From 39115b3901b0ba6ac579ddd5ecc2a75ef06737ed Mon Sep 17 00:00:00 2001
From: Jonathan Cooper <j.p.cooper@ucl.ac.uk>
Date: Wed, 21 Feb 2018 11:37:06 +0000
Subject: [PATCH 01/13] Add first equation in test CellML file

---
 tests/cellml_files/test_simple_odes.cellml | 71 ++++++++++++++++++++++
 1 file changed, 71 insertions(+)
 create mode 100644 tests/cellml_files/test_simple_odes.cellml

diff --git a/tests/cellml_files/test_simple_odes.cellml b/tests/cellml_files/test_simple_odes.cellml
new file mode 100644
index 00000000..d346d5bf
--- /dev/null
+++ b/tests/cellml_files/test_simple_odes.cellml
@@ -0,0 +1,71 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!--
+This model is designed to test the following kinds of equations:
+
+    dV/dt = 1, V(0) = 1
+    dx/dt = 1, dy/dt = -1, x(0) = y(0) = 1
+    dx/dt = -y, dy/dt = x, x(0) = 0, y(0) = 1
+    dx/dt1 = -y, dy/dt2 = x, t1 = t2, x(0) = 0, y(0) = 1
+
+The last case checks whether connecting 'time' across components will work naturally. To check connecting V we could use:
+
+    dV/dt = 1, derived = V1 * 2, V1 = V, V(0) = 1
+
+We will also check some connection features (units conversions, encapsulation) and annotations.
+
+-->
+<model name="test_simple_odes" cmeta:id="test_simple_odes" xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#">
+
+   <units name="millisecond">
+      <unit units="second" prefix="milli"/>
+   </units>
+   <units name="per_millisecond">
+      <unit units="millisecond" exponent="-1"/>
+   </units>
+   <units name="millivolt">
+      <unit units="volt" prefix="milli"/>
+   </units>
+   <units name="per_millivolt">
+      <unit units="volt" prefix="milli" exponent="-1"/>
+   </units>
+   <units name="millivolt_per_millisecond">
+      <unit units="millivolt" exponent="1"/>
+      <unit units="millisecond" exponent="-1"/>
+   </units>
+
+   <component name="environment">
+      <variable name="time" public_interface="out" units="millisecond" cmeta:id="time">
+         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#time">
+               <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#time"/>
+            </rdf:Description>
+         </rdf:RDF>
+      </variable>
+   </component>
+
+   <component name="single_independent_ode">
+      <!-- d(sv1)/d(time) = 1, sv1(0) = 1 -->
+      <variable name="time" public_interface="in" units="millisecond"/>
+      <variable name="sv1" units="millivolt" cmeta:id="sv1" initial_value="1">
+         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#sv1">
+               <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#sodium_reversal_potential"/>
+            </rdf:Description>
+         </rdf:RDF>
+      </variable>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+         <apply>
+            <eq/>
+            <apply>
+               <diff/>
+               <bvar>
+                  <ci>time</ci>
+               </bvar>
+               <ci>sv1</ci>
+            </apply>
+            <cn cellml:units="millivolt_per_millisecond">1</cn>
+         </apply>
+      </math>
+   </component>
+
+</model>

From a89e30b71823772f0c929cf84a2800c88431c9d3 Mon Sep 17 00:00:00 2001
From: Jonathan Cooper <j.p.cooper@ucl.ac.uk>
Date: Wed, 21 Feb 2018 14:09:53 +0000
Subject: [PATCH 02/13] Add 2 more independent ODEs

Note that these have variables with the same names but different ids.
---
 tests/cellml_files/test_simple_odes.cellml | 73 +++++++++++++++++++++-
 1 file changed, 70 insertions(+), 3 deletions(-)

diff --git a/tests/cellml_files/test_simple_odes.cellml b/tests/cellml_files/test_simple_odes.cellml
index d346d5bf..709d0e4e 100644
--- a/tests/cellml_files/test_simple_odes.cellml
+++ b/tests/cellml_files/test_simple_odes.cellml
@@ -14,7 +14,10 @@ The last case checks whether connecting 'time' across components will work natur
 We will also check some connection features (units conversions, encapsulation) and annotations.
 
 -->
-<model name="test_simple_odes" cmeta:id="test_simple_odes" xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#">
+<model name="test_simple_odes" cmeta:id="test_simple_odes"
+   xmlns="http://www.cellml.org/cellml/1.0#"
+   xmlns:cellml="http://www.cellml.org/cellml/1.0#"
+   xmlns:cmeta="http://www.cellml.org/metadata/1.0#">
 
    <units name="millisecond">
       <unit units="second" prefix="milli"/>
@@ -46,9 +49,9 @@ We will also check some connection features (units conversions, encapsulation) a
    <component name="single_independent_ode">
       <!-- d(sv1)/d(time) = 1, sv1(0) = 1 -->
       <variable name="time" public_interface="in" units="millisecond"/>
-      <variable name="sv1" units="millivolt" cmeta:id="sv1" initial_value="1">
+      <variable name="sv1" units="millivolt" cmeta:id="sv11" initial_value="1">
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#sv1">
+            <rdf:Description rdf:about="#sv11">
                <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#sodium_reversal_potential"/>
             </rdf:Description>
          </rdf:RDF>
@@ -68,4 +71,68 @@ We will also check some connection features (units conversions, encapsulation) a
       </math>
    </component>
 
