diff --git a/examples/README.md b/examples/README.md
new file mode 100644
index 0000000..b434b13
--- /dev/null
+++ b/examples/README.md
@@ -0,0 +1,2 @@
+## Examples
+The examples in this folder are encoded in the 0.92 format of the spacial specification. 
\ No newline at end of file
diff --git a/examples/The_Brusselator.xml b/examples/The_Brusselator.xml
index d40c2f8..3ca1516 100644
--- a/examples/The_Brusselator.xml
+++ b/examples/The_Brusselator.xml
@@ -1,15 +1,15 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" spatial:required="true">
   <model id="The_Brusselator_Application0" name="The Brusselator_Application0">
-	<annotation>
-        <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+    <annotation>
+      <oldspatialInfo xmlns="http://fbergmann.github.io/oldspatial-sbml/settings">
         <update step="0.1" freq="50"/>
         <items>
           <item sbmlId="X" palette="black-green" max="3"/>
           <item sbmlId="Y" palette="black-red" max="3"/>
         </items>
-      </spatialInfo>
-	</annotation>
+      </oldspatialInfo>
+    </annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
         <listOfUnits>
@@ -18,17 +18,17 @@
       </unitDefinition>
       <unitDefinition id="volume">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="area">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="length">
         <listOfUnits>
-          <unit kind="metre" exponent="1" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="1" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="time">
@@ -43,17 +43,17 @@
       </unitDefinition>
       <unitDefinition id="um3">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um2">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um">
         <listOfUnits>
-          <unit kind="metre" exponent="1" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="1" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="s">
@@ -63,12 +63,12 @@
       </unitDefinition>
       <unitDefinition id="umol_um3_litre_1">
         <listOfUnits>
-          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-21"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="uM_um3_molecules_1">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-21"/>
           <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
           <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
         </listOfUnits>
@@ -88,7 +88,7 @@
       </unitDefinition>
       <unitDefinition id="_one__0E_21">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-21"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="_one_000000">
@@ -99,17 +99,17 @@
     </listOfUnitDefinitions>
     <listOfCompartments>
       <compartment id="cell" name="cell" spatialDimensions="3" size="1" units="um3" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain1cell" spatial:compartment="cell" spatial:domainType="subdomain0" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain1cell" spatial:domainType="subdomain0" spatial:unitSize="1"/>
       </compartment>
       <compartment id="EC" name="EC" spatialDimensions="3" size="1" units="um3" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain0EC" spatial:compartment="EC" spatial:domainType="subdomain1" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain0EC" spatial:domainType="subdomain1" spatial:unitSize="1"/>
       </compartment>
       <compartment id="Membrane0" name="Membrane0" spatialDimensions="2" size="1" units="um2" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain0_subdomain1_membraneMembrane0" spatial:compartment="Membrane0" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="11"/>
+        <spatial:compartmentMapping spatial:id="subdomain0_subdomain1_membraneMembrane0" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="11"/>
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species id="X" compartment="cell" initialConcentration="2.5" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+      <species id="X" compartment="cell" initialConcentration="2.5" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -118,7 +118,7 @@
           </vcell:VCellInfo>
         </annotation>
       </species>
-      <species id="Y" compartment="cell" initialConcentration="2" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+      <species id="Y" compartment="cell" initialConcentration="2" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -129,47 +129,47 @@
       </species>
     </listOfSpecies>
     <listOfParameters>
-      <parameter id="x" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      <parameter id="x" value="0" constant="false">
+        <spatial:spatialSymbolReference spatial:spatialRef="x"/>
       </parameter>
-      <parameter id="y" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      <parameter id="y" value="0" constant="false">
+        <spatial:spatialSymbolReference spatial:spatialRef="y"/>
       </parameter>
-      <parameter id="X_diff" value="0.16" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="X" spatial:coordinateIndex="0"/>
+      <parameter id="X_diff" value="0.16" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="X" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="X_diff1" value="0.16" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="X" spatial:coordinateIndex="1"/>
+      <parameter id="X_diff1" value="0.16" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="X" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="X_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="X" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="X_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="X" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="X_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="X" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="X_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="X" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="X_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="X" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="X_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="X" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="X_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="X" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="X_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="X" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
-      <parameter id="Y_diff" value="0.8" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="Y" spatial:coordinateIndex="0"/>
+      <parameter id="Y_diff" value="0.8" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="Y" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="Y_diff1" value="0.8" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="Y" spatial:coordinateIndex="1"/>
+      <parameter id="Y_diff1" value="0.8" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="Y" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="Y_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="Y" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="Y_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="Y" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="Y_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="Y" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="Y_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="Y" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="Y_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="Y" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="Y_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="Y" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="Y_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="Y" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="Y_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="Y" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
       <parameter id="J0_k_1" value="0.1" units="_one_" constant="true"/>
       <parameter id="J1_k_2" value="0.1" units="_one_" constant="true"/>
@@ -181,7 +181,7 @@
       <parameter id="E" value="0" units="_one_" constant="true"/>
     </listOfParameters>
     <listOfReactions>
-      <reaction id="J0" name="J0" reversible="true" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction id="J0" name="J0" reversible="true" fast="false" spatial:isLocal="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -203,7 +203,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction id="J1" name="J1" reversible="true" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction id="J1" name="J1" reversible="true" fast="false" spatial:isLocal="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -230,7 +230,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction id="J2" name="J2" reversible="true" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction id="J2" name="J2" reversible="true" fast="false" spatial:isLocal="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -256,7 +256,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction id="J3" name="J3" reversible="true" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction id="J3" name="J3" reversible="true" fast="false" spatial:isLocal="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -279,43 +279,43 @@
         </kineticLaw>
       </reaction>
     </listOfReactions>
-    <spatial:geometry spatial:coordinateSystem="Cartesian">
+    <spatial:geometry spatial:id="newGeometry" spatial:coordinateSystem="cartesian">
       <spatial:listOfCoordinateComponents>
-        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
-          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="100"/>
+        <spatial:coordinateComponent spatial:id="x" spatial:type="cartesianX">
+          <spatial:boundaryMin spatial:id="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Xmax" spatial:value="100"/>
         </spatial:coordinateComponent>
-        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
-          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="100"/>
+        <spatial:coordinateComponent spatial:id="y" spatial:type="cartesianY">
+          <spatial:boundaryMin spatial:id="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Ymax" spatial:value="100"/>
         </spatial:coordinateComponent>
       </spatial:listOfCoordinateComponents>
       <spatial:listOfDomainTypes>
-        <spatial:domainType spatial:spatialId="subdomain1" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain0" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
+        <spatial:domainType spatial:id="subdomain1" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain0" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
       </spatial:listOfDomainTypes>
       <spatial:listOfDomains>
-        <spatial:domain spatial:spatialId="subdomain00" spatial:domainType="subdomain1">
+        <spatial:domain spatial:id="subdomain00" spatial:domainType="subdomain1">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="subdomain11" spatial:domainType="subdomain0">
+        <spatial:domain spatial:id="subdomain11" spatial:domainType="subdomain0">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="1" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="membrane_subdomain00_subdomain11" spatial:domainType="subdomain0_subdomain1_membrane"/>
+        <spatial:domain spatial:id="membrane_subdomain00_subdomain11" spatial:domainType="subdomain0_subdomain1_membrane"/>
       </spatial:listOfDomains>
       <spatial:listOfAdjacentDomains>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain00_subdomain11_subdomain11" spatial:domain1="membrane_subdomain00_subdomain11" spatial:domain2="subdomain11"/>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain00_subdomain11_subdomain00" spatial:domain1="membrane_subdomain00_subdomain11" spatial:domain2="subdomain00"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain00_subdomain11_subdomain11" spatial:domain1="membrane_subdomain00_subdomain11" spatial:domain2="subdomain11"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain00_subdomain11_subdomain00" spatial:domain1="membrane_subdomain00_subdomain11" spatial:domain2="subdomain00"/>
       </spatial:listOfAdjacentDomains>
       <spatial:listOfGeometryDefinitions>
-        <spatial:analyticGeometry spatial:spatialId="Geometry3">
+        <spatial:analyticGeometry spatial:id="Geometry3" spatial:isActive="true">
           <spatial:listOfAnalyticVolumes>
-            <spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="1">
+            <spatial:analyticVolume spatial:id="subdomain0" spatial:functionType="layered" spatial:ordinal="1" spatial:domainType="subdomain0">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <piecewise>
                   <piece>
@@ -350,7 +350,7 @@
                 </piecewise>
               </math>
             </spatial:analyticVolume>
-            <spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="0">
+            <spatial:analyticVolume spatial:id="subdomain1" spatial:functionType="layered" spatial:ordinal="0" spatial:domainType="subdomain1">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <cn type="integer"> 1 </cn>
               </math>
diff --git a/examples/The_Brusselator_300x300.xml b/examples/The_Brusselator_300x300.xml
index 9e72453..2a73bd5 100644
--- a/examples/The_Brusselator_300x300.xml
+++ b/examples/The_Brusselator_300x300.xml
@@ -1,16 +1,16 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" spatial:required="true">
   <model id="The_Brusselator_Application0" name="The Brusselator_Application0">
-	<annotation>
-        <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+    <annotation>
+      <oldspatialInfo xmlns="http://fbergmann.github.io/oldspatial-sbml/settings">
         <update step="0.1" freq="500"/>
         <items>
           <item sbmlId="X" palette="black-blue.txt" max="6"/>
           <item sbmlId="Y" palette="black-green.txt" max="6"/>
         </items>
-      </spatialInfo>
-	</annotation>
-	<listOfUnitDefinitions>
+      </oldspatialInfo>
+    </annotation>
+    <listOfUnitDefinitions>
       <unitDefinition id="substance">
         <listOfUnits>
           <unit kind="item" exponent="1" scale="0" multiplier="1"/>
@@ -18,17 +18,17 @@
       </unitDefinition>
       <unitDefinition id="volume">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="area">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="length">
         <listOfUnits>
-          <unit kind="metre" exponent="1" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="1" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="time">
@@ -43,17 +43,17 @@
       </unitDefinition>
       <unitDefinition id="um3">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um2">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um">
         <listOfUnits>
-          <unit kind="metre" exponent="1" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="1" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="s">
@@ -63,12 +63,12 @@
       </unitDefinition>
       <unitDefinition id="umol_um3_litre_1">
         <listOfUnits>
-          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-21"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="uM_um3_molecules_1">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-21"/>
           <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
           <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
         </listOfUnits>
@@ -88,7 +88,7 @@
       </unitDefinition>
       <unitDefinition id="_one__0E_21">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-21"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="_one_000000">
@@ -99,17 +99,17 @@
     </listOfUnitDefinitions>
     <listOfCompartments>
       <compartment id="cell" name="cell" spatialDimensions="3" size="1" units="um3" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain1cell" spatial:compartment="cell" spatial:domainType="subdomain0" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain1cell" spatial:domainType="subdomain0" spatial:unitSize="1"/>
       </compartment>
       <compartment id="EC" name="EC" spatialDimensions="3" size="1" units="um3" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain0EC" spatial:compartment="EC" spatial:domainType="subdomain1" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain0EC" spatial:domainType="subdomain1" spatial:unitSize="1"/>
       </compartment>
       <compartment id="Membrane0" name="Membrane0" spatialDimensions="2" size="1" units="um2" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain0_subdomain1_membraneMembrane0" spatial:compartment="Membrane0" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="11"/>
+        <spatial:compartmentMapping spatial:id="subdomain0_subdomain1_membraneMembrane0" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="11"/>
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species id="X" compartment="cell" initialConcentration="2.5" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+      <species id="X" compartment="cell" initialConcentration="2.5" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -118,7 +118,7 @@
           </vcell:VCellInfo>
         </annotation>
       </species>
-      <species id="Y" compartment="cell" initialConcentration="2" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+      <species id="Y" compartment="cell" initialConcentration="2" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -129,47 +129,47 @@
       </species>
     </listOfSpecies>
     <listOfParameters>
-      <parameter id="x" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      <parameter id="x" value="0" constant="false">
+        <spatial:spatialSymbolReference spatial:spatialRef="x"/>
       </parameter>
-      <parameter id="y" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      <parameter id="y" value="0" constant="false">
+        <spatial:spatialSymbolReference spatial:spatialRef="y"/>
       </parameter>
-      <parameter id="X_diff" value="0.16" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="X" spatial:coordinateIndex="0"/>
+      <parameter id="X_diff" value="0.16" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="X" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="X_diff1" value="0.16" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="X" spatial:coordinateIndex="1"/>
+      <parameter id="X_diff1" value="0.16" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="X" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="X_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="X" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="X_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="X" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="X_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="X" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="X_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="X" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="X_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="X" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="X_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="X" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="X_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="X" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="X_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="X" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
-      <parameter id="Y_diff" value="0.8" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="Y" spatial:coordinateIndex="0"/>
+      <parameter id="Y_diff" value="0.8" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="Y" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="Y_diff1" value="0.8" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="Y" spatial:coordinateIndex="1"/>
+      <parameter id="Y_diff1" value="0.8" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="Y" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="Y_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="Y" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="Y_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="Y" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="Y_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="Y" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="Y_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="Y" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="Y_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="Y" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="Y_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="Y" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="Y_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="Y" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="Y_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="Y" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
       <parameter id="J0_k_1" value="0.1" units="_one_" constant="true"/>
       <parameter id="J1_k_2" value="0.1" units="_one_" constant="true"/>
@@ -181,7 +181,7 @@
       <parameter id="E" value="0" units="_one_" constant="true"/>
     </listOfParameters>
     <listOfReactions>
-      <reaction id="J0" name="J0" reversible="true" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction id="J0" name="J0" reversible="true" fast="false" spatial:isLocal="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -203,7 +203,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction id="J1" name="J1" reversible="true" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction id="J1" name="J1" reversible="true" fast="false" spatial:isLocal="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -230,7 +230,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction id="J2" name="J2" reversible="true" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction id="J2" name="J2" reversible="true" fast="false" spatial:isLocal="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -256,7 +256,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction id="J3" name="J3" reversible="true" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction id="J3" name="J3" reversible="true" fast="false" spatial:isLocal="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -279,43 +279,43 @@
         </kineticLaw>
       </reaction>
     </listOfReactions>
-    <spatial:geometry spatial:coordinateSystem="Cartesian">
+    <spatial:geometry spatial:id="newGeometry" spatial:coordinateSystem="cartesian">
       <spatial:listOfCoordinateComponents>
-        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
-          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="300"/>
+        <spatial:coordinateComponent spatial:id="x" spatial:type="cartesianX">
+          <spatial:boundaryMin spatial:id="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Xmax" spatial:value="300"/>
         </spatial:coordinateComponent>
-        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
-          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="300"/>
+        <spatial:coordinateComponent spatial:id="y" spatial:type="cartesianY">
+          <spatial:boundaryMin spatial:id="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Ymax" spatial:value="300"/>
         </spatial:coordinateComponent>
       </spatial:listOfCoordinateComponents>
       <spatial:listOfDomainTypes>
-        <spatial:domainType spatial:spatialId="subdomain1" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain0" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
+        <spatial:domainType spatial:id="subdomain1" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain0" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
       </spatial:listOfDomainTypes>
       <spatial:listOfDomains>
-        <spatial:domain spatial:spatialId="subdomain00" spatial:domainType="subdomain1">
+        <spatial:domain spatial:id="subdomain00" spatial:domainType="subdomain1">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="subdomain11" spatial:domainType="subdomain0">
+        <spatial:domain spatial:id="subdomain11" spatial:domainType="subdomain0">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="1" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="membrane_subdomain00_subdomain11" spatial:domainType="subdomain0_subdomain1_membrane"/>
+        <spatial:domain spatial:id="membrane_subdomain00_subdomain11" spatial:domainType="subdomain0_subdomain1_membrane"/>
       </spatial:listOfDomains>
       <spatial:listOfAdjacentDomains>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain00_subdomain11_subdomain11" spatial:domain1="membrane_subdomain00_subdomain11" spatial:domain2="subdomain11"/>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain00_subdomain11_subdomain00" spatial:domain1="membrane_subdomain00_subdomain11" spatial:domain2="subdomain00"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain00_subdomain11_subdomain11" spatial:domain1="membrane_subdomain00_subdomain11" spatial:domain2="subdomain11"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain00_subdomain11_subdomain00" spatial:domain1="membrane_subdomain00_subdomain11" spatial:domain2="subdomain00"/>
       </spatial:listOfAdjacentDomains>
       <spatial:listOfGeometryDefinitions>
-        <spatial:analyticGeometry spatial:spatialId="Geometry3">
+        <spatial:analyticGeometry spatial:id="Geometry3" spatial:isActive="true">
           <spatial:listOfAnalyticVolumes>
-            <spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="1">
+            <spatial:analyticVolume spatial:id="subdomain0" spatial:functionType="layered" spatial:ordinal="1" spatial:domainType="subdomain0">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <piecewise>
                   <piece>
@@ -350,7 +350,7 @@
                 </piecewise>
               </math>
             </spatial:analyticVolume>
-            <spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="0">
+            <spatial:analyticVolume spatial:id="subdomain1" spatial:functionType="layered" spatial:ordinal="0" spatial:domainType="subdomain1">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <cn type="integer"> 1 </cn>
               </math>
diff --git a/examples/advection.xml b/examples/advection.xml
index 195dcff..803a34f 100644
--- a/examples/advection.xml
+++ b/examples/advection.xml
@@ -1,15 +1,15 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" spatial:required="true">
   <model id="advection_test_simulation" name="advection_test_simulation">
     <annotation>
-      <spatialInfo xmlns="http://spatial-sbml/settings">
+      <oldspatialInfo xmlns="http://oldspatial-sbml/settings">
         <update step="0.05" freq="50"/>
         <items>
           <item sbmlId="B_cytosol" palette="black-blue.txt" max="6"/>
           <item sbmlId="C_cytosol" palette="black-green.txt" max="1000"/>
           <item sbmlId="A_cytosol" palette="black-red.txt" max="6"/>
         </items>
-      </spatialInfo>
+      </oldspatialInfo>
       <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
         <vcell:VCMLSpecific>
           <vcell:BioModel Name="advection_test" KeyValue="62900696"/>
@@ -25,12 +25,12 @@
       </unitDefinition>
       <unitDefinition id="volume">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="area">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="molecules">
@@ -40,22 +40,22 @@
       </unitDefinition>
       <unitDefinition id="umol_um3_litre_1">
         <listOfUnits>
-          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-21"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um3">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um2">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="uM_um3_molecules_1">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-21"/>
           <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
           <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
         </listOfUnits>
@@ -63,7 +63,7 @@
     </listOfUnitDefinitions>
     <listOfCompartments>
       <compartment id="extracellular" name="extracellular" spatialDimensions="3" units="um3" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain0extracellular" spatial:compartment="extracellular" spatial:domainType="subdomain0" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain0extracellular" spatial:domainType="subdomain0" spatial:unitSize="1"/>
       </compartment>
       <compartment id="cytosol" name="cytosol" spatialDimensions="3" units="um3" constant="true">
         <annotation>
@@ -73,7 +73,7 @@
             </vcell:VCMLSpecific>
           </vcell:VCellInfo>
         </annotation>
-        <spatial:compartmentMapping spatial:spatialId="subdomain1cytosol" spatial:compartment="cytosol" spatial:domainType="subdomain1" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain1cytosol" spatial:domainType="subdomain1" spatial:unitSize="1"/>
       </compartment>
       <compartment id="membrane0" name="membrane0" spatialDimensions="2" units="um2" constant="true">
         <annotation>
@@ -83,11 +83,11 @@
             </vcell:VCMLSpecific>
           </vcell:VCellInfo>
         </annotation>
-        <spatial:compartmentMapping spatial:spatialId="subdomain0_subdomain1_membranemembrane0" spatial:compartment="membrane0" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain0_subdomain1_membranemembrane0" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species id="B_cytosol" compartment="cytosol" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+      <species id="B_cytosol" compartment="cytosol" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -96,7 +96,7 @@
           </vcell:VCellInfo>
         </annotation>
       </species>
-      <species id="C_cytosol" compartment="cytosol" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+      <species id="C_cytosol" compartment="cytosol" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -105,7 +105,7 @@
           </vcell:VCellInfo>
         </annotation>
       </species>
-      <species id="A_cytosol" compartment="cytosol" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+      <species id="A_cytosol" compartment="cytosol" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -116,62 +116,62 @@
       </species>
     </listOfSpecies>
     <listOfParameters>
-      <parameter id="x" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      <parameter id="x" value="0" constant="false">
+        <spatial:spatialSymbolReference spatial:spatialRef="x"/>
       </parameter>
-      <parameter id="y" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      <parameter id="y" value="0" constant="false">
+        <spatial:spatialSymbolReference spatial:spatialRef="y"/>
       </parameter>
-      <parameter id="B_cytosol_diff" value="2" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="B_cytosol"/>
+      <parameter id="B_cytosol_diff" value="2" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="B_cytosol" spatial:type="isotropic"/>
       </parameter>
-      <parameter id="B_cytosol_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="B_cytosol" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="B_cytosol_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="B_cytosol" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="B_cytosol_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="B_cytosol" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="B_cytosol_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="B_cytosol" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="B_cytosol_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="B_cytosol" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="B_cytosol_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="B_cytosol" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="B_cytosol_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="B_cytosol" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="B_cytosol_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="B_cytosol" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
-      <parameter id="C_cytosol_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="C_cytosol" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="C_cytosol_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="C_cytosol" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="C_cytosol_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="C_cytosol" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="C_cytosol_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="C_cytosol" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="C_cytosol_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="C_cytosol" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="C_cytosol_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="C_cytosol" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="C_cytosol_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="C_cytosol" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="C_cytosol_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="C_cytosol" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
-      <parameter id="C_cytosol_Vel_X" value="2" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:advectionCoefficient spatial:variable="C_cytosol" spatial:coordinateIndex="0"/>
+      <parameter id="C_cytosol_Vel_X" value="2" constant="true">
+        <spatial:advectionCoefficient spatial:variable="C_cytosol" spatial:coordinate="cartesianX"/>
       </parameter>
-      <parameter id="C_cytosol_Vel_Y" value="-2" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:advectionCoefficient spatial:variable="C_cytosol" spatial:coordinateIndex="1"/>
+      <parameter id="C_cytosol_Vel_Y" value="-2" constant="true">
+        <spatial:advectionCoefficient spatial:variable="C_cytosol" spatial:coordinate="cartesianY"/>
       </parameter>
-      <parameter id="A_cytosol_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="A_cytosol" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="A_cytosol_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="A_cytosol" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="A_cytosol_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="A_cytosol" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="A_cytosol_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="A_cytosol" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="A_cytosol_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="A_cytosol" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="A_cytosol_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="A_cytosol" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="A_cytosol_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="A_cytosol" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="A_cytosol_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="A_cytosol" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
-      <parameter id="A_cytosol_Vel_X" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:advectionCoefficient spatial:variable="A_cytosol" spatial:coordinateIndex="0"/>
+      <parameter id="A_cytosol_Vel_X" value="4" constant="true">
+        <spatial:advectionCoefficient spatial:variable="A_cytosol" spatial:coordinate="cartesianX"/>
       </parameter>
-      <parameter id="A_cytosol_Vel_Y" value="-3" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:advectionCoefficient spatial:variable="A_cytosol" spatial:coordinateIndex="1"/>
+      <parameter id="A_cytosol_Vel_Y" value="-3" constant="true">
