Initial nml model run

app.py

@@ -128,11 +128,23 @@ with tab_model:
 
         from model import run_model
 
-        text = st.text_area("Current injection level:", "100pA")
+        text = st.text_area("Current injection level:", "4.1 pA")
 
         submitted = st.form_submit_button("Submit")
 
         if submitted:
-            response = run_model(text)
+            try:
+                response = run_model(text)
+                st.info(response)
+
+                import numpy as np
+                import matplotlib.pyplot as plt
+
+                arr = np.random.normal(1, 1, size=100)
+                fig, ax = plt.subplots()
+                ax.hist(arr, bins=20)
+
+                st.pyplot(fig)
+            except Exception as e:
+                st.info('There was a problem...\n\n%s'%e)
 
-            st.info(response)

model.py

@@ -5,13 +5,46 @@
 import os
 import re
 
+from neuromllite.utils import load_simulation_json
+from neuromllite.utils import load_network_json
+from neuromllite.NetworkGenerator import generate_and_run
 
-def run_model(text):
+def run_model(text, verbose = False):
 
-    info = 'Running models with: %s'%text
+    info = '''Running models with: [%s]...
+
+'''%text
+
+    sim_file = "models/Sim_IClamp_GenericMuscleCell.json"
+    net_file = "models/IClamp_GenericMuscleCell.json"
+
+    sim = load_simulation_json(sim_file)
+    net = load_network_json(net_file)
+    
+
+    net.parameters["stim_amp"] = text.strip()
+
+
+    if verbose:
+        info+="""```%s```
+
+"""%sim.to_json()
+        info+="""```%s```
+
+"""%net.to_json()
+
+    traces, events = generate_and_run(sim, 
+                                      network=net, 
+                                      simulator="jNeuroML",
+                                      base_dir='./models',
+                                      return_results=True)
+
+    info+="""Results returned: %s"""%(list(traces.keys()))
 
     
 
+    print(info)
+
     return info
 
 

models/GenericMuscleCell.cell.nml

@@ -0,0 +1,33 @@
+<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_v2beta5.xsd" id="GenericCell">
+    <notes>
+
+...
+</notes>
+    <include href="cell_C.xml"/>
+    
+    <fixedFactorConcentrationModel id="CaPool" ion="ca" restingConc="0 mM" decayConstant="20 ms" rho="0.0002 mol_per_m_per_A_per_s"/>
+    <cell id="GenericMuscleCell">
+        <morphology id="morphology_GenericMuscleCell">
+            <segment id="0" name="soma">
+                <proximal x="0.000000e+00" y="0.000000e+00" z="0.000000e+00" diameter="5.0"/>
+                <distal x="0.000000e+00" y="2.000000e+01" z="0.000000e+00" diameter="5.0"/>
+            </segment>
+        </morphology>
+        <biophysicalProperties id="biophys_GenericMuscleCell">
+            <membraneProperties>
+                <channelDensity id="Leak_all" ionChannel="Leak" condDensity="0.00105 mS_per_cm2" erev="-44 mV" ion="non_specific"/>
+                <channelDensity id="k_slow_all" ionChannel="k_slow" condDensity="0.3 mS_per_cm2" erev="-80 mV" ion="k"/>
+                <channelDensity id="ca_simple_all" ionChannel="ca_simple" condDensity="0.25 mS_per_cm2" erev="50 mV" ion="ca"/>
+                <spikeThresh value="-20 mV"/>
+                <specificCapacitance value=".6860 uF_per_cm2"/>
+                <initMembPotential value="-50 mV"/>
+            </membraneProperties>
+            <intracellularProperties>
+                <species id="ca" concentrationModel="CaPool" ion="ca" initialConcentration="0 mM" initialExtConcentration="2E-6 mol_per_cm3"/>
+                <resistivity value="0.1 kohm_cm"/>
+            </intracellularProperties>
+        </biophysicalProperties>
+    </cell>
+    
+    
+</neuroml>