+   <component name="single_ode_rhs_const_var">
+      <!-- d(sv1)/d(time) = a, sv1(0) = 1 -->
+      <variable name="time" public_interface="in" units="millisecond"/>
+      <variable name="sv1" units="millivolt" cmeta:id="sv12" initial_value="1">
+         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#sv12">
+               <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#potassium_reversal_potential"/>
+            </rdf:Description>
+         </rdf:RDF>
+      </variable>
+      <variable name="a" units="millivolt_per_millisecond" initial_value="1" cmeta:id="a1"/>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+         <apply>
+            <eq/>
+            <apply>
+               <diff/>
+               <bvar>
+                  <ci>time</ci>
+               </bvar>
+               <ci>sv1</ci>
+            </apply>
+            <ci>a</ci>
+         </apply>
+      </math>
+   </component>
+
+   <component name="single_ode_rhs_computed_var">
+      <!-- d(sv1)/d(time) = a, sv1(0) = 1 -->
+      <variable name="time" public_interface="in" units="millisecond"/>
+      <variable name="sv1" units="millivolt" cmeta:id="sv13" initial_value="1">
+         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#sv13">
+               <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#calcium_reversal_potential"/>
+            </rdf:Description>
+         </rdf:RDF>
+      </variable>
+      <variable name="a" units="millivolt_per_millisecond" cmeta:id="a2"/>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+         <apply>
+            <eq/>
+            <apply>
+               <diff/>
+               <bvar>
+                  <ci>time</ci>
+               </bvar>
+               <ci>sv1</ci>
+            </apply>
+            <ci>a</ci>
+         </apply>
+         <apply><eq/>
+            <ci>a</ci>
+            <cn cellml:units="millivolt_per_millisecond">-1</cn>
+         </apply>
+      </math>
+   </component>
+
+   <!-- RDF can appear outside components too -->
+   <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+            xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+      <rdf:Description rdf:about="#a1">
+         <bqbiol:is rdf:resource="urn:test-ns#parameter_a1"/>
+      </rdf:Description>
+   </rdf:RDF>
+    
 </model>

From 78cc2a7e180c39b823dfe43881f48ad40d306785 Mon Sep 17 00:00:00 2001
From: Jonathan Cooper <j.p.cooper@ucl.ac.uk>
Date: Wed, 21 Feb 2018 14:12:24 +0000
Subject: [PATCH 03/13] Connect up time

---
 tests/cellml_files/test_simple_odes.cellml | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/tests/cellml_files/test_simple_odes.cellml b/tests/cellml_files/test_simple_odes.cellml
index 709d0e4e..2d1e8a63 100644
--- a/tests/cellml_files/test_simple_odes.cellml
+++ b/tests/cellml_files/test_simple_odes.cellml
@@ -127,6 +127,24 @@ We will also check some connection features (units conversions, encapsulation) a
       </math>
    </component>
 
+   <!-- Encapsulation hierarchy - empty at present - all components top-level -->
+   <group>
+      <relationship_ref relationship="encapsulation"/>
+   </group>
+
+   <connection>
+      <map_components component_1="single_independent_ode" component_2="environment"/>
+      <map_variables variable_1="time" variable_2="time"/>
+   </connection>
+   <connection>
+      <map_components component_1="single_ode_rhs_const_var" component_2="environment"/>
+      <map_variables variable_1="time" variable_2="time"/>
+   </connection>
+   <connection>
+      <map_components component_1="single_ode_rhs_computed_var" component_2="environment"/>
+      <map_variables variable_1="time" variable_2="time"/>
+   </connection>
+
    <!-- RDF can appear outside components too -->
    <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
             xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">

From 5e51edf9fad7830da3dfead2700b21c87a779491 Mon Sep 17 00:00:00 2001
From: Jonathan Cooper <j.p.cooper@ucl.ac.uk>
Date: Wed, 21 Feb 2018 14:23:31 +0000
Subject: [PATCH 04/13] Rename units

---
 tests/cellml_files/test_simple_odes.cellml | 36 +++++++++++-----------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/tests/cellml_files/test_simple_odes.cellml b/tests/cellml_files/test_simple_odes.cellml
index 2d1e8a63..2b3a28e6 100644
--- a/tests/cellml_files/test_simple_odes.cellml
+++ b/tests/cellml_files/test_simple_odes.cellml
@@ -19,25 +19,25 @@ We will also check some connection features (units conversions, encapsulation) a
    xmlns:cellml="http://www.cellml.org/cellml/1.0#"
    xmlns:cmeta="http://www.cellml.org/metadata/1.0#">
 
-   <units name="millisecond">
+   <units name="ms">
       <unit units="second" prefix="milli"/>
    </units>
-   <units name="per_millisecond">
-      <unit units="millisecond" exponent="-1"/>
+   <units name="per_ms">
+      <unit units="ms" exponent="-1"/>
    </units>
-   <units name="millivolt">
+   <units name="mV">
       <unit units="volt" prefix="milli"/>
    </units>
-   <units name="per_millivolt">
+   <units name="per_mV">
       <unit units="volt" prefix="milli" exponent="-1"/>
    </units>
-   <units name="millivolt_per_millisecond">
-      <unit units="millivolt" exponent="1"/>
-      <unit units="millisecond" exponent="-1"/>
+   <units name="mV_per_ms">
+      <unit units="mV" exponent="1"/>
+      <unit units="ms" exponent="-1"/>
    </units>
 
    <component name="environment">
-      <variable name="time" public_interface="out" units="millisecond" cmeta:id="time">
+      <variable name="time" public_interface="out" units="ms" cmeta:id="time">
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#time">
                <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#time"/>
@@ -48,8 +48,8 @@ We will also check some connection features (units conversions, encapsulation) a
 
    <component name="single_independent_ode">
       <!-- d(sv1)/d(time) = 1, sv1(0) = 1 -->
-      <variable name="time" public_interface="in" units="millisecond"/>
-      <variable name="sv1" units="millivolt" cmeta:id="sv11" initial_value="1">
+      <variable name="time" public_interface="in" units="ms"/>
+      <variable name="sv1" units="mV" cmeta:id="sv11" initial_value="1">
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#sv11">
                <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#sodium_reversal_potential"/>
@@ -66,22 +66,22 @@ We will also check some connection features (units conversions, encapsulation) a
                </bvar>
                <ci>sv1</ci>
             </apply>
-            <cn cellml:units="millivolt_per_millisecond">1</cn>
+            <cn cellml:units="mV_per_ms">1</cn>
          </apply>
       </math>
    </component>
 