+        <spatial:advectionCoefficient spatial:variable="A_cytosol" spatial:coordinate="cartesianY"/>
       </parameter>
       <parameter id="KMOLE" value="0.00166112956810631" units="uM_um3_molecules_1" constant="true"/>
     </listOfParameters>
@@ -282,43 +282,43 @@
         </math>
       </initialAssignment>
     </listOfInitialAssignments>
-    <spatial:geometry spatial:coordinateSystem="Cartesian">
+    <spatial:geometry spatial:id="newGeometry" spatial:coordinateSystem="cartesian">
       <spatial:listOfCoordinateComponents>
-        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
-          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="100"/>
+        <spatial:coordinateComponent spatial:id="x" spatial:type="cartesianX">
+          <spatial:boundaryMin spatial:id="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Xmax" spatial:value="100"/>
         </spatial:coordinateComponent>
-        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
-          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="100"/>
+        <spatial:coordinateComponent spatial:id="y" spatial:type="cartesianY">
+          <spatial:boundaryMin spatial:id="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Ymax" spatial:value="100"/>
         </spatial:coordinateComponent>
       </spatial:listOfCoordinateComponents>
       <spatial:listOfDomainTypes>
-        <spatial:domainType spatial:spatialId="subdomain1" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain0" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
+        <spatial:domainType spatial:id="subdomain1" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain0" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
       </spatial:listOfDomainTypes>
       <spatial:listOfDomains>
-        <spatial:domain spatial:spatialId="subdomain00" spatial:domainType="subdomain0">
+        <spatial:domain spatial:id="subdomain00" spatial:domainType="subdomain0">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="subdomain11" spatial:domainType="subdomain1">
+        <spatial:domain spatial:id="subdomain11" spatial:domainType="subdomain1">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="45" spatial:coord2="17" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="membrane_subdomain00_subdomain11" spatial:domainType="subdomain0_subdomain1_membrane"/>
+        <spatial:domain spatial:id="membrane_subdomain00_subdomain11" spatial:domainType="subdomain0_subdomain1_membrane"/>
       </spatial:listOfDomains>
       <spatial:listOfAdjacentDomains>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain00_subdomain11_subdomain11" spatial:domain1="membrane_subdomain00_subdomain11" spatial:domain2="subdomain11"/>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain00_subdomain11_subdomain00" spatial:domain1="membrane_subdomain00_subdomain11" spatial:domain2="subdomain00"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain00_subdomain11_subdomain11" spatial:domain1="membrane_subdomain00_subdomain11" spatial:domain2="subdomain11"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain00_subdomain11_subdomain00" spatial:domain1="membrane_subdomain00_subdomain11" spatial:domain2="subdomain00"/>
       </spatial:listOfAdjacentDomains>
       <spatial:listOfGeometryDefinitions>
-        <spatial:analyticGeometry spatial:spatialId="cyt">
+        <spatial:analyticGeometry spatial:id="cyt" spatial:isActive="true">
           <spatial:listOfAnalyticVolumes>
-            <spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="1">
+            <spatial:analyticVolume spatial:id="subdomain1" spatial:functionType="layered" spatial:ordinal="1" spatial:domainType="subdomain1">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <piecewise>
                   <piece>
@@ -369,7 +369,7 @@
                 </piecewise>
               </math>
             </spatial:analyticVolume>
-            <spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="0">
+            <spatial:analyticVolume spatial:id="subdomain0" spatial:functionType="layered" spatial:ordinal="0" spatial:domainType="subdomain0">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <cn type="integer"> 1 </cn>
               </math>
diff --git a/examples/fish.xml b/examples/fish.xml
index 365527d..a0a60bc 100644
--- a/examples/fish.xml
+++ b/examples/fish.xml
@@ -1,15 +1,15 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" spatial:required="true">
   <model metaid="meta_fish_skin_pnas2_Application0" id="fish_skin_pnas2_Application0" name="fish-skin-pnas2_Application0">
     <annotation>
-      <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+      <oldspatialInfo xmlns="http://fbergmann.github.io/oldspatial-sbml/settings">
         <update step="1" freq="50"/>
         <items>
           <item sbmlId="u" palette="black-blue.txt" max="6"/>
           <item sbmlId="v" palette="black-green.txt" max="6"/>
           <item sbmlId="w" palette="black-red.txt" max="6"/>
         </items>
-      </spatialInfo>
+      </oldspatialInfo>
     </annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
@@ -19,12 +19,12 @@
       </unitDefinition>
       <unitDefinition id="volume">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="area">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="molecules">
@@ -34,22 +34,22 @@
       </unitDefinition>
       <unitDefinition id="umol_um3_litre_1">
         <listOfUnits>
-          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-21"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um3">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um2">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="uM_um3_molecules_1">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-21"/>
           <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
           <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
         </listOfUnits>
@@ -70,10 +70,10 @@
     </listOfUnitDefinitions>
     <listOfCompartments>
       <compartment id="outside" name="outside" spatialDimensions="3" size="50000" units="um3" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="outsideoutside" spatial:compartment="outside" spatial:domainType="outside" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="outsideoutside" spatial:domainType="outside" spatial:unitSize="1"/>
       </compartment>
       <compartment id="eye" name="eye" spatialDimensions="3" size="500" units="um3" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="fish_eyeeye" spatial:compartment="eye" spatial:domainType="fish_eye" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="fish_eyeeye" spatial:domainType="fish_eye" spatial:unitSize="1"/>
       </compartment>
       <compartment id="fish" name="fish" spatialDimensions="3" size="5000" units="um3" constant="true">
         <annotation>
@@ -83,7 +83,7 @@
             </vcell:VCMLSpecific>
           </vcell:VCellInfo>
         </annotation>
-        <spatial:compartmentMapping spatial:spatialId="fish_bodyfish" spatial:compartment="fish" spatial:domainType="fish_body" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="fish_bodyfish" spatial:domainType="fish_body" spatial:unitSize="1"/>
       </compartment>
       <compartment id="Membrane0" name="Membrane0" spatialDimensions="2" size="1414" units="um2" constant="true">
         <annotation>
@@ -93,7 +93,7 @@
             </vcell:VCMLSpecific>
           </vcell:VCellInfo>
         </annotation>
-        <spatial:compartmentMapping spatial:spatialId="fish_body_outside_membraneMembrane0" spatial:compartment="Membrane0" spatial:domainType="fish_body_outside_membrane" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="fish_body_outside_membraneMembrane0" spatial:domainType="fish_body_outside_membrane" spatial:unitSize="1"/>
       </compartment>
       <compartment id="Membrane1" name="Membrane1" spatialDimensions="2" size="304.6" units="um2" constant="true">
         <annotation>
@@ -103,11 +103,11 @@
             </vcell:VCMLSpecific>
           </vcell:VCellInfo>
         </annotation>
-        <spatial:compartmentMapping spatial:spatialId="fish_body_fish_eye_membraneMembrane1" spatial:compartment="Membrane1" spatial:domainType="fish_body_fish_eye_membrane" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="fish_body_fish_eye_membraneMembrane1" spatial:domainType="fish_body_fish_eye_membrane" spatial:unitSize="1"/>
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species id="u" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+      <species id="u" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -116,7 +116,7 @@
           </vcell:VCellInfo>
         </annotation>
       </species>
-      <species id="v" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+      <species id="v" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -125,7 +125,7 @@
           </vcell:VCellInfo>
         </annotation>
       </species>
-      <species id="X" compartment="fish" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+      <species id="X" compartment="fish" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -134,7 +134,7 @@
           </vcell:VCellInfo>
         </annotation>
       </species>
-      <species id="w" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+      <species id="w" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -145,65 +145,65 @@
       </species>
     </listOfSpecies>
     <listOfParameters>
-      <parameter id="x" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      <parameter id="x" value="0" constant="false">
+        <spatial:spatialSymbolReference spatial:spatialRef="x"/>
       </parameter>
-      <parameter id="y" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      <parameter id="y" value="0" constant="false">
+        <spatial:spatialSymbolReference spatial:spatialRef="y"/>
       </parameter>
-      <parameter id="u_diff_X" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="u" spatial:coordinateIndex="0"/>
+      <parameter id="u_diff_X" value="0.02" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="u" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="u_diff_Y" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="u" spatial:coordinateIndex="1"/>
+      <parameter id="u_diff_Y" value="0.02" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="u" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="u_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="u_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="u_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="u_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="u_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="u_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="u_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="u_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
-      <parameter id="v_diff_X" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="v" spatial:coordinateIndex="0"/>
+      <parameter id="v_diff_X" value="0.02" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="v" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="v_diff_Y" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="v" spatial:coordinateIndex="1"/>
+      <parameter id="v_diff_Y" value="0.02" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="v" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="v_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="v_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="v_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="v_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="v_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="v_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="v_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="v_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
-      <parameter id="w_diff_X" value="0.2" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="w" spatial:coordinateIndex="0"/>
+      <parameter id="w_diff_X" value="0.2" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="w" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="w_diff_Y" value="0.2" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="w" spatial:coordinateIndex="1"/>
+      <parameter id="w_diff_Y" value="0.2" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="w" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="w_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="w_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="w_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="w_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="w_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="w_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="w_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="w_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
       <parameter id="KMOLE" value="0.00166112956810631" units="uM_um3_molecules_1" constant="true"/>
     </listOfParameters>
@@ -285,7 +285,7 @@
       </initialAssignment>
     </listOfInitialAssignments>
     <listOfReactions>
-      <reaction id="re0" name="re0" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction id="re0" name="re0" reversible="false" fast="false" spatial:isLocal="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -413,7 +413,7 @@
           </listOfLocalParameters>
         </kineticLaw>
       </reaction>
-      <reaction id="re1" name="re1" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction id="re1" name="re1" reversible="false" fast="false" spatial:isLocal="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -541,7 +541,7 @@
           </listOfLocalParameters>
         </kineticLaw>
       </reaction>
-      <reaction id="re2" name="re2" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction id="re2" name="re2" reversible="false" fast="false" spatial:isLocal="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -670,53 +670,53 @@
         </kineticLaw>
       </reaction>
     </listOfReactions>
-    <spatial:geometry spatial:coordinateSystem="Cartesian">
+    <spatial:geometry spatial:id="newGeometry" spatial:coordinateSystem="cartesian">
       <spatial:listOfCoordinateComponents>
-        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
-          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="100"/>
+        <spatial:coordinateComponent spatial:id="x" spatial:type="cartesianX">
+          <spatial:boundaryMin spatial:id="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Xmax" spatial:value="100"/>
         </spatial:coordinateComponent>
-        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
-          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="100"/>
+        <spatial:coordinateComponent spatial:id="y" spatial:type="cartesianY">
+          <spatial:boundaryMin spatial:id="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Ymax" spatial:value="100"/>
         </spatial:coordinateComponent>
       </spatial:listOfCoordinateComponents>
       <spatial:listOfDomainTypes>
-        <spatial:domainType spatial:spatialId="fish_eye" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="fish_body" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="outside" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="fish_body_outside_membrane" spatial:spatialDimensions="2"/>
-        <spatial:domainType spatial:spatialId="fish_body_fish_eye_membrane" spatial:spatialDimensions="2"/>
+        <spatial:domainType spatial:id="fish_eye" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="fish_body" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="outside" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="fish_body_outside_membrane" spatial:spatialDimensions="2"/>
+        <spatial:domainType spatial:id="fish_body_fish_eye_membrane" spatial:spatialDimensions="2"/>
       </spatial:listOfDomainTypes>
       <spatial:listOfDomains>
-        <spatial:domain spatial:spatialId="outside0" spatial:domainType="outside">
+        <spatial:domain spatial:id="outside0" spatial:domainType="outside">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="fish_body1" spatial:domainType="fish_body">
+        <spatial:domain spatial:id="fish_body1" spatial:domainType="fish_body">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="89" spatial:coord2="22" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="fish_eye2" spatial:domainType="fish_eye">
+        <spatial:domain spatial:id="fish_eye2" spatial:domainType="fish_eye">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="22" spatial:coord2="38" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="membrane_outside0_fish_body1" spatial:domainType="fish_body_outside_membrane"/>
-        <spatial:domain spatial:spatialId="membrane_fish_body1_fish_eye2" spatial:domainType="fish_body_fish_eye_membrane"/>
+        <spatial:domain spatial:id="membrane_outside0_fish_body1" spatial:domainType="fish_body_outside_membrane"/>
+        <spatial:domain spatial:id="membrane_fish_body1_fish_eye2" spatial:domainType="fish_body_fish_eye_membrane"/>
       </spatial:listOfDomains>
       <spatial:listOfAdjacentDomains>
-        <spatial:adjacentDomains spatial:spatialId="membrane_outside0_fish_body1_fish_body1" spatial:domain1="membrane_outside0_fish_body1" spatial:domain2="fish_body1"/>
-        <spatial:adjacentDomains spatial:spatialId="membrane_outside0_fish_body1_outside0" spatial:domain1="membrane_outside0_fish_body1" spatial:domain2="outside0"/>
-        <spatial:adjacentDomains spatial:spatialId="membrane_fish_body1_fish_eye2_fish_eye2" spatial:domain1="membrane_fish_body1_fish_eye2" spatial:domain2="fish_eye2"/>
-        <spatial:adjacentDomains spatial:spatialId="membrane_fish_body1_fish_eye2_fish_body1" spatial:domain1="membrane_fish_body1_fish_eye2" spatial:domain2="fish_body1"/>
+        <spatial:adjacentDomains spatial:id="membrane_outside0_fish_body1_fish_body1" spatial:domain1="membrane_outside0_fish_body1" spatial:domain2="fish_body1"/>
+        <spatial:adjacentDomains spatial:id="membrane_outside0_fish_body1_outside0" spatial:domain1="membrane_outside0_fish_body1" spatial:domain2="outside0"/>
+        <spatial:adjacentDomains spatial:id="membrane_fish_body1_fish_eye2_fish_eye2" spatial:domain1="membrane_fish_body1_fish_eye2" spatial:domain2="fish_eye2"/>
+        <spatial:adjacentDomains spatial:id="membrane_fish_body1_fish_eye2_fish_body1" spatial:domain1="membrane_fish_body1_fish_eye2" spatial:domain2="fish_body1"/>
       </spatial:listOfAdjacentDomains>
       <spatial:listOfGeometryDefinitions>
-        <spatial:analyticGeometry spatial:spatialId="Geometry225509093">
+        <spatial:analyticGeometry spatial:id="Geometry225509093" spatial:isActive="true">
           <spatial:listOfAnalyticVolumes>
-            <spatial:analyticVolume spatial:spatialId="fish_body" spatial:domainType="fish_body" spatial:functionType="layered" spatial:ordinal="1">
+            <spatial:analyticVolume spatial:id="fish_body" spatial:functionType="layered" spatial:ordinal="1" spatial:domainType="fish_body">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <piecewise>
                   <piece>
@@ -895,7 +895,7 @@
                 </piecewise>
               </math>
             </spatial:analyticVolume>
-            <spatial:analyticVolume spatial:spatialId="fish_eye" spatial:domainType="fish_eye" spatial:functionType="layered" spatial:ordinal="2">
+            <spatial:analyticVolume spatial:id="fish_eye" spatial:functionType="layered" spatial:ordinal="2" spatial:domainType="fish_eye">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <piecewise>
                   <piece>
@@ -964,7 +964,7 @@
                 </piecewise>
               </math>
             </spatial:analyticVolume>
-            <spatial:analyticVolume spatial:spatialId="outside" spatial:domainType="outside" spatial:functionType="layered" spatial:ordinal="0">
+            <spatial:analyticVolume spatial:id="outside" spatial:functionType="layered" spatial:ordinal="0" spatial:domainType="outside">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <cn type="integer"> 1 </cn>
               </math>
diff --git a/examples/fish_300x300.xml b/examples/fish_300x300.xml
index 1773865..84772f3 100644
--- a/examples/fish_300x300.xml
+++ b/examples/fish_300x300.xml
@@ -1,15 +1,15 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" spatial:required="true">
   <model metaid="meta_fish_skin_pnas2_Application0" id="fish_skin_pnas2_Application0" name="fish-skin-pnas2_Application0">
     <annotation>
-      <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+      <oldspatialInfo xmlns="http://fbergmann.github.io/oldspatial-sbml/settings">
         <update step="1" freq="100"/>
         <items>
           <item sbmlId="u" palette="black-blue.txt" max="6"/>
           <item sbmlId="v" palette="black-green.txt" max="6"/>
           <item sbmlId="w" palette="black-red.txt" max="6"/>
         </items>
-      </spatialInfo>
+      </oldspatialInfo>
     </annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
@@ -19,12 +19,12 @@
       </unitDefinition>
       <unitDefinition id="volume">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="area">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="molecules">
@@ -34,22 +34,22 @@
       </unitDefinition>
       <unitDefinition id="umol_um3_litre_1">
         <listOfUnits>
-          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-21"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um3">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um2">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="uM_um3_molecules_1">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-21"/>
           <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
           <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
         </listOfUnits>
@@ -70,10 +70,10 @@
     </listOfUnitDefinitions>
     <listOfCompartments>
       <compartment id="outside" name="outside" spatialDimensions="3" size="50000" units="um3" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="outsideoutside" spatial:compartment="outside" spatial:domainType="outside" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="outsideoutside" spatial:domainType="outside" spatial:unitSize="1"/>
       </compartment>
       <compartment id="eye" name="eye" spatialDimensions="3" size="500" units="um3" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="fish_eyeeye" spatial:compartment="eye" spatial:domainType="fish_eye" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="fish_eyeeye" spatial:domainType="fish_eye" spatial:unitSize="1"/>
       </compartment>
       <compartment id="fish" name="fish" spatialDimensions="3" size="5000" units="um3" constant="true">
         <annotation>
@@ -83,7 +83,7 @@
             </vcell:VCMLSpecific>
           </vcell:VCellInfo>
         </annotation>
-        <spatial:compartmentMapping spatial:spatialId="fish_bodyfish" spatial:compartment="fish" spatial:domainType="fish_body" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="fish_bodyfish" spatial:domainType="fish_body" spatial:unitSize="1"/>
       </compartment>
       <compartment id="Membrane0" name="Membrane0" spatialDimensions="2" size="1414" units="um2" constant="true">
         <annotation>
@@ -93,7 +93,7 @@
             </vcell:VCMLSpecific>
           </vcell:VCellInfo>
         </annotation>
-        <spatial:compartmentMapping spatial:spatialId="fish_body_outside_membraneMembrane0" spatial:compartment="Membrane0" spatial:domainType="fish_body_outside_membrane" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="fish_body_outside_membraneMembrane0" spatial:domainType="fish_body_outside_membrane" spatial:unitSize="1"/>
       </compartment>
       <compartment id="Membrane1" name="Membrane1" spatialDimensions="2" size="304.6" units="um2" constant="true">
         <annotation>
@@ -103,11 +103,11 @@
             </vcell:VCMLSpecific>
           </vcell:VCellInfo>
         </annotation>
-        <spatial:compartmentMapping spatial:spatialId="fish_body_fish_eye_membraneMembrane1" spatial:compartment="Membrane1" spatial:domainType="fish_body_fish_eye_membrane" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="fish_body_fish_eye_membraneMembrane1" spatial:domainType="fish_body_fish_eye_membrane" spatial:unitSize="1"/>
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species id="u" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+      <species id="u" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -116,7 +116,7 @@
           </vcell:VCellInfo>
         </annotation>
       </species>
-      <species id="v" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+      <species id="v" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -125,7 +125,7 @@
           </vcell:VCellInfo>
         </annotation>
       </species>
-      <species id="X" compartment="fish" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+      <species id="X" compartment="fish" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -134,7 +134,7 @@
           </vcell:VCellInfo>
         </annotation>
       </species>
-      <species id="w" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+      <species id="w" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -145,65 +145,65 @@
       </species>
     </listOfSpecies>
     <listOfParameters>
-      <parameter id="x" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      <parameter id="x" value="0" constant="false">
+        <spatial:spatialSymbolReference spatial:spatialRef="x"/>
       </parameter>
-      <parameter id="y" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      <parameter id="y" value="0" constant="false">
+        <spatial:spatialSymbolReference spatial:spatialRef="y"/>
       </parameter>
-      <parameter id="u_diff_X" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="u" spatial:coordinateIndex="0"/>
+      <parameter id="u_diff_X" value="0.02" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="u" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="u_diff_Y" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="u" spatial:coordinateIndex="1"/>
+      <parameter id="u_diff_Y" value="0.02" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="u" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="u_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="u_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="u_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="u_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="u_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="u_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="u_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="u_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
-      <parameter id="v_diff_X" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="v" spatial:coordinateIndex="0"/>
+      <parameter id="v_diff_X" value="0.02" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="v" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="v_diff_Y" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="v" spatial:coordinateIndex="1"/>
+      <parameter id="v_diff_Y" value="0.02" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="v" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="v_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="v_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="v_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="v_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="v_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="v_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="v_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="v_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
-      <parameter id="w_diff_X" value="0.2" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="w" spatial:coordinateIndex="0"/>
+      <parameter id="w_diff_X" value="0.2" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="w" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="w_diff_Y" value="0.2" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="w" spatial:coordinateIndex="1"/>
+      <parameter id="w_diff_Y" value="0.2" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="w" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="w_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="w_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="w_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="w_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="w_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="w_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="w_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="w_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
       <parameter id="KMOLE" value="0.00166112956810631" units="uM_um3_molecules_1" constant="true"/>
     </listOfParameters>
@@ -285,7 +285,7 @@
       </initialAssignment>
     </listOfInitialAssignments>
     <listOfReactions>
-      <reaction id="re0" name="re0" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction id="re0" name="re0" reversible="false" fast="false" spatial:isLocal="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -413,7 +413,7 @@
           </listOfLocalParameters>
         </kineticLaw>
       </reaction>
-      <reaction id="re1" name="re1" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction id="re1" name="re1" reversible="false" fast="false" spatial:isLocal="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -541,7 +541,7 @@
           </listOfLocalParameters>
         </kineticLaw>
       </reaction>
-      <reaction id="re2" name="re2" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction id="re2" name="re2" reversible="false" fast="false" spatial:isLocal="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -670,53 +670,53 @@
         </kineticLaw>
       </reaction>
     </listOfReactions>
-    <spatial:geometry spatial:coordinateSystem="Cartesian">
+    <spatial:geometry spatial:id="newGeometry" spatial:coordinateSystem="cartesian">
       <spatial:listOfCoordinateComponents>
-        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
-          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="300"/>
+        <spatial:coordinateComponent spatial:id="x" spatial:type="cartesianX">
+          <spatial:boundaryMin spatial:id="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Xmax" spatial:value="300"/>
         </spatial:coordinateComponent>
-        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
-          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="300"/>
+        <spatial:coordinateComponent spatial:id="y" spatial:type="cartesianY">
+          <spatial:boundaryMin spatial:id="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Ymax" spatial:value="300"/>
         </spatial:coordinateComponent>
       </spatial:listOfCoordinateComponents>
       <spatial:listOfDomainTypes>
-        <spatial:domainType spatial:spatialId="fish_eye" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="fish_body" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="outside" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="fish_body_outside_membrane" spatial:spatialDimensions="2"/>
-        <spatial:domainType spatial:spatialId="fish_body_fish_eye_membrane" spatial:spatialDimensions="2"/>
+        <spatial:domainType spatial:id="fish_eye" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="fish_body" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="outside" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="fish_body_outside_membrane" spatial:spatialDimensions="2"/>
+        <spatial:domainType spatial:id="fish_body_fish_eye_membrane" spatial:spatialDimensions="2"/>
       </spatial:listOfDomainTypes>
       <spatial:listOfDomains>
-        <spatial:domain spatial:spatialId="outside0" spatial:domainType="outside">
+        <spatial:domain spatial:id="outside0" spatial:domainType="outside">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="fish_body1" spatial:domainType="fish_body">
+        <spatial:domain spatial:id="fish_body1" spatial:domainType="fish_body">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="267" spatial:coord2="66" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="fish_eye2" spatial:domainType="fish_eye">
+        <spatial:domain spatial:id="fish_eye2" spatial:domainType="fish_eye">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="66" spatial:coord2="114" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="membrane_outside0_fish_body1" spatial:domainType="fish_body_outside_membrane"/>
-        <spatial:domain spatial:spatialId="membrane_fish_body1_fish_eye2" spatial:domainType="fish_body_fish_eye_membrane"/>
+        <spatial:domain spatial:id="membrane_outside0_fish_body1" spatial:domainType="fish_body_outside_membrane"/>
+        <spatial:domain spatial:id="membrane_fish_body1_fish_eye2" spatial:domainType="fish_body_fish_eye_membrane"/>
       </spatial:listOfDomains>
       <spatial:listOfAdjacentDomains>
-        <spatial:adjacentDomains spatial:spatialId="membrane_outside0_fish_body1_fish_body1" spatial:domain1="membrane_outside0_fish_body1" spatial:domain2="fish_body1"/>
-        <spatial:adjacentDomains spatial:spatialId="membrane_outside0_fish_body1_outside0" spatial:domain1="membrane_outside0_fish_body1" spatial:domain2="outside0"/>
-        <spatial:adjacentDomains spatial:spatialId="membrane_fish_body1_fish_eye2_fish_eye2" spatial:domain1="membrane_fish_body1_fish_eye2" spatial:domain2="fish_eye2"/>
-        <spatial:adjacentDomains spatial:spatialId="membrane_fish_body1_fish_eye2_fish_body1" spatial:domain1="membrane_fish_body1_fish_eye2" spatial:domain2="fish_body1"/>
+        <spatial:adjacentDomains spatial:id="membrane_outside0_fish_body1_fish_body1" spatial:domain1="membrane_outside0_fish_body1" spatial:domain2="fish_body1"/>
+        <spatial:adjacentDomains spatial:id="membrane_outside0_fish_body1_outside0" spatial:domain1="membrane_outside0_fish_body1" spatial:domain2="outside0"/>
+        <spatial:adjacentDomains spatial:id="membrane_fish_body1_fish_eye2_fish_eye2" spatial:domain1="membrane_fish_body1_fish_eye2" spatial:domain2="fish_eye2"/>
+        <spatial:adjacentDomains spatial:id="membrane_fish_body1_fish_eye2_fish_body1" spatial:domain1="membrane_fish_body1_fish_eye2" spatial:domain2="fish_body1"/>
       </spatial:listOfAdjacentDomains>
       <spatial:listOfGeometryDefinitions>
-        <spatial:analyticGeometry spatial:spatialId="Geometry225509093">
+        <spatial:analyticGeometry spatial:id="Geometry225509093" spatial:isActive="true">
           <spatial:listOfAnalyticVolumes>
-            <spatial:analyticVolume spatial:spatialId="fish_body" spatial:domainType="fish_body" spatial:functionType="layered" spatial:ordinal="1">
+            <spatial:analyticVolume spatial:id="fish_body" spatial:functionType="layered" spatial:ordinal="1" spatial:domainType="fish_body">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <piecewise>
                   <piece>
@@ -895,7 +895,7 @@
                 </piecewise>
               </math>
             </spatial:analyticVolume>
-            <spatial:analyticVolume spatial:spatialId="fish_eye" spatial:domainType="fish_eye" spatial:functionType="layered" spatial:ordinal="2">
