From ed428e9138709d8d787f3866c5e69e5613af8e5e Mon Sep 17 00:00:00 2001
From: Boris Marin <borismarin@gmail.com>
Date: Wed, 6 Apr 2016 15:19:50 +0100
Subject: [PATCH 1/3] child annotation/notes -> children (optional)

---
 NeuroML2CoreTypes/Channels.xml | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/NeuroML2CoreTypes/Channels.xml b/NeuroML2CoreTypes/Channels.xml
index 4434264..76c8c69 100644
--- a/NeuroML2CoreTypes/Channels.xml
+++ b/NeuroML2CoreTypes/Channels.xml
@@ -225,7 +225,7 @@
                    extends="gate"
                    description="Gate which follows the general Hodgkin Huxley formalism">
 
-        <Child name="notes" type="notes"/>
+        <Children name="notes" type="notes"/>
 
         <Child name="forwardRate" type="baseVoltageDepRate"/>
         <Child name="reverseRate" type="baseVoltageDepRate"/>
@@ -269,7 +269,7 @@
                    extends="gate"
                    description="Gate which follows the general Hodgkin Huxley formalism">
 
-        <Child name="notes" type="notes"/>
+        <Children name="notes" type="notes"/>
 
         <Child name="timeCourse" type="baseVoltageDepTime" />
         <Child name="steadyState" type="baseVoltageDepVariable" />
@@ -307,7 +307,7 @@
 
         <Constant name="SEC" dimension="time" value="1 s"/>
         
-        <Child name="notes" type="notes"/>
+        <Children name="notes" type="notes"/>
 
         <Child name="steadyState" type="baseVoltageDepVariable" />
         
@@ -332,7 +332,7 @@
                    extends="gate"
                    description="Gate which follows the general Hodgkin Huxley formalism">
 
-        <Child name="notes" type="notes"/>
+        <Children name="notes" type="notes"/>
 
         <Child name="forwardRate" type="baseVoltageDepRate"/>
         <Child name="reverseRate" type="baseVoltageDepRate"/>
@@ -376,7 +376,7 @@
                    extends="gate"
                    description="Gate which follows the general Hodgkin Huxley formalism">
 
-        <Child name="notes" type="notes"/>
+        <Children name="notes" type="notes"/>
 
         <Child name="forwardRate" type="baseVoltageDepRate"/>
         <Child name="reverseRate" type="baseVoltageDepRate"/>
@@ -416,7 +416,7 @@
                    extends="gate"
                    description="Gate which follows the general Hodgkin Huxley formalism">
 
-        <Child name="notes" type="notes"/>
+        <Children name="notes" type="notes"/>
 
         <Child name="forwardRate" type="baseVoltageDepRate"/>
         <Child name="reverseRate" type="baseVoltageDepRate"/>
@@ -472,7 +472,7 @@
     <ComponentType name="subGate"
                    description="Gate composed of subgates contributing with fractional conductance">
 
-        <Child name="notes" type="notes"/>
+        <Children name="notes" type="notes"/>
 
         <Child name="timeCourse" type="baseVoltageDepTime" />
         <Child name="steadyState" type="baseVoltageDepVariable" />
@@ -511,8 +511,8 @@
     <ComponentType name="ionChannelPassive" 
                    extends="ionChannel"
                    description="Simple passive ion channel where the constant conductance through the channel is equal to _conductance">
-        <Child name="notes" type="notes"/>
-        <Child name="annotation" type="annotation"/>
+        <Children name="notes" type="notes"/>
+        <Children name="annotation" type="annotation"/>
         <Text name="neuroLexId"/>
 
         <Dynamics>
@@ -525,8 +525,8 @@
     <ComponentType name="ionChannelHH" 
                    extends="baseIonChannel"
                    description="Note _ionChannel_ and _ionChannelHH_ are currently functionally identical. This is needed since many existing examples use ionChannel, some use ionChannelHH. NeuroML v2beta4 should remove one of these, probably ionChannelHH.">
-        <Child name="notes" type="notes"/>
-        <Child name="annotation" type="annotation"/>
+        <Children name="notes" type="notes"/>
+        <Children name="annotation" type="annotation"/>
         
         <Children name="conductanceScaling" type="baseConductanceScaling"/>
         <Children name="gates" type="gate"/>
@@ -560,7 +560,7 @@
     <ComponentType name="KSState"
                    description="One of the states in which a _gateKS_ can be. The rates of transitions between these states are given by _KSTransition_s">
         <Parameter name="relativeConductance" dimension="none"/>
-        <Child name="notes" type="notes"/>
+        <Children name="notes" type="notes"/>
         <Exposure name="occupancy" dimension="none"/>
         <Exposure name="q" dimension="none"/>
 
@@ -684,7 +684,7 @@
 
 
     <ComponentType name="gateKS"
-                   extends="baseGate"
+                   extends="gate"
                    description="A gate which consists of multiple _KSState_s and _KSTransition_s giving the rates of transition between them">
         <Children name="states" type="KSState"/>
         <Children name="transitions" type="KSTransition"/>

From 24a13b539d964ed491f8bd5a21b1e466f8f006dd Mon Sep 17 00:00:00 2001
From: Boris Marin <borismarin@gmail.com>
Date: Wed, 6 Apr 2016 15:32:08 +0100
Subject: [PATCH 2/3] children name collision (gates) for ionChannelKS

---
 NeuroML2CoreTypes/Channels.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NeuroML2CoreTypes/Channels.xml b/NeuroML2CoreTypes/Channels.xml
index 4434264..73d886d 100644
--- a/NeuroML2CoreTypes/Channels.xml
+++ b/NeuroML2CoreTypes/Channels.xml
@@ -588,7 +588,7 @@
     <ComponentType name="ionChannelKS" 
                    extends="ionChannel"
                    description="A kinetic scheme based ion channel with multiple _gateKS_s, each of which consists of multiple _KSState_s and _KSTransition_s giving the rates of transition between them">
-        <Children name="gates" type="gateKS"/>
+        <Children name="gatesKS" type="gateKS"/>
     
         <Text name="species"/>
     

From 9c9516d5aaefa11aa63e8bd87ff9dd8b1b4bf7c2 Mon Sep 17 00:00:00 2001
From: Boris Marin <borismarin@gmail.com>
Date: Wed, 6 Apr 2016 15:37:37 +0100
Subject: [PATCH 3/3] corrected path for gatesKS

---
 NeuroML2CoreTypes/Channels.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NeuroML2CoreTypes/Channels.xml b/NeuroML2CoreTypes/Channels.xml
index 8d13667..910580c 100644
--- a/NeuroML2CoreTypes/Channels.xml
+++ b/NeuroML2CoreTypes/Channels.xml
@@ -593,7 +593,7 @@
         <Text name="species"/>
     
         <Dynamics>
-            <DerivedVariable name="fopen" exposure="fopen" dimension="none" select="gates[*]/fcond" reduce="multiply"/>
+            <DerivedVariable name="fopen" exposure="fopen" dimension="none" select="gatesKS[*]/fcond" reduce="multiply"/>
             <DerivedVariable name="g" exposure="g" dimension="conductance" value="fopen * conductance"/>
 
         </Dynamics>