Update x nmllite model to have bias/gain params

.gitignore

@@ -109,3 +109,4 @@ arm64
 /examples/parametersweep/IClamp_GenericNeuronCellX__lems.xml
 /examples/parametersweep/LEMS_SimCanonical_X.png
 /examples/parametersweep/Canonical_X__lems.xml
+/examples/parametersweep/average_last_1percent_GenericNeuronCellX.png

examples/parametersweep/CanonicalCircuit.py

@@ -80,10 +80,18 @@ def generate(duration=1000, paramset="C"):
 
     net = Network(id=reference)
     net.parameters = {}
+
+    cell_params = {"bias": 0, "gain": 1, "tau": "100ms"}
+
     if paramset == "X":
         neuron_id = "GenericNeuronCellX"
 
-        neuron_nmllite = Cell(id=neuron_id, lems_source_file='cell_X.xml')
+        neuron_nmllite = Cell(id=neuron_id, lems_source_file="cell_X.xml")
+        neuron_nmllite.parameters = {}
+
+        for p in cell_params:
+            neuron_nmllite.parameters[p] = p
+            net.parameters[p] = cell_params[p]
 
         exc_syn = Synapse(
             id="neuron_to_neuron_exc_syn_x", neuroml2_source_file="test_syns.xml"
@@ -126,11 +134,11 @@ def generate(duration=1000, paramset="C"):
     net.parameters["scaleDinout"] = 0.5
 
     if paramset == "X":
-        net.parameters["stim_duration"] = "250ms"
-        net.parameters["stim_amp"] = "1pA"
+        net.parameters["stim_duration"] = "2000ms"
+        net.parameters["stim_amp"] = "0.2pA"
         net.parameters["weight_IN_MN"] = 1
         net.parameters["weight_MN_MN_Exc"] = 1
-        net.parameters["weight_MN_MN_Inh"] = -1
+        net.parameters["weight_MN_MN_Inh"] = -5
         net.parameters["scaleDinout"] = 0.5
 
     mode = "circ"
@@ -150,20 +158,22 @@ def generate(duration=1000, paramset="C"):
         add_connection(net, "DD", "DB", inh_syn, "weight_MN_MN_Inh")
 
     if mode == "iclamp":
-
-        add_connection(net, "AVB", "VD", exc_syn, "weight_IN_MN")
-        add_connection(net, "VD", "VB", exc_syn, "weight_MN_MN_Inh")
+        add_connection(net, "AVB", "VB", exc_syn, "weight_IN_MN")
+        add_connection(net, "VB", "VD", exc_syn, "weight_MN_MN_Exc")
+        # add_connection(net, "VB", "DD", exc_syn, "weight_MN_MN_Exc")
+
+        add_connection(net, "VD", "VB", inh_syn, "weight_MN_MN_Inh")
 
     if paramset == "X":
-            input_source = InputSource(
-                id="iclamp_0",
-                neuroml2_input="PulseGenerator",
-                parameters={
-                    "amplitude": "stim_amp",
-                    "delay": "500ms",
-                    "duration": "stim_duration",
-                },
-            )
+        input_source = InputSource(
+            id="iclamp_0",
+            neuroml2_input="PulseGenerator",
+            parameters={
+                "amplitude": "stim_amp",
+                "delay": "500ms",
+                "duration": "stim_duration",
+            },
+        )
 
     else:
         input_source = InputSource(
@@ -202,13 +212,15 @@ def generate(duration=1000, paramset="C"):
         },
     )
 
-    if paramset=="X":
-
-        sim.record_traces={}
-        sim.record_variables={"state": {"all": "*"}, "output": {"all": "*"}} # "V": {"all": "*"}, 
-        sim.plots2D={
+    if paramset == "X":
+        sim.record_traces = {}
+        sim.record_variables = {
+            "state": {"all": "*"},
+            "output": {"all": "*"},
+        }  # "V": {"all": "*"},
+        sim.plots2D = {
             "DB-VB": {
-                "x_axis": "DB/0/%s/output" % neuron_id,
+                "x_axis": "VD/0/%s/output" % neuron_id,
                 "y_axis": "VB/0/%s/output" % neuron_id,
             }
         }