+            <spatial:analyticVolume spatial:id="fish_eye" spatial:functionType="layered" spatial:ordinal="2" spatial:domainType="fish_eye">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <piecewise>
                   <piece>
@@ -964,7 +964,7 @@
                 </piecewise>
               </math>
             </spatial:analyticVolume>
-            <spatial:analyticVolume spatial:spatialId="outside" spatial:domainType="outside" spatial:functionType="layered" spatial:ordinal="0">
+            <spatial:analyticVolume spatial:id="outside" spatial:functionType="layered" spatial:ordinal="0" spatial:domainType="outside">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <cn type="integer"> 1 </cn>
               </math>
diff --git a/examples/fish_big.xml b/examples/fish_big.xml
index 2614e41..2030c72 100644
--- a/examples/fish_big.xml
+++ b/examples/fish_big.xml
@@ -1,16 +1,16 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" spatial:required="true">
   <model metaid="meta_fish_skin_pnas2_Application0" id="fish_skin_pnas2_Application0" name="fish-skin-pnas2_Application0">
-	<annotation>
-        <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+    <annotation>
+      <oldspatialInfo xmlns="http://fbergmann.github.io/oldspatial-sbml/settings">
         <update step="1" freq="50"/>
         <items>
           <item sbmlId="u" palette="black-blue.txt" max="6"/>
           <item sbmlId="v" palette="black-green.txt" max="6"/>
           <item sbmlId="w" palette="black-red.txt" max="6"/>
         </items>
-      </spatialInfo>
-	</annotation>
+      </oldspatialInfo>
+    </annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
         <listOfUnits>
@@ -19,12 +19,12 @@
       </unitDefinition>
       <unitDefinition id="volume">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="area">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="molecules">
@@ -34,22 +34,22 @@
       </unitDefinition>
       <unitDefinition id="umol_um3_litre_1">
         <listOfUnits>
-          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-21"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um3">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um2">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="uM_um3_molecules_1">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-21"/>
           <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
           <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
         </listOfUnits>
@@ -70,10 +70,10 @@
     </listOfUnitDefinitions>
     <listOfCompartments>
       <compartment id="outside" name="outside" spatialDimensions="3" size="50000" units="um3" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="outsideoutside" spatial:compartment="outside" spatial:domainType="outside" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="outsideoutside" spatial:domainType="outside" spatial:unitSize="1"/>
       </compartment>
       <compartment id="eye" name="eye" spatialDimensions="3" size="500" units="um3" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="fish_eyeeye" spatial:compartment="eye" spatial:domainType="fish_eye" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="fish_eyeeye" spatial:domainType="fish_eye" spatial:unitSize="1"/>
       </compartment>
       <compartment id="fish" name="fish" spatialDimensions="3" size="5000" units="um3" constant="true">
         <annotation>
@@ -83,7 +83,7 @@
             </vcell:VCMLSpecific>
           </vcell:VCellInfo>
         </annotation>
-        <spatial:compartmentMapping spatial:spatialId="fish_bodyfish" spatial:compartment="fish" spatial:domainType="fish_body" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="fish_bodyfish" spatial:domainType="fish_body" spatial:unitSize="1"/>
       </compartment>
       <compartment id="Membrane0" name="Membrane0" spatialDimensions="2" size="1414" units="um2" constant="true">
         <annotation>
@@ -93,7 +93,7 @@
             </vcell:VCMLSpecific>
           </vcell:VCellInfo>
         </annotation>
-        <spatial:compartmentMapping spatial:spatialId="fish_body_outside_membraneMembrane0" spatial:compartment="Membrane0" spatial:domainType="fish_body_outside_membrane" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="fish_body_outside_membraneMembrane0" spatial:domainType="fish_body_outside_membrane" spatial:unitSize="1"/>
       </compartment>
       <compartment id="Membrane1" name="Membrane1" spatialDimensions="2" size="304.6" units="um2" constant="true">
         <annotation>
@@ -103,11 +103,11 @@
             </vcell:VCMLSpecific>
           </vcell:VCellInfo>
         </annotation>
-        <spatial:compartmentMapping spatial:spatialId="fish_body_fish_eye_membraneMembrane1" spatial:compartment="Membrane1" spatial:domainType="fish_body_fish_eye_membrane" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="fish_body_fish_eye_membraneMembrane1" spatial:domainType="fish_body_fish_eye_membrane" spatial:unitSize="1"/>
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species id="u" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+      <species id="u" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -116,7 +116,7 @@
           </vcell:VCellInfo>
         </annotation>
       </species>
-      <species id="v" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+      <species id="v" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -125,7 +125,7 @@
           </vcell:VCellInfo>
         </annotation>
       </species>
-      <species id="X" compartment="fish" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+      <species id="X" compartment="fish" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -134,7 +134,7 @@
           </vcell:VCellInfo>
         </annotation>
       </species>
-      <species id="w" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+      <species id="w" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -145,65 +145,65 @@
       </species>
     </listOfSpecies>
     <listOfParameters>
-      <parameter id="x" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      <parameter id="x" value="0" constant="false">
+        <spatial:spatialSymbolReference spatial:spatialRef="x"/>
       </parameter>
-      <parameter id="y" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      <parameter id="y" value="0" constant="false">
+        <spatial:spatialSymbolReference spatial:spatialRef="y"/>
       </parameter>
-      <parameter id="u_diff_X" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="u" spatial:coordinateIndex="0"/>
+      <parameter id="u_diff_X" value="0.02" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="u" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="u_diff_Y" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="u" spatial:coordinateIndex="1"/>
+      <parameter id="u_diff_Y" value="0.02" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="u" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="u_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="u_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="u_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="u_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="u_BC_Ym" value="5" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Ymin" spatial:type="Value"/>
+      <parameter id="u_BC_Ym" value="5" constant="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:type="Dirichlet" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="u_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="u_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
-      <parameter id="v_diff_X" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="v" spatial:coordinateIndex="0"/>
+      <parameter id="v_diff_X" value="0.02" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="v" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="v_diff_Y" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="v" spatial:coordinateIndex="1"/>
+      <parameter id="v_diff_Y" value="0.02" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="v" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="v_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="v_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="v_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="v_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="v_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="v_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="v_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="v_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
-      <parameter id="w_diff_X" value="0.2" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="w" spatial:coordinateIndex="0"/>
+      <parameter id="w_diff_X" value="0.2" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="w" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="w_diff_Y" value="0.2" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="w" spatial:coordinateIndex="1"/>
+      <parameter id="w_diff_Y" value="0.2" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="w" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="w_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="w_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="w_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="w_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="w_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="w_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="w_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="w_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
       <parameter id="KMOLE" value="0.00166112956810631" units="uM_um3_molecules_1" constant="true"/>
     </listOfParameters>
@@ -285,7 +285,7 @@
       </initialAssignment>
     </listOfInitialAssignments>
     <listOfReactions>
-      <reaction id="re0" name="re0" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction id="re0" name="re0" reversible="false" fast="false" spatial:isLocal="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -413,7 +413,7 @@
           </listOfLocalParameters>
         </kineticLaw>
       </reaction>
-      <reaction id="re1" name="re1" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction id="re1" name="re1" reversible="false" fast="false" spatial:isLocal="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -541,7 +541,7 @@
           </listOfLocalParameters>
         </kineticLaw>
       </reaction>
-      <reaction id="re2" name="re2" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction id="re2" name="re2" reversible="false" fast="false" spatial:isLocal="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -670,53 +670,53 @@
         </kineticLaw>
       </reaction>
     </listOfReactions>
-    <spatial:geometry spatial:coordinateSystem="Cartesian">
+    <spatial:geometry spatial:id="newGeometry" spatial:coordinateSystem="cartesian">
       <spatial:listOfCoordinateComponents>
-        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
-          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="100"/>
+        <spatial:coordinateComponent spatial:id="x" spatial:type="cartesianX">
+          <spatial:boundaryMin spatial:id="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Xmax" spatial:value="100"/>
         </spatial:coordinateComponent>
-        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
-          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="100"/>
+        <spatial:coordinateComponent spatial:id="y" spatial:type="cartesianY">
+          <spatial:boundaryMin spatial:id="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Ymax" spatial:value="100"/>
         </spatial:coordinateComponent>
       </spatial:listOfCoordinateComponents>
       <spatial:listOfDomainTypes>
-        <spatial:domainType spatial:spatialId="fish_eye" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="fish_body" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="outside" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="fish_body_outside_membrane" spatial:spatialDimensions="2"/>
-        <spatial:domainType spatial:spatialId="fish_body_fish_eye_membrane" spatial:spatialDimensions="2"/>
+        <spatial:domainType spatial:id="fish_eye" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="fish_body" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="outside" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="fish_body_outside_membrane" spatial:spatialDimensions="2"/>
+        <spatial:domainType spatial:id="fish_body_fish_eye_membrane" spatial:spatialDimensions="2"/>
       </spatial:listOfDomainTypes>
       <spatial:listOfDomains>
-        <spatial:domain spatial:spatialId="outside0" spatial:domainType="outside">
+        <spatial:domain spatial:id="outside0" spatial:domainType="outside">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="fish_body1" spatial:domainType="fish_body">
+        <spatial:domain spatial:id="fish_body1" spatial:domainType="fish_body">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="89" spatial:coord2="22" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="fish_eye2" spatial:domainType="fish_eye">
+        <spatial:domain spatial:id="fish_eye2" spatial:domainType="fish_eye">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="22" spatial:coord2="38" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="membrane_outside0_fish_body1" spatial:domainType="fish_body_outside_membrane"/>
-        <spatial:domain spatial:spatialId="membrane_fish_body1_fish_eye2" spatial:domainType="fish_body_fish_eye_membrane"/>
+        <spatial:domain spatial:id="membrane_outside0_fish_body1" spatial:domainType="fish_body_outside_membrane"/>
+        <spatial:domain spatial:id="membrane_fish_body1_fish_eye2" spatial:domainType="fish_body_fish_eye_membrane"/>
       </spatial:listOfDomains>
       <spatial:listOfAdjacentDomains>
-        <spatial:adjacentDomains spatial:spatialId="membrane_outside0_fish_body1_fish_body1" spatial:domain1="membrane_outside0_fish_body1" spatial:domain2="fish_body1"/>
-        <spatial:adjacentDomains spatial:spatialId="membrane_outside0_fish_body1_outside0" spatial:domain1="membrane_outside0_fish_body1" spatial:domain2="outside0"/>
-        <spatial:adjacentDomains spatial:spatialId="membrane_fish_body1_fish_eye2_fish_eye2" spatial:domain1="membrane_fish_body1_fish_eye2" spatial:domain2="fish_eye2"/>
-        <spatial:adjacentDomains spatial:spatialId="membrane_fish_body1_fish_eye2_fish_body1" spatial:domain1="membrane_fish_body1_fish_eye2" spatial:domain2="fish_body1"/>
+        <spatial:adjacentDomains spatial:id="membrane_outside0_fish_body1_fish_body1" spatial:domain1="membrane_outside0_fish_body1" spatial:domain2="fish_body1"/>
+        <spatial:adjacentDomains spatial:id="membrane_outside0_fish_body1_outside0" spatial:domain1="membrane_outside0_fish_body1" spatial:domain2="outside0"/>
+        <spatial:adjacentDomains spatial:id="membrane_fish_body1_fish_eye2_fish_eye2" spatial:domain1="membrane_fish_body1_fish_eye2" spatial:domain2="fish_eye2"/>
+        <spatial:adjacentDomains spatial:id="membrane_fish_body1_fish_eye2_fish_body1" spatial:domain1="membrane_fish_body1_fish_eye2" spatial:domain2="fish_body1"/>
       </spatial:listOfAdjacentDomains>
       <spatial:listOfGeometryDefinitions>
-        <spatial:analyticGeometry spatial:spatialId="Geometry225509093">
+        <spatial:analyticGeometry spatial:id="Geometry225509093" spatial:isActive="true">
           <spatial:listOfAnalyticVolumes>
-            <spatial:analyticVolume spatial:spatialId="fish_eye" spatial:domainType="fish_eye" spatial:functionType="layered" spatial:ordinal="2">
+            <spatial:analyticVolume spatial:id="fish_eye" spatial:functionType="layered" spatial:ordinal="2" spatial:domainType="fish_eye">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <piecewise>
                   <piece>
@@ -753,7 +753,7 @@
                 </piecewise>
               </math>
             </spatial:analyticVolume>
-            <spatial:analyticVolume spatial:spatialId="fish_body" spatial:domainType="fish_body" spatial:functionType="layered" spatial:ordinal="1">
+            <spatial:analyticVolume spatial:id="fish_body" spatial:functionType="layered" spatial:ordinal="1" spatial:domainType="fish_body">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <piecewise>
                   <piece>
@@ -830,7 +830,7 @@
                 </piecewise>
               </math>
             </spatial:analyticVolume>
-            <spatial:analyticVolume spatial:spatialId="outside" spatial:domainType="outside" spatial:functionType="layered" spatial:ordinal="0">
+            <spatial:analyticVolume spatial:id="outside" spatial:functionType="layered" spatial:ordinal="0" spatial:domainType="outside">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <cn type="integer"> 1 </cn>
               </math>
diff --git a/examples/no_spatial.xml b/examples/no_spatial.xml
index 0fa2775..d365d7d 100644
--- a/examples/no_spatial.xml
+++ b/examples/no_spatial.xml
@@ -1,6 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" 
-level="3" version="1">
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
   <model metaid="COPASI1" id="New_Model_Application0" name="New Model_Application0">
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
@@ -10,12 +9,12 @@ level="3" version="1">
       </unitDefinition>
       <unitDefinition id="volume">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="area">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="molecules">
@@ -25,22 +24,22 @@ level="3" version="1">
       </unitDefinition>
       <unitDefinition id="umol_um3_litre_1">
         <listOfUnits>
-          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-21"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um3">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um2">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="uM_um3_molecules_1">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-21"/>
           <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
           <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
         </listOfUnits>
@@ -63,7 +62,7 @@ level="3" version="1">
       </unitDefinition>
       <unitDefinition id="_one__0E_6">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-006"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="_one_000000_0">
@@ -91,8 +90,8 @@ level="3" version="1">
       <compartment id="compartment_1" name="compartment_1" spatialDimensions="3" size="1" constant="true"/>
     </listOfCompartments>
     <listOfSpecies>
-      <species id="species_1" initialConcentration="6" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" />
-      <species id="species_2" initialConcentration="0.1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" />
+      <species id="species_1" compartment="compartment_1" initialConcentration="6" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="species_2" compartment="compartment_1" initialConcentration="0.1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
     </listOfSpecies>
     <listOfParameters>
       <parameter id="v1" value="0.06" constant="true"/>
diff --git a/examples/transport.xml b/examples/transport.xml
index 7098d28..87d1f8d 100644
--- a/examples/transport.xml
+++ b/examples/transport.xml
@@ -1,15 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" spatial:required="true">
   <model id="simple_transport_simulation" name="simple_transport_simulation">
     <annotation>
-        <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+      <oldspatialInfo xmlns="http://fbergmann.github.io/oldspatial-sbml/settings">
         <update step="1" freq="50"/>
         <items>
           <item sbmlId="s1" palette="black-blue.txt" max="6"/>
           <item sbmlId="s0" palette="black-green.txt" max="6"/>
         </items>
-      </spatialInfo>
-
+      </oldspatialInfo>
       <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
         <vcell:VCMLSpecific>
           <vcell:BioModel Name="simple_transport" KeyValue="60099072"/>
@@ -25,12 +24,12 @@
       </unitDefinition>
       <unitDefinition id="volume">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="area">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="molecules">
@@ -40,22 +39,22 @@
       </unitDefinition>
       <unitDefinition id="umol_um3_litre_1">
         <listOfUnits>
-          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-21"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um3">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um2">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="uM_um3_molecules_1">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-21"/>
           <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
           <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
         </listOfUnits>
@@ -78,7 +77,7 @@
     </listOfUnitDefinitions>
     <listOfCompartments>
       <compartment id="extracellular" name="extracellular" spatialDimensions="3" units="um3" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain0extracellular" spatial:compartment="extracellular" spatial:domainType="subdomain0" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain0extracellular" spatial:domainType="subdomain0" spatial:unitSize="1"/>
       </compartment>
       <compartment id="cytosol" name="cytosol" spatialDimensions="3" units="um3" constant="true">
         <annotation>
@@ -88,7 +87,7 @@
             </vcell:VCMLSpecific>
           </vcell:VCellInfo>
         </annotation>
-        <spatial:compartmentMapping spatial:spatialId="subdomain2cytosol" spatial:compartment="cytosol" spatial:domainType="subdomain2" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain2cytosol" spatial:domainType="subdomain2" spatial:unitSize="1"/>
       </compartment>
       <compartment id="nucleus" name="nucleus" spatialDimensions="3" units="um3" constant="true">
         <annotation>
@@ -98,7 +97,7 @@
             </vcell:VCMLSpecific>
           </vcell:VCellInfo>
         </annotation>
-        <spatial:compartmentMapping spatial:spatialId="subdomain1nucleus" spatial:compartment="nucleus" spatial:domainType="subdomain1" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain1nucleus" spatial:domainType="subdomain1" spatial:unitSize="1"/>
       </compartment>
       <compartment id="membrane0" name="membrane0" spatialDimensions="2" units="um2" constant="true">
         <annotation>
@@ -108,7 +107,7 @@
             </vcell:VCMLSpecific>
           </vcell:VCellInfo>
         </annotation>
-        <spatial:compartmentMapping spatial:spatialId="subdomain0_subdomain2_membranemembrane0" spatial:compartment="membrane0" spatial:domainType="subdomain0_subdomain2_membrane" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain0_subdomain2_membranemembrane0" spatial:domainType="subdomain0_subdomain2_membrane" spatial:unitSize="1"/>
       </compartment>
       <compartment id="membrane1" name="membrane1" spatialDimensions="2" units="um2" constant="true">
         <annotation>
@@ -118,11 +117,11 @@
             </vcell:VCMLSpecific>
           </vcell:VCellInfo>
         </annotation>
-        <spatial:compartmentMapping spatial:spatialId="subdomain1_subdomain2_membranemembrane1" spatial:compartment="membrane1" spatial:domainType="subdomain1_subdomain2_membrane" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain1_subdomain2_membranemembrane1" spatial:domainType="subdomain1_subdomain2_membrane" spatial:unitSize="1"/>
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species id="s1" compartment="nucleus" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+      <species id="s1" compartment="nucleus" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -131,7 +130,7 @@
           </vcell:VCellInfo>
         </annotation>
       </species>
-      <species id="s0" compartment="cytosol" initialConcentration="3010" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+      <species id="s0" compartment="cytosol" initialConcentration="3010" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -142,45 +141,45 @@
       </species>
     </listOfSpecies>
     <listOfParameters>
-      <parameter id="s1_diff" value="0.1" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="s1"/>
+      <parameter id="s1_diff" value="0.1" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="s1" spatial:type="isotropic"/>
       </parameter>
-      <parameter id="s1_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="s1" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="s1_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="s1" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="s1_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="s1" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="s1_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="s1" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="s1_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="s1" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="s1_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="s1" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="s1_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="s1" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="s1_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="s1" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
-      <parameter id="s0_diff" value="0.1" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="s0"/>
+      <parameter id="s0_diff" value="0.1" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="s0" spatial:type="isotropic"/>
       </parameter>
-      <parameter id="s0_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="s0" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="s0_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="s0" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="s0_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="s0" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="s0_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="s0" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="s0_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="s0" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="s0_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="s0" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="s0_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="s0" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="s0_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="s0" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
-      <parameter id="x" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      <parameter id="x" value="0" constant="true">
+        <spatial:spatialSymbolReference spatial:spatialRef="x"/>
       </parameter>
-      <parameter id="y" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      <parameter id="y" value="0" constant="true">
+        <spatial:spatialSymbolReference spatial:spatialRef="y"/>
       </parameter>
     </listOfParameters>
     <listOfReactions>
-      <reaction id="transport0" name="transport0" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction id="transport0" name="transport0" reversible="false" fast="false" spatial:isLocal="true">
         <annotation>
           <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
             <vcell:VCMLSpecific>
@@ -209,53 +208,53 @@
         </kineticLaw>
       </reaction>
     </listOfReactions>
-    <spatial:geometry spatial:coordinateSystem="Cartesian">
+    <spatial:geometry spatial:id="newGeometry" spatial:coordinateSystem="cartesian">
       <spatial:listOfCoordinateComponents>
-        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
-          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="100"/>
+        <spatial:coordinateComponent spatial:id="x" spatial:type="cartesianX">
+          <spatial:boundaryMin spatial:id="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Xmax" spatial:value="100"/>
         </spatial:coordinateComponent>
-        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
-          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="100"/>
+        <spatial:coordinateComponent spatial:id="y" spatial:type="cartesianY">
+          <spatial:boundaryMin spatial:id="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Ymax" spatial:value="100"/>
         </spatial:coordinateComponent>
       </spatial:listOfCoordinateComponents>
       <spatial:listOfDomainTypes>
-        <spatial:domainType spatial:spatialId="subdomain1" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain2" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain0" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain0_subdomain2_membrane" spatial:spatialDimensions="2"/>
-        <spatial:domainType spatial:spatialId="subdomain1_subdomain2_membrane" spatial:spatialDimensions="2"/>
+        <spatial:domainType spatial:id="subdomain1" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain2" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain0" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain0_subdomain2_membrane" spatial:spatialDimensions="2"/>
+        <spatial:domainType spatial:id="subdomain1_subdomain2_membrane" spatial:spatialDimensions="2"/>
       </spatial:listOfDomainTypes>
       <spatial:listOfDomains>
-        <spatial:domain spatial:spatialId="subdomain00" spatial:domainType="subdomain0">
+        <spatial:domain spatial:id="subdomain00" spatial:domainType="subdomain0">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="subdomain21" spatial:domainType="subdomain2">
+        <spatial:domain spatial:id="subdomain21" spatial:domainType="subdomain2">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="16" spatial:coord2="16" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="subdomain12" spatial:domainType="subdomain1">
+        <spatial:domain spatial:id="subdomain12" spatial:domainType="subdomain1">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="24" spatial:coord2="24" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="membrane_subdomain00_subdomain21" spatial:domainType="subdomain0_subdomain2_membrane"/>
-        <spatial:domain spatial:spatialId="membrane_subdomain21_subdomain12" spatial:domainType="subdomain1_subdomain2_membrane"/>
+        <spatial:domain spatial:id="membrane_subdomain00_subdomain21" spatial:domainType="subdomain0_subdomain2_membrane"/>
+        <spatial:domain spatial:id="membrane_subdomain21_subdomain12" spatial:domainType="subdomain1_subdomain2_membrane"/>
       </spatial:listOfDomains>
       <spatial:listOfAdjacentDomains>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain00_subdomain21_subdomain21" spatial:domain1="membrane_subdomain00_subdomain21" spatial:domain2="subdomain21"/>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain00_subdomain21_subdomain00" spatial:domain1="membrane_subdomain00_subdomain21" spatial:domain2="subdomain00"/>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain21_subdomain12_subdomain12" spatial:domain1="membrane_subdomain21_subdomain12" spatial:domain2="subdomain12"/>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain21_subdomain12_subdomain21" spatial:domain1="membrane_subdomain21_subdomain12" spatial:domain2="subdomain21"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain00_subdomain21_subdomain21" spatial:domain1="membrane_subdomain00_subdomain21" spatial:domain2="subdomain21"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain00_subdomain21_subdomain00" spatial:domain1="membrane_subdomain00_subdomain21" spatial:domain2="subdomain00"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain21_subdomain12_subdomain12" spatial:domain1="membrane_subdomain21_subdomain12" spatial:domain2="subdomain12"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain21_subdomain12_subdomain21" spatial:domain1="membrane_subdomain21_subdomain12" spatial:domain2="subdomain21"/>
       </spatial:listOfAdjacentDomains>
       <spatial:listOfGeometryDefinitions>
-        <spatial:analyticGeometry spatial:spatialId="spatial2d8sq">
+        <spatial:analyticGeometry spatial:id="oldspatial2d8sq" spatial:isActive="true">
           <spatial:listOfAnalyticVolumes>
-            <spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="2">
+            <spatial:analyticVolume spatial:id="subdomain1" spatial:functionType="layered" spatial:ordinal="2" spatial:domainType="subdomain1">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <piecewise>
                   <piece>
@@ -290,7 +289,7 @@
                 </piecewise>
               </math>
             </spatial:analyticVolume>
-            <spatial:analyticVolume spatial:spatialId="subdomain2" spatial:domainType="subdomain2" spatial:functionType="layered" spatial:ordinal="1">
+            <spatial:analyticVolume spatial:id="subdomain2" spatial:functionType="layered" spatial:ordinal="1" spatial:domainType="subdomain2">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <piecewise>
                   <piece>
@@ -325,7 +324,7 @@
                 </piecewise>
               </math>
             </spatial:analyticVolume>
-            <spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="0">
+            <spatial:analyticVolume spatial:id="subdomain0" spatial:functionType="layered" spatial:ordinal="0" spatial:domainType="subdomain0">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <cn type="integer"> 1 </cn>
               </math>
diff --git a/examples/turing.xml b/examples/turing.xml
index e48879c..a6e06a3 100644
--- a/examples/turing.xml
+++ b/examples/turing.xml
@@ -1,14 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="true" spatial:required="true">
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" spatial:required="true">
   <model metaid="COPASI1" id="New_Model_Application0" name="New Model_Application0">
     <annotation>
-      <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+      <oldspatialInfo xmlns="http://fbergmann.github.io/oldspatial-sbml/settings">
         <update step="0.07" freq="50"/>
         <items>
           <item sbmlId="species_1" palette="black-blue.txt" max="2"/>
           <item sbmlId="species_2" palette="black-green.txt" max="2"/>
         </items>
-      </spatialInfo>
+      </oldspatialInfo>
     </annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
@@ -18,12 +18,12 @@
       </unitDefinition>
       <unitDefinition id="volume">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="area">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="molecules">
@@ -33,22 +33,22 @@
       </unitDefinition>
       <unitDefinition id="umol_um3_litre_1">
         <listOfUnits>
-          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-21"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um3">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um2">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="uM_um3_molecules_1">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-21"/>
           <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
           <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
         </listOfUnits>
@@ -71,7 +71,7 @@
       </unitDefinition>
       <unitDefinition id="_one__0E_6">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-006"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="_one_000000_0">
@@ -97,61 +97,61 @@
     </listOfUnitDefinitions>
     <listOfCompartments>
