']
+
 
-all_g = ['gshal','gkir','gshak','gegl36','gunc2','gegl19','gcca1','gslo1','gbk','gbk2','gslo2','gca','gsc','gnca']
+channels_to_include = ['leak']
+channels_to_include = ['leak','shal','egl36','kir','shak','cca','unc2']
 
-all_g.remove('gkir')
-all_g.remove('gcca1')
+for c in channels_to_include:
+    print('Including channel: %s'%c)
+    if c =='cca': c='cca1'
+    all_g.remove('g%s'%c)
 
 for p in all_g:
     parsed_data['parameters'][p] = 0
 
 new_ode_file = 'Test_RMD.ode'
+parsed_data['settings']['total'] = 800
 new_ode = to_xpp(parsed_data, new_ode_file)
 
 

diff --git a/NeuroML2/clean.sh b/NeuroML2/clean.sh
@@ -0,0 +1 @@
+mv *dat *txt LEMS_Test*.xml /tmp