examples/parametersweep/Canonical_X.json

@@ -2,15 +2,23 @@
     "Canonical_X": {
         "version": "NeuroMLlite v0.6.1",
         "parameters": {
-            "stim_duration": "250ms",
-            "stim_amp": "1pA",
+            "bias": 0,
+            "gain": 1,
+            "tau": "100ms",
+            "stim_duration": "2000ms",
+            "stim_amp": "0.2pA",
             "weight_IN_MN": 1,
             "weight_MN_MN_Exc": 1,
-            "weight_MN_MN_Inh": -1,
+            "weight_MN_MN_Inh": -5,
             "scaleDinout": 0.5
         },
         "cells": {
             "GenericNeuronCellX": {
+                "parameters": {
+                    "bias": "bias",
+                    "gain": "gain",
+                    "tau": "tau"
+                },
                 "lems_source_file": "cell_X.xml"
             }
         },
@@ -119,9 +127,9 @@
             }
         },
         "projections": {
-            "proj_AVB_VD": {
+            "proj_AVB_VB": {
                 "presynaptic": "AVB",
-                "postsynaptic": "VD",
+                "postsynaptic": "VB",
                 "synapse": "neuron_to_neuron_exc_syn_x",
                 "type": "continuousProjection",
                 "delay": 0,
@@ -130,10 +138,21 @@
                     "probability": 1
                 }
             },
+            "proj_VB_VD": {
+                "presynaptic": "VB",
+                "postsynaptic": "VD",
+                "synapse": "neuron_to_neuron_exc_syn_x",
+                "type": "continuousProjection",
+                "delay": 0,
+                "weight": "weight_MN_MN_Exc",
+                "random_connectivity": {
+                    "probability": 1
+                }
+            },
             "proj_VD_VB": {
                 "presynaptic": "VD",
                 "postsynaptic": "VB",
-                "synapse": "neuron_to_neuron_exc_syn_x",
+                "synapse": "neuron_to_neuron_inh_syn_x",
                 "type": "continuousProjection",
                 "delay": 0,
                 "weight": "weight_MN_MN_Inh",

examples/parametersweep/Canonical_X.net.nml

@@ -3,17 +3,21 @@
     Generated network: Canonical_X
     Generation seed: 1234
     NeuroMLlite parameters: 
+        bias = 0
+        gain = 1
         scaleDinout = 0.5
-        stim_amp = 1pA
-        stim_duration = 250ms
+        stim_amp = 0.2pA
+        stim_duration = 2000ms
+        tau = 100ms
         weight_IN_MN = 1
         weight_MN_MN_Exc = 1
-        weight_MN_MN_Inh = -1</notes>
+        weight_MN_MN_Inh = -5</notes>
     <include href="Canonical_X__lems.xml"/>
     <include href="test_syns.xml"/>
-    <silentSynapse id="silentSyn_proj_AVB_VD"/>
+    <silentSynapse id="silentSyn_proj_AVB_VB"/>
+    <silentSynapse id="silentSyn_proj_VB_VD"/>
     <silentSynapse id="silentSyn_proj_VD_VB"/>
-    <pulseGenerator id="iclamp_0" delay="500ms" duration="250ms" amplitude="1pA"/>
+    <pulseGenerator id="iclamp_0" delay="500ms" duration="2000ms" amplitude="0.2pA"/>
     <network id="Canonical_X">
         <property tag="recommended_dt_ms" value="0.1"/>
         <property tag="recommended_duration_ms" value="3000.0"/>
@@ -52,11 +56,14 @@
                 <location x="234.608896559712321" y="62.328147503916853" z="61.581569510361525"/>
             </instance>
         </population>
-        <continuousProjection id="proj_AVB_VD" presynapticPopulation="AVB" postsynapticPopulation="VD">
-            <continuousConnectionInstance id="0" preCell="../AVB/0/GenericNeuronCellX" postCell="../VD/0/GenericNeuronCellX" preComponent="silentSyn_proj_AVB_VD" postComponent="neuron_to_neuron_exc_syn_x"/>
+        <continuousProjection id="proj_AVB_VB" presynapticPopulation="AVB" postsynapticPopulation="VB">
+            <continuousConnectionInstance id="0" preCell="../AVB/0/GenericNeuronCellX" postCell="../VB/0/GenericNeuronCellX" preComponent="silentSyn_proj_AVB_VB" postComponent="neuron_to_neuron_exc_syn_x"/>
+        </continuousProjection>
+        <continuousProjection id="proj_VB_VD" presynapticPopulation="VB" postsynapticPopulation="VD">
+            <continuousConnectionInstance id="0" preCell="../VB/0/GenericNeuronCellX" postCell="../VD/0/GenericNeuronCellX" preComponent="silentSyn_proj_VB_VD" postComponent="neuron_to_neuron_exc_syn_x"/>
         </continuousProjection>
         <continuousProjection id="proj_VD_VB" presynapticPopulation="VD" postsynapticPopulation="VB">
-            <continuousConnectionInstanceW id="0" preCell="../VD/0/GenericNeuronCellX" postCell="../VB/0/GenericNeuronCellX" preComponent="silentSyn_proj_VD_VB" postComponent="neuron_to_neuron_exc_syn_x" weight="-1.0"/>
+            <continuousConnectionInstanceW id="0" preCell="../VD/0/GenericNeuronCellX" postCell="../VB/0/GenericNeuronCellX" preComponent="silentSyn_proj_VD_VB" postComponent="neuron_to_neuron_inh_syn_x" weight="-5.0"/>
         </continuousProjection>
         <inputList id="stim" population="AVB" component="iclamp_0">
             <input id="0" target="../AVB/0/GenericNeuronCellX" destination="synapses"/>

