Merge pull request #6 from OpenSourceBrain/master

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OpenSourceBrain · May 31, 2024 · d992e40 · d992e40
2 parents b044d69 + d1c86af
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diff --git a/NEURON/mb/mod/Steady_state(s)_of_activation_variables_in_kst_at_6.3_degC.png b/NEURON/mb/mod/Steady_state(s)_of_activation_variables_in_kst_at_6.3_degC.png
diff --git a/NEURON/mb/mod/Time_course(s)_of_activation_variables_in_kst_at_6.3_degC.png b/NEURON/mb/mod/Time_course(s)_of_activation_variables_in_kst_at_6.3_degC.png
diff --git a/NeuroML2/KC.cell.nml b/NeuroML2/KC.cell.nml
@@ -0,0 +1,39 @@
+<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="KC_doc">
+    <include href="channels/pas.channel.nml"/>
+    <include href="channels/nas.channel.nml"/>
+    <include href="channels/naf.channel.nml"/>
+    <include href="channels/kv.channel.nml"/>
+    <include href="channels/ka.channel.nml"/>
+    <include href="channels/kst.channel.nml"/>
+    <cell id="KC">
+        <morphology id="morphology">
+            <segment id="0" name="Seg0">
+                <proximal x="0.0" y="0.0" z="0.0" diameter="20.0"/>
+                <distal x="0.0" y="0.0" z="6.366" diameter="20.0"/>
+            </segment>
+            <segmentGroup id="soma_group" neuroLexId="GO:0043025">
+                <notes>Default soma segment group for the cell</notes>
+                <member segment="0"/>
+            </segmentGroup>
+            <segmentGroup id="all">
+                <notes>Default segment group for all segments in the cell</notes>
+                <member segment="0"/>
+            </segmentGroup>
+        </morphology>
+        <biophysicalProperties id="biophys">
+            <membraneProperties>
+                <channelDensity id="pas" ionChannel="pas" condDensity=".0000975 S_per_cm2" erev="-70 mV" ion="non_specific"/>
+                <channelDensity id="nas" ionChannel="nas" condDensity="3e-3 S_per_cm2" erev="-58 mV" ion="na"/>
+                <channelDensity id="naf" ionChannel="naf" condDensity="3.5e-2 S_per_cm2" erev="-58 mV" ion="na"/>
+                <channelDensity id="kv" ionChannel="kv" condDensity="1.5e-3 S_per_cm2" erev="-81 mV" ion="k"/>
+                <channelDensity id="ka" ionChannel="ka" condDensity="1.4525e-2 S_per_cm2" erev="-81 mV" ion="k"/>
+                <channelDensity id="kst" ionChannel="kst" condDensity="2.0275e-3 S_per_cm2" erev="-81 mV" ion="k"/>
+                <specificCapacitance value="1 uF_per_cm2"/>
+                <initMembPotential value="-80mV"/>
+            </membraneProperties>
+            <intracellularProperties>
+                <resistivity value="35.4 ohm_cm"/>
+            </intracellularProperties>
+        </biophysicalProperties>
+    </cell>
+</neuroml>
diff --git a/...dy_state(s)_of_activation_variables_of_naf_from_naf.channel.nml_at_6.3_degC.png b/...dy_state(s)_of_activation_variables_of_naf_from_naf.channel.nml_at_6.3_degC.png
diff --git a/...e_Course(s)_of_activation_variables_of_naf_from_naf.channel.nml_at_6.3_degC.png b/...e_Course(s)_of_activation_variables_of_naf_from_naf.channel.nml_at_6.3_degC.png
diff --git a/NeuroML2/channels/kst.channel.nml b/NeuroML2/channels/kst.channel.nml
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" 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_v2beta4.xsd" id="NeuroML_ionChannel">
+
+    <notes>NeuroML file containing a single ion channel</notes>
+    <include href="RaySigmoid.nml" />
+
+    <ionChannel id="kst" conductance="1pS" type="ionChannelHH" species="k">
+
+        <notes>
+            NEURON implementation of slow transient K+ channel ( KST ) from Wustenberg DG, Boytcheva M, Grunewald B, Byrne JH, Menzel R, Baxter DA
+
+            This is slow transient K+ channel in Apis mellifera Kenyon cells (cultured).
+        </notes>
+
+        <gate id="m" type="gateHHtauInf" instances="3">
+            <steadyState type="Ray_inf" rate="1" midpoint="-20.1mV" scale="16.1mV"/>
+            <timeCourse type="Ray_tau" min_tau="0.5 per_s" max_tau="5.0 per_s" midpoint="20.0 mV" scale="-20.0mV"/>
+        </gate>
+
+        <gate id="h" type="gateHHtauInf" instances="1">
+            <steadyState type="Ray_inf" rate="1" midpoint="-74.7mV" scale="-7.0mV"/>
+            <timeCourse type="Ray_tau" min_tau="150.0 per_s" max_tau="200.0 per_s" midpoint="52.0 mV" scale="-15.0mV"/>
+        </gate>
+    </ionChannel>
+</neuroml>
diff --git a/NeuroML2/channels/nas.channel.nml b/NeuroML2/channels/nas.channel.nml
@@ -4,7 +4,7 @@
     <notes>NeuroML file containing a single ion channel</notes>
     <include href="RaySigmoid.nml" />
 