       <compartment id="compartment_1" name="compartment_1" spatialDimensions="3" size="1" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain0compartment_1" spatial:compartment="compartment_1" spatial:domainType="subdomain0" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain0compartment_1" spatial:domainType="subdomain0" spatial:unitSize="1"/>
       </compartment>
       <compartment id="c2" name="c2" spatialDimensions="3" size="1" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain1c2" spatial:compartment="c2" spatial:domainType="subdomain1" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain1c2" spatial:domainType="subdomain1" spatial:unitSize="1"/>
       </compartment>
       <compartment id="Membrane2" name="Membrane2" spatialDimensions="2" size="1" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain0_subdomain1_membraneMembrane2" spatial:compartment="Membrane2" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain0_subdomain1_membraneMembrane2" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species id="species_1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
-      <species id="species_2" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
+      <species id="species_1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true"/>
+      <species id="species_2" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true"/>
     </listOfSpecies>
     <listOfParameters>
-      <parameter id="x" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      <parameter id="x" value="0" constant="true">
+        <spatial:spatialSymbolReference spatial:spatialRef="x"/>
       </parameter>
-      <parameter id="y" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      <parameter id="y" value="0" constant="true">
+        <spatial:spatialSymbolReference spatial:spatialRef="y"/>
       </parameter>
-      <parameter id="species_1_diff" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="0"/>
+      <parameter id="species_1_diff" value="4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="species_1_diff_Y" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="1"/>
+      <parameter id="species_1_diff_Y" value="4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="species_1_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="species_1_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="species_1_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="species_1_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
-      <parameter id="species_2_diff" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="0"/>
+      <parameter id="species_2_diff" value="0.4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="species_2_diff_y" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="1"/>
+      <parameter id="species_2_diff_y" value="0.4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="species_2_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="species_2_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="species_2_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="species_2_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
       <parameter id="v1" value="0.06" constant="true"/>
       <parameter id="v2" value="0.12" constant="true"/>
@@ -208,7 +208,7 @@
       </initialAssignment>
     </listOfInitialAssignments>
     <listOfReactions>
-      <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false" spatial:isLocal="true">
         <listOfReactants>
           <speciesReference species="species_1" stoichiometry="1" constant="true"/>
         </listOfReactants>
@@ -226,7 +226,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false" spatial:isLocal="true">
         <listOfProducts>
           <speciesReference species="species_1" stoichiometry="1" constant="true"/>
         </listOfProducts>
@@ -236,7 +236,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false" spatial:isLocal="true">
         <listOfProducts>
           <speciesReference species="species_2" stoichiometry="1" constant="true"/>
         </listOfProducts>
@@ -246,7 +246,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false" spatial:isLocal="true">
         <listOfReactants>
           <speciesReference species="species_2" stoichiometry="1" constant="true"/>
         </listOfReactants>
@@ -270,43 +270,43 @@
         </kineticLaw>
       </reaction>
     </listOfReactions>
-    <spatial:geometry spatial:coordinateSystem="Cartesian">
+    <spatial:geometry spatial:id="newGeometry" spatial:coordinateSystem="cartesian">
       <spatial:listOfCoordinateComponents>
-        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
-          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="100"/>
+        <spatial:coordinateComponent spatial:id="x" spatial:type="cartesianX">
+          <spatial:boundaryMin spatial:id="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Xmax" spatial:value="100"/>
         </spatial:coordinateComponent>
-        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
-          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="100"/>
+        <spatial:coordinateComponent spatial:id="y" spatial:type="cartesianY">
+          <spatial:boundaryMin spatial:id="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Ymax" spatial:value="100"/>
         </spatial:coordinateComponent>
       </spatial:listOfCoordinateComponents>
       <spatial:listOfDomainTypes>
-        <spatial:domainType spatial:spatialId="subdomain1" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain0" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
+        <spatial:domainType spatial:id="subdomain1" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain0" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
       </spatial:listOfDomainTypes>
       <spatial:listOfDomains>
-        <spatial:domain spatial:spatialId="subdomain10" spatial:domainType="subdomain1">
+        <spatial:domain spatial:id="subdomain10" spatial:domainType="subdomain1">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="subdomain01" spatial:domainType="subdomain0">
+        <spatial:domain spatial:id="subdomain01" spatial:domainType="subdomain0">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="1" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="membrane_subdomain10_subdomain01" spatial:domainType="subdomain0_subdomain1_membrane"/>
+        <spatial:domain spatial:id="membrane_subdomain10_subdomain01" spatial:domainType="subdomain0_subdomain1_membrane"/>
       </spatial:listOfDomains>
       <spatial:listOfAdjacentDomains>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain01" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain01"/>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain10" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain10"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain10_subdomain01_subdomain01" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain01"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain10_subdomain01_subdomain10" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain10"/>
       </spatial:listOfAdjacentDomains>
       <spatial:listOfGeometryDefinitions>
-        <spatial:analyticGeometry spatial:spatialId="Geometry4">
+        <spatial:analyticGeometry spatial:id="Geometry4" spatial:isActive="true">
           <spatial:listOfAnalyticVolumes>
-            <spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="1">
+            <spatial:analyticVolume spatial:id="subdomain0" spatial:functionType="layered" spatial:ordinal="1" spatial:domainType="subdomain0">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <piecewise>
                   <piece>
@@ -341,7 +341,7 @@
                 </piecewise>
               </math>
             </spatial:analyticVolume>
-            <spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="0">
+            <spatial:analyticVolume spatial:id="subdomain1" spatial:functionType="layered" spatial:ordinal="0" spatial:domainType="subdomain1">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <cn type="integer"> 1 </cn>
               </math>
diff --git a/examples/turing_300x300.xml b/examples/turing_300x300.xml
index 2afa301..92581eb 100644
--- a/examples/turing_300x300.xml
+++ b/examples/turing_300x300.xml
@@ -1,14 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="true" spatial:required="true">
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" spatial:required="true">
   <model metaid="COPASI1" id="New_Model_Application0" name="New Model_Application0">
     <annotation>
-      <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+      <oldspatialInfo xmlns="http://fbergmann.github.io/oldspatial-sbml/settings">
         <update step="0.07" freq="500"/>
         <items>
           <item sbmlId="species_1" palette="black-blue.txt" max="2"/>
           <item sbmlId="species_2" palette="black-green.txt" max="2"/>
         </items>
-      </spatialInfo>
+      </oldspatialInfo>
     </annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
@@ -18,12 +18,12 @@
       </unitDefinition>
       <unitDefinition id="volume">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="area">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="molecules">
@@ -33,22 +33,22 @@
       </unitDefinition>
       <unitDefinition id="umol_um3_litre_1">
         <listOfUnits>
-          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-21"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um3">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um2">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="uM_um3_molecules_1">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-21"/>
           <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
           <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
         </listOfUnits>
@@ -71,7 +71,7 @@
       </unitDefinition>
       <unitDefinition id="_one__0E_6">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-006"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="_one_000000_0">
@@ -97,61 +97,61 @@
     </listOfUnitDefinitions>
     <listOfCompartments>
       <compartment id="compartment_1" name="compartment_1" spatialDimensions="3" size="1" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain0compartment_1" spatial:compartment="compartment_1" spatial:domainType="subdomain0" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain0compartment_1" spatial:domainType="subdomain0" spatial:unitSize="1"/>
       </compartment>
       <compartment id="c2" name="c2" spatialDimensions="3" size="1" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain1c2" spatial:compartment="c2" spatial:domainType="subdomain1" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain1c2" spatial:domainType="subdomain1" spatial:unitSize="1"/>
       </compartment>
       <compartment id="Membrane2" name="Membrane2" spatialDimensions="2" size="1" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain0_subdomain1_membraneMembrane2" spatial:compartment="Membrane2" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain0_subdomain1_membraneMembrane2" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species id="species_1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
-      <species id="species_2" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
+      <species id="species_1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true"/>
+      <species id="species_2" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true"/>
     </listOfSpecies>
     <listOfParameters>
-      <parameter id="x" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      <parameter id="x" value="0" constant="true">
+        <spatial:spatialSymbolReference spatial:spatialRef="x"/>
       </parameter>
-      <parameter id="y" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      <parameter id="y" value="0" constant="true">
+        <spatial:spatialSymbolReference spatial:spatialRef="y"/>
       </parameter>
-      <parameter id="species_1_diff" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="0"/>
+      <parameter id="species_1_diff" value="4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="species_1_diff_Y" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="1"/>
+      <parameter id="species_1_diff_Y" value="4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="species_1_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="species_1_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="species_1_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="species_1_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
-      <parameter id="species_2_diff" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="0"/>
+      <parameter id="species_2_diff" value="0.4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="species_2_diff_y" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="1"/>
+      <parameter id="species_2_diff_y" value="0.4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="species_2_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="species_2_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="species_2_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="species_2_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
       <parameter id="v1" value="0.06" constant="true"/>
       <parameter id="v2" value="0.12" constant="true"/>
@@ -208,7 +208,7 @@
       </initialAssignment>
     </listOfInitialAssignments>
     <listOfReactions>
-      <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false" spatial:isLocal="true">
         <listOfReactants>
           <speciesReference species="species_1" stoichiometry="1" constant="true"/>
         </listOfReactants>
@@ -226,7 +226,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false" spatial:isLocal="true">
         <listOfProducts>
           <speciesReference species="species_1" stoichiometry="1" constant="true"/>
         </listOfProducts>
@@ -236,7 +236,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false" spatial:isLocal="true">
         <listOfProducts>
           <speciesReference species="species_2" stoichiometry="1" constant="true"/>
         </listOfProducts>
@@ -246,7 +246,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false" spatial:isLocal="true">
         <listOfReactants>
           <speciesReference species="species_2" stoichiometry="1" constant="true"/>
         </listOfReactants>
@@ -270,43 +270,43 @@
         </kineticLaw>
       </reaction>
     </listOfReactions>
-    <spatial:geometry spatial:coordinateSystem="Cartesian">
+    <spatial:geometry spatial:id="newGeometry" spatial:coordinateSystem="cartesian">
       <spatial:listOfCoordinateComponents>
-        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
-          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="300"/>
+        <spatial:coordinateComponent spatial:id="x" spatial:type="cartesianX">
+          <spatial:boundaryMin spatial:id="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Xmax" spatial:value="300"/>
         </spatial:coordinateComponent>
-        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
-          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="300"/>
+        <spatial:coordinateComponent spatial:id="y" spatial:type="cartesianY">
+          <spatial:boundaryMin spatial:id="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Ymax" spatial:value="300"/>
         </spatial:coordinateComponent>
       </spatial:listOfCoordinateComponents>
       <spatial:listOfDomainTypes>
-        <spatial:domainType spatial:spatialId="subdomain1" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain0" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
+        <spatial:domainType spatial:id="subdomain1" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain0" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
       </spatial:listOfDomainTypes>
       <spatial:listOfDomains>
-        <spatial:domain spatial:spatialId="subdomain10" spatial:domainType="subdomain1">
+        <spatial:domain spatial:id="subdomain10" spatial:domainType="subdomain1">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="subdomain01" spatial:domainType="subdomain0">
+        <spatial:domain spatial:id="subdomain01" spatial:domainType="subdomain0">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="1" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="membrane_subdomain10_subdomain01" spatial:domainType="subdomain0_subdomain1_membrane"/>
+        <spatial:domain spatial:id="membrane_subdomain10_subdomain01" spatial:domainType="subdomain0_subdomain1_membrane"/>
       </spatial:listOfDomains>
       <spatial:listOfAdjacentDomains>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain01" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain01"/>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain10" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain10"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain10_subdomain01_subdomain01" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain01"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain10_subdomain01_subdomain10" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain10"/>
       </spatial:listOfAdjacentDomains>
       <spatial:listOfGeometryDefinitions>
-        <spatial:analyticGeometry spatial:spatialId="Geometry4">
+        <spatial:analyticGeometry spatial:id="Geometry4" spatial:isActive="true">
           <spatial:listOfAnalyticVolumes>
-            <spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="1">
+            <spatial:analyticVolume spatial:id="subdomain0" spatial:functionType="layered" spatial:ordinal="1" spatial:domainType="subdomain0">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <piecewise>
                   <piece>
@@ -341,7 +341,7 @@
                 </piecewise>
               </math>
             </spatial:analyticVolume>
-            <spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="0">
+            <spatial:analyticVolume spatial:id="subdomain1" spatial:functionType="layered" spatial:ordinal="0" spatial:domainType="subdomain1">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <cn type="integer"> 1 </cn>
               </math>
diff --git a/examples/turing_parameters-stripe.xml b/examples/turing_parameters-stripe.xml
index 13de1f5..66f351d 100644
--- a/examples/turing_parameters-stripe.xml
+++ b/examples/turing_parameters-stripe.xml
@@ -1,14 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="true" spatial:required="true">
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" spatial:required="true">
   <model metaid="COPASI1" id="New_Model_Application0" name="New Model_Application0">
-      <annotation>
-      <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+    <annotation>
+      <oldspatialInfo xmlns="http://fbergmann.github.io/oldspatial-sbml/settings">
         <update step="0.05" freq="50"/>
         <items>
           <item sbmlId="species_1" palette="black-blue.txt" max="2"/>
           <item sbmlId="species_2" palette="black-green.txt" max="2"/>
         </items>
-      </spatialInfo>
+      </oldspatialInfo>
     </annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
@@ -18,12 +18,12 @@
       </unitDefinition>
       <unitDefinition id="volume">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="area">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="molecules">
@@ -33,22 +33,22 @@
       </unitDefinition>
       <unitDefinition id="umol_um3_litre_1">
         <listOfUnits>
-          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-21"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um3">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um2">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="uM_um3_molecules_1">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-21"/>
           <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
           <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
         </listOfUnits>
@@ -71,7 +71,7 @@
       </unitDefinition>
       <unitDefinition id="_one__0E_6">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-006"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="_one_000000_0">
@@ -97,61 +97,61 @@
     </listOfUnitDefinitions>
     <listOfCompartments>
       <compartment id="compartment_1" name="compartment_1" spatialDimensions="3" size="1" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain0compartment_1" spatial:compartment="compartment_1" spatial:domainType="subdomain0" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain0compartment_1" spatial:domainType="subdomain0" spatial:unitSize="1"/>
       </compartment>
       <compartment id="c2" name="c2" spatialDimensions="3" size="1" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain1c2" spatial:compartment="c2" spatial:domainType="subdomain1" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain1c2" spatial:domainType="subdomain1" spatial:unitSize="1"/>
       </compartment>
       <compartment id="Membrane2" name="Membrane2" spatialDimensions="2" size="1" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain0_subdomain1_membraneMembrane2" spatial:compartment="Membrane2" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain0_subdomain1_membraneMembrane2" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species id="species_1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
-      <species id="species_2" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
+      <species id="species_1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true"/>
+      <species id="species_2" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true"/>
     </listOfSpecies>
     <listOfParameters>
-      <parameter id="x" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      <parameter id="x" value="0" constant="true">
+        <spatial:spatialSymbolReference spatial:spatialRef="x"/>
       </parameter>
-      <parameter id="y" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      <parameter id="y" value="0" constant="true">
+        <spatial:spatialSymbolReference spatial:spatialRef="y"/>
       </parameter>
-      <parameter id="species_1_diff" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="0"/>
+      <parameter id="species_1_diff" value="4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="species_1_diff_Y" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="1"/>
+      <parameter id="species_1_diff_Y" value="4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="species_1_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="species_1_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="species_1_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="species_1_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
-      <parameter id="species_2_diff" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="0"/>
+      <parameter id="species_2_diff" value="0.4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="species_2_diff_y" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="1"/>
+      <parameter id="species_2_diff_y" value="0.4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="species_2_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="species_2_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="species_2_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="species_2_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
       <parameter id="v1" value="0.06" constant="true"/>
       <parameter id="v2" value="0.12" constant="true"/>
@@ -208,7 +208,7 @@
       </initialAssignment>
     </listOfInitialAssignments>
     <listOfReactions>
-      <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false" spatial:isLocal="true">
         <listOfReactants>
           <speciesReference species="species_1" stoichiometry="1" constant="true"/>
         </listOfReactants>
@@ -226,7 +226,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false" spatial:isLocal="true">
         <listOfProducts>
           <speciesReference species="species_1" stoichiometry="1" constant="true"/>
         </listOfProducts>
@@ -236,7 +236,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false" spatial:isLocal="true">
         <listOfProducts>
           <speciesReference species="species_2" stoichiometry="1" constant="true"/>
         </listOfProducts>
@@ -246,7 +246,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false" spatial:isLocal="true">
         <listOfReactants>
           <speciesReference species="species_2" stoichiometry="1" constant="true"/>
         </listOfReactants>
@@ -270,43 +270,43 @@
         </kineticLaw>
       </reaction>
     </listOfReactions>
-    <spatial:geometry spatial:coordinateSystem="Cartesian">
+    <spatial:geometry spatial:id="newGeometry" spatial:coordinateSystem="cartesian">
       <spatial:listOfCoordinateComponents>
-        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
-          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="100"/>
+        <spatial:coordinateComponent spatial:id="x" spatial:type="cartesianX">
+          <spatial:boundaryMin spatial:id="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Xmax" spatial:value="100"/>
         </spatial:coordinateComponent>
-        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
-          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="100"/>
+        <spatial:coordinateComponent spatial:id="y" spatial:type="cartesianY">
+          <spatial:boundaryMin spatial:id="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Ymax" spatial:value="100"/>
         </spatial:coordinateComponent>
       </spatial:listOfCoordinateComponents>
       <spatial:listOfDomainTypes>
-        <spatial:domainType spatial:spatialId="subdomain1" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain0" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
+        <spatial:domainType spatial:id="subdomain1" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain0" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
       </spatial:listOfDomainTypes>
       <spatial:listOfDomains>
-        <spatial:domain spatial:spatialId="subdomain10" spatial:domainType="subdomain1">
+        <spatial:domain spatial:id="subdomain10" spatial:domainType="subdomain1">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="subdomain01" spatial:domainType="subdomain0">
+        <spatial:domain spatial:id="subdomain01" spatial:domainType="subdomain0">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="1" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="membrane_subdomain10_subdomain01" spatial:domainType="subdomain0_subdomain1_membrane"/>
+        <spatial:domain spatial:id="membrane_subdomain10_subdomain01" spatial:domainType="subdomain0_subdomain1_membrane"/>
       </spatial:listOfDomains>
       <spatial:listOfAdjacentDomains>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain01" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain01"/>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain10" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain10"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain10_subdomain01_subdomain01" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain01"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain10_subdomain01_subdomain10" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain10"/>
       </spatial:listOfAdjacentDomains>
       <spatial:listOfGeometryDefinitions>
-        <spatial:analyticGeometry spatial:spatialId="Geometry4">
+        <spatial:analyticGeometry spatial:id="Geometry4" spatial:isActive="true">
           <spatial:listOfAnalyticVolumes>
-            <spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="1">
+            <spatial:analyticVolume spatial:id="subdomain0" spatial:functionType="layered" spatial:ordinal="1" spatial:domainType="subdomain0">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <piecewise>
                   <piece>
@@ -341,7 +341,7 @@
                 </piecewise>
               </math>
             </spatial:analyticVolume>
-            <spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="0">
+            <spatial:analyticVolume spatial:id="subdomain1" spatial:functionType="layered" spatial:ordinal="0" spatial:domainType="subdomain1">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <cn type="integer"> 1 </cn>
               </math>
diff --git a/examples/turing_parameters.xml b/examples/turing_parameters.xml
index af89961..122f07b 100644
--- a/examples/turing_parameters.xml
+++ b/examples/turing_parameters.xml
@@ -1,14 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="true" spatial:required="true">
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" spatial:required="true">
   <model metaid="COPASI1" id="New_Model_Application0" name="New Model_Application0">
-      <annotation>
-      <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+    <annotation>
+      <oldspatialInfo xmlns="http://fbergmann.github.io/oldspatial-sbml/settings">
         <update step="0.07" freq="50"/>
         <items>
           <item sbmlId="species_1" palette="black-blue.txt" max="2"/>
           <item sbmlId="species_2" palette="black-green.txt" max="2"/>
         </items>
-      </spatialInfo>
+      </oldspatialInfo>
     </annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
@@ -18,12 +18,12 @@
       </unitDefinition>
       <unitDefinition id="volume">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="area">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="molecules">
@@ -33,22 +33,22 @@
       </unitDefinition>
       <unitDefinition id="umol_um3_litre_1">
         <listOfUnits>
-          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-21"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um3">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um2">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="uM_um3_molecules_1">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-21"/>
           <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
           <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
         </listOfUnits>
@@ -71,7 +71,7 @@
       </unitDefinition>
       <unitDefinition id="_one__0E_6">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-006"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="_one_000000_0">
@@ -97,61 +97,61 @@
     </listOfUnitDefinitions>
     <listOfCompartments>
       <compartment id="compartment_1" name="compartment_1" spatialDimensions="3" size="1" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain0compartment_1" spatial:compartment="compartment_1" spatial:domainType="subdomain0" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain0compartment_1" spatial:domainType="subdomain0" spatial:unitSize="1"/>
       </compartment>
       <compartment id="c2" name="c2" spatialDimensions="3" size="1" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain1c2" spatial:compartment="c2" spatial:domainType="subdomain1" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain1c2" spatial:domainType="subdomain1" spatial:unitSize="1"/>
       </compartment>
       <compartment id="Membrane2" name="Membrane2" spatialDimensions="2" size="1" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain0_subdomain1_membraneMembrane2" spatial:compartment="Membrane2" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain0_subdomain1_membraneMembrane2" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species id="species_1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
-      <species id="species_2" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
+      <species id="species_1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true"/>
+      <species id="species_2" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true"/>
     </listOfSpecies>
     <listOfParameters>
-      <parameter id="x" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      <parameter id="x" value="0" constant="true">
+        <spatial:spatialSymbolReference spatial:spatialRef="x"/>
       </parameter>
-      <parameter id="y" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      <parameter id="y" value="0" constant="true">
+        <spatial:spatialSymbolReference spatial:spatialRef="y"/>
       </parameter>
-      <parameter id="species_1_diff" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="0"/>
+      <parameter id="species_1_diff" value="4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="species_1_diff_Y" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="1"/>
+      <parameter id="species_1_diff_Y" value="4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="species_1_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="species_1_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="species_1_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="species_1_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
-      <parameter id="species_2_diff" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="0"/>
+      <parameter id="species_2_diff" value="0.4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="species_2_diff_y" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="1"/>
+      <parameter id="species_2_diff_y" value="0.4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="species_2_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="species_2_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="species_2_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="species_2_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
       <parameter id="v1" value="0.06" constant="true"/>
       <parameter id="v2" value="0.12" constant="true"/>
@@ -208,7 +208,7 @@
       </initialAssignment>
     </listOfInitialAssignments>
     <listOfReactions>
-      <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false" spatial:isLocal="true">
         <listOfReactants>
           <speciesReference species="species_1" stoichiometry="1" constant="true"/>
         </listOfReactants>
@@ -226,7 +226,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false" spatial:isLocal="true">
         <listOfProducts>
           <speciesReference species="species_1" stoichiometry="1" constant="true"/>
         </listOfProducts>
@@ -236,7 +236,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false" spatial:isLocal="true">
         <listOfProducts>
           <speciesReference species="species_2" stoichiometry="1" constant="true"/>
         </listOfProducts>
@@ -246,7 +246,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false" spatial:isLocal="true">
         <listOfReactants>
           <speciesReference species="species_2" stoichiometry="1" constant="true"/>
         </listOfReactants>
@@ -270,43 +270,43 @@
         </kineticLaw>
       </reaction>
     </listOfReactions>
-    <spatial:geometry spatial:coordinateSystem="Cartesian">
+    <spatial:geometry spatial:id="newGeometry" spatial:coordinateSystem="cartesian">
       <spatial:listOfCoordinateComponents>
-        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
-          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="100"/>
+        <spatial:coordinateComponent spatial:id="x" spatial:type="cartesianX">
+          <spatial:boundaryMin spatial:id="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Xmax" spatial:value="100"/>
         </spatial:coordinateComponent>
-        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
-          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="100"/>
