From 971694c9a97a002fad293bc1a27a90f49e8769a4 Mon Sep 17 00:00:00 2001
From: Padraig Gleeson <p.gleeson@gmail.com>
Date: Wed, 11 Nov 2015 19:50:11 +0000
Subject: [PATCH] Improved values for testing full cell

---
 NeuroML2/L23_NoHotSpot.cell.nml      | 22 +++++++++++-----------
 NeuroML2/LEMS_L23Test.xml            |  7 +++----
 NeuroML2/singleCompAllChans.cell.nml |  2 +-
 3 files changed, 15 insertions(+), 16 deletions(-)

diff --git a/NeuroML2/L23_NoHotSpot.cell.nml b/NeuroML2/L23_NoHotSpot.cell.nml
index ae7d4c3..08b38b8 100644
--- a/NeuroML2/L23_NoHotSpot.cell.nml
+++ b/NeuroML2/L23_NoHotSpot.cell.nml
@@ -16643,27 +16643,27 @@
 
       <membraneProperties> 
 
-        <channelDensity ionChannel="pas" id="pas_all"  condDensity = "0.142857 mS_per_cm2" erev="-75 mV" />
+        <channelDensity ionChannel="pas" id="pas_all"  condDensity = "0.000142857 S_per_cm2" ion="non_specific" erev="-75 mV" />
 
-        <channelDensity ionChannel="kca" id="kca_all"  condDensity = "3000 mS_per_cm2" erev="-90 mV" />
+        <channelDensity ionChannel="kca" id="kca_all"  condDensity = "3.0e-4 S_per_cm2" ion="k" erev="-90 mV" />
 
-        <channelDensity ionChannel="km" id="km_dends"  condDensity = "1000 mS_per_cm2" segmentGroup="dendrite_group"  erev="-90 mV" />
+        <channelDensity ionChannel="km" id="km_dends"  condDensity = "1e-4 S_per_cm2" ion="k" segmentGroup="dendrite_group"  erev="-90 mV" />
 
-        <channelDensity ionChannel="km" id="km_soma"  condDensity = "2200 mS_per_cm2" segmentGroup="soma_group"  erev="-90 mV" />
+        <channelDensity ionChannel="km" id="km_soma"  condDensity = "2.2e-4 S_per_cm2" ion="k" segmentGroup="soma_group"  erev="-90 mV" />
 
-        <channelDensity ionChannel="kv" id="kv_dends"  condDensity = "3000 mS_per_cm2" segmentGroup="dendrite_group"  erev="-90 mV" />
+        <channelDensity ionChannel="kv" id="kv_dends"  condDensity = "0.03 S_per_cm2" ion="k" segmentGroup="dendrite_group"  erev="-90 mV" />
 
-        <channelDensity ionChannel="kv" id="kv_soma"  condDensity = "100000 mS_per_cm2" segmentGroup="soma_group"  erev="-90 mV" />
+        <channelDensity ionChannel="kv" id="kv_soma"  condDensity = "0.01 S_per_cm2" ion="k" segmentGroup="soma_group"  erev="-90 mV" />
 
-        <channelDensity ionChannel="na" id="na_dends"  condDensity = "80000 mS_per_cm2" segmentGroup="dendrite_group"  erev="60 mV" />
+        <channelDensity ionChannel="na" id="na_dends"  condDensity = "0.008 S_per_cm2" ion="na" segmentGroup="dendrite_group"  erev="60 mV" />
 
-        <channelDensity ionChannel="na" id="na_soma"  condDensity = "1e6 mS_per_cm2" segmentGroup="soma_group"  erev="60 mV" />
+        <channelDensity ionChannel="na" id="na_soma"  condDensity = "0.1 S_per_cm2" ion="na" segmentGroup="soma_group"  erev="60 mV" />
 