examples/parametersweep/GenerateExamples.py

@@ -17,9 +17,9 @@ def generate(cell, duration=3000, config="IClamp", parameters=None):
     reference = "%s_%s" % (config, cell)
 
     cell_id = "%s" % cell
-    
-    if cell_id=='GenericNeuronCellX':
-        cell_nmll = Cell(id=cell_id, lems_source_file='cell_X.xml')
+
+    if cell_id == "GenericNeuronCellX":
+        cell_nmll = Cell(id=cell_id, lems_source_file="cell_X.xml")
     else:
         cell_nmll = Cell(id=cell_id, neuroml2_source_file="%s.cell.nml" % (cell))
 
@@ -30,15 +30,21 @@ def generate(cell, duration=3000, config="IClamp", parameters=None):
         if not parameters:
             parameters = {}
             parameters["stim_amp"] = "350pA"
+
+        parameters["stim_delay"] = "2000ms"
+        parameters["stim_duration"] = "6000ms"
+
+        if cell_id is not "GenericNeuronCellX":
 
-        if cell_id is not 'GenericNeuronCellX':
+            parameters["stim_delay"] = "500ms"
+            parameters["stim_duration"] = "2000ms"
             input_source = InputSource(
                 id="iclamp_0",
                 neuroml2_input="PulseGenerator",
                 parameters={
                     "amplitude": "stim_amp",
-                    "delay": "500ms",
-                    "duration": "2000ms",
+                    "delay": "stim_delay",
+                    "duration": "stim_duration",
                 },
             )
         else:
@@ -47,8 +53,8 @@ def generate(cell, duration=3000, config="IClamp", parameters=None):
                 neuroml2_input="PulseGenerator",
                 parameters={
                     "amplitude": "stim_amp",
-                    "delay": "2000ms",
-                    "duration": "6000ms",
+                    "delay": "stim_delay",
+                    "duration": "stim_duration",
                 },
             )
 
@@ -80,25 +86,28 @@ def generate(cell, duration=3000, config="IClamp", parameters=None):
         input_for_default_population=input_source,
     )
 
-    if cell_id=='GenericNeuronCellX':
-        sim.record_traces={}
-        sim.record_variables={"v": {"all": "*"}, "state": {"all": "*"}, "output": {"all": "*"}}
+    if cell_id == "GenericNeuronCellX":
+        sim.record_traces={"all": "*"}
+        sim.record_variables = {
+            "state": {"all": "*"},
+            "output": {"all": "*"},
+        }
 