+        <spatial:coordinateComponent spatial:id="y" spatial:type="cartesianY">
+          <spatial:boundaryMin spatial:id="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Ymax" spatial:value="100"/>
         </spatial:coordinateComponent>
       </spatial:listOfCoordinateComponents>
       <spatial:listOfDomainTypes>
-        <spatial:domainType spatial:spatialId="subdomain1" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain0" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
+        <spatial:domainType spatial:id="subdomain1" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain0" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
       </spatial:listOfDomainTypes>
       <spatial:listOfDomains>
-        <spatial:domain spatial:spatialId="subdomain10" spatial:domainType="subdomain1">
+        <spatial:domain spatial:id="subdomain10" spatial:domainType="subdomain1">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="subdomain01" spatial:domainType="subdomain0">
+        <spatial:domain spatial:id="subdomain01" spatial:domainType="subdomain0">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="1" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="membrane_subdomain10_subdomain01" spatial:domainType="subdomain0_subdomain1_membrane"/>
+        <spatial:domain spatial:id="membrane_subdomain10_subdomain01" spatial:domainType="subdomain0_subdomain1_membrane"/>
       </spatial:listOfDomains>
       <spatial:listOfAdjacentDomains>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain01" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain01"/>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain10" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain10"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain10_subdomain01_subdomain01" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain01"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain10_subdomain01_subdomain10" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain10"/>
       </spatial:listOfAdjacentDomains>
       <spatial:listOfGeometryDefinitions>
-        <spatial:analyticGeometry spatial:spatialId="Geometry4">
+        <spatial:analyticGeometry spatial:id="Geometry4" spatial:isActive="true">
           <spatial:listOfAnalyticVolumes>
-            <spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="1">
+            <spatial:analyticVolume spatial:id="subdomain0" spatial:functionType="layered" spatial:ordinal="1" spatial:domainType="subdomain0">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <piecewise>
                   <piece>
@@ -341,7 +341,7 @@
                 </piecewise>
               </math>
             </spatial:analyticVolume>
-            <spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="0">
+            <spatial:analyticVolume spatial:id="subdomain1" spatial:functionType="layered" spatial:ordinal="0" spatial:domainType="subdomain1">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <cn type="integer"> 1 </cn>
               </math>
diff --git a/examples/turing_parameters_50x50.xml b/examples/turing_parameters_50x50.xml
index 9b17a18..f48e21f 100644
--- a/examples/turing_parameters_50x50.xml
+++ b/examples/turing_parameters_50x50.xml
@@ -1,14 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="true" spatial:required="true">
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" spatial:required="true">
   <model metaid="COPASI1" id="New_Model_Application0" name="New Model_Application0">
-      <annotation>
-      <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+    <annotation>
+      <oldspatialInfo xmlns="http://fbergmann.github.io/oldspatial-sbml/settings">
         <update step="0.07" freq="50"/>
         <items>
           <item sbmlId="species_1" palette="black-blue.txt" max="2"/>
           <item sbmlId="species_2" palette="black-green.txt" max="2"/>
         </items>
-      </spatialInfo>
+      </oldspatialInfo>
     </annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
@@ -18,12 +18,12 @@
       </unitDefinition>
       <unitDefinition id="volume">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="area">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="molecules">
@@ -33,22 +33,22 @@
       </unitDefinition>
       <unitDefinition id="umol_um3_litre_1">
         <listOfUnits>
-          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-21"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um3">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um2">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="uM_um3_molecules_1">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-21"/>
           <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
           <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
         </listOfUnits>
@@ -71,7 +71,7 @@
       </unitDefinition>
       <unitDefinition id="_one__0E_6">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-006"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="_one_000000_0">
@@ -97,61 +97,61 @@
     </listOfUnitDefinitions>
     <listOfCompartments>
       <compartment id="compartment_1" name="compartment_1" spatialDimensions="3" size="1" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain0compartment_1" spatial:compartment="compartment_1" spatial:domainType="subdomain0" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain0compartment_1" spatial:domainType="subdomain0" spatial:unitSize="1"/>
       </compartment>
       <compartment id="c2" name="c2" spatialDimensions="3" size="1" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain1c2" spatial:compartment="c2" spatial:domainType="subdomain1" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain1c2" spatial:domainType="subdomain1" spatial:unitSize="1"/>
       </compartment>
       <compartment id="Membrane2" name="Membrane2" spatialDimensions="2" size="1" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain0_subdomain1_membraneMembrane2" spatial:compartment="Membrane2" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain0_subdomain1_membraneMembrane2" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species id="species_1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
-      <species id="species_2" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
+      <species id="species_1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true"/>
+      <species id="species_2" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true"/>
     </listOfSpecies>
     <listOfParameters>
-      <parameter id="x" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      <parameter id="x" value="0" constant="true">
+        <spatial:spatialSymbolReference spatial:spatialRef="x"/>
       </parameter>
-      <parameter id="y" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      <parameter id="y" value="0" constant="true">
+        <spatial:spatialSymbolReference spatial:spatialRef="y"/>
       </parameter>
-      <parameter id="species_1_diff" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="0"/>
+      <parameter id="species_1_diff" value="4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="species_1_diff_Y" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="1"/>
+      <parameter id="species_1_diff_Y" value="4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="species_1_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="species_1_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="species_1_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="species_1_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
-      <parameter id="species_2_diff" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="0"/>
+      <parameter id="species_2_diff" value="0.4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="species_2_diff_y" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="1"/>
+      <parameter id="species_2_diff_y" value="0.4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="species_2_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="species_2_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="species_2_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="species_2_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
       <parameter id="v1" value="0.06" constant="true"/>
       <parameter id="v2" value="0.12" constant="true"/>
@@ -208,7 +208,7 @@
       </initialAssignment>
     </listOfInitialAssignments>
     <listOfReactions>
-      <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false" spatial:isLocal="true">
         <listOfReactants>
           <speciesReference species="species_1" stoichiometry="1" constant="true"/>
         </listOfReactants>
@@ -226,7 +226,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false" spatial:isLocal="true">
         <listOfProducts>
           <speciesReference species="species_1" stoichiometry="1" constant="true"/>
         </listOfProducts>
@@ -236,7 +236,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false" spatial:isLocal="true">
         <listOfProducts>
           <speciesReference species="species_2" stoichiometry="1" constant="true"/>
         </listOfProducts>
@@ -246,7 +246,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false" spatial:isLocal="true">
         <listOfReactants>
           <speciesReference species="species_2" stoichiometry="1" constant="true"/>
         </listOfReactants>
@@ -270,43 +270,43 @@
         </kineticLaw>
       </reaction>
     </listOfReactions>
-    <spatial:geometry spatial:coordinateSystem="Cartesian">
+    <spatial:geometry spatial:id="newGeometry" spatial:coordinateSystem="cartesian">
       <spatial:listOfCoordinateComponents>
-        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
-          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="50"/>
+        <spatial:coordinateComponent spatial:id="x" spatial:type="cartesianX">
+          <spatial:boundaryMin spatial:id="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Xmax" spatial:value="50"/>
         </spatial:coordinateComponent>
-        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
-          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="50"/>
+        <spatial:coordinateComponent spatial:id="y" spatial:type="cartesianY">
+          <spatial:boundaryMin spatial:id="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Ymax" spatial:value="50"/>
         </spatial:coordinateComponent>
       </spatial:listOfCoordinateComponents>
       <spatial:listOfDomainTypes>
-        <spatial:domainType spatial:spatialId="subdomain1" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain0" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
+        <spatial:domainType spatial:id="subdomain1" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain0" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
       </spatial:listOfDomainTypes>
       <spatial:listOfDomains>
-        <spatial:domain spatial:spatialId="subdomain10" spatial:domainType="subdomain1">
+        <spatial:domain spatial:id="subdomain10" spatial:domainType="subdomain1">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="subdomain01" spatial:domainType="subdomain0">
+        <spatial:domain spatial:id="subdomain01" spatial:domainType="subdomain0">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="1" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="membrane_subdomain10_subdomain01" spatial:domainType="subdomain0_subdomain1_membrane"/>
+        <spatial:domain spatial:id="membrane_subdomain10_subdomain01" spatial:domainType="subdomain0_subdomain1_membrane"/>
       </spatial:listOfDomains>
       <spatial:listOfAdjacentDomains>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain01" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain01"/>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain10" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain10"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain10_subdomain01_subdomain01" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain01"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain10_subdomain01_subdomain10" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain10"/>
       </spatial:listOfAdjacentDomains>
       <spatial:listOfGeometryDefinitions>
-        <spatial:analyticGeometry spatial:spatialId="Geometry4">
+        <spatial:analyticGeometry spatial:id="Geometry4" spatial:isActive="true">
           <spatial:listOfAnalyticVolumes>
-            <spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="1">
+            <spatial:analyticVolume spatial:id="subdomain0" spatial:functionType="layered" spatial:ordinal="1" spatial:domainType="subdomain0">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <piecewise>
                   <piece>
@@ -341,7 +341,7 @@
                 </piecewise>
               </math>
             </spatial:analyticVolume>
-            <spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="0">
+            <spatial:analyticVolume spatial:id="subdomain1" spatial:functionType="layered" spatial:ordinal="0" spatial:domainType="subdomain1">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <cn type="integer"> 1 </cn>
               </math>
diff --git a/examples/turing_parameters_tiny.xml b/examples/turing_parameters_tiny.xml
index e2b92d8..897d16d 100644
--- a/examples/turing_parameters_tiny.xml
+++ b/examples/turing_parameters_tiny.xml
@@ -1,14 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="true" spatial:required="true">
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" spatial:required="true">
   <model metaid="COPASI1" id="New_Model_Application0" name="New Model_Application0">
-      <annotation>
-      <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+    <annotation>
+      <oldspatialInfo xmlns="http://fbergmann.github.io/oldspatial-sbml/settings">
         <update step="0.07" freq="30"/>
         <items>
           <item sbmlId="species_1" palette="black-blue.txt" max="2"/>
           <item sbmlId="species_2" palette="black-green.txt" max="2"/>
         </items>
-      </spatialInfo>
+      </oldspatialInfo>
     </annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
@@ -18,12 +18,12 @@
       </unitDefinition>
       <unitDefinition id="volume">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="area">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="molecules">
@@ -33,22 +33,22 @@
       </unitDefinition>
       <unitDefinition id="umol_um3_litre_1">
         <listOfUnits>
-          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-21"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um3">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um2">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="uM_um3_molecules_1">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-21"/>
           <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
           <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
         </listOfUnits>
@@ -71,7 +71,7 @@
       </unitDefinition>
       <unitDefinition id="_one__0E_6">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-006"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="_one_000000_0">
@@ -97,61 +97,61 @@
     </listOfUnitDefinitions>
     <listOfCompartments>
       <compartment id="compartment_1" name="compartment_1" spatialDimensions="3" size="1" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain0compartment_1" spatial:compartment="compartment_1" spatial:domainType="subdomain0" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain0compartment_1" spatial:domainType="subdomain0" spatial:unitSize="1"/>
       </compartment>
       <compartment id="c2" name="c2" spatialDimensions="3" size="1" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain1c2" spatial:compartment="c2" spatial:domainType="subdomain1" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain1c2" spatial:domainType="subdomain1" spatial:unitSize="1"/>
       </compartment>
       <compartment id="Membrane2" name="Membrane2" spatialDimensions="2" size="1" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain0_subdomain1_membraneMembrane2" spatial:compartment="Membrane2" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain0_subdomain1_membraneMembrane2" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species id="species_1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
-      <species id="species_2" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
+      <species id="species_1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true"/>
+      <species id="species_2" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true"/>
     </listOfSpecies>
     <listOfParameters>
-      <parameter id="x" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      <parameter id="x" value="0" constant="true">
+        <spatial:spatialSymbolReference spatial:spatialRef="x"/>
       </parameter>
-      <parameter id="y" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      <parameter id="y" value="0" constant="true">
+        <spatial:spatialSymbolReference spatial:spatialRef="y"/>
       </parameter>
-      <parameter id="species_1_diff" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="0"/>
+      <parameter id="species_1_diff" value="4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="species_1_diff_Y" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="1"/>
+      <parameter id="species_1_diff_Y" value="4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="species_1_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="species_1_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="species_1_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="species_1_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
-      <parameter id="species_2_diff" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="0"/>
+      <parameter id="species_2_diff" value="0.4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="species_2_diff_y" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="1"/>
+      <parameter id="species_2_diff_y" value="0.4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="species_2_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="species_2_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="species_2_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="species_2_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
       <parameter id="v1" value="0.06" constant="true"/>
       <parameter id="v2" value="0.12" constant="true"/>
@@ -208,7 +208,7 @@
       </initialAssignment>
     </listOfInitialAssignments>
     <listOfReactions>
-      <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false" spatial:isLocal="true">
         <listOfReactants>
           <speciesReference species="species_1" stoichiometry="1" constant="true"/>
         </listOfReactants>
@@ -226,7 +226,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false" spatial:isLocal="true">
         <listOfProducts>
           <speciesReference species="species_1" stoichiometry="1" constant="true"/>
         </listOfProducts>
@@ -236,7 +236,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false" spatial:isLocal="true">
         <listOfProducts>
           <speciesReference species="species_2" stoichiometry="1" constant="true"/>
         </listOfProducts>
@@ -246,7 +246,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false" spatial:isLocal="true">
         <listOfReactants>
           <speciesReference species="species_2" stoichiometry="1" constant="true"/>
         </listOfReactants>
@@ -270,43 +270,43 @@
         </kineticLaw>
       </reaction>
     </listOfReactions>
-    <spatial:geometry spatial:coordinateSystem="Cartesian">
+    <spatial:geometry spatial:id="newGeometry" spatial:coordinateSystem="cartesian">
       <spatial:listOfCoordinateComponents>
-        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
-          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="21"/>
+        <spatial:coordinateComponent spatial:id="x" spatial:type="cartesianX">
+          <spatial:boundaryMin spatial:id="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Xmax" spatial:value="21"/>
         </spatial:coordinateComponent>
-        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
-          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="21"/>
+        <spatial:coordinateComponent spatial:id="y" spatial:type="cartesianY">
+          <spatial:boundaryMin spatial:id="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Ymax" spatial:value="21"/>
         </spatial:coordinateComponent>
       </spatial:listOfCoordinateComponents>
       <spatial:listOfDomainTypes>
-        <spatial:domainType spatial:spatialId="subdomain1" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain0" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
+        <spatial:domainType spatial:id="subdomain1" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain0" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
       </spatial:listOfDomainTypes>
       <spatial:listOfDomains>
-        <spatial:domain spatial:spatialId="subdomain10" spatial:domainType="subdomain1">
+        <spatial:domain spatial:id="subdomain10" spatial:domainType="subdomain1">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="subdomain01" spatial:domainType="subdomain0">
+        <spatial:domain spatial:id="subdomain01" spatial:domainType="subdomain0">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="1" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="membrane_subdomain10_subdomain01" spatial:domainType="subdomain0_subdomain1_membrane"/>
+        <spatial:domain spatial:id="membrane_subdomain10_subdomain01" spatial:domainType="subdomain0_subdomain1_membrane"/>
       </spatial:listOfDomains>
       <spatial:listOfAdjacentDomains>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain01" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain01"/>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain10" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain10"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain10_subdomain01_subdomain01" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain01"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain10_subdomain01_subdomain10" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain10"/>
       </spatial:listOfAdjacentDomains>
       <spatial:listOfGeometryDefinitions>
-        <spatial:analyticGeometry spatial:spatialId="Geometry4">
+        <spatial:analyticGeometry spatial:id="Geometry4" spatial:isActive="true">
           <spatial:listOfAnalyticVolumes>
-            <spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="1">
+            <spatial:analyticVolume spatial:id="subdomain0" spatial:functionType="layered" spatial:ordinal="1" spatial:domainType="subdomain0">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <piecewise>
                   <piece>
@@ -341,7 +341,7 @@
                 </piecewise>
               </math>
             </spatial:analyticVolume>
-            <spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="0">
+            <spatial:analyticVolume spatial:id="subdomain1" spatial:functionType="layered" spatial:ordinal="0" spatial:domainType="subdomain1">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <cn type="integer"> 1 </cn>
               </math>
diff --git a/examples/turing_uniform.xml b/examples/turing_uniform.xml
index 27c8ae1..0362219 100644
--- a/examples/turing_uniform.xml
+++ b/examples/turing_uniform.xml
@@ -1,14 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="true" spatial:required="true">
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" spatial:required="true">
   <model metaid="COPASI1" id="New_Model_Application0" name="New Model_Application0">
-      <annotation>
-      <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+    <annotation>
+      <oldspatialInfo xmlns="http://fbergmann.github.io/oldspatial-sbml/settings">
         <update step="0.07" freq="50"/>
         <items>
           <item sbmlId="species_1" palette="black-blue.txt" max="2"/>
           <item sbmlId="species_2" palette="black-green.txt" max="2"/>
         </items>
-      </spatialInfo>
+      </oldspatialInfo>
     </annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
@@ -18,12 +18,12 @@
       </unitDefinition>
       <unitDefinition id="volume">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="area">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="molecules">
@@ -33,22 +33,22 @@
       </unitDefinition>
       <unitDefinition id="umol_um3_litre_1">
         <listOfUnits>
-          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-21"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um3">
         <listOfUnits>
-          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="um2">
         <listOfUnits>
-          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="uM_um3_molecules_1">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-21"/>
           <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
           <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
         </listOfUnits>
@@ -71,7 +71,7 @@
       </unitDefinition>
       <unitDefinition id="_one__0E_6">
         <listOfUnits>
-          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-006"/>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-06"/>
         </listOfUnits>
       </unitDefinition>
       <unitDefinition id="_one_000000_0">
@@ -97,61 +97,61 @@
     </listOfUnitDefinitions>
     <listOfCompartments>
       <compartment id="compartment_1" name="compartment_1" spatialDimensions="3" size="1" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain0compartment_1" spatial:compartment="compartment_1" spatial:domainType="subdomain0" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain0compartment_1" spatial:domainType="subdomain0" spatial:unitSize="1"/>
       </compartment>
       <compartment id="c2" name="c2" spatialDimensions="3" size="1" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain1c2" spatial:compartment="c2" spatial:domainType="subdomain1" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain1c2" spatial:domainType="subdomain1" spatial:unitSize="1"/>
       </compartment>
       <compartment id="Membrane2" name="Membrane2" spatialDimensions="2" size="1" constant="true">
-        <spatial:compartmentMapping spatial:spatialId="subdomain0_subdomain1_membraneMembrane2" spatial:compartment="Membrane2" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
+        <spatial:compartmentMapping spatial:id="subdomain0_subdomain1_membraneMembrane2" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species id="species_1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
-      <species id="species_2" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
+      <species id="species_1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true"/>
+      <species id="species_2" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true"/>
     </listOfSpecies>
     <listOfParameters>
-      <parameter id="x" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      <parameter id="x" value="0" constant="true">
+        <spatial:spatialSymbolReference spatial:spatialRef="x"/>
       </parameter>
-      <parameter id="y" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
-        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      <parameter id="y" value="0" constant="true">
+        <spatial:spatialSymbolReference spatial:spatialRef="y"/>
       </parameter>
-      <parameter id="species_1_diff" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="0"/>
+      <parameter id="species_1_diff" value="4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="species_1_diff_Y" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="1"/>
+      <parameter id="species_1_diff_Y" value="4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="species_1_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="species_1_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="species_1_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="species_1_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="species_1_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
-      <parameter id="species_2_diff" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="0"/>
+      <parameter id="species_2_diff" value="0.4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:type="isotropic" spatial:coordinateReference1="cartesianX"/>
       </parameter>
-      <parameter id="species_2_diff_y" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="1"/>
+      <parameter id="species_2_diff_y" value="0.4" constant="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:type="isotropic" spatial:coordinateReference1="cartesianY"/>
       </parameter>
-      <parameter id="species_2_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Xm" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Xmin"/>
       </parameter>
-      <parameter id="species_2_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Xp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Xmax"/>
       </parameter>
-      <parameter id="species_2_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Ym" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Ymin"/>
       </parameter>
-      <parameter id="species_2_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
-        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      <parameter id="species_2_BC_Yp" value="0" constant="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:type="Neumann" spatial:coordinateBoundary="Ymax"/>
       </parameter>
       <parameter id="v1" value="0.06" constant="true"/>
       <parameter id="v2" value="0.12" constant="true"/>
@@ -172,7 +172,7 @@
       </initialAssignment>
     </listOfInitialAssignments>
     <listOfReactions>
-      <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false" spatial:isLocal="true">
         <listOfReactants>
           <speciesReference species="species_1" stoichiometry="1" constant="true"/>
         </listOfReactants>
@@ -190,7 +190,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false" spatial:isLocal="true">
         <listOfProducts>
           <speciesReference species="species_1" stoichiometry="1" constant="true"/>
         </listOfProducts>
@@ -200,7 +200,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false" spatial:isLocal="true">
         <listOfProducts>
           <speciesReference species="species_2" stoichiometry="1" constant="true"/>
         </listOfProducts>
@@ -210,7 +210,7 @@
           </math>
         </kineticLaw>
       </reaction>
-      <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+      <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false" spatial:isLocal="true">
         <listOfReactants>
           <speciesReference species="species_2" stoichiometry="1" constant="true"/>
         </listOfReactants>
@@ -234,43 +234,43 @@
         </kineticLaw>
       </reaction>
     </listOfReactions>
-    <spatial:geometry spatial:coordinateSystem="Cartesian">
+    <spatial:geometry spatial:id="newGeometry" spatial:coordinateSystem="cartesian">
       <spatial:listOfCoordinateComponents>
-        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
-          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="100"/>
+        <spatial:coordinateComponent spatial:id="x" spatial:type="cartesianX">
+          <spatial:boundaryMin spatial:id="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Xmax" spatial:value="100"/>
         </spatial:coordinateComponent>
-        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
-          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
-          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="100"/>
+        <spatial:coordinateComponent spatial:id="y" spatial:type="cartesianY">
+          <spatial:boundaryMin spatial:id="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:id="Ymax" spatial:value="100"/>
         </spatial:coordinateComponent>
       </spatial:listOfCoordinateComponents>
       <spatial:listOfDomainTypes>
-        <spatial:domainType spatial:spatialId="subdomain1" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain0" spatial:spatialDimensions="3"/>
-        <spatial:domainType spatial:spatialId="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
+        <spatial:domainType spatial:id="subdomain1" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain0" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:id="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
       </spatial:listOfDomainTypes>
       <spatial:listOfDomains>
-        <spatial:domain spatial:spatialId="subdomain10" spatial:domainType="subdomain1">
+        <spatial:domain spatial:id="subdomain10" spatial:domainType="subdomain1">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="subdomain01" spatial:domainType="subdomain0">
+        <spatial:domain spatial:id="subdomain01" spatial:domainType="subdomain0">
           <spatial:listOfInteriorPoints>
             <spatial:interiorPoint spatial:coord1="1" spatial:coord2="0" spatial:coord3="5"/>
           </spatial:listOfInteriorPoints>
         </spatial:domain>
-        <spatial:domain spatial:spatialId="membrane_subdomain10_subdomain01" spatial:domainType="subdomain0_subdomain1_membrane"/>
+        <spatial:domain spatial:id="membrane_subdomain10_subdomain01" spatial:domainType="subdomain0_subdomain1_membrane"/>
       </spatial:listOfDomains>
       <spatial:listOfAdjacentDomains>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain01" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain01"/>
-        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain10" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain10"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain10_subdomain01_subdomain01" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain01"/>
+        <spatial:adjacentDomains spatial:id="membrane_subdomain10_subdomain01_subdomain10" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain10"/>
       </spatial:listOfAdjacentDomains>
       <spatial:listOfGeometryDefinitions>
-        <spatial:analyticGeometry spatial:spatialId="Geometry4">
+        <spatial:analyticGeometry spatial:id="Geometry4" spatial:isActive="true">
           <spatial:listOfAnalyticVolumes>
-            <spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="1">
+            <spatial:analyticVolume spatial:id="subdomain0" spatial:functionType="layered" spatial:ordinal="1" spatial:domainType="subdomain0">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <piecewise>
                   <piece>
@@ -305,7 +305,7 @@
                 </piecewise>
               </math>
             </spatial:analyticVolume>
-            <spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="0">
+            <spatial:analyticVolume spatial:id="subdomain1" spatial:functionType="layered" spatial:ordinal="0" spatial:domainType="subdomain1">
               <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <cn type="integer"> 1 </cn>
               </math>
diff --git a/examples/v0.84/README.md b/examples/v0.84/README.md
new file mode 100644
index 0000000..86b2212
--- /dev/null
+++ b/examples/v0.84/README.md
@@ -0,0 +1,2 @@
+## Examples
+The examples in this folder are encoded in the 0.84 format of the spacial specification. 