    <component name="single_ode_rhs_const_var">
       <!-- d(sv1)/d(time) = a, sv1(0) = 1 -->
-      <variable name="time" public_interface="in" units="millisecond"/>
-      <variable name="sv1" units="millivolt" cmeta:id="sv12" initial_value="1">
+      <variable name="time" public_interface="in" units="ms"/>
+      <variable name="sv1" units="mV" cmeta:id="sv12" initial_value="1">
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#sv12">
                <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#potassium_reversal_potential"/>
             </rdf:Description>
          </rdf:RDF>
       </variable>
-      <variable name="a" units="millivolt_per_millisecond" initial_value="1" cmeta:id="a1"/>
+      <variable name="a" units="mV_per_ms" initial_value="1" cmeta:id="a1"/>
       <math xmlns="http://www.w3.org/1998/Math/MathML">
          <apply>
             <eq/>
@@ -99,15 +99,15 @@ We will also check some connection features (units conversions, encapsulation) a
 
    <component name="single_ode_rhs_computed_var">
       <!-- d(sv1)/d(time) = a, sv1(0) = 1 -->
-      <variable name="time" public_interface="in" units="millisecond"/>
-      <variable name="sv1" units="millivolt" cmeta:id="sv13" initial_value="1">
+      <variable name="time" public_interface="in" units="ms"/>
+      <variable name="sv1" units="mV" cmeta:id="sv13" initial_value="1">
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#sv13">
                <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#calcium_reversal_potential"/>
             </rdf:Description>
          </rdf:RDF>
       </variable>
-      <variable name="a" units="millivolt_per_millisecond" cmeta:id="a2"/>
+      <variable name="a" units="mV_per_ms" cmeta:id="a2"/>
       <math xmlns="http://www.w3.org/1998/Math/MathML">
          <apply>
             <eq/>

From 0d22b430c92d33af158cde4700d5326938a48c12 Mon Sep 17 00:00:00 2001
From: Jonathan Cooper <j.p.cooper@ucl.ac.uk>
Date: Wed, 21 Feb 2018 14:51:24 +0000
Subject: [PATCH 05/13] Add a coupled pair of ODEs with encapsulation

---
 tests/cellml_files/test_simple_odes.cellml | 96 +++++++++++++++++++++-
 1 file changed, 94 insertions(+), 2 deletions(-)

diff --git a/tests/cellml_files/test_simple_odes.cellml b/tests/cellml_files/test_simple_odes.cellml
index 2b3a28e6..6e992b6f 100644
--- a/tests/cellml_files/test_simple_odes.cellml
+++ b/tests/cellml_files/test_simple_odes.cellml
@@ -35,6 +35,14 @@ We will also check some connection features (units conversions, encapsulation) a
       <unit units="mV" exponent="1"/>
       <unit units="ms" exponent="-1"/>
    </units>
+   <units name="mM">
+      <unit prefix="milli" units="mole"/>
+      <unit units="litre" exponent="-1"/>
+   </units>
+   <units name="mM_per_ms">
+      <unit units="mM"/>
+      <unit units="ms" exponent="-1"/>
+   </units>
 
    <component name="environment">
       <variable name="time" public_interface="out" units="ms" cmeta:id="time">
@@ -122,14 +130,78 @@ We will also check some connection features (units conversions, encapsulation) a
          </apply>
          <apply><eq/>
             <ci>a</ci>
-            <cn cellml:units="millivolt_per_millisecond">-1</cn>
+            <cn cellml:units="mV_per_ms">-1</cn>
+         </apply>
+      </math>
+   </component>
+
+   <!--
+      This trio of components define a coupled pair of ODEs, encapsulated within a parent:
+      dx/dt = -y, dy/dt = x, x(0) = 0, y(0) = 1
+    -->
+   <component name="circle_parent">
+      <variable name="time" public_interface="in" private_interface="out" units="ms"/>
+      <variable name="x" units="mM" private_interface="in"/>
+      <variable name="y" units="mM" private_interface="in"/>
+   </component>
+   <component name="circle_x">
+      <variable name="time" public_interface="in" units="ms"/>
+      <variable name="x" units="mM" cmeta:id="x1" initial_value="0" public_interface="out">
+      <variable name="y" units="mM" public_interface="in">
+         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#x1">
+               <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#cytosolic_calcium_concentration"/>
+            </rdf:Description>
+         </rdf:RDF>
+      </variable>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+         <apply>
+            <eq/>
+            <apply>
+               <diff/>
+               <bvar>
+                  <ci>time</ci>
+               </bvar>
+               <ci>x</ci>
+            </apply>
+            <apply><minus/>
+               <ci>y</ci>
+            </apply>
+         </apply>
+      </math>
+   </component>
+   <component name="circle_y">
+      <variable name="time" public_interface="in" units="ms"/>
+      <variable name="y" units="mM" cmeta:id="y1" initial_value="1" public_interface="out">
+      <variable name="x" units="mM" public_interface="in">
+         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#y1">
+               <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#extracellular_calcium_concentration"/>
+            </rdf:Description>
+         </rdf:RDF>
+      </variable>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+         <apply>
+            <eq/>
+            <apply>
+               <diff/>
+               <bvar>
+                  <ci>time</ci>
+               </bvar>
+               <ci>y</ci>
+            </apply>
+            <ci>x</ci>
          </apply>
       </math>
    </component>
 
-   <!-- Encapsulation hierarchy - empty at present - all components top-level -->
+   <!-- Encapsulation hierarchy - non-mentioned components are top-level -->
    <group>
       <relationship_ref relationship="encapsulation"/>
+      <component_ref component="circle_parent">
+         <component_ref component="circle_x"/>
+         <component_ref component="circle_y"/>
+      </component_ref>
    </group>
 
    <connection>
@@ -145,6 +217,26 @@ We will also check some connection features (units conversions, encapsulation) a
       <map_variables variable_1="time" variable_2="time"/>
    </connection>
 