models/GenericNeuronCell.cell.nml

@@ -0,0 +1,31 @@
+<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_v2beta5.xsd" id="GenericCell">
+    <notes>
+...
+</notes>
+    <include href="cell_C.xml"/>
+    <fixedFactorConcentrationModel id="CaPool" ion="ca" restingConc="0 mM" decayConstant="20 ms" rho="0.0002 mol_per_m_per_A_per_s"/>
+ 
+    <cell id="GenericNeuronCell">
+        <morphology id="morphology_GenericNeuronCell">
+            <segment id="0" name="soma">
+                <proximal x="0.000000e+00" y="0.000000e+00" z="0.000000e+00" diameter="5.0"/>
+                <distal x="0.000000e+00" y="0.000000e+00" z="0.000000e+00" diameter="5.0"/>
+            </segment>
+        </morphology>
+        <biophysicalProperties id="biophys_GenericNeuronCell">
+            <membraneProperties>
+                <channelDensity id="Leak_all" ionChannel="Leak" condDensity="0.05 mS_per_cm2" erev="-44 mV" ion="non_specific"/>
+                <channelDensity id="k_slow_all" ionChannel="k_slow" condDensity="0.1 mS_per_cm2" erev="-80 mV" ion="k"/>
+                <channelDensity id="ca_simple_all" ionChannel="ca_simple" condDensity="0.06 mS_per_cm2" erev="50 mV" ion="ca"/>
+                <spikeThresh value="-20 mV"/>
+                <specificCapacitance value="5 uF_per_cm2"/>
+                <initMembPotential value="-50 mV"/>
+            </membraneProperties>
+            <intracellularProperties>
+                <species id="ca" concentrationModel="CaPool" ion="ca" initialConcentration="0 mM" initialExtConcentration="2E-6 mol_per_cm3"/>
+                <resistivity value="0.1 kohm_cm"/>
+            </intracellularProperties>
+        </biophysicalProperties>
+    </cell>
+    
+</neuroml>

models/IClamp_GenericMuscleCell.json

@@ -0,0 +1,54 @@
+{
+    "IClamp_GenericMuscleCell": {
+        "version": "NeuroMLlite v0.5.9",
+        "notes": "A network model: IClamp_GenericMuscleCell",
+        "parameters": {
+            "stim_amp": "4pA"
+        },
+        "cells": {
+            "GenericMuscleCell": {
+                "neuroml2_source_file": "GenericMuscleCell.cell.nml"
+            }
+        },
+        "input_sources": {
+            "iclamp_0": {
+                "parameters": {
+                    "amplitude": "stim_amp",
+                    "delay": "500ms",
+                    "duration": "2000ms"
+                },
+                "neuroml2_input": "PulseGenerator"
+            }
+        },
+        "regions": {
+            "Worm": {
+                "x": 0.0,
+                "y": 0.0,
+                "z": 0.0,
+                "width": 1000.0,
+                "height": 100.0,
+                "depth": 1000.0
+            }
+        },
+        "populations": {
+            "pop_GenericMuscleCell": {
+                "size": 1,
+                "component": "GenericMuscleCell",
+                "properties": {
+                    "color": "0.8 0 0"
+                },
+                "random_layout": {
+                    "region": "Worm"
+                }
+            }
+        },
+        "inputs": {
+            "Stim_iclamp_0": {
+                "input_source": "iclamp_0",
+                "population": "pop_GenericMuscleCell",
+                "percentage": 100
+            }
+        },
+        "temperature": 34.0
+    }
+}