\ No newline at end of file
diff --git a/examples/v0.84/The_Brusselator.xml b/examples/v0.84/The_Brusselator.xml
new file mode 100644
index 0000000..d40c2f8
--- /dev/null
+++ b/examples/v0.84/The_Brusselator.xml
@@ -0,0 +1,363 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
+  <model id="The_Brusselator_Application0" name="The Brusselator_Application0">
+	<annotation>
+        <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+        <update step="0.1" freq="50"/>
+        <items>
+          <item sbmlId="X" palette="black-green" max="3"/>
+          <item sbmlId="Y" palette="black-red" max="3"/>
+        </items>
+      </spatialInfo>
+	</annotation>
+    <listOfUnitDefinitions>
+      <unitDefinition id="substance">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="volume">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="area">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="length">
+        <listOfUnits>
+          <unit kind="metre" exponent="1" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="time">
+        <listOfUnits>
+          <unit kind="second" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="molecules">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um3">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um2">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um">
+        <listOfUnits>
+          <unit kind="metre" exponent="1" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="s">
+        <listOfUnits>
+          <unit kind="second" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="umol_um3_litre_1">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_um3_molecules_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one_">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one__0E_21">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one_000000">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000000"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="cell" name="cell" spatialDimensions="3" size="1" units="um3" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain1cell" spatial:compartment="cell" spatial:domainType="subdomain0" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="EC" name="EC" spatialDimensions="3" size="1" units="um3" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain0EC" spatial:compartment="EC" spatial:domainType="subdomain1" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="Membrane0" name="Membrane0" spatialDimensions="2" size="1" units="um2" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain0_subdomain1_membraneMembrane0" spatial:compartment="Membrane0" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="11"/>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="X" compartment="cell" initialConcentration="2.5" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:Compound Name="X"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+      </species>
+      <species id="Y" compartment="cell" initialConcentration="2" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:Compound Name="Y"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+      </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="x" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="y" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="X_diff" value="0.16" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="X" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="X_diff1" value="0.16" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="X" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="X_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="X" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="X_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="X" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="X_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="X" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="X_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="X" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="Y_diff" value="0.8" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="Y" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="Y_diff1" value="0.8" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="Y" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="Y_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="Y" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="Y_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="Y" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="Y_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="Y" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="Y_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="Y" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="J0_k_1" value="0.1" units="_one_" constant="true"/>
+      <parameter id="J1_k_2" value="0.1" units="_one_" constant="true"/>
+      <parameter id="J2_k_3" value="0.1" units="_one_" constant="true"/>
+      <parameter id="J3_k_4" value="0.1" units="_one_" constant="true"/>
+      <parameter id="A" value="2.5" units="_one_" constant="true"/>
+      <parameter id="B" value="5.24" units="_one_" constant="true"/>
+      <parameter id="D" value="0" units="_one_" constant="true"/>
+      <parameter id="E" value="0" units="_one_" constant="true"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction id="J0" name="J0" reversible="true" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:SimpleReaction Structure="cell"/>
+              <vcell:ReactionRate Name="J"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <listOfProducts>
+          <speciesReference species="X" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> J0_k_1 </ci>
+              <ci> A </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction id="J1" name="J1" reversible="true" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:SimpleReaction Structure="cell"/>
+              <vcell:ReactionRate Name="J"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="Y" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="X" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> J1_k_2 </ci>
+              <ci> X </ci>
+              <ci> X </ci>
+              <ci> Y </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction id="J2" name="J2" reversible="true" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:SimpleReaction Structure="cell"/>
+              <vcell:ReactionRate Name="J"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="X" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="Y" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> J2_k_3 </ci>
+              <ci> X </ci>
+              <ci> B </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction id="J3" name="J3" reversible="true" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:SimpleReaction Structure="cell"/>
+              <vcell:ReactionRate Name="J"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="X" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> J3_k_4 </ci>
+              <ci> X </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+    <spatial:geometry spatial:coordinateSystem="Cartesian">
+      <spatial:listOfCoordinateComponents>
+        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
+          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="100"/>
+        </spatial:coordinateComponent>
+        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
+          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="100"/>
+        </spatial:coordinateComponent>
+      </spatial:listOfCoordinateComponents>
+      <spatial:listOfDomainTypes>
+        <spatial:domainType spatial:spatialId="subdomain1" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain0" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
+      </spatial:listOfDomainTypes>
+      <spatial:listOfDomains>
+        <spatial:domain spatial:spatialId="subdomain00" spatial:domainType="subdomain1">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="subdomain11" spatial:domainType="subdomain0">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="1" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="membrane_subdomain00_subdomain11" spatial:domainType="subdomain0_subdomain1_membrane"/>
+      </spatial:listOfDomains>
+      <spatial:listOfAdjacentDomains>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain00_subdomain11_subdomain11" spatial:domain1="membrane_subdomain00_subdomain11" spatial:domain2="subdomain11"/>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain00_subdomain11_subdomain00" spatial:domain1="membrane_subdomain00_subdomain11" spatial:domain2="subdomain00"/>
+      </spatial:listOfAdjacentDomains>
+      <spatial:listOfGeometryDefinitions>
+        <spatial:analyticGeometry spatial:spatialId="Geometry3">
+          <spatial:listOfAnalyticVolumes>
+            <spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="1">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <piecewise>
+                  <piece>
+                    <cn type="integer"> 1 </cn>
+                    <apply>
+                      <and/>
+                      <apply>
+                        <geq/>
+                        <ci> x </ci>
+                        <cn type="integer"> 2 </cn>
+                      </apply>
+                      <apply>
+                        <leq/>
+                        <ci> x </ci>
+                        <cn type="integer"> 98 </cn>
+                      </apply>
+                      <apply>
+                        <geq/>
+                        <ci> y </ci>
+                        <cn type="integer"> 2 </cn>
+                      </apply>
+                      <apply>
+                        <leq/>
+                        <ci> y </ci>
+                        <cn type="integer"> 98 </cn>
+                      </apply>
+                    </apply>
+                  </piece>
+                  <otherwise>
+                    <cn type="integer"> 0 </cn>
+                  </otherwise>
+                </piecewise>
+              </math>
+            </spatial:analyticVolume>
+            <spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="0">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <cn type="integer"> 1 </cn>
+              </math>
+            </spatial:analyticVolume>
+          </spatial:listOfAnalyticVolumes>
+        </spatial:analyticGeometry>
+      </spatial:listOfGeometryDefinitions>
+    </spatial:geometry>
+  </model>
+</sbml>
diff --git a/examples/v0.84/The_Brusselator_300x300.xml b/examples/v0.84/The_Brusselator_300x300.xml
new file mode 100644
index 0000000..9e72453
--- /dev/null
+++ b/examples/v0.84/The_Brusselator_300x300.xml
@@ -0,0 +1,363 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
+  <model id="The_Brusselator_Application0" name="The Brusselator_Application0">
+	<annotation>
+        <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+        <update step="0.1" freq="500"/>
+        <items>
+          <item sbmlId="X" palette="black-blue.txt" max="6"/>
+          <item sbmlId="Y" palette="black-green.txt" max="6"/>
+        </items>
+      </spatialInfo>
+	</annotation>
+	<listOfUnitDefinitions>
+      <unitDefinition id="substance">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="volume">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="area">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="length">
+        <listOfUnits>
+          <unit kind="metre" exponent="1" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="time">
+        <listOfUnits>
+          <unit kind="second" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="molecules">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um3">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um2">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um">
+        <listOfUnits>
+          <unit kind="metre" exponent="1" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="s">
+        <listOfUnits>
+          <unit kind="second" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="umol_um3_litre_1">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_um3_molecules_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one_">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one__0E_21">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one_000000">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000000"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="cell" name="cell" spatialDimensions="3" size="1" units="um3" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain1cell" spatial:compartment="cell" spatial:domainType="subdomain0" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="EC" name="EC" spatialDimensions="3" size="1" units="um3" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain0EC" spatial:compartment="EC" spatial:domainType="subdomain1" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="Membrane0" name="Membrane0" spatialDimensions="2" size="1" units="um2" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain0_subdomain1_membraneMembrane0" spatial:compartment="Membrane0" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="11"/>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="X" compartment="cell" initialConcentration="2.5" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:Compound Name="X"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+      </species>
+      <species id="Y" compartment="cell" initialConcentration="2" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:Compound Name="Y"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+      </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="x" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="y" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="X_diff" value="0.16" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="X" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="X_diff1" value="0.16" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="X" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="X_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="X" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="X_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="X" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="X_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="X" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="X_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="X" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="Y_diff" value="0.8" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="Y" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="Y_diff1" value="0.8" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="Y" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="Y_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="Y" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="Y_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="Y" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="Y_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="Y" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="Y_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="Y" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="J0_k_1" value="0.1" units="_one_" constant="true"/>
+      <parameter id="J1_k_2" value="0.1" units="_one_" constant="true"/>
+      <parameter id="J2_k_3" value="0.1" units="_one_" constant="true"/>
+      <parameter id="J3_k_4" value="0.1" units="_one_" constant="true"/>
+      <parameter id="A" value="2.5" units="_one_" constant="true"/>
+      <parameter id="B" value="5.24" units="_one_" constant="true"/>
+      <parameter id="D" value="0" units="_one_" constant="true"/>
+      <parameter id="E" value="0" units="_one_" constant="true"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction id="J0" name="J0" reversible="true" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:SimpleReaction Structure="cell"/>
+              <vcell:ReactionRate Name="J"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <listOfProducts>
+          <speciesReference species="X" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> J0_k_1 </ci>
+              <ci> A </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction id="J1" name="J1" reversible="true" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:SimpleReaction Structure="cell"/>
+              <vcell:ReactionRate Name="J"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="Y" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="X" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> J1_k_2 </ci>
+              <ci> X </ci>
+              <ci> X </ci>
+              <ci> Y </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction id="J2" name="J2" reversible="true" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:SimpleReaction Structure="cell"/>
+              <vcell:ReactionRate Name="J"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="X" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="Y" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> J2_k_3 </ci>
+              <ci> X </ci>
+              <ci> B </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction id="J3" name="J3" reversible="true" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:SimpleReaction Structure="cell"/>
+              <vcell:ReactionRate Name="J"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="X" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> J3_k_4 </ci>
+              <ci> X </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+    <spatial:geometry spatial:coordinateSystem="Cartesian">
+      <spatial:listOfCoordinateComponents>
+        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
+          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="300"/>
+        </spatial:coordinateComponent>
+        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
+          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="300"/>
+        </spatial:coordinateComponent>
+      </spatial:listOfCoordinateComponents>
+      <spatial:listOfDomainTypes>
+        <spatial:domainType spatial:spatialId="subdomain1" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain0" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
+      </spatial:listOfDomainTypes>
+      <spatial:listOfDomains>
+        <spatial:domain spatial:spatialId="subdomain00" spatial:domainType="subdomain1">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="subdomain11" spatial:domainType="subdomain0">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="1" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="membrane_subdomain00_subdomain11" spatial:domainType="subdomain0_subdomain1_membrane"/>
+      </spatial:listOfDomains>
+      <spatial:listOfAdjacentDomains>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain00_subdomain11_subdomain11" spatial:domain1="membrane_subdomain00_subdomain11" spatial:domain2="subdomain11"/>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain00_subdomain11_subdomain00" spatial:domain1="membrane_subdomain00_subdomain11" spatial:domain2="subdomain00"/>
+      </spatial:listOfAdjacentDomains>
+      <spatial:listOfGeometryDefinitions>
+        <spatial:analyticGeometry spatial:spatialId="Geometry3">
+          <spatial:listOfAnalyticVolumes>
+            <spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="1">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <piecewise>
+                  <piece>
+                    <cn type="integer"> 1 </cn>
+                    <apply>
+                      <and/>
+                      <apply>
+                        <geq/>
+                        <ci> x </ci>
+                        <cn type="integer"> 2 </cn>
+                      </apply>
+                      <apply>
+                        <leq/>
+                        <ci> x </ci>
+                        <cn type="integer"> 298 </cn>
+                      </apply>
+                      <apply>
+                        <geq/>
+                        <ci> y </ci>
+                        <cn type="integer"> 2 </cn>
+                      </apply>
+                      <apply>
+                        <leq/>
+                        <ci> y </ci>
+                        <cn type="integer"> 298 </cn>
+                      </apply>
+                    </apply>
+                  </piece>
+                  <otherwise>
+                    <cn type="integer"> 0 </cn>
+                  </otherwise>
+                </piecewise>
+              </math>
+            </spatial:analyticVolume>
+            <spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="0">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <cn type="integer"> 1 </cn>
+              </math>
+            </spatial:analyticVolume>
+          </spatial:listOfAnalyticVolumes>
+        </spatial:analyticGeometry>
+      </spatial:listOfGeometryDefinitions>
+    </spatial:geometry>
+  </model>
+</sbml>
diff --git a/examples/v0.84/advection.xml b/examples/v0.84/advection.xml
new file mode 100644
index 0000000..195dcff
--- /dev/null
+++ b/examples/v0.84/advection.xml
@@ -0,0 +1,382 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
+  <model id="advection_test_simulation" name="advection_test_simulation">
+    <annotation>
+      <spatialInfo xmlns="http://spatial-sbml/settings">
+        <update step="0.05" freq="50"/>
+        <items>
+          <item sbmlId="B_cytosol" palette="black-blue.txt" max="6"/>
+          <item sbmlId="C_cytosol" palette="black-green.txt" max="1000"/>
+          <item sbmlId="A_cytosol" palette="black-red.txt" max="6"/>
+        </items>
+      </spatialInfo>
+      <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+        <vcell:VCMLSpecific>
+          <vcell:BioModel Name="advection_test" KeyValue="62900696"/>
+          <vcell:SimulationSpec Name="simulation" KeyValue="62900686"/>
+        </vcell:VCMLSpecific>
+      </vcell:VCellInfo>
+    </annotation>
+    <listOfUnitDefinitions>
+      <unitDefinition id="substance">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="volume">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="area">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="molecules">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="umol_um3_litre_1">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um3">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um2">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_um3_molecules_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="extracellular" name="extracellular" spatialDimensions="3" units="um3" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain0extracellular" spatial:compartment="extracellular" spatial:domainType="subdomain0" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="cytosol" name="cytosol" spatialDimensions="3" units="um3" constant="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:OutsideCompartment Name="membrane0"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <spatial:compartmentMapping spatial:spatialId="subdomain1cytosol" spatial:compartment="cytosol" spatial:domainType="subdomain1" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="membrane0" name="membrane0" spatialDimensions="2" units="um2" constant="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:OutsideCompartment Name="extracellular"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <spatial:compartmentMapping spatial:spatialId="subdomain0_subdomain1_membranemembrane0" spatial:compartment="membrane0" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="B_cytosol" compartment="cytosol" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:Compound Name="B"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+      </species>
+      <species id="C_cytosol" compartment="cytosol" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:Compound Name="C"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+      </species>
+      <species id="A_cytosol" compartment="cytosol" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:Compound Name="A"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+      </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="x" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="y" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="B_cytosol_diff" value="2" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="B_cytosol"/>
+      </parameter>
+      <parameter id="B_cytosol_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="B_cytosol" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="B_cytosol_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="B_cytosol" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="B_cytosol_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="B_cytosol" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="B_cytosol_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="B_cytosol" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="C_cytosol_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="C_cytosol" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="C_cytosol_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="C_cytosol" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="C_cytosol_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="C_cytosol" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="C_cytosol_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="C_cytosol" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="C_cytosol_Vel_X" value="2" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:advectionCoefficient spatial:variable="C_cytosol" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="C_cytosol_Vel_Y" value="-2" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:advectionCoefficient spatial:variable="C_cytosol" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="A_cytosol_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="A_cytosol" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="A_cytosol_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="A_cytosol" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="A_cytosol_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="A_cytosol" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="A_cytosol_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="A_cytosol" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="A_cytosol_Vel_X" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:advectionCoefficient spatial:variable="A_cytosol" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="A_cytosol_Vel_Y" value="-3" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:advectionCoefficient spatial:variable="A_cytosol" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="KMOLE" value="0.00166112956810631" units="uM_um3_molecules_1" constant="true"/>
+    </listOfParameters>
+    <listOfInitialAssignments>
+      <initialAssignment symbol="A_cytosol">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <apply>
+            <times/>
+            <cn type="integer"> 4 </cn>
+            <apply>
+              <exp/>
+              <apply>
+                <plus/>
+                <apply>
+                  <minus/>
+                  <apply>
+                    <power/>
+                    <apply>
+                      <times/>
+                      <cn> 0.1 </cn>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <minus/>
+                          <cn type="integer"> 30 </cn>
+                        </apply>
+                        <ci> x </ci>
+                      </apply>
+                    </apply>
+                    <cn type="integer"> 2 </cn>
+                  </apply>
+                </apply>
+                <apply>
+                  <minus/>
+                  <apply>
+                    <power/>
+                    <apply>
+                      <times/>
+                      <cn> 0.16 </cn>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <minus/>
+                          <cn type="integer"> 55 </cn>
+                        </apply>
+                        <ci> y </ci>
+                      </apply>
+                    </apply>
+                    <cn type="integer"> 2 </cn>
+                  </apply>
+                </apply>
+              </apply>
+            </apply>
+            <cn type="integer"> 1 </cn>
+          </apply>
+        </math>
+      </initialAssignment>
+      <initialAssignment symbol="C_cytosol">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <apply>
+            <times/>
+            <piecewise>
+              <piece>
+                <cn type="integer"> 4 </cn>
+                <apply>
+                  <and/>
+                  <apply>
+                    <geq/>
+                    <ci> x </ci>
+                    <cn type="integer"> 18 </cn>
+                  </apply>
+                  <apply>
+                    <leq/>
+                    <ci> x </ci>
+                    <cn type="integer"> 21 </cn>
+                  </apply>
+                  <apply>
+                    <geq/>
+                    <ci> y </ci>
+                    <cn type="integer"> 27 </cn>
+                  </apply>
+                  <apply>
+                    <leq/>
+                    <ci> y </ci>
+                    <cn type="integer"> 30 </cn>
+                  </apply>
+                </apply>
+              </piece>
+              <otherwise>
+                <cn type="integer"> 0 </cn>
+              </otherwise>
+            </piecewise>
+            <cn type="integer"> 1 </cn>
+            <apply>
+              <divide/>
+              <cn type="integer"> 1 </cn>
+              <apply>
+                <times/>
+                <cn type="integer"> 1 </cn>
+                <apply>
+                  <divide/>
+                  <cn type="integer"> 1 </cn>
+                  <cn type="integer"> 602 </cn>
+                </apply>
+              </apply>
+            </apply>
+          </apply>
+        </math>
+      </initialAssignment>
+    </listOfInitialAssignments>
+    <spatial:geometry spatial:coordinateSystem="Cartesian">
+      <spatial:listOfCoordinateComponents>
+        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
+          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="100"/>
+        </spatial:coordinateComponent>
+        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
+          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="100"/>
+        </spatial:coordinateComponent>
+      </spatial:listOfCoordinateComponents>
+      <spatial:listOfDomainTypes>
+        <spatial:domainType spatial:spatialId="subdomain1" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain0" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
+      </spatial:listOfDomainTypes>
+      <spatial:listOfDomains>
+        <spatial:domain spatial:spatialId="subdomain00" spatial:domainType="subdomain0">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="subdomain11" spatial:domainType="subdomain1">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="45" spatial:coord2="17" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="membrane_subdomain00_subdomain11" spatial:domainType="subdomain0_subdomain1_membrane"/>
+      </spatial:listOfDomains>
+      <spatial:listOfAdjacentDomains>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain00_subdomain11_subdomain11" spatial:domain1="membrane_subdomain00_subdomain11" spatial:domain2="subdomain11"/>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain00_subdomain11_subdomain00" spatial:domain1="membrane_subdomain00_subdomain11" spatial:domain2="subdomain00"/>
+      </spatial:listOfAdjacentDomains>
+      <spatial:listOfGeometryDefinitions>
+        <spatial:analyticGeometry spatial:spatialId="cyt">
+          <spatial:listOfAnalyticVolumes>
+            <spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="1">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <piecewise>
+                  <piece>
+                    <cn type="integer"> 1 </cn>
+                    <apply>
+                      <lt/>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <power/>
+                          <apply>
+                            <times/>
+                            <cn> 0.025 </cn>
+                            <apply>
+                              <plus/>
+                              <cn type="integer"> 50 </cn>
+                              <apply>
+                                <minus/>
+                                <ci> x </ci>
+                              </apply>
+                            </apply>
+                          </apply>
+                          <cn type="integer"> 2 </cn>
+                        </apply>
+                        <apply>
+                          <power/>
+                          <apply>
+                            <times/>
+                            <cn> 0.03 </cn>
+                            <apply>
+                              <plus/>
+                              <cn type="integer"> 50 </cn>
+                              <apply>
+                                <minus/>
+                                <ci> y </ci>
+                              </apply>
+                            </apply>
+                          </apply>
+                          <cn type="integer"> 2 </cn>
+                        </apply>
+                      </apply>
+                      <cn type="integer"> 1 </cn>
+                    </apply>
+                  </piece>
+                  <otherwise>
+                    <cn type="integer"> 0 </cn>
+                  </otherwise>
+                </piecewise>
+              </math>
+            </spatial:analyticVolume>
+            <spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="0">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <cn type="integer"> 1 </cn>
+              </math>
+            </spatial:analyticVolume>
+          </spatial:listOfAnalyticVolumes>
+        </spatial:analyticGeometry>
+      </spatial:listOfGeometryDefinitions>
+    </spatial:geometry>
+  </model>
+</sbml>
diff --git a/examples/v0.84/fish.xml b/examples/v0.84/fish.xml
new file mode 100644
index 0000000..365527d
--- /dev/null
+++ b/examples/v0.84/fish.xml
@@ -0,0 +1,977 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
+  <model metaid="meta_fish_skin_pnas2_Application0" id="fish_skin_pnas2_Application0" name="fish-skin-pnas2_Application0">
+    <annotation>
+      <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+        <update step="1" freq="50"/>
+        <items>
+          <item sbmlId="u" palette="black-blue.txt" max="6"/>
+          <item sbmlId="v" palette="black-green.txt" max="6"/>
+          <item sbmlId="w" palette="black-red.txt" max="6"/>
+        </items>
+      </spatialInfo>
+    </annotation>
+    <listOfUnitDefinitions>
+      <unitDefinition id="substance">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="volume">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="area">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="molecules">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="umol_um3_litre_1">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um3">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um2">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_um3_molecules_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="s_1">
+        <listOfUnits>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="outside" name="outside" spatialDimensions="3" size="50000" units="um3" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="outsideoutside" spatial:compartment="outside" spatial:domainType="outside" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="eye" name="eye" spatialDimensions="3" size="500" units="um3" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="fish_eyeeye" spatial:compartment="eye" spatial:domainType="fish_eye" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="fish" name="fish" spatialDimensions="3" size="5000" units="um3" constant="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:OutsideCompartment Name="Membrane0"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <spatial:compartmentMapping spatial:spatialId="fish_bodyfish" spatial:compartment="fish" spatial:domainType="fish_body" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="Membrane0" name="Membrane0" spatialDimensions="2" size="1414" units="um2" constant="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:OutsideCompartment Name="outside"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <spatial:compartmentMapping spatial:spatialId="fish_body_outside_membraneMembrane0" spatial:compartment="Membrane0" spatial:domainType="fish_body_outside_membrane" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="Membrane1" name="Membrane1" spatialDimensions="2" size="304.6" units="um2" constant="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:OutsideCompartment Name="fish"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <spatial:compartmentMapping spatial:spatialId="fish_body_fish_eye_membraneMembrane1" spatial:compartment="Membrane1" spatial:domainType="fish_body_fish_eye_membrane" spatial:unitSize="1"/>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="u" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:Compound Name="s0"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+      </species>
+      <species id="v" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:Compound Name="s1"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+      </species>
+      <species id="X" compartment="fish" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:Compound Name="s2"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+      </species>
+      <species id="w" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:Compound Name="s3"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+      </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="x" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="y" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="u_diff_X" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="u" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="u_diff_Y" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="u" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="u_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="u_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="u_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="u_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="v_diff_X" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="v" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="v_diff_Y" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="v" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="v_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="v_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="v_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="v_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="w_diff_X" value="0.2" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="w" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="w_diff_Y" value="0.2" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="w" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="w_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="w_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="w_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="w_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="KMOLE" value="0.00166112956810631" units="uM_um3_molecules_1" constant="true"/>