+   <connection>
+      <map_components component_1="circle_parent" component_2="environment"/>
+      <map_variables variable_1="time" variable_2="time"/>
+   </connection>
+   <connection>
+      <map_components component_1="circle_parent" component_2="circle_x"/>
+      <map_variables variable_1="time" variable_2="time"/>
+      <map_variables variable_1="x" variable_2="x"/>
+   </connection>
+   <connection>
+      <map_components component_1="circle_parent" component_2="circle_y"/>
+      <map_variables variable_1="time" variable_2="time"/>
+      <map_variables variable_1="y" variable_2="y"/>
+   </connection>
+   <connection>
+      <map_components component_1="circle_x" component_2="circle_y"/>
+      <map_variables variable_1="x" variable_2="x"/>
+      <map_variables variable_1="y" variable_2="y"/>
+   </connection>
+
    <!-- RDF can appear outside components too -->
    <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
             xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">

From 80f829b20b41c34e5c2b961f9972421608a6041e Mon Sep 17 00:00:00 2001
From: Jonathan Cooper <j.p.cooper@ucl.ac.uk>
Date: Thu, 1 Mar 2018 12:15:10 +0000
Subject: [PATCH 06/13] Fix CellML validation issues

---
 tests/cellml_files/test_simple_odes.cellml | 27 +++++++++++++---------
 1 file changed, 16 insertions(+), 11 deletions(-)

diff --git a/tests/cellml_files/test_simple_odes.cellml b/tests/cellml_files/test_simple_odes.cellml
index 6e992b6f..bbf5319b 100644
--- a/tests/cellml_files/test_simple_odes.cellml
+++ b/tests/cellml_files/test_simple_odes.cellml
@@ -146,7 +146,7 @@ We will also check some connection features (units conversions, encapsulation) a
    </component>
    <component name="circle_x">
       <variable name="time" public_interface="in" units="ms"/>
-      <variable name="x" units="mM" cmeta:id="x1" initial_value="0" public_interface="out">
+      <variable name="x" units="mM" cmeta:id="x1" initial_value="0" public_interface="out"/>
       <variable name="y" units="mM" public_interface="in">
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#x1">
@@ -165,21 +165,23 @@ We will also check some connection features (units conversions, encapsulation) a
                <ci>x</ci>
             </apply>
             <apply><minus/>
-               <ci>y</ci>
+               <apply><times/>
+                  <ci>y</ci>
+                  <cn cellml:units="per_ms">1</cn>
+               </apply>
             </apply>
          </apply>
       </math>
    </component>
    <component name="circle_y">
       <variable name="time" public_interface="in" units="ms"/>
-      <variable name="y" units="mM" cmeta:id="y1" initial_value="1" public_interface="out">
-      <variable name="x" units="mM" public_interface="in">
-         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#y1">
-               <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#extracellular_calcium_concentration"/>
-            </rdf:Description>
-         </rdf:RDF>
-      </variable>
+      <variable name="y" units="mM" cmeta:id="y1" initial_value="1" public_interface="out"/>
+      <variable name="x" units="mM" public_interface="in"/>
+      <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+         <rdf:Description rdf:about="#y1">
+            <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#extracellular_calcium_concentration"/>
+         </rdf:Description>
+      </rdf:RDF>
       <math xmlns="http://www.w3.org/1998/Math/MathML">
          <apply>
             <eq/>
@@ -190,7 +192,10 @@ We will also check some connection features (units conversions, encapsulation) a
                </bvar>
                <ci>y</ci>
             </apply>
-            <ci>x</ci>
+            <apply><times/>
+               <ci>x</ci>
+               <cn cellml:units="per_ms">1</cn>
+            </apply>
          </apply>
       </math>
    </component>

From 9a366e28e5d89026c6ffc309179cbed3d53e9145 Mon Sep 17 00:00:00 2001
From: Jonathan Cooper <j.p.cooper@ucl.ac.uk>
Date: Fri, 2 Mar 2018 16:24:04 +0000
Subject: [PATCH 07/13] Add more detailed notes on test cases

---
 tests/cellml_files/test_simple_odes.cellml | 32 +++++++++++++++-------
 1 file changed, 22 insertions(+), 10 deletions(-)

diff --git a/tests/cellml_files/test_simple_odes.cellml b/tests/cellml_files/test_simple_odes.cellml
index bbf5319b..68e90a0d 100644
--- a/tests/cellml_files/test_simple_odes.cellml
+++ b/tests/cellml_files/test_simple_odes.cellml
@@ -1,17 +1,29 @@
 <?xml version="1.0" encoding="utf-8"?>
 <!--
 This model is designed to test the following kinds of equations:
+* single_independent_ode: d(sv1)/d(time) = 1, sv1(0) = 1
+* single_ode_rhs_const_var: d(sv1)/d(time) = a, sv1(0) = 1, a=1 set by initial_value
+  Note that sv1 here is not the same as sv1 elsewhere! Similarly below.
+  This means we're also testing multiple independent ODEs.
+* single_ode_rhs_computed_var: d(sv1)/d(time) = a, sv1(0) = 1, a=-1 set by equation
+* derived_from_state_var: dbl_sv1 = sv1 * 2, where sv1 is connected to single_ode_rhs_computed_var
+* deriv_on_rhs: sv1_rate = d(sv1)/d(time), where sv1 & time are connected to single_ode_rhs_computed_var
+* circle_parent: dx/dt = -y, dy/dt = x, x(0) = 0, y(0) = 1
+  This one also checks encapsulation: x and y ODEs are within child components.
+  All information flow directions are covered.
+* time_units_conversion1: d(sv1)/d(time) = 0.0001, sv1(0) = 1, time in seconds locally
+* time_units_conversion2: d(sv1)/d(time) = 1000, sv1(0) = 1, time in microseconds locally
+* state_units_conversion1: d(sv1)/d(time) = 0.0001, sv1(0) = 1, sv1 in volts locally, exported to proto in mV
+* state_units_conversion2: d(sv1)/d(time) = 1000, sv1(0) = 1, sv1 in microvolts locally, exported to proto in mV
+* deriv_on_rhs1a: sv1_rate = d(sv1)/d(time), where sv1 & time are connected to parent time_units_conversion1
+* deriv_on_rhs2a: sv1_rate = d(sv1)/d(time), where sv1 & time are connected to parent time_units_conversion2
+* deriv_on_rhs1b: sv1_rate = d(sv1)/d(time), where sv1 & time are connected to parent state_units_conversion1
+* deriv_on_rhs2b: sv1_rate = d(sv1)/d(time), where sv1 & time are connected to parent state_units_conversion2
 