-        <channelDensity ionChannel="it" id="it_soma"  condDensity = "0.3 mS_per_cm2" segmentGroup="soma_group" erev="127.57323 mV" />
+        <channelDensity ionChannel="it" id="it_soma"  condDensity = "0.0003 S_per_cm2" ion="ca" segmentGroup="soma_group" erev="127.57323 mV" />
 
-        <channelDensity ionChannel="it" id="it_dends" condDensity = "0.15 mS_per_cm2" segmentGroup="dendrite_group" erev="127.57323 mV" />        
+        <channelDensity ionChannel="it" id="it_dends" condDensity = "0.00015 S_per_cm2" ion="ca" segmentGroup="dendrite_group" erev="127.57323 mV" />        
         
-        <channelDensity ionChannel="ca" id="ca_all" condDensity = "500 mS_per_cm2" erev="127.57323 mV"/>
+        <channelDensity ionChannel="ca" id="ca_all" condDensity = "5e-5 S_per_cm2" ion="ca" erev="127.57323 mV"/>
         
         <specificCapacitance  value="1 uF_per_cm2" />
 
diff --git a/NeuroML2/LEMS_L23Test.xml b/NeuroML2/LEMS_L23Test.xml
index dc4bb02..94873e1 100644
--- a/NeuroML2/LEMS_L23Test.xml
+++ b/NeuroML2/LEMS_L23Test.xml
@@ -23,10 +23,9 @@
         <!--   Cell files-->
     <Include file="L23_NoHotSpot.cell.nml"/>
     
-    <pulseGenerator id="stim" delay="100ms" duration="400ms" amplitude="350pA"/>
+    <pulseGenerator id="stim" delay="50ms" duration="250ms" amplitude="0.7nA"/>
 
     
-    
     <network id="TestNetwork" type="networkWithTemperature" temperature="35.0 degC">
         
         <population id="PopL23" size="1" type="populationList" component="L23_NoHotSpot">
@@ -37,12 +36,12 @@
             
         </population>
         <inputList id="stim_input" component="stim" population="PopL23">
-            <input destination="synapses" id="0" target="../PopL23/0/L23_NoHotSpot/v"/>
+            <input destination="synapses" id="0" target="../PopL23/0/L23_NoHotSpot"/>
         </inputList>
     </network>
     
 
-    <Component type="Simulation" id="sim1" length="600.0ms" step="0.025ms" target="TestNetwork">
+    <Component type="Simulation" id="sim1" length="400.0ms" step="0.01ms" target="TestNetwork">
         
         <Display id="v" title="Soma VOLTAGE" xmin="-60.0" xmax="660.0" ymin="-104.0" ymax="64.0" timeScale="1ms">
             <Line id="VOLTAGE" timeScale="1ms" quantity="PopL23/0/L23_NoHotSpot/v" scale="1 mV" color="#000000"/>
diff --git a/NeuroML2/singleCompAllChans.cell.nml b/NeuroML2/singleCompAllChans.cell.nml
index 3e935fb..a2bf88e 100644
--- a/NeuroML2/singleCompAllChans.cell.nml
+++ b/NeuroML2/singleCompAllChans.cell.nml
@@ -48,7 +48,7 @@
                 <channelDensity condDensity="0.5e-4 S_per_cm2" id="ca_all" ionChannel="ca" ion="ca" erev="140.0 mV"/>
                 <channelDensity condDensity="3.0e-4 S_per_cm2" id="kca_all" ionChannel="kca" ion="k" erev="-90 mV"/>
                 <channelDensity condDensity="0.0003 S_per_cm2" id="it_all" ionChannel="it" ion="ca" erev="140.0 mV"/>
-                <channelDensity condDensity="0.000142857142857 S_per_cm2" id="pas_all" ionChannel="pas" ion="non_specific" erev="-75 mV"/>
+                <channelDensity condDensity="0.00014285 S_per_cm2" id="pas_all" ionChannel="pas" ion="non_specific" erev="-75 mV"/>
 
                 <spikeThresh value="0 mV"/>
                 <specificCapacitance value="1.0 uF_per_cm2"/>