-    #qprint(dir(sim))
+    # qprint(dir(sim))
     sim.to_json_file()
 
     return sim, net
 
 
 if __name__ == "__main__":
-
     if "-all" in sys.argv:
         for cell in colors:
             generate(cell, 3000, config="IClamp", parameters={"stim_amp": "4pA"})
 
     elif "-x" in sys.argv:
-
-        sim, net = generate("GenericNeuronCellX", 10000, config="IClamp", parameters={"stim_amp": "1pA"})
+        sim, net = generate(
+            "GenericNeuronCellX", 10000, config="IClamp", parameters={"stim_amp": "1pA"}
+        )
         check_to_generate_or_run(sys.argv, sim)
 
     else:

examples/parametersweep/IClamp_GenericMuscleCell.json

@@ -3,7 +3,9 @@
         "version": "NeuroMLlite v0.6.1",
         "notes": "A network model: IClamp_GenericMuscleCell",
         "parameters": {
-            "stim_amp": "4pA"
+            "stim_amp": "4pA",
+            "stim_delay": "500ms",
+            "stim_duration": "2000ms"
         },
         "cells": {
             "GenericMuscleCell": {
@@ -14,8 +16,8 @@
             "iclamp_0": {
                 "parameters": {
                     "amplitude": "stim_amp",
-                    "delay": "500ms",
-                    "duration": "2000ms"
+                    "delay": "stim_delay",
+                    "duration": "stim_duration"
                 },
                 "neuroml2_input": "PulseGenerator"
             }

examples/parametersweep/IClamp_GenericMuscleCell.net.nml

@@ -3,7 +3,9 @@
     Generated network: IClamp_GenericMuscleCell
     Generation seed: 1234
     NeuroMLlite parameters: 
-        stim_amp = 4pA</notes>
+        stim_amp = 4pA
+        stim_delay = 500ms
+        stim_duration = 2000ms</notes>
     <include href="GenericMuscleCell.cell.nml"/>
     <pulseGenerator id="iclamp_0" delay="500ms" duration="2000ms" amplitude="4pA"/>
     <network id="IClamp_GenericMuscleCell" type="networkWithTemperature" temperature="34.0degC">

examples/parametersweep/IClamp_GenericNeuronCell.json

@@ -3,7 +3,9 @@
         "version": "NeuroMLlite v0.6.1",
         "notes": "A network model: IClamp_GenericNeuronCell",
         "parameters": {
-            "stim_amp": "4pA"
+            "stim_amp": "4pA",
+            "stim_delay": "500ms",
+            "stim_duration": "2000ms"
         },
         "cells": {
             "GenericNeuronCell": {
@@ -14,8 +16,8 @@
             "iclamp_0": {
                 "parameters": {
                     "amplitude": "stim_amp",
-                    "delay": "500ms",
-                    "duration": "2000ms"
+                    "delay": "stim_delay",
+                    "duration": "stim_duration"
                 },
                 "neuroml2_input": "PulseGenerator"
             }

examples/parametersweep/IClamp_GenericNeuronCell.net.nml

@@ -3,7 +3,9 @@
     Generated network: IClamp_GenericNeuronCell
     Generation seed: 1234
     NeuroMLlite parameters: 
-        stim_amp = 4pA</notes>
+        stim_amp = 4pA
+        stim_delay = 500ms
+        stim_duration = 2000ms</notes>
     <include href="GenericNeuronCell.cell.nml"/>
     <pulseGenerator id="iclamp_0" delay="500ms" duration="2000ms" amplitude="4pA"/>
     <network id="IClamp_GenericNeuronCell" type="networkWithTemperature" temperature="34.0degC">

examples/parametersweep/SimCanonical_X.json

@@ -15,7 +15,7 @@
         },
         "plots2D": {
             "DB-VB": {
-                "x_axis": "DB/0/GenericNeuronCellX/output",
+                "x_axis": "VD/0/GenericNeuronCellX/output",
                 "y_axis": "VB/0/GenericNeuronCellX/output"
             }
         }