-    dV/dt = 1, V(0) = 1
-    dx/dt = 1, dy/dt = -1, x(0) = y(0) = 1
-    dx/dt = -y, dy/dt = x, x(0) = 0, y(0) = 1
-    dx/dt1 = -y, dy/dt2 = x, t1 = t2, x(0) = 0, y(0) = 1
-
-The last case checks whether connecting 'time' across components will work naturally. To check connecting V we could use:
-
-    dV/dt = 1, derived = V1 * 2, V1 = V, V(0) = 1
-
-We will also check some connection features (units conversions, encapsulation) and annotations.
+For annotations, we check:
+* RDF within <variable> elements
+* RDF within a <component> but not inside a <variable>
+* RDF directly within <model>
 
 -->
 <model name="test_simple_odes" cmeta:id="test_simple_odes"

From 181e426312a230c5b681450db15db9b909821f6a Mon Sep 17 00:00:00 2001
From: Jonathan Cooper <j.p.cooper@ucl.ac.uk>
Date: Fri, 2 Mar 2018 16:24:30 +0000
Subject: [PATCH 08/13] Add derived_from_state_var test case

---
 tests/cellml_files/test_simple_odes.cellml | 31 ++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/tests/cellml_files/test_simple_odes.cellml b/tests/cellml_files/test_simple_odes.cellml
index 68e90a0d..b7843fed 100644
--- a/tests/cellml_files/test_simple_odes.cellml
+++ b/tests/cellml_files/test_simple_odes.cellml
@@ -147,6 +147,28 @@ For annotations, we check:
       </math>
    </component>
 
+   <component name="derived_from_state_var">
+      <!-- dbl_sv1 = sv1 * 2, where sv1 is connected to single_ode_rhs_computed_var -->
+      <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+         <rdf:Description rdf:about="#dbl_sv1">
+            <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#chloride_reversal_potential"/>
+         </rdf:Description>
+      </rdf:RDF>
+      <!-- Here the RDF comes *before* the annotated variable, just for fun! -->
+      <variable name="time" public_interface="in" units="ms"/>
+      <variable name="sv1" units="mV" public_interface="in"/>
+      <variable name="dbl_sv1" units="mV" cmeta:id="dbl_sv1"/>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+         <apply><eq/>
+            <ci>dbl_sv1</ci>
+            <apply><times/>
+               <ci>sv1</ci>
+               <cn cellml:units="dimensionless">2</cn>
+            </apply>
+         </apply>
+      </math>
+   </component>
+
    <!--
       This trio of components define a coupled pair of ODEs, encapsulated within a parent:
       dx/dt = -y, dy/dt = x, x(0) = 0, y(0) = 1
@@ -234,6 +256,15 @@ For annotations, we check:
       <map_variables variable_1="time" variable_2="time"/>
    </connection>
 
+   <connection>
+      <map_components component_1="derived_from_state_var" component_2="environment"/>
+      <map_variables variable_1="time" variable_2="time"/>
+   </connection>
+   <connection>
+      <map_components component_1="single_ode_rhs_computed_var" component_2="derived_from_state_var"/>
+      <map_variables variable_1="sv1" variable_2="sv1"/>
+   </connection>
+
    <connection>
       <map_components component_1="circle_parent" component_2="environment"/>
       <map_variables variable_1="time" variable_2="time"/>

From ba1ff6db8266fa00586831595d8be3be3307196f Mon Sep 17 00:00:00 2001
From: Jonathan Cooper <j.p.cooper@ucl.ac.uk>
Date: Fri, 2 Mar 2018 16:25:42 +0000
Subject: [PATCH 09/13] Add missing public_interface

---
 tests/cellml_files/test_simple_odes.cellml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/cellml_files/test_simple_odes.cellml b/tests/cellml_files/test_simple_odes.cellml
index b7843fed..088d746d 100644
--- a/tests/cellml_files/test_simple_odes.cellml
+++ b/tests/cellml_files/test_simple_odes.cellml
@@ -120,7 +120,7 @@ For annotations, we check:
    <component name="single_ode_rhs_computed_var">
       <!-- d(sv1)/d(time) = a, sv1(0) = 1 -->
       <variable name="time" public_interface="in" units="ms"/>
-      <variable name="sv1" units="mV" cmeta:id="sv13" initial_value="1">
+      <variable name="sv1" units="mV" cmeta:id="sv13" initial_value="1" public_interface="out">
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#sv13">
                <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#calcium_reversal_potential"/>

From dd7218f13b7e9c743d2920b15a57223e3decf105 Mon Sep 17 00:00:00 2001
From: Jonathan Cooper <j.p.cooper@ucl.ac.uk>
Date: Fri, 2 Mar 2018 16:30:20 +0000
Subject: [PATCH 10/13] Add deriv_on_rhs test case

---
 tests/cellml_files/test_simple_odes.cellml | 32 ++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/tests/cellml_files/test_simple_odes.cellml b/tests/cellml_files/test_simple_odes.cellml
index 088d746d..f5b904c3 100644
--- a/tests/cellml_files/test_simple_odes.cellml
+++ b/tests/cellml_files/test_simple_odes.cellml
@@ -169,6 +169,29 @@ For annotations, we check:
       </math>
    </component>
 
+   <component name="deriv_on_rhs">
+      <!-- sv1_rate = d(sv1)/d(time), where sv1 & time are connected to single_ode_rhs_computed_var -->
+      <variable name="time" public_interface="in" units="ms"/>
+      <variable name="sv1" units="mV" public_interface="in"/>
+      <variable name="sv1_rate" units="mV_per_ms" cmeta:id="sv1_rate"/>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+         <apply><eq/>
+            <ci>sv1_rate</ci>
+            <apply><diff/>
+               <bvar>
+                  <ci>time</ci>
+               </bvar>
+               <ci>sv1</ci>
+            </apply>
+         </apply>
+      </math>
+      <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+         <rdf:Description rdf:about="#sv1_rate">
+            <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#membrane_potassium_current"/>
+         </rdf:Description>
+      </rdf:RDF>
+   </component>
+
    <!--
       This trio of components define a coupled pair of ODEs, encapsulated within a parent:
       dx/dt = -y, dy/dt = x, x(0) = 0, y(0) = 1
@@ -265,6 +288,15 @@ For annotations, we check:
       <map_variables variable_1="sv1" variable_2="sv1"/>
    </connection>
 