+    </listOfParameters>
+    <listOfInitialAssignments>
+      <initialAssignment symbol="u">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <piecewise>
+            <piece>
+              <cn> 4 </cn>
+              <apply>
+                <and/>
+                <apply>
+                  <gt/>
+                  <ci> y </ci>
+                  <cn> 47 </cn>
+                </apply>
+                <apply>
+                  <lt/>
+                  <ci> y </ci>
+                  <cn> 51 </cn>
+                </apply>
+              </apply>
+            </piece>
+            <otherwise>
+              <cn> 0 </cn>
+            </otherwise>
+          </piecewise>
+        </math>
+      </initialAssignment>
+      <initialAssignment symbol="v">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <piecewise>
+            <piece>
+              <cn> 4 </cn>
+              <apply>
+                <and/>
+                <apply>
+                  <gt/>
+                  <ci> y </ci>
+                  <cn> 47 </cn>
+                </apply>
+                <apply>
+                  <lt/>
+                  <ci> y </ci>
+                  <cn> 51 </cn>
+                </apply>
+              </apply>
+            </piece>
+            <otherwise>
+              <cn> 0 </cn>
+            </otherwise>
+          </piecewise>
+        </math>
+      </initialAssignment>
+      <initialAssignment symbol="w">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <piecewise>
+            <piece>
+              <cn> 4 </cn>
+              <apply>
+                <and/>
+                <apply>
+                  <gt/>
+                  <ci> y </ci>
+                  <cn> 47 </cn>
+                </apply>
+                <apply>
+                  <lt/>
+                  <ci> y </ci>
+                  <cn> 51 </cn>
+                </apply>
+              </apply>
+            </piece>
+            <otherwise>
+              <cn> 0 </cn>
+            </otherwise>
+          </piecewise>
+        </math>
+      </initialAssignment>
+    </listOfInitialAssignments>
+    <listOfReactions>
+      <reaction id="re0" name="re0" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:SimpleReaction Structure="fish"/>
+              <vcell:ReactionRate Name="J"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="X" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="u" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference species="v"/>
+          <modifierSpeciesReference species="w"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <plus/>
+              <piecewise>
+                <piece>
+                  <ci> U </ci>
+                  <apply>
+                    <geq/>
+                    <apply>
+                      <plus/>
+                      <apply>
+                        <times/>
+                        <ci> c1 </ci>
+                        <ci> v </ci>
+                      </apply>
+                      <apply>
+                        <times/>
+                        <ci> c2 </ci>
+                        <ci> w </ci>
+                      </apply>
+                      <ci> c3 </ci>
+                    </apply>
+                    <ci> U </ci>
+                  </apply>
+                </piece>
+                <otherwise>
+                  <cn> 0 </cn>
+                </otherwise>
+              </piecewise>
+              <piecewise>
+                <piece>
+                  <apply>
+                    <plus/>
+                    <apply>
+                      <times/>
+                      <ci> c1 </ci>
+                      <ci> v </ci>
+                    </apply>
+                    <apply>
+                      <times/>
+                      <ci> c2 </ci>
+                      <ci> w </ci>
+                    </apply>
+                    <ci> c3 </ci>
+                  </apply>
+                  <apply>
+                    <and/>
+                    <apply>
+                      <gt/>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <times/>
+                          <ci> c1 </ci>
+                          <ci> v </ci>
+                        </apply>
+                        <apply>
+                          <times/>
+                          <ci> c2 </ci>
+                          <ci> w </ci>
+                        </apply>
+                        <ci> c3 </ci>
+                      </apply>
+                      <cn> 0 </cn>
+                    </apply>
+                    <apply>
+                      <lt/>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <times/>
+                          <ci> c1 </ci>
+                          <ci> v </ci>
+                        </apply>
+                        <apply>
+                          <times/>
+                          <ci> c2 </ci>
+                          <ci> w </ci>
+                        </apply>
+                        <ci> c3 </ci>
+                      </apply>
+                      <ci> U </ci>
+                    </apply>
+                  </apply>
+                </piece>
+                <otherwise>
+                  <cn> 0 </cn>
+                </otherwise>
+              </piecewise>
+              <apply>
+                <minus/>
+                <apply>
+                  <times/>
+                  <ci> cu </ci>
+                  <ci> u </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+          <listOfLocalParameters>
+            <localParameter id="U" value="0.5" units="uM_s_1"/>
+            <localParameter id="c1" value="-0.04" units="s_1"/>
+            <localParameter id="c2" value="-0.055" units="s_1"/>
+            <localParameter id="c3" value="0.37" units="uM_s_1"/>
+            <localParameter id="cu" value="0.02" units="s_1"/>
+          </listOfLocalParameters>
+        </kineticLaw>
+      </reaction>
+      <reaction id="re1" name="re1" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:SimpleReaction Structure="fish"/>
+              <vcell:ReactionRate Name="J"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="X" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="v" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference species="u"/>
+          <modifierSpeciesReference species="w"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <plus/>
+              <piecewise>
+                <piece>
+                  <ci> V </ci>
+                  <apply>
+                    <geq/>
+                    <apply>
+                      <plus/>
+                      <apply>
+                        <times/>
+                        <ci> c4 </ci>
+                        <ci> u </ci>
+                      </apply>
+                      <apply>
+                        <times/>
+                        <ci> c5 </ci>
+                        <ci> w </ci>
+                      </apply>
+                      <ci> c6 </ci>
+                    </apply>
+                    <ci> V </ci>
+                  </apply>
+                </piece>
+                <otherwise>
+                  <cn> 0 </cn>
+                </otherwise>
+              </piecewise>
+              <piecewise>
+                <piece>
+                  <apply>
+                    <plus/>
+                    <apply>
+                      <times/>
+                      <ci> c4 </ci>
+                      <ci> u </ci>
+                    </apply>
+                    <apply>
+                      <times/>
+                      <ci> c5 </ci>
+                      <ci> w </ci>
+                    </apply>
+                    <ci> c6 </ci>
+                  </apply>
+                  <apply>
+                    <and/>
+                    <apply>
+                      <gt/>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <times/>
+                          <ci> c4 </ci>
+                          <ci> u </ci>
+                        </apply>
+                        <apply>
+                          <times/>
+                          <ci> c5 </ci>
+                          <ci> w </ci>
+                        </apply>
+                        <ci> c6 </ci>
+                      </apply>
+                      <cn> 0 </cn>
+                    </apply>
+                    <apply>
+                      <lt/>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <times/>
+                          <ci> c4 </ci>
+                          <ci> u </ci>
+                        </apply>
+                        <apply>
+                          <times/>
+                          <ci> c5 </ci>
+                          <ci> w </ci>
+                        </apply>
+                        <ci> c6 </ci>
+                      </apply>
+                      <ci> V </ci>
+                    </apply>
+                  </apply>
+                </piece>
+                <otherwise>
+                  <cn> 0 </cn>
+                </otherwise>
+              </piecewise>
+              <apply>
+                <minus/>
+                <apply>
+                  <times/>
+                  <ci> cv </ci>
+                  <ci> v </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+          <listOfLocalParameters>
+            <localParameter id="V" value="0.5" units="uM_s_1"/>
+            <localParameter id="c4" value="-0.05" units="s_1"/>
+            <localParameter id="c5" value="0" units="s_1"/>
+            <localParameter id="c6" value="0.25" units="uM_s_1"/>
+            <localParameter id="cv" value="0.025" units="s_1"/>
+          </listOfLocalParameters>
+        </kineticLaw>
+      </reaction>
+      <reaction id="re2" name="re2" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:SimpleReaction Structure="fish"/>
+              <vcell:ReactionRate Name="J"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="X" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="w" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference species="u"/>
+          <modifierSpeciesReference species="v"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <plus/>
+              <piecewise>
+                <piece>
+                  <ci> W </ci>
+                  <apply>
+                    <geq/>
+                    <apply>
+                      <plus/>
+                      <apply>
+                        <times/>
+                        <ci> c7 </ci>
+                        <ci> u </ci>
+                      </apply>
+                      <apply>
+                        <times/>
+                        <ci> c8 </ci>
+                        <ci> v </ci>
+                      </apply>
+                      <ci> c9 </ci>
+                    </apply>
+                    <ci> W </ci>
+                  </apply>
+                </piece>
+                <otherwise>
+                  <cn> 0 </cn>
+                </otherwise>
+              </piecewise>
+              <piecewise>
+                <piece>
+                  <apply>
+                    <plus/>
+                    <apply>
+                      <times/>
+                      <ci> c7 </ci>
+                      <ci> u </ci>
+                    </apply>
+                    <apply>
+                      <times/>
+                      <ci> c8 </ci>
+                      <ci> v </ci>
+                    </apply>
+                    <ci> c9 </ci>
+                  </apply>
+                  <apply>
+                    <and/>
+                    <apply>
+                      <gt/>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <times/>
+                          <ci> c7 </ci>
+                          <ci> u </ci>
+                        </apply>
+                        <apply>
+                          <times/>
+                          <ci> c8 </ci>
+                          <ci> v </ci>
+                        </apply>
+                        <ci> c9 </ci>
+                      </apply>
+                      <cn> 0 </cn>
+                    </apply>
+                    <apply>
+                      <lt/>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <times/>
+                          <ci> c7 </ci>
+                          <ci> u </ci>
+                        </apply>
+                        <apply>
+                          <times/>
+                          <ci> c8 </ci>
+                          <ci> v </ci>
+                        </apply>
+                        <ci> c9 </ci>
+                      </apply>
+                      <ci> W </ci>
+                    </apply>
+                  </apply>
+                </piece>
+                <otherwise>
+                  <cn> 0 </cn>
+                </otherwise>
+              </piecewise>
+              <apply>
+                <minus/>
+                <apply>
+                  <times/>
+                  <ci> cw </ci>
+                  <ci> w </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+          <listOfLocalParameters>
+            <localParameter id="W" value="0.5" units="uM_s_1"/>
+            <localParameter id="c7" value="0.016" units="s_1"/>
+            <localParameter id="c8" value="-0.03" units="s_1"/>
+            <localParameter id="c9" value="0.24" units="uM_s_1"/>
+            <localParameter id="cw" value="0.06" units="s_1"/>
+          </listOfLocalParameters>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+    <spatial:geometry spatial:coordinateSystem="Cartesian">
+      <spatial:listOfCoordinateComponents>
+        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
+          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="100"/>
+        </spatial:coordinateComponent>
+        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
+          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="100"/>
+        </spatial:coordinateComponent>
+      </spatial:listOfCoordinateComponents>
+      <spatial:listOfDomainTypes>
+        <spatial:domainType spatial:spatialId="fish_eye" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="fish_body" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="outside" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="fish_body_outside_membrane" spatial:spatialDimensions="2"/>
+        <spatial:domainType spatial:spatialId="fish_body_fish_eye_membrane" spatial:spatialDimensions="2"/>
+      </spatial:listOfDomainTypes>
+      <spatial:listOfDomains>
+        <spatial:domain spatial:spatialId="outside0" spatial:domainType="outside">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="fish_body1" spatial:domainType="fish_body">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="89" spatial:coord2="22" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="fish_eye2" spatial:domainType="fish_eye">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="22" spatial:coord2="38" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="membrane_outside0_fish_body1" spatial:domainType="fish_body_outside_membrane"/>
+        <spatial:domain spatial:spatialId="membrane_fish_body1_fish_eye2" spatial:domainType="fish_body_fish_eye_membrane"/>
+      </spatial:listOfDomains>
+      <spatial:listOfAdjacentDomains>
+        <spatial:adjacentDomains spatial:spatialId="membrane_outside0_fish_body1_fish_body1" spatial:domain1="membrane_outside0_fish_body1" spatial:domain2="fish_body1"/>
+        <spatial:adjacentDomains spatial:spatialId="membrane_outside0_fish_body1_outside0" spatial:domain1="membrane_outside0_fish_body1" spatial:domain2="outside0"/>
+        <spatial:adjacentDomains spatial:spatialId="membrane_fish_body1_fish_eye2_fish_eye2" spatial:domain1="membrane_fish_body1_fish_eye2" spatial:domain2="fish_eye2"/>
+        <spatial:adjacentDomains spatial:spatialId="membrane_fish_body1_fish_eye2_fish_body1" spatial:domain1="membrane_fish_body1_fish_eye2" spatial:domain2="fish_body1"/>
+      </spatial:listOfAdjacentDomains>
+      <spatial:listOfGeometryDefinitions>
+        <spatial:analyticGeometry spatial:spatialId="Geometry225509093">
+          <spatial:listOfAnalyticVolumes>
+            <spatial:analyticVolume spatial:spatialId="fish_body" spatial:domainType="fish_body" spatial:functionType="layered" spatial:ordinal="1">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <piecewise>
+                  <piece>
+                    <cn type="integer"> 1 </cn>
+                    <apply>
+                      <and/>
+                      <apply>
+                        <or/>
+                        <apply>
+                          <lt/>
+                          <apply>
+                            <plus/>
+                            <apply>
+                              <divide/>
+                              <apply>
+                                <power/>
+                                <apply>
+                                  <minus/>
+                                  <ci> x </ci>
+                                  <apply>
+                                    <times/>
+                                    <cn type="integer"> 100 </cn>
+                                    <cn> 0.42 </cn>
+                                  </apply>
+                                </apply>
+                                <cn type="integer"> 2 </cn>
+                              </apply>
+                              <apply>
+                                <power/>
+                                <apply>
+                                  <times/>
+                                  <cn type="integer"> 100 </cn>
+                                  <cn> 0.37 </cn>
+                                </apply>
+                                <cn type="integer"> 2 </cn>
+                              </apply>
+                            </apply>
+                            <apply>
+                              <divide/>
+                              <apply>
+                                <power/>
+                                <apply>
+                                  <minus/>
+                                  <ci> y </ci>
+                                  <apply>
+                                    <divide/>
+                                    <cn type="integer"> 100 </cn>
+                                    <cn type="integer"> 2 </cn>
+                                  </apply>
+                                </apply>
+                                <cn type="integer"> 2 </cn>
+                              </apply>
+                              <apply>
+                                <power/>
+                                <apply>
+                                  <times/>
+                                  <cn type="integer"> 100 </cn>
+                                  <cn> 0.25 </cn>
+                                </apply>
+                                <cn type="integer"> 2 </cn>
+                              </apply>
+                            </apply>
+                          </apply>
+                          <cn type="integer"> 1 </cn>
+                        </apply>
+                        <apply>
+                          <and/>
+                          <apply>
+                            <lt/>
+                            <ci> y </ci>
+                            <apply>
+                              <plus/>
+                              <apply>
+                                <minus/>
+                                <apply>
+                                  <times/>
+                                  <cn type="integer"> 100 </cn>
+                                  <cn> 0.1 </cn>
+                                </apply>
+                              </apply>
+                              <ci> x </ci>
+                            </apply>
+                          </apply>
+                          <apply>
+                            <gt/>
+                            <ci> y </ci>
+                            <apply>
+                              <plus/>
+                              <apply>
+                                <times/>
+                                <cn type="integer"> 100 </cn>
+                                <cn> 1.1 </cn>
+                              </apply>
+                              <apply>
+                                <minus/>
+                                <ci> x </ci>
+                              </apply>
+                            </apply>
+                          </apply>
+                          <apply>
+                            <lt/>
+                            <ci> x </ci>
+                            <apply>
+                              <times/>
+                              <cn type="integer"> 100 </cn>
+                              <cn> 0.9 </cn>
+                            </apply>
+                          </apply>
+                        </apply>
+                      </apply>
+                      <apply>
+                        <not/>
+                        <apply>
+                          <lt/>
+                          <apply>
+                            <plus/>
+                            <apply>
+                              <divide/>
+                              <apply>
+                                <power/>
+                                <apply>
+                                  <minus/>
+                                  <ci> x </ci>
+                                  <apply>
+                                    <times/>
+                                    <cn type="integer"> 100 </cn>
+                                    <cn> 0.25 </cn>
+                                  </apply>
+                                </apply>
+                                <cn type="integer"> 2 </cn>
+                              </apply>
+                              <apply>
+                                <power/>
+                                <apply>
+                                  <times/>
+                                  <cn> 0.08 </cn>
+                                  <cn type="integer"> 100 </cn>
+                                </apply>
+                                <cn type="integer"> 2 </cn>
+                              </apply>
+                            </apply>
+                            <apply>
+                              <divide/>
+                              <apply>
+                                <power/>
+                                <apply>
+                                  <minus/>
+                                  <ci> y </ci>
+                                  <apply>
+                                    <times/>
+                                    <cn type="integer"> 100 </cn>
+                                    <cn> 0.45 </cn>
+                                  </apply>
+                                </apply>
+                                <cn type="integer"> 2 </cn>
+                              </apply>
+                              <apply>
+                                <power/>
+                                <apply>
+                                  <times/>
+                                  <cn> 0.08 </cn>
+                                  <cn type="integer"> 100 </cn>
+                                </apply>
+                                <cn type="integer"> 2 </cn>
+                              </apply>
+                            </apply>
+                          </apply>
+                          <cn type="integer"> 1 </cn>
+                        </apply>
+                      </apply>
+                    </apply>
+                  </piece>
+                  <otherwise>
+                    <cn type="integer"> 0 </cn>
+                  </otherwise>
+                </piecewise>
+              </math>
+            </spatial:analyticVolume>
+            <spatial:analyticVolume spatial:spatialId="fish_eye" spatial:domainType="fish_eye" spatial:functionType="layered" spatial:ordinal="2">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <piecewise>
+                  <piece>
+                    <cn type="integer"> 1 </cn>
+                    <apply>
+                      <lt/>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <divide/>
+                          <apply>
+                            <power/>
+                            <apply>
+                              <minus/>
+                              <ci> x </ci>
+                              <apply>
+                                <times/>
+                                <cn type="integer"> 100 </cn>
+                                <cn> 0.25 </cn>
+                              </apply>
+                            </apply>
+                            <cn type="integer"> 2 </cn>
+                          </apply>
+                          <apply>
+                            <power/>
+                            <apply>
+                              <times/>
+                              <cn> 0.08 </cn>
+                              <cn type="integer"> 100 </cn>
+                            </apply>
+                            <cn type="integer"> 2 </cn>
+                          </apply>
+                        </apply>
+                        <apply>
+                          <divide/>
+                          <apply>
+                            <power/>
+                            <apply>
+                              <minus/>
+                              <ci> y </ci>
+                              <apply>
+                                <times/>
+                                <cn type="integer"> 100 </cn>
+                                <cn> 0.45 </cn>
+                              </apply>
+                            </apply>
+                            <cn type="integer"> 2 </cn>
+                          </apply>
+                          <apply>
+                            <power/>
+                            <apply>
+                              <times/>
+                              <cn> 0.08 </cn>
+                              <cn type="integer"> 100 </cn>
+                            </apply>
+                            <cn type="integer"> 2 </cn>
+                          </apply>
+                        </apply>
+                      </apply>
+                      <cn type="integer"> 1 </cn>
+                    </apply>
+                  </piece>
+                  <otherwise>
+                    <cn type="integer"> 0 </cn>
+                  </otherwise>
+                </piecewise>
+              </math>
+            </spatial:analyticVolume>
+            <spatial:analyticVolume spatial:spatialId="outside" spatial:domainType="outside" spatial:functionType="layered" spatial:ordinal="0">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <cn type="integer"> 1 </cn>
+              </math>
+            </spatial:analyticVolume>
+          </spatial:listOfAnalyticVolumes>
+        </spatial:analyticGeometry>
+      </spatial:listOfGeometryDefinitions>
+    </spatial:geometry>
+  </model>
+</sbml>
diff --git a/examples/v0.84/fish_300x300.xml b/examples/v0.84/fish_300x300.xml
new file mode 100644
index 0000000..1773865
--- /dev/null
+++ b/examples/v0.84/fish_300x300.xml
@@ -0,0 +1,977 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
+  <model metaid="meta_fish_skin_pnas2_Application0" id="fish_skin_pnas2_Application0" name="fish-skin-pnas2_Application0">
+    <annotation>
+      <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+        <update step="1" freq="100"/>
+        <items>
+          <item sbmlId="u" palette="black-blue.txt" max="6"/>
+          <item sbmlId="v" palette="black-green.txt" max="6"/>
+          <item sbmlId="w" palette="black-red.txt" max="6"/>
+        </items>
+      </spatialInfo>
+    </annotation>
+    <listOfUnitDefinitions>
+      <unitDefinition id="substance">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="volume">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="area">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="molecules">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="umol_um3_litre_1">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um3">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um2">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_um3_molecules_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="s_1">
+        <listOfUnits>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="outside" name="outside" spatialDimensions="3" size="50000" units="um3" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="outsideoutside" spatial:compartment="outside" spatial:domainType="outside" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="eye" name="eye" spatialDimensions="3" size="500" units="um3" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="fish_eyeeye" spatial:compartment="eye" spatial:domainType="fish_eye" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="fish" name="fish" spatialDimensions="3" size="5000" units="um3" constant="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:OutsideCompartment Name="Membrane0"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <spatial:compartmentMapping spatial:spatialId="fish_bodyfish" spatial:compartment="fish" spatial:domainType="fish_body" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="Membrane0" name="Membrane0" spatialDimensions="2" size="1414" units="um2" constant="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:OutsideCompartment Name="outside"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <spatial:compartmentMapping spatial:spatialId="fish_body_outside_membraneMembrane0" spatial:compartment="Membrane0" spatial:domainType="fish_body_outside_membrane" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="Membrane1" name="Membrane1" spatialDimensions="2" size="304.6" units="um2" constant="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:OutsideCompartment Name="fish"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <spatial:compartmentMapping spatial:spatialId="fish_body_fish_eye_membraneMembrane1" spatial:compartment="Membrane1" spatial:domainType="fish_body_fish_eye_membrane" spatial:unitSize="1"/>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="u" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:Compound Name="s0"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+      </species>
+      <species id="v" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:Compound Name="s1"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+      </species>
+      <species id="X" compartment="fish" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:Compound Name="s2"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+      </species>
+      <species id="w" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:Compound Name="s3"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+      </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="x" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="y" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="u_diff_X" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="u" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="u_diff_Y" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="u" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="u_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="u_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="u_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="u_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="v_diff_X" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="v" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="v_diff_Y" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="v" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="v_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="v_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="v_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="v_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="w_diff_X" value="0.2" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="w" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="w_diff_Y" value="0.2" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="w" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="w_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="w_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="w_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="w_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="KMOLE" value="0.00166112956810631" units="uM_um3_molecules_1" constant="true"/>
+    </listOfParameters>
+    <listOfInitialAssignments>
+      <initialAssignment symbol="u">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <piecewise>
+            <piece>
+              <cn> 4 </cn>
+              <apply>
+                <and/>
+                <apply>
+                  <gt/>
+                  <ci> y </ci>
+                  <cn> 141 </cn>
+                </apply>
+                <apply>
+                  <lt/>
+                  <ci> y </ci>
+                  <cn> 153 </cn>
+                </apply>
+              </apply>
+            </piece>
+            <otherwise>
+              <cn> 0 </cn>
+            </otherwise>
+          </piecewise>
+        </math>
+      </initialAssignment>
+      <initialAssignment symbol="v">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <piecewise>
+            <piece>
+              <cn> 4 </cn>
+              <apply>
+                <and/>
+                <apply>
+                  <gt/>
+                  <ci> y </ci>
+                  <cn> 141 </cn>
+                </apply>
+                <apply>
+                  <lt/>
+                  <ci> y </ci>
+                  <cn> 153 </cn>
+                </apply>
+              </apply>
+            </piece>
+            <otherwise>
+              <cn> 0 </cn>
+            </otherwise>
+          </piecewise>
+        </math>
+      </initialAssignment>
+      <initialAssignment symbol="w">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <piecewise>
+            <piece>
+              <cn> 4 </cn>
+              <apply>
+                <and/>
+                <apply>
+                  <gt/>
+                  <ci> y </ci>
+                  <cn> 141 </cn>
+                </apply>
+                <apply>
+                  <lt/>
+                  <ci> y </ci>
+                  <cn> 153 </cn>
+                </apply>
+              </apply>
+            </piece>
+            <otherwise>
+              <cn> 0 </cn>
+            </otherwise>
+          </piecewise>
+        </math>
+      </initialAssignment>
+    </listOfInitialAssignments>
+    <listOfReactions>
+      <reaction id="re0" name="re0" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:SimpleReaction Structure="fish"/>
+              <vcell:ReactionRate Name="J"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="X" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="u" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference species="v"/>
+          <modifierSpeciesReference species="w"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <plus/>
+              <piecewise>
+                <piece>
+                  <ci> U </ci>
+                  <apply>
+                    <geq/>
+                    <apply>
+                      <plus/>
+                      <apply>
+                        <times/>
+                        <ci> c1 </ci>
+                        <ci> v </ci>
+                      </apply>
+                      <apply>
+                        <times/>
+                        <ci> c2 </ci>
+                        <ci> w </ci>
+                      </apply>
+                      <ci> c3 </ci>
+                    </apply>
+                    <ci> U </ci>
+                  </apply>
+                </piece>
+                <otherwise>
+                  <cn> 0 </cn>
+                </otherwise>
+              </piecewise>
+              <piecewise>
+                <piece>
+                  <apply>
+                    <plus/>
+                    <apply>
+                      <times/>
+                      <ci> c1 </ci>
+                      <ci> v </ci>
+                    </apply>
+                    <apply>
+                      <times/>
+                      <ci> c2 </ci>
+                      <ci> w </ci>
+                    </apply>
+                    <ci> c3 </ci>
+                  </apply>
+                  <apply>
+                    <and/>
+                    <apply>
+                      <gt/>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <times/>
+                          <ci> c1 </ci>
+                          <ci> v </ci>
+                        </apply>
+                        <apply>
+                          <times/>
+                          <ci> c2 </ci>
+                          <ci> w </ci>
+                        </apply>
+                        <ci> c3 </ci>
+                      </apply>
+                      <cn> 0 </cn>
+                    </apply>
+                    <apply>
+                      <lt/>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <times/>
+                          <ci> c1 </ci>
+                          <ci> v </ci>
+                        </apply>
+                        <apply>
+                          <times/>
+                          <ci> c2 </ci>
+                          <ci> w </ci>
+                        </apply>
+                        <ci> c3 </ci>
+                      </apply>
+                      <ci> U </ci>
+                    </apply>
+                  </apply>
+                </piece>
+                <otherwise>
+                  <cn> 0 </cn>
+                </otherwise>
+              </piecewise>
+              <apply>
+                <minus/>
+                <apply>
+                  <times/>
+                  <ci> cu </ci>
+                  <ci> u </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+          <listOfLocalParameters>
+            <localParameter id="U" value="0.5" units="uM_s_1"/>
+            <localParameter id="c1" value="-0.04" units="s_1"/>
+            <localParameter id="c2" value="-0.055" units="s_1"/>
+            <localParameter id="c3" value="0.37" units="uM_s_1"/>
+            <localParameter id="cu" value="0.02" units="s_1"/>
+          </listOfLocalParameters>
+        </kineticLaw>
+      </reaction>
+      <reaction id="re1" name="re1" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:SimpleReaction Structure="fish"/>
+              <vcell:ReactionRate Name="J"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="X" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="v" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference species="u"/>