models/IClamp_GenericNeuronCell.json

@@ -0,0 +1,54 @@
+{
+    "IClamp_GenericNeuronCell": {
+        "version": "NeuroMLlite v0.5.9",
+        "notes": "A network model: IClamp_GenericNeuronCell",
+        "parameters": {
+            "stim_amp": "4pA"
+        },
+        "cells": {
+            "GenericNeuronCell": {
+                "neuroml2_source_file": "GenericNeuronCell.cell.nml"
+            }
+        },
+        "input_sources": {
+            "iclamp_0": {
+                "parameters": {
+                    "amplitude": "stim_amp",
+                    "delay": "500ms",
+                    "duration": "2000ms"
+                },
+                "neuroml2_input": "PulseGenerator"
+            }
+        },
+        "regions": {
+            "Worm": {
+                "x": 0.0,
+                "y": 0.0,
+                "z": 0.0,
+                "width": 1000.0,
+                "height": 100.0,
+                "depth": 1000.0
+            }
+        },
+        "populations": {
+            "pop_GenericNeuronCell": {
+                "size": 1,
+                "component": "GenericNeuronCell",
+                "properties": {
+                    "color": "0 0 0.8"
+                },
+                "random_layout": {
+                    "region": "Worm"
+                }
+            }
+        },
+        "inputs": {
+            "Stim_iclamp_0": {
+                "input_source": "iclamp_0",
+                "population": "pop_GenericNeuronCell",
+                "percentage": 100
+            }
+        },
+        "temperature": 34.0
+    }
+}

models/Sim_IClamp_GenericMuscleCell.json

@@ -0,0 +1,12 @@
+{
+    "Sim_IClamp_GenericMuscleCell": {
+        "version": "NeuroMLlite v0.5.9",
+        "network": "IClamp_GenericMuscleCell.json",
+        "duration": 3000.0,
+        "dt": 0.025,
+        "seed": 12345,
+        "record_traces": {
+            "all": "*"
+        }
+    }
+}

models/Sim_IClamp_GenericNeuronCell.json

@@ -0,0 +1,12 @@
+{
+    "Sim_IClamp_GenericNeuronCell": {
+        "version": "NeuroMLlite v0.5.9",
+        "network": "IClamp_GenericNeuronCell.json",
+        "duration": 3000.0,
+        "dt": 0.025,
+        "seed": 12345,
+        "record_traces": {
+            "all": "*"
+        }
+    }
+}