+   <connection>
+      <map_components component_1="deriv_on_rhs" component_2="environment"/>
+      <map_variables variable_1="time" variable_2="time"/>
+   </connection>
+   <connection>
+      <map_components component_1="single_ode_rhs_computed_var" component_2="deriv_on_rhs"/>
+      <map_variables variable_1="sv1" variable_2="sv1"/>
+   </connection>
+
    <connection>
       <map_components component_1="circle_parent" component_2="environment"/>
       <map_variables variable_1="time" variable_2="time"/>

From 27f32147a1749427f5a146e6cff85f569738e6c0 Mon Sep 17 00:00:00 2001
From: Jonathan Cooper <j.p.cooper@ucl.ac.uk>
Date: Fri, 2 Mar 2018 16:42:27 +0000
Subject: [PATCH 11/13] Add time units conversion test cases

---
 tests/cellml_files/test_simple_odes.cellml | 67 ++++++++++++++++++++++
 1 file changed, 67 insertions(+)

diff --git a/tests/cellml_files/test_simple_odes.cellml b/tests/cellml_files/test_simple_odes.cellml
index f5b904c3..d7ae24b8 100644
--- a/tests/cellml_files/test_simple_odes.cellml
+++ b/tests/cellml_files/test_simple_odes.cellml
@@ -47,6 +47,14 @@ For annotations, we check:
       <unit units="mV" exponent="1"/>
       <unit units="ms" exponent="-1"/>
    </units>
+   <units name="mV_per_s">
+      <unit units="mV" exponent="1"/>
+      <unit units="second" exponent="-1"/>
+   </units>
+   <units name="mV_per_usec">
+      <unit units="mV" exponent="1"/>
+      <unit prefix="micro" units="second" exponent="-1"/>
+   </units>
    <units name="mM">
       <unit prefix="milli" units="mole"/>
       <unit units="litre" exponent="-1"/>
@@ -257,6 +265,56 @@ For annotations, we check:
       </math>
    </component>
 
+   <component name="time_units_conversion1">
+      <!-- d(sv1)/d(time) = 0.001, sv1(0) = 1, time in seconds locally -->
+      <variable name="time" public_interface="in" units="second" private_interface="out"/>
+      <variable name="sv1" units="mV" cmeta:id="sv1_time1" initial_value="1" private_interface="out">
+         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#sv1_time1">
+               <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#membrane_potassium_current_conductance"/>
+            </rdf:Description>
+         </rdf:RDF>
+      </variable>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+         <apply>
+            <eq/>
+            <apply>
+               <diff/>
+               <bvar>
+                  <ci>time</ci>
+               </bvar>
+               <ci>sv1</ci>
+            </apply>
+            <cn cellml:units="mV_per_s">0.001</cn>
+         </apply>
+      </math>
+   </component>
+
+   <component name="time_units_conversion2">
+      <!-- d(sv1)/d(time) = 1000, sv1(0) = 1, time in microseconds locally -->
+      <variable name="time" public_interface="in" units="second" private_interface="out"/>
+      <variable name="sv1" units="mV" cmeta:id="sv1_time2" initial_value="1" private_interface="out">
+         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#sv1_time2">
+               <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#membrane_plateau_potassium_current_conductance"/>
+            </rdf:Description>
+         </rdf:RDF>
+      </variable>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+         <apply>
+            <eq/>
+            <apply>
+               <diff/>
+               <bvar>
+                  <ci>time</ci>
+               </bvar>
+               <ci>sv1</ci>
+            </apply>
+            <cn cellml:units="mV_per_usec">1000</cn>
+         </apply>
+      </math>
+   </component>
+
    <!-- Encapsulation hierarchy - non-mentioned components are top-level -->
    <group>
       <relationship_ref relationship="encapsulation"/>
@@ -317,6 +375,15 @@ For annotations, we check:
       <map_variables variable_1="y" variable_2="y"/>
    </connection>
 
+   <connection>
+      <map_components component_1="time_units_conversion1" component_2="environment"/>
+      <map_variables variable_1="time" variable_2="time"/>
+   </connection>
+   <connection>
+      <map_components component_1="time_units_conversion2" component_2="environment"/>
+      <map_variables variable_1="time" variable_2="time"/>
+   </connection>
+
    <!-- RDF can appear outside components too -->
    <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
             xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">

From d0b12e6882db30acb149bcbbb24dcf02cc7cb77e Mon Sep 17 00:00:00 2001
From: Jonathan Cooper <j.p.cooper@ucl.ac.uk>
Date: Fri, 2 Mar 2018 17:18:25 +0000
Subject: [PATCH 12/13] Add state var units conversion cases

---
 tests/cellml_files/test_simple_odes.cellml | 71 +++++++++++++++++++++-
 1 file changed, 68 insertions(+), 3 deletions(-)

