Some minimal documentation

openworm · Jun 6, 2024 · cf47415 · cf47415
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diff --git a/NeuroML2/AWC_RMD_NeuroML.png b/NeuroML2/AWC_RMD_NeuroML.png
diff --git a/NeuroML2/Fig4C_AWCon.net.nml b/NeuroML2/Fig4C_AWCon.net.nml
@@ -3,17 +3,17 @@
     Generated network: Fig4C_AWCon
     Generation seed: 1234</notes>
     <include href="AWCon.cell.nml"/>
-    <pulseGenerator id="iclamp_stim_min4" delay="200ms" duration="500ms" amplitude="-4pA"/>
-    <pulseGenerator id="iclamp_stim_0" delay="200ms" duration="500ms" amplitude="0pA"/>
-    <pulseGenerator id="iclamp_stim_4" delay="200ms" duration="500ms" amplitude="4pA"/>
-    <pulseGenerator id="iclamp_stim_8" delay="200ms" duration="500ms" amplitude="8pA"/>
-    <pulseGenerator id="iclamp_stim_12" delay="200ms" duration="500ms" amplitude="12pA"/>
-    <pulseGenerator id="iclamp_stim_16" delay="200ms" duration="500ms" amplitude="16pA"/>
-    <pulseGenerator id="iclamp_stim_20" delay="200ms" duration="500ms" amplitude="20pA"/>
+    <pulseGenerator id="iclamp_stim_min4" delay="100ms" duration="500ms" amplitude="-4pA"/>
+    <pulseGenerator id="iclamp_stim_0" delay="100ms" duration="500ms" amplitude="0pA"/>
+    <pulseGenerator id="iclamp_stim_4" delay="100ms" duration="500ms" amplitude="4pA"/>
+    <pulseGenerator id="iclamp_stim_8" delay="100ms" duration="500ms" amplitude="8pA"/>
+    <pulseGenerator id="iclamp_stim_12" delay="100ms" duration="500ms" amplitude="12pA"/>
+    <pulseGenerator id="iclamp_stim_16" delay="100ms" duration="500ms" amplitude="16pA"/>
+    <pulseGenerator id="iclamp_stim_20" delay="100ms" duration="500ms" amplitude="20pA"/>
     <network id="Fig4C_AWCon" type="networkWithTemperature" temperature="34.0degC">
         <notes>A network model: Fig4C_AWCon</notes>
         <property tag="recommended_dt_ms" value="0.025"/>
-        <property tag="recommended_duration_ms" value="800.0"/>
+        <property tag="recommended_duration_ms" value="700.0"/>
         <population id="pop_AWCon" component="AWCon" size="7" type="populationList">
             <property tag="color" value="0.8 0 0"/>
             <property tag="region" value="Worm"/>

diff --git a/NeuroML2/Fig7B_RMD.net.nml b/NeuroML2/Fig7B_RMD.net.nml
@@ -3,15 +3,15 @@
     Generated network: Fig7B_RMD
     Generation seed: 1234</notes>
     <include href="RMD.cell.nml"/>
-    <pulseGenerator id="iclamp_stim_min2" delay="110ms" duration="50ms" amplitude="-2pA"/>
-    <pulseGenerator id="iclamp_stim_2" delay="110ms" duration="50ms" amplitude="2pA"/>
-    <pulseGenerator id="iclamp_stim_6" delay="110ms" duration="50ms" amplitude="6pA"/>
-    <pulseGenerator id="iclamp_stim_10" delay="110ms" duration="50ms" amplitude="10pA"/>
-    <pulseGenerator id="iclamp_hyp" delay="210ms" duration="20ms" amplitude="-15pA"/>
+    <pulseGenerator id="iclamp_stim_min2" delay="10ms" duration="50ms" amplitude="-2pA"/>
+    <pulseGenerator id="iclamp_stim_2" delay="10ms" duration="50ms" amplitude="2pA"/>
+    <pulseGenerator id="iclamp_stim_6" delay="10ms" duration="50ms" amplitude="6pA"/>
+    <pulseGenerator id="iclamp_stim_10" delay="10ms" duration="50ms" amplitude="10pA"/>
+    <pulseGenerator id="iclamp_hyp" delay="110ms" duration="20ms" amplitude="-15pA"/>
     <network id="Fig7B_RMD" type="networkWithTemperature" temperature="34.0degC">
         <notes>A network model: Fig7B_RMD</notes>
         <property tag="recommended_dt_ms" value="0.025"/>
-        <property tag="recommended_duration_ms" value="250.0"/>
+        <property tag="recommended_duration_ms" value="150.0"/>
         <population id="pop_RMD" component="RMD" size="4" type="populationList">
             <property tag="color" value="0.8 0 0"/>
             <property tag="region" value="Worm"/>

diff --git a/NeuroML2/GenerateExamples.py b/NeuroML2/GenerateExamples.py
@@ -14,14 +14,14 @@ def generate(cell, config, parameters=None):
     stim_delay = 100
     stim_dur = 500
     post_stim = 100
-    extra_init = 100
+    extra_init = 0
 
     if cell == "RMD":
         amps = [-2, 2, 6, 10]
         stim_delay = 10
         stim_dur = 50
         post_stim = 90
-        extra_init = 100
+        extra_init = 0
 
     sim, net = create_new_model(
         reference,

diff --git a/NeuroML2/LEMS_Sim_Fig4C_AWCon.xml b/NeuroML2/LEMS_Sim_Fig4C_AWCon.xml
@@ -18,8 +18,8 @@
     <Include file="Fig4C_AWCon.net.nml"/>
     <Include file="AWCon.cell.nml"/>
 