-    <ionChannel id="Nas" conductance="1pS" type="ionChannelHH" species="na">
+    <ionChannel id="nas" conductance="1pS" type="ionChannelHH" species="na">
 
         <notes>
             Implementation of slow Na+ channel ( NAS ) from Wustenberg DG, Boytcheva M, Grunewald B, Byrne JH, Menzel R, Baxter DA

diff --git a/NeuroML2/postprocess_cells.py b/NeuroML2/postprocess_cells.py
@@ -117,77 +117,64 @@ def postprocess_KC():
     cell.set_specific_capacitance("1 uF_per_cm2", group_id="all")
     cell.set_init_memb_potential("-80mV")
 
-    # L1 validation
-    # cell.validate(recursive=True)
-    cell.summary(morph=False, biophys=True)
-    # use pynml writer to also run L2 validation
-    write_neuroml2_file(celldoc, "KC.cell.nml")
-
-
-def KC_create_na_channel():
-    """Create the Na channel.
-
-    This will create the Na channel and save it to a file.
-    It will also validate this file.
-
-    returns: name of the created file
-    """
-    na_channel = component_factory(
-        "IonChannelHH",
-        id="na_channel",
-        notes="Sodium channel for HH cell",
-        conductance="10pS",
-        species="na",
-        validate=False,
-    )
-    gate_m = component_factory(
-        "GateHHRates",
-        id="m",
-        instances="3",
-        notes="m gate for na channel",
-        validate=False,
-    )
-    m_forward_rate = component_factory(
-        "HHRate", type="HHExpLinearRate", rate="1per_ms", midpoint="-40mV", scale="10mV"
-    )
-    m_reverse_rate = component_factory(
-        "HHRate", type="HHExpRate", rate="4per_ms", midpoint="-65mV", scale="-18mV"
-    )
-
-    gate_m.add(m_forward_rate, hint="forward_rate", validate=False)
-    gate_m.add(m_reverse_rate, hint="reverse_rate")
-    na_channel.add(gate_m)
-
-    gate_h = component_factory(
-        "GateHHRates",
-        id="h",
-        instances="1",
-        notes="h gate for na channel",
-        validate=False,
+    cell.add_channel_density(
+        nml_cell_doc=celldoc,
+        cd_id="nas",
+        ion_channel="nas",
+        cond_density="3e-3 S_per_cm2",
+        erev="-58 mV",
+        group_id="all",
+        ion="na",
+        ion_chan_def_file="channels/nas.channel.nml",
     )
-    h_forward_rate = component_factory(
-        "HHRate", type="HHExpRate", rate="0.07per_ms", midpoint="-65mV", scale="-20mV"
+    cell.add_channel_density(
+        nml_cell_doc=celldoc,
+        cd_id="naf",
+        ion_channel="naf",
+        cond_density="3.5e-2 S_per_cm2",
+        erev="-58 mV",
+        group_id="all",
+        ion="na",
+        ion_chan_def_file="channels/naf.channel.nml",
     )
-    h_reverse_rate = component_factory(
-        "HHRate", type="HHSigmoidRate", rate="1per_ms", midpoint="-35mV", scale="10mV"
+    cell.add_channel_density(
+        nml_cell_doc=celldoc,
+        cd_id="kv",
+        ion_channel="kv",
+        cond_density="1.5e-3 S_per_cm2",
+        erev="-81 mV",
+        group_id="all",
+        ion="k",
+        ion_chan_def_file="channels/kv.channel.nml",
     )
-    gate_h.add(h_forward_rate, hint="forward_rate", validate=False)
-    gate_h.add(h_reverse_rate, hint="reverse_rate")
-    na_channel.add(gate_h)
-
-    na_channel_doc = component_factory(
-        "NeuroMLDocument", id="na_channel", notes="Na channel for HH neuron"
+    cell.add_channel_density(
+        nml_cell_doc=celldoc,
+        cd_id="ka",
+        ion_channel="ka",
+        cond_density="1.4525e-2 S_per_cm2",
+        erev="-81 mV",
+        group_id="all",
+        ion="k",
+        ion_chan_def_file="channels/ka.channel.nml",
     )
-    na_channel_fn = "HH_example_na_channel.nml"
-    na_channel_doc.add(na_channel)
-    na_channel_doc.validate(recursive=True)
-
-    write_neuroml2_file(
-        nml2_doc=na_channel_doc, nml2_file_name=na_channel_fn, validate=True
+    cell.add_channel_density(
+        nml_cell_doc=celldoc,
+        cd_id="kst",
+        ion_channel="kst",
+        cond_density="2.0275e-3 S_per_cm2",
+        erev="-81 mV",
+        group_id="all",
+        ion="k",
+        ion_chan_def_file="channels/kst.channel.nml",
     )
 
-    return na_channel_fn
+    # L1 validation
+    # cell.validate(recursive=True)
+    cell.summary(morph=False, biophys=True)
+    # use pynml writer to also run L2 validation
+    write_neuroml2_file(celldoc, "KC.cell.nml")
 
 
 if __name__ == "__main__":
     postprocess_GGN()
+    postprocess_KC()