diff --git a/tests/cellml_files/test_simple_odes.cellml b/tests/cellml_files/test_simple_odes.cellml
index d7ae24b8..5bc19d50 100644
--- a/tests/cellml_files/test_simple_odes.cellml
+++ b/tests/cellml_files/test_simple_odes.cellml
@@ -11,9 +11,9 @@ This model is designed to test the following kinds of equations:
 * circle_parent: dx/dt = -y, dy/dt = x, x(0) = 0, y(0) = 1
   This one also checks encapsulation: x and y ODEs are within child components.
   All information flow directions are covered.
-* time_units_conversion1: d(sv1)/d(time) = 0.0001, sv1(0) = 1, time in seconds locally
+* time_units_conversion1: d(sv1)/d(time) = 0.001, sv1(0) = 1, time in seconds locally
 * time_units_conversion2: d(sv1)/d(time) = 1000, sv1(0) = 1, time in microseconds locally
-* state_units_conversion1: d(sv1)/d(time) = 0.0001, sv1(0) = 1, sv1 in volts locally, exported to proto in mV
+* state_units_conversion1: d(sv1)/d(time) = 0.001, sv1(0) = 1, sv1 in volts locally, exported to proto in mV
 * state_units_conversion2: d(sv1)/d(time) = 1000, sv1(0) = 1, sv1 in microvolts locally, exported to proto in mV
 * deriv_on_rhs1a: sv1_rate = d(sv1)/d(time), where sv1 & time are connected to parent time_units_conversion1
 * deriv_on_rhs2a: sv1_rate = d(sv1)/d(time), where sv1 & time are connected to parent time_units_conversion2
@@ -37,12 +37,18 @@ For annotations, we check:
    <units name="per_ms">
       <unit units="ms" exponent="-1"/>
    </units>
+   <units name="usec">
+      <unit units="second" prefix="micro"/>
+   </units>
    <units name="mV">
       <unit units="volt" prefix="milli"/>
    </units>
    <units name="per_mV">
       <unit units="volt" prefix="milli" exponent="-1"/>
    </units>
+   <units name="uV">
+      <unit units="volt" prefix="micro"/>
+   </units>
    <units name="mV_per_ms">
       <unit units="mV" exponent="1"/>
       <unit units="ms" exponent="-1"/>
@@ -292,7 +298,7 @@ For annotations, we check:
 
    <component name="time_units_conversion2">
       <!-- d(sv1)/d(time) = 1000, sv1(0) = 1, time in microseconds locally -->
-      <variable name="time" public_interface="in" units="second" private_interface="out"/>
+      <variable name="time" public_interface="in" units="usec" private_interface="out"/>
       <variable name="sv1" units="mV" cmeta:id="sv1_time2" initial_value="1" private_interface="out">
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#sv1_time2">
@@ -315,6 +321,56 @@ For annotations, we check:
       </math>
    </component>
 
+   <component name="state_units_conversion1">
+      <!-- d(sv1)/d(time) = 0.001, sv1(0) = 1, sv1 in volts locally, exported to proto in mV -->
+      <variable name="time" public_interface="in" units="ms" private_interface="out"/>
+      <variable name="sv1" units="volt" cmeta:id="sv1_state1" initial_value="1" private_interface="out">
+         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#sv1_state1">
+               <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#membrane_delayed_rectifier_potassium_current"/>
+            </rdf:Description>
+         </rdf:RDF>
+      </variable>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+         <apply>
+            <eq/>
+            <apply>
+               <diff/>
+               <bvar>
+                  <ci>time</ci>
+               </bvar>
+               <ci>sv1</ci>
+            </apply>
+            <cn cellml:units="mV_per_s">0.001</cn>
+         </apply>
+      </math>
+   </component>
+
+   <component name="state_units_conversion2">
+      <!-- d(sv1)/d(time) = 1000, sv1(0) = 1, sv1 in microvolts locally, exported to proto in mV -->
+      <variable name="time" public_interface="in" units="ms" private_interface="out"/>
+      <variable name="sv1" units="uV" cmeta:id="sv1_state2" initial_value="1" private_interface="out">
+         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#sv1_state2">
+               <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#membrane_delayed_rectifier_potassium_current_conductance"/>
+            </rdf:Description>
+         </rdf:RDF>
+      </variable>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+         <apply>
+            <eq/>
+            <apply>
+               <diff/>
+               <bvar>
+                  <ci>time</ci>
+               </bvar>
+               <ci>sv1</ci>
+            </apply>
+            <cn cellml:units="mV_per_usec">1000</cn>
+         </apply>
+      </math>
+   </component>
+
    <!-- Encapsulation hierarchy - non-mentioned components are top-level -->
    <group>
       <relationship_ref relationship="encapsulation"/>
@@ -384,6 +440,15 @@ For annotations, we check:
       <map_variables variable_1="time" variable_2="time"/>
    </connection>
 
+   <connection>
+      <map_components component_1="state_units_conversion1" component_2="environment"/>
+      <map_variables variable_1="time" variable_2="time"/>
+   </connection>
+   <connection>
+      <map_components component_1="state_units_conversion2" component_2="environment"/>
+      <map_variables variable_1="time" variable_2="time"/>
+   </connection>
+
    <!-- RDF can appear outside components too -->
    <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
             xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">

From 6cf7da5792b717ccf79abbd9122119ec025bad04 Mon Sep 17 00:00:00 2001
From: Jonathan Cooper <j.p.cooper@ucl.ac.uk>
Date: Thu, 22 Mar 2018 08:47:54 +0000
Subject: [PATCH 13/13] Add egs of derivatives on the RHS

---
 tests/cellml_files/test_simple_odes.cellml | 134 +++++++++++++++++++++
 1 file changed, 134 insertions(+)

diff --git a/tests/cellml_files/test_simple_odes.cellml b/tests/cellml_files/test_simple_odes.cellml
index 5bc19d50..684c0c88 100644
--- a/tests/cellml_files/test_simple_odes.cellml
+++ b/tests/cellml_files/test_simple_odes.cellml
@@ -296,6 +296,31 @@ For annotations, we check:
       </math>
    </component>
 
+   <component name="deriv_on_rhs1a">
+      <!-- sv1_rate = d(sv1)/d(time), where sv1 & time are connected to parent time_units_conversion1 -->
+      <variable name="time" public_interface="in" units="second"/>
+      <variable name="sv1" units="mV" public_interface="in"/>
+      <variable name="sv1_rate" units="mV_per_s" cmeta:id="sv1_rate1a"/>
+      <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+         <rdf:Description rdf:about="#sv1_rate1a">
+            <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#rapid_time_dependent_potassium_current_Xr1_gate"/>
+         </rdf:Description>
+      </rdf:RDF>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+         <apply>
+            <eq/>
+            <ci>sv1_rate</ci>
+            <apply>
+               <diff/>
+               <bvar>
+                  <ci>time</ci>
+               </bvar>
+               <ci>sv1</ci>
+            </apply>
+         </apply>
+      </math>
+   </component>
+
    <component name="time_units_conversion2">
       <!-- d(sv1)/d(time) = 1000, sv1(0) = 1, time in microseconds locally -->
       <variable name="time" public_interface="in" units="usec" private_interface="out"/>
@@ -321,6 +346,31 @@ For annotations, we check:
       </math>
    </component>
 