-    <Simulation id="Sim_Fig4C_AWCon" length="800.0ms" step="0.025ms" target="Fig4C_AWCon" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
-        <Display id="pop_AWCon_v" title="Plots of pop_AWCon_v" timeScale="1ms" xmin="-80.0" xmax="880.0000000000001" ymin="-80" ymax="40">
+    <Simulation id="Sim_Fig4C_AWCon" length="700.0ms" step="0.025ms" target="Fig4C_AWCon" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
+        <Display id="pop_AWCon_v" title="Plots of pop_AWCon_v" timeScale="1ms" xmin="-70.0" xmax="770.0000000000001" ymin="-80" ymax="40">
             <Line id="pop_AWCon_0_AWCon_v" quantity="pop_AWCon/0/AWCon/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
             <Line id="pop_AWCon_1_AWCon_v" quantity="pop_AWCon/1/AWCon/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
             <Line id="pop_AWCon_2_AWCon_v" quantity="pop_AWCon/2/AWCon/v" scale="1mV" color="#98e752" timeScale="1ms"/>

diff --git a/NeuroML2/LEMS_Sim_Fig7B_RMD.xml b/NeuroML2/LEMS_Sim_Fig7B_RMD.xml
@@ -18,8 +18,8 @@
     <Include file="Fig7B_RMD.net.nml"/>
     <Include file="RMD.cell.nml"/>
 
-    <Simulation id="Sim_Fig7B_RMD" length="250.0ms" step="0.025ms" target="Fig7B_RMD" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
-        <Display id="pop_RMD_v" title="Plots of pop_RMD_v" timeScale="1ms" xmin="-25.0" xmax="275.0" ymin="-80" ymax="40">
+    <Simulation id="Sim_Fig7B_RMD" length="150.0ms" step="0.025ms" target="Fig7B_RMD" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
+        <Display id="pop_RMD_v" title="Plots of pop_RMD_v" timeScale="1ms" xmin="-15.0" xmax="165.0" ymin="-80" ymax="40">
             <Line id="pop_RMD_0_RMD_v" quantity="pop_RMD/0/RMD/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
             <Line id="pop_RMD_1_RMD_v" quantity="pop_RMD/1/RMD/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
             <Line id="pop_RMD_2_RMD_v" quantity="pop_RMD/2/RMD/v" scale="1mV" color="#98e752" timeScale="1ms"/>

diff --git a/NeuroML2/regenerateAndTest.sh b/NeuroML2/regenerateAndTest.sh
@@ -1,13 +1,21 @@
 #!/bin/bash
 set -ex
 
+# Format the code
 black *.py
 
+# This script loads in the XPP using the parser in pyNeuroML, and converts the channels to NeuroML
+# It will also run a test simulation of the cells and save the results
+# NOTE: make sure to update to a recent version of pyNeuroML!
 python GenerateNeuroML.py -jnml
 
-python TestXPP.py
-
+# This will use the generated NeuroML cells and create networks with a number of (unconnected cells) and 
+# inject current steps into them to replicate the currnt clamp protocols in Figs 4C and 7B in the paper
 python GenerateExamples.py -jnml
 
+# This will load the original XPP using pyNeuroML, run it, save the results and plot them against the 
+# results generated by the NeuroML in GenerateNeuroML.py
+python TestXPP.py
+
 omv all -V 
 
diff --git a/README.md b/README.md
@@ -13,5 +13,17 @@ The XPP files for the 2 cells are:
 
 [NeuroML](http://www.neuroml.org) compliant versions of the cells and all the ion channels can be found in [this folder](NeuroML2):
 
-- [RMD.cell.nml](RMD.cell.nml)
-- [AWCon.cell.nml](AWC.cell.nml)
+- [RMD.cell.nml](NeuroML2/RMD.cell.nml)
+- [AWCon.cell.nml](NeuroML2/AWC.cell.nml)
+
+These cell models can be run with [pyNeuroML](https://docs.neuroml.org/Userdocs/Software/pyNeuroML.html):
+```
+    pynml LEMS_Sim_Fig4C_AWCon.xml
+
+    pynml Fig7B_RMD.net.nml
+```
+and will produce the following:
+
+![](NeuroML2/AWC_RMD_NeuroML.png)
+
+These cells have been tested against the original XPP versions, see [regenerateAndTest.sh](NeuroML2/regenerateAndTest.sh).