models/cell_C.xml

@@ -0,0 +1,141 @@
+<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_v2beta4.xsd" id="cell_C">
+
+    <!-- Note: Not fully valid NML2: <customHGate> -->
+
+    <!--
+    
+    Parameters C for c302 still under developemnt!!
+    
+    Subject to change without notice!!
+    
+  
+    The fixed values for the parameters here will have to be replaced by parameters set in parameters_C.py & 
+    built using libNeuroML classes
+    
+    -->
+    
+    
+    <ionChannel id="Leak" conductance="10pS" type="ionChannelPassive"/>
+    
+    
+    <ionChannel id="k_fast" conductance="10pS" type="ionChannelHH" species="k">
+
+        <notes>K fast channel from Boyle and Cohen 2008</notes>
+
+        <gateHHtauInf id="p" instances="4">
+
+            <timeCourse type="fixedTimeCourse" tau="2.25518 ms"/>
+            <steadyState type="HHSigmoidVariable" rate="1" scale="7.42636 mV" midpoint="-8.05232 mV"/>
+
+        </gateHHtauInf>
+        
+        <gateHHtauInf id="q" instances="1">
+
+            <timeCourse type="fixedTimeCourse" tau="149.963 ms"/>
+            <steadyState type="HHSigmoidVariable" rate="1" scale="-9.97468 mV" midpoint="-15.6456 mV"/>
+
+        </gateHHtauInf>
+
+    </ionChannel>
+    
+    
+    <ionChannel id="k_slow" conductance="10pS" type="ionChannelHH" species="k">
+
+        <notes>K slow channel from Boyle and Cohen 2008</notes>
+
+        <gateHHtauInf id="n" instances="1">
+
+            <timeCourse type="fixedTimeCourse" tau="25.0007 ms"/>
+            <steadyState type="HHSigmoidVariable" rate="1" scale="15.8512 mV" midpoint="19.8741 mV"/>
+            
+        </gateHHtauInf>
+        
+    </ionChannel>
+    
+    
+    <ionChannel id="ca_boyle" conductance="10pS" type="ionChannelHH" species="ca">
+
+        <notes>Ca channel from Boyle and Cohen 2008</notes>
+
+        <gateHHtauInf id="e" instances="2">
+
+            <timeCourse type="fixedTimeCourse" tau="0.100027 ms"/>
+            <steadyState type="HHSigmoidVariable" rate="1" scale="6.74821 mV" midpoint="-3.3568 mV"/>
+
+        </gateHHtauInf>
+
+        <gateHHtauInf id="f" instances="1">
+
+            <timeCourse type="fixedTimeCourse" tau="150.88 ms"/>
+            
+            <!-- Note!!! 
+
+                f gate is "inactivation" a/c B&C 2008 p172 
+                but the scale value from Table A1 (kf) is positive (5mV), i.e. steady 
+                state is zero for v << midpoint and 1 for v >> midpoint 
+                Couple this with a very slow time course & the ion channel never 
+                conducts as e^2 x f is always ~0 
+
+                Using -5.03176mV NOT 5mV for k/scale to make this INACTIVATION 
+                
+                This is suggested by the value used here:
+                https://github.com/openworm/muscle_model/blob/master/BoyleCohen2008/MatlabSupport/Main_Version/data/input.csv#L20
+                
+                see also
+                https://github.com/openworm/muscle_model/blob/master/BoyleCohen2008/PythonSupport/Main_Version/compareToNeuroML2.py
+            -->
+            <steadyState type="HHSigmoidVariable" rate="1" scale="-5.03176 mV" midpoint="25.1815 mV"/>
+
+        </gateHHtauInf>
+
+        <customHGate id="h" instances="1" alpha="0.282473" ca_half="6.41889e-8 mM" k="-1.00056e-8 mM"/>
+
+    </ionChannel>
+    
+    <ionChannel id="ca_simple" conductance="10pS" type="ionChannelHH" species="ca">
+
+        <notes>Simplified Ca channel</notes>
+
+        <gateHHtauInf id="e" instances="2">
+
+            <timeCourse type="fixedTimeCourse" tau="0.100027 ms"/>
+            <steadyState type="HHSigmoidVariable" rate="1" scale="6.74821 mV" midpoint="-3.3568 mV"/>
+
+        </gateHHtauInf>
+
+    </ionChannel>
+    
+
+    <ComponentType name="customHGate"
+                   extends="gateHHtauInf"
+                   description="Custom gate for h">
+
+        <Parameter name="alpha" dimension="none"/>
+        <Parameter name="k" dimension="concentration"/>
+        <Parameter name="ca_half" dimension="concentration"/>
+
+
+        <Constant name="SEC" dimension="time" value="1s"/>
+
+
+        <Exposure name="tau" dimension="time"/>
+        <Exposure name="inf" dimension="none"/>
+
+        <Requirement name="caConc" dimension="concentration"/>
+
+        <Dynamics>
+
+            <DerivedVariable name="rateScale" exposure="rateScale" dimension="none" value="1"/>
+
+            <DerivedVariable name="inf" dimension="none" exposure="inf" value="1 / (1 + (exp( (ca_half - caConc) / k)))"/>
+
+
+            <DerivedVariable name="tau" dimension="time" exposure="tau" value="0 * SEC"/>
+            <DerivedVariable name="q" exposure="q" dimension="none" value="inf"/>
+            <DerivedVariable name="fcond" exposure="fcond" dimension="none" value="1 +((q-1) * alpha)"/>
+
+        </Dynamics>
+    </ComponentType>
+    
+    
+</neuroml>

requirements.txt

@@ -5,4 +5,5 @@ llamaapi
 asyncio
 langchain_experimental
 wormneuroatlas
-pprint
+neuromllite
+matplotlib