+   <component name="deriv_on_rhs2a">
+      <!-- sv1_rate = d(sv1)/d(time), where sv1 & time are connected to parent time_units_conversion2 -->
+      <variable name="time" public_interface="in" units="usec"/>
+      <variable name="sv1" units="mV" public_interface="in"/>
+      <variable name="sv1_rate" units="mV_per_usec" cmeta:id="sv1_rate2a"/>
+      <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+         <rdf:Description rdf:about="#sv1_rate2a">
+            <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#rapid_time_dependent_potassium_current_Xr2_gate"/>
+         </rdf:Description>
+      </rdf:RDF>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+         <apply>
+            <eq/>
+            <ci>sv1_rate</ci>
+            <apply>
+               <diff/>
+               <bvar>
+                  <ci>time</ci>
+               </bvar>
+               <ci>sv1</ci>
+            </apply>
+         </apply>
+      </math>
+   </component>
+
    <component name="state_units_conversion1">
       <!-- d(sv1)/d(time) = 0.001, sv1(0) = 1, sv1 in volts locally, exported to proto in mV -->
       <variable name="time" public_interface="in" units="ms" private_interface="out"/>
@@ -346,6 +396,31 @@ For annotations, we check:
       </math>
    </component>
 
+   <component name="deriv_on_rhs1b">
+      <!-- sv1_rate = d(sv1)/d(time), where sv1 & time are connected to parent state_units_conversion1 -->
+      <variable name="time" public_interface="in" units="ms"/>
+      <variable name="sv1" units="volt" public_interface="in"/>
+      <variable name="sv1_rate" units="mV_per_s" cmeta:id="sv1_rate1b"/>
+      <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+         <rdf:Description rdf:about="#sv1_rate1b">
+            <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#slow_time_dependent_potassium_current_conductance"/>
+         </rdf:Description>
+      </rdf:RDF>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+         <apply>
+            <eq/>
+            <ci>sv1_rate</ci>
+            <apply>
+               <diff/>
+               <bvar>
+                  <ci>time</ci>
+               </bvar>
+               <ci>sv1</ci>
+            </apply>
+         </apply>
+      </math>
+   </component>
+
    <component name="state_units_conversion2">
       <!-- d(sv1)/d(time) = 1000, sv1(0) = 1, sv1 in microvolts locally, exported to proto in mV -->
       <variable name="time" public_interface="in" units="ms" private_interface="out"/>
@@ -371,6 +446,31 @@ For annotations, we check:
       </math>
    </component>
 
+   <component name="deriv_on_rhs2b">
+      <!-- sv1_rate = d(sv1)/d(time), where sv1 & time are connected to parent state_units_conversion2 -->
+      <variable name="time" public_interface="in" units="ms"/>
+      <variable name="sv1" units="uV" public_interface="in"/>
+      <variable name="sv1_rate" units="mV_per_usec" cmeta:id="sv1_rate2b"/>
+      <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+         <rdf:Description rdf:about="#sv1_rate2b">
+            <bqbiol:is rdf:resource="https://chaste.comlab.ox.ac.uk/cellml/ns/oxford-metadata#rapid_time_dependent_potassium_current_conductance"/>
+         </rdf:Description>
+      </rdf:RDF>
+      <math xmlns="http://www.w3.org/1998/Math/MathML">
+         <apply>
+            <eq/>
+            <ci>sv1_rate</ci>
+            <apply>
+               <diff/>
+               <bvar>
+                  <ci>time</ci>
+               </bvar>
+               <ci>sv1</ci>
+            </apply>
+         </apply>
+      </math>
+   </component>
+
    <!-- Encapsulation hierarchy - non-mentioned components are top-level -->
    <group>
       <relationship_ref relationship="encapsulation"/>
@@ -378,6 +478,18 @@ For annotations, we check:
          <component_ref component="circle_x"/>
          <component_ref component="circle_y"/>
       </component_ref>
+      <component_ref component="time_units_conversion1">
+         <component_ref component="deriv_on_rhs1a"/>
+      </component_ref>
+      <component_ref component="time_units_conversion2">
+         <component_ref component="deriv_on_rhs2a"/>
+      </component_ref>
+      <component_ref component="state_units_conversion1">
+         <component_ref component="deriv_on_rhs1b"/>
+      </component_ref>
+      <component_ref component="state_units_conversion2">
+         <component_ref component="deriv_on_rhs2b"/>
+      </component_ref>
    </group>
 
    <connection>
@@ -449,6 +561,28 @@ For annotations, we check:
       <map_variables variable_1="time" variable_2="time"/>
    </connection>
 
+   <connection>
+      <map_components component_1="time_units_conversion1" component_2="deriv_on_rhs1a"/>
+      <map_variables variable_1="time" variable_2="time"/>
+      <map_variables variable_1="sv1" variable_2="sv1"/>
+   </connection>
+   <connection>
+      <map_components component_1="time_units_conversion2" component_2="deriv_on_rhs2a"/>
+      <map_variables variable_1="time" variable_2="time"/>
+      <map_variables variable_1="sv1" variable_2="sv1"/>
+   </connection>
+   <connection>
+      <map_components component_1="state_units_conversion1" component_2="deriv_on_rhs1b"/>
+      <map_variables variable_1="time" variable_2="time"/>
+      <map_variables variable_1="sv1" variable_2="sv1"/>
+   </connection>
+   <connection>
+      <map_components component_1="state_units_conversion2" component_2="deriv_on_rhs2b"/>
+      <map_variables variable_1="time" variable_2="time"/>
+      <map_variables variable_1="sv1" variable_2="sv1"/>
+   </connection>
+
+
    <!-- RDF can appear outside components too -->
    <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
             xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">