+          <modifierSpeciesReference species="w"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <plus/>
+              <piecewise>
+                <piece>
+                  <ci> V </ci>
+                  <apply>
+                    <geq/>
+                    <apply>
+                      <plus/>
+                      <apply>
+                        <times/>
+                        <ci> c4 </ci>
+                        <ci> u </ci>
+                      </apply>
+                      <apply>
+                        <times/>
+                        <ci> c5 </ci>
+                        <ci> w </ci>
+                      </apply>
+                      <ci> c6 </ci>
+                    </apply>
+                    <ci> V </ci>
+                  </apply>
+                </piece>
+                <otherwise>
+                  <cn> 0 </cn>
+                </otherwise>
+              </piecewise>
+              <piecewise>
+                <piece>
+                  <apply>
+                    <plus/>
+                    <apply>
+                      <times/>
+                      <ci> c4 </ci>
+                      <ci> u </ci>
+                    </apply>
+                    <apply>
+                      <times/>
+                      <ci> c5 </ci>
+                      <ci> w </ci>
+                    </apply>
+                    <ci> c6 </ci>
+                  </apply>
+                  <apply>
+                    <and/>
+                    <apply>
+                      <gt/>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <times/>
+                          <ci> c4 </ci>
+                          <ci> u </ci>
+                        </apply>
+                        <apply>
+                          <times/>
+                          <ci> c5 </ci>
+                          <ci> w </ci>
+                        </apply>
+                        <ci> c6 </ci>
+                      </apply>
+                      <cn> 0 </cn>
+                    </apply>
+                    <apply>
+                      <lt/>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <times/>
+                          <ci> c4 </ci>
+                          <ci> u </ci>
+                        </apply>
+                        <apply>
+                          <times/>
+                          <ci> c5 </ci>
+                          <ci> w </ci>
+                        </apply>
+                        <ci> c6 </ci>
+                      </apply>
+                      <ci> V </ci>
+                    </apply>
+                  </apply>
+                </piece>
+                <otherwise>
+                  <cn> 0 </cn>
+                </otherwise>
+              </piecewise>
+              <apply>
+                <minus/>
+                <apply>
+                  <times/>
+                  <ci> cv </ci>
+                  <ci> v </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+          <listOfLocalParameters>
+            <localParameter id="V" value="0.5" units="uM_s_1"/>
+            <localParameter id="c4" value="-0.05" units="s_1"/>
+            <localParameter id="c5" value="0" units="s_1"/>
+            <localParameter id="c6" value="0.25" units="uM_s_1"/>
+            <localParameter id="cv" value="0.025" units="s_1"/>
+          </listOfLocalParameters>
+        </kineticLaw>
+      </reaction>
+      <reaction id="re2" name="re2" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:SimpleReaction Structure="fish"/>
+              <vcell:ReactionRate Name="J"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="X" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="w" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference species="u"/>
+          <modifierSpeciesReference species="v"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <plus/>
+              <piecewise>
+                <piece>
+                  <ci> W </ci>
+                  <apply>
+                    <geq/>
+                    <apply>
+                      <plus/>
+                      <apply>
+                        <times/>
+                        <ci> c7 </ci>
+                        <ci> u </ci>
+                      </apply>
+                      <apply>
+                        <times/>
+                        <ci> c8 </ci>
+                        <ci> v </ci>
+                      </apply>
+                      <ci> c9 </ci>
+                    </apply>
+                    <ci> W </ci>
+                  </apply>
+                </piece>
+                <otherwise>
+                  <cn> 0 </cn>
+                </otherwise>
+              </piecewise>
+              <piecewise>
+                <piece>
+                  <apply>
+                    <plus/>
+                    <apply>
+                      <times/>
+                      <ci> c7 </ci>
+                      <ci> u </ci>
+                    </apply>
+                    <apply>
+                      <times/>
+                      <ci> c8 </ci>
+                      <ci> v </ci>
+                    </apply>
+                    <ci> c9 </ci>
+                  </apply>
+                  <apply>
+                    <and/>
+                    <apply>
+                      <gt/>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <times/>
+                          <ci> c7 </ci>
+                          <ci> u </ci>
+                        </apply>
+                        <apply>
+                          <times/>
+                          <ci> c8 </ci>
+                          <ci> v </ci>
+                        </apply>
+                        <ci> c9 </ci>
+                      </apply>
+                      <cn> 0 </cn>
+                    </apply>
+                    <apply>
+                      <lt/>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <times/>
+                          <ci> c7 </ci>
+                          <ci> u </ci>
+                        </apply>
+                        <apply>
+                          <times/>
+                          <ci> c8 </ci>
+                          <ci> v </ci>
+                        </apply>
+                        <ci> c9 </ci>
+                      </apply>
+                      <ci> W </ci>
+                    </apply>
+                  </apply>
+                </piece>
+                <otherwise>
+                  <cn> 0 </cn>
+                </otherwise>
+              </piecewise>
+              <apply>
+                <minus/>
+                <apply>
+                  <times/>
+                  <ci> cw </ci>
+                  <ci> w </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+          <listOfLocalParameters>
+            <localParameter id="W" value="0.5" units="uM_s_1"/>
+            <localParameter id="c7" value="0.016" units="s_1"/>
+            <localParameter id="c8" value="-0.03" units="s_1"/>
+            <localParameter id="c9" value="0.24" units="uM_s_1"/>
+            <localParameter id="cw" value="0.06" units="s_1"/>
+          </listOfLocalParameters>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+    <spatial:geometry spatial:coordinateSystem="Cartesian">
+      <spatial:listOfCoordinateComponents>
+        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
+          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="300"/>
+        </spatial:coordinateComponent>
+        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
+          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="300"/>
+        </spatial:coordinateComponent>
+      </spatial:listOfCoordinateComponents>
+      <spatial:listOfDomainTypes>
+        <spatial:domainType spatial:spatialId="fish_eye" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="fish_body" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="outside" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="fish_body_outside_membrane" spatial:spatialDimensions="2"/>
+        <spatial:domainType spatial:spatialId="fish_body_fish_eye_membrane" spatial:spatialDimensions="2"/>
+      </spatial:listOfDomainTypes>
+      <spatial:listOfDomains>
+        <spatial:domain spatial:spatialId="outside0" spatial:domainType="outside">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="fish_body1" spatial:domainType="fish_body">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="267" spatial:coord2="66" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="fish_eye2" spatial:domainType="fish_eye">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="66" spatial:coord2="114" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="membrane_outside0_fish_body1" spatial:domainType="fish_body_outside_membrane"/>
+        <spatial:domain spatial:spatialId="membrane_fish_body1_fish_eye2" spatial:domainType="fish_body_fish_eye_membrane"/>
+      </spatial:listOfDomains>
+      <spatial:listOfAdjacentDomains>
+        <spatial:adjacentDomains spatial:spatialId="membrane_outside0_fish_body1_fish_body1" spatial:domain1="membrane_outside0_fish_body1" spatial:domain2="fish_body1"/>
+        <spatial:adjacentDomains spatial:spatialId="membrane_outside0_fish_body1_outside0" spatial:domain1="membrane_outside0_fish_body1" spatial:domain2="outside0"/>
+        <spatial:adjacentDomains spatial:spatialId="membrane_fish_body1_fish_eye2_fish_eye2" spatial:domain1="membrane_fish_body1_fish_eye2" spatial:domain2="fish_eye2"/>
+        <spatial:adjacentDomains spatial:spatialId="membrane_fish_body1_fish_eye2_fish_body1" spatial:domain1="membrane_fish_body1_fish_eye2" spatial:domain2="fish_body1"/>
+      </spatial:listOfAdjacentDomains>
+      <spatial:listOfGeometryDefinitions>
+        <spatial:analyticGeometry spatial:spatialId="Geometry225509093">
+          <spatial:listOfAnalyticVolumes>
+            <spatial:analyticVolume spatial:spatialId="fish_body" spatial:domainType="fish_body" spatial:functionType="layered" spatial:ordinal="1">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <piecewise>
+                  <piece>
+                    <cn type="integer"> 1 </cn>
+                    <apply>
+                      <and/>
+                      <apply>
+                        <or/>
+                        <apply>
+                          <lt/>
+                          <apply>
+                            <plus/>
+                            <apply>
+                              <divide/>
+                              <apply>
+                                <power/>
+                                <apply>
+                                  <minus/>
+                                  <ci> x </ci>
+                                  <apply>
+                                    <times/>
+                                    <cn type="integer"> 300 </cn>
+                                    <cn> 0.42 </cn>
+                                  </apply>
+                                </apply>
+                                <cn type="integer"> 2 </cn>
+                              </apply>
+                              <apply>
+                                <power/>
+                                <apply>
+                                  <times/>
+                                  <cn type="integer"> 300 </cn>
+                                  <cn> 0.37 </cn>
+                                </apply>
+                                <cn type="integer"> 2 </cn>
+                              </apply>
+                            </apply>
+                            <apply>
+                              <divide/>
+                              <apply>
+                                <power/>
+                                <apply>
+                                  <minus/>
+                                  <ci> y </ci>
+                                  <apply>
+                                    <divide/>
+                                    <cn type="integer"> 300 </cn>
+                                    <cn type="integer"> 2 </cn>
+                                  </apply>
+                                </apply>
+                                <cn type="integer"> 2 </cn>
+                              </apply>
+                              <apply>
+                                <power/>
+                                <apply>
+                                  <times/>
+                                  <cn type="integer"> 300 </cn>
+                                  <cn> 0.25 </cn>
+                                </apply>
+                                <cn type="integer"> 2 </cn>
+                              </apply>
+                            </apply>
+                          </apply>
+                          <cn type="integer"> 1 </cn>
+                        </apply>
+                        <apply>
+                          <and/>
+                          <apply>
+                            <lt/>
+                            <ci> y </ci>
+                            <apply>
+                              <plus/>
+                              <apply>
+                                <minus/>
+                                <apply>
+                                  <times/>
+                                  <cn type="integer"> 300 </cn>
+                                  <cn> 0.1 </cn>
+                                </apply>
+                              </apply>
+                              <ci> x </ci>
+                            </apply>
+                          </apply>
+                          <apply>
+                            <gt/>
+                            <ci> y </ci>
+                            <apply>
+                              <plus/>
+                              <apply>
+                                <times/>
+                                <cn type="integer"> 300 </cn>
+                                <cn> 1.1 </cn>
+                              </apply>
+                              <apply>
+                                <minus/>
+                                <ci> x </ci>
+                              </apply>
+                            </apply>
+                          </apply>
+                          <apply>
+                            <lt/>
+                            <ci> x </ci>
+                            <apply>
+                              <times/>
+                              <cn type="integer"> 300 </cn>
+                              <cn> 0.9 </cn>
+                            </apply>
+                          </apply>
+                        </apply>
+                      </apply>
+                      <apply>
+                        <not/>
+                        <apply>
+                          <lt/>
+                          <apply>
+                            <plus/>
+                            <apply>
+                              <divide/>
+                              <apply>
+                                <power/>
+                                <apply>
+                                  <minus/>
+                                  <ci> x </ci>
+                                  <apply>
+                                    <times/>
+                                    <cn type="integer"> 300 </cn>
+                                    <cn> 0.25 </cn>
+                                  </apply>
+                                </apply>
+                                <cn type="integer"> 2 </cn>
+                              </apply>
+                              <apply>
+                                <power/>
+                                <apply>
+                                  <times/>
+                                  <cn> 0.08 </cn>
+                                  <cn type="integer"> 300 </cn>
+                                </apply>
+                                <cn type="integer"> 2 </cn>
+                              </apply>
+                            </apply>
+                            <apply>
+                              <divide/>
+                              <apply>
+                                <power/>
+                                <apply>
+                                  <minus/>
+                                  <ci> y </ci>
+                                  <apply>
+                                    <times/>
+                                    <cn type="integer"> 300 </cn>
+                                    <cn> 0.45 </cn>
+                                  </apply>
+                                </apply>
+                                <cn type="integer"> 2 </cn>
+                              </apply>
+                              <apply>
+                                <power/>
+                                <apply>
+                                  <times/>
+                                  <cn> 0.08 </cn>
+                                  <cn type="integer"> 300 </cn>
+                                </apply>
+                                <cn type="integer"> 2 </cn>
+                              </apply>
+                            </apply>
+                          </apply>
+                          <cn type="integer"> 1 </cn>
+                        </apply>
+                      </apply>
+                    </apply>
+                  </piece>
+                  <otherwise>
+                    <cn type="integer"> 0 </cn>
+                  </otherwise>
+                </piecewise>
+              </math>
+            </spatial:analyticVolume>
+            <spatial:analyticVolume spatial:spatialId="fish_eye" spatial:domainType="fish_eye" spatial:functionType="layered" spatial:ordinal="2">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <piecewise>
+                  <piece>
+                    <cn type="integer"> 1 </cn>
+                    <apply>
+                      <lt/>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <divide/>
+                          <apply>
+                            <power/>
+                            <apply>
+                              <minus/>
+                              <ci> x </ci>
+                              <apply>
+                                <times/>
+                                <cn type="integer"> 300 </cn>
+                                <cn> 0.25 </cn>
+                              </apply>
+                            </apply>
+                            <cn type="integer"> 2 </cn>
+                          </apply>
+                          <apply>
+                            <power/>
+                            <apply>
+                              <times/>
+                              <cn> 0.08 </cn>
+                              <cn type="integer"> 300 </cn>
+                            </apply>
+                            <cn type="integer"> 2 </cn>
+                          </apply>
+                        </apply>
+                        <apply>
+                          <divide/>
+                          <apply>
+                            <power/>
+                            <apply>
+                              <minus/>
+                              <ci> y </ci>
+                              <apply>
+                                <times/>
+                                <cn type="integer"> 300 </cn>
+                                <cn> 0.45 </cn>
+                              </apply>
+                            </apply>
+                            <cn type="integer"> 2 </cn>
+                          </apply>
+                          <apply>
+                            <power/>
+                            <apply>
+                              <times/>
+                              <cn> 0.08 </cn>
+                              <cn type="integer"> 300 </cn>
+                            </apply>
+                            <cn type="integer"> 2 </cn>
+                          </apply>
+                        </apply>
+                      </apply>
+                      <cn type="integer"> 1 </cn>
+                    </apply>
+                  </piece>
+                  <otherwise>
+                    <cn type="integer"> 0 </cn>
+                  </otherwise>
+                </piecewise>
+              </math>
+            </spatial:analyticVolume>
+            <spatial:analyticVolume spatial:spatialId="outside" spatial:domainType="outside" spatial:functionType="layered" spatial:ordinal="0">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <cn type="integer"> 1 </cn>
+              </math>
+            </spatial:analyticVolume>
+          </spatial:listOfAnalyticVolumes>
+        </spatial:analyticGeometry>
+      </spatial:listOfGeometryDefinitions>
+    </spatial:geometry>
+  </model>
+</sbml>
diff --git a/examples/v0.84/fish_big.xml b/examples/v0.84/fish_big.xml
new file mode 100644
index 0000000..2614e41
--- /dev/null
+++ b/examples/v0.84/fish_big.xml
@@ -0,0 +1,843 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
+  <model metaid="meta_fish_skin_pnas2_Application0" id="fish_skin_pnas2_Application0" name="fish-skin-pnas2_Application0">
+	<annotation>
+        <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+        <update step="1" freq="50"/>
+        <items>
+          <item sbmlId="u" palette="black-blue.txt" max="6"/>
+          <item sbmlId="v" palette="black-green.txt" max="6"/>
+          <item sbmlId="w" palette="black-red.txt" max="6"/>
+        </items>
+      </spatialInfo>
+	</annotation>
+    <listOfUnitDefinitions>
+      <unitDefinition id="substance">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="volume">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="area">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="molecules">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="umol_um3_litre_1">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um3">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um2">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_um3_molecules_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="s_1">
+        <listOfUnits>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="outside" name="outside" spatialDimensions="3" size="50000" units="um3" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="outsideoutside" spatial:compartment="outside" spatial:domainType="outside" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="eye" name="eye" spatialDimensions="3" size="500" units="um3" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="fish_eyeeye" spatial:compartment="eye" spatial:domainType="fish_eye" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="fish" name="fish" spatialDimensions="3" size="5000" units="um3" constant="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:OutsideCompartment Name="Membrane0"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <spatial:compartmentMapping spatial:spatialId="fish_bodyfish" spatial:compartment="fish" spatial:domainType="fish_body" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="Membrane0" name="Membrane0" spatialDimensions="2" size="1414" units="um2" constant="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:OutsideCompartment Name="outside"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <spatial:compartmentMapping spatial:spatialId="fish_body_outside_membraneMembrane0" spatial:compartment="Membrane0" spatial:domainType="fish_body_outside_membrane" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="Membrane1" name="Membrane1" spatialDimensions="2" size="304.6" units="um2" constant="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:OutsideCompartment Name="fish"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <spatial:compartmentMapping spatial:spatialId="fish_body_fish_eye_membraneMembrane1" spatial:compartment="Membrane1" spatial:domainType="fish_body_fish_eye_membrane" spatial:unitSize="1"/>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="u" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:Compound Name="s0"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+      </species>
+      <species id="v" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:Compound Name="s1"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+      </species>
+      <species id="X" compartment="fish" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:Compound Name="s2"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+      </species>
+      <species id="w" compartment="fish" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:Compound Name="s3"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+      </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="x" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="y" value="0" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="u_diff_X" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="u" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="u_diff_Y" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="u" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="u_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="u_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="u_BC_Ym" value="5" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Ymin" spatial:type="Value"/>
+      </parameter>
+      <parameter id="u_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="u" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="v_diff_X" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="v" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="v_diff_Y" value="0.02" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="v" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="v_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="v_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="v_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="v_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="v" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="w_diff_X" value="0.2" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="w" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="w_diff_Y" value="0.2" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="w" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="w_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="w_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="w_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="w_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="w" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="KMOLE" value="0.00166112956810631" units="uM_um3_molecules_1" constant="true"/>
+    </listOfParameters>
+    <listOfInitialAssignments>
+      <initialAssignment symbol="u">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <piecewise>
+            <piece>
+              <cn> 4 </cn>
+              <apply>
+                <and/>
+                <apply>
+                  <gt/>
+                  <ci> y </ci>
+                  <cn> 47 </cn>
+                </apply>
+                <apply>
+                  <lt/>
+                  <ci> y </ci>
+                  <cn> 51 </cn>
+                </apply>
+              </apply>
+            </piece>
+            <otherwise>
+              <cn> 0 </cn>
+            </otherwise>
+          </piecewise>
+        </math>
+      </initialAssignment>
+      <initialAssignment symbol="v">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <piecewise>
+            <piece>
+              <cn> 4 </cn>
+              <apply>
+                <and/>
+                <apply>
+                  <gt/>
+                  <ci> y </ci>
+                  <cn> 47 </cn>
+                </apply>
+                <apply>
+                  <lt/>
+                  <ci> y </ci>
+                  <cn> 51 </cn>
+                </apply>
+              </apply>
+            </piece>
+            <otherwise>
+              <cn> 0 </cn>
+            </otherwise>
+          </piecewise>
+        </math>
+      </initialAssignment>
+      <initialAssignment symbol="w">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <piecewise>
+            <piece>
+              <cn> 4 </cn>
+              <apply>
+                <and/>
+                <apply>
+                  <gt/>
+                  <ci> y </ci>
+                  <cn> 47 </cn>
+                </apply>
+                <apply>
+                  <lt/>
+                  <ci> y </ci>
+                  <cn> 51 </cn>
+                </apply>
+              </apply>
+            </piece>
+            <otherwise>
+              <cn> 0 </cn>
+            </otherwise>
+          </piecewise>
+        </math>
+      </initialAssignment>
+    </listOfInitialAssignments>
+    <listOfReactions>
+      <reaction id="re0" name="re0" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:SimpleReaction Structure="fish"/>
+              <vcell:ReactionRate Name="J"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="X" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="u" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference species="v"/>
+          <modifierSpeciesReference species="w"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <plus/>
+              <piecewise>
+                <piece>
+                  <ci> U </ci>
+                  <apply>
+                    <geq/>
+                    <apply>
+                      <plus/>
+                      <apply>
+                        <times/>
+                        <ci> c1 </ci>
+                        <ci> v </ci>
+                      </apply>
+                      <apply>
+                        <times/>
+                        <ci> c2 </ci>
+                        <ci> w </ci>
+                      </apply>
+                      <ci> c3 </ci>
+                    </apply>
+                    <ci> U </ci>
+                  </apply>
+                </piece>
+                <otherwise>
+                  <cn> 0 </cn>
+                </otherwise>
+              </piecewise>
+              <piecewise>
+                <piece>
+                  <apply>
+                    <plus/>
+                    <apply>
+                      <times/>
+                      <ci> c1 </ci>
+                      <ci> v </ci>
+                    </apply>
+                    <apply>
+                      <times/>
+                      <ci> c2 </ci>
+                      <ci> w </ci>
+                    </apply>
+                    <ci> c3 </ci>
+                  </apply>
+                  <apply>
+                    <and/>
+                    <apply>
+                      <gt/>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <times/>
+                          <ci> c1 </ci>
+                          <ci> v </ci>
+                        </apply>
+                        <apply>
+                          <times/>
+                          <ci> c2 </ci>
+                          <ci> w </ci>
+                        </apply>
+                        <ci> c3 </ci>
+                      </apply>
+                      <cn> 0 </cn>
+                    </apply>
+                    <apply>
+                      <lt/>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <times/>
+                          <ci> c1 </ci>
+                          <ci> v </ci>
+                        </apply>
+                        <apply>
+                          <times/>
+                          <ci> c2 </ci>
+                          <ci> w </ci>
+                        </apply>
+                        <ci> c3 </ci>
+                      </apply>
+                      <ci> U </ci>
+                    </apply>
+                  </apply>
+                </piece>
+                <otherwise>
+                  <cn> 0 </cn>
+                </otherwise>
+              </piecewise>
+              <apply>
+                <minus/>
+                <apply>
+                  <times/>
+                  <ci> cu </ci>
+                  <ci> u </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+          <listOfLocalParameters>
+            <localParameter id="U" value="0.5" units="uM_s_1"/>
+            <localParameter id="c1" value="-0.04" units="s_1"/>
+            <localParameter id="c2" value="-0.055" units="s_1"/>
+            <localParameter id="c3" value="0.37" units="uM_s_1"/>
+            <localParameter id="cu" value="0.02" units="s_1"/>
+          </listOfLocalParameters>
+        </kineticLaw>
+      </reaction>
+      <reaction id="re1" name="re1" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:SimpleReaction Structure="fish"/>
+              <vcell:ReactionRate Name="J"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="X" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="v" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference species="u"/>
+          <modifierSpeciesReference species="w"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <plus/>
+              <piecewise>
+                <piece>
+                  <ci> V </ci>
+                  <apply>
+                    <geq/>
+                    <apply>
+                      <plus/>
+                      <apply>
+                        <times/>
+                        <ci> c4 </ci>
+                        <ci> u </ci>
+                      </apply>
+                      <apply>
+                        <times/>
+                        <ci> c5 </ci>
+                        <ci> w </ci>
+                      </apply>
+                      <ci> c6 </ci>
+                    </apply>
+                    <ci> V </ci>
+                  </apply>
+                </piece>
+                <otherwise>
+                  <cn> 0 </cn>
+                </otherwise>
+              </piecewise>
+              <piecewise>
+                <piece>
+                  <apply>
+                    <plus/>
+                    <apply>
+                      <times/>
+                      <ci> c4 </ci>
+                      <ci> u </ci>
+                    </apply>
+                    <apply>
+                      <times/>
+                      <ci> c5 </ci>
+                      <ci> w </ci>
+                    </apply>
+                    <ci> c6 </ci>
+                  </apply>
+                  <apply>
+                    <and/>
+                    <apply>
+                      <gt/>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <times/>
+                          <ci> c4 </ci>
+                          <ci> u </ci>
+                        </apply>
+                        <apply>
+                          <times/>
+                          <ci> c5 </ci>
+                          <ci> w </ci>
+                        </apply>
+                        <ci> c6 </ci>
+                      </apply>
+                      <cn> 0 </cn>
+                    </apply>
+                    <apply>
+                      <lt/>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <times/>
+                          <ci> c4 </ci>
+                          <ci> u </ci>
+                        </apply>
+                        <apply>
+                          <times/>
+                          <ci> c5 </ci>
+                          <ci> w </ci>
+                        </apply>
+                        <ci> c6 </ci>
+                      </apply>
+                      <ci> V </ci>
+                    </apply>
+                  </apply>
+                </piece>
+                <otherwise>
+                  <cn> 0 </cn>
+                </otherwise>
+              </piecewise>
+              <apply>
+                <minus/>
+                <apply>
+                  <times/>
+                  <ci> cv </ci>
+                  <ci> v </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+          <listOfLocalParameters>
+            <localParameter id="V" value="0.5" units="uM_s_1"/>
+            <localParameter id="c4" value="-0.05" units="s_1"/>
+            <localParameter id="c5" value="0" units="s_1"/>
+            <localParameter id="c6" value="0.25" units="uM_s_1"/>
+            <localParameter id="cv" value="0.025" units="s_1"/>
+          </listOfLocalParameters>
+        </kineticLaw>
+      </reaction>
+      <reaction id="re2" name="re2" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:SimpleReaction Structure="fish"/>
+              <vcell:ReactionRate Name="J"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="X" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="w" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference species="u"/>
+          <modifierSpeciesReference species="v"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <plus/>
+              <piecewise>
+                <piece>
+                  <ci> W </ci>
+                  <apply>
+                    <geq/>
+                    <apply>
+                      <plus/>
+                      <apply>
+                        <times/>
+                        <ci> c7 </ci>
+                        <ci> u </ci>
+                      </apply>
+                      <apply>
+                        <times/>
+                        <ci> c8 </ci>
+                        <ci> v </ci>
+                      </apply>
+                      <ci> c9 </ci>
+                    </apply>
+                    <ci> W </ci>
+                  </apply>
+                </piece>
+                <otherwise>
+                  <cn> 0 </cn>
+                </otherwise>
+              </piecewise>
+              <piecewise>
+                <piece>
+                  <apply>
+                    <plus/>
+                    <apply>
+                      <times/>
+                      <ci> c7 </ci>
+                      <ci> u </ci>
+                    </apply>
+                    <apply>
+                      <times/>
+                      <ci> c8 </ci>
+                      <ci> v </ci>
+                    </apply>
+                    <ci> c9 </ci>
+                  </apply>
+                  <apply>
+                    <and/>
+                    <apply>
+                      <gt/>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <times/>
+                          <ci> c7 </ci>
+                          <ci> u </ci>
+                        </apply>
+                        <apply>
+                          <times/>
+                          <ci> c8 </ci>
+                          <ci> v </ci>
+                        </apply>
+                        <ci> c9 </ci>
+                      </apply>
+                      <cn> 0 </cn>
+                    </apply>
+                    <apply>
+                      <lt/>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <times/>
+                          <ci> c7 </ci>
+                          <ci> u </ci>
+                        </apply>
+                        <apply>
+                          <times/>
+                          <ci> c8 </ci>
+                          <ci> v </ci>
+                        </apply>
+                        <ci> c9 </ci>
+                      </apply>
+                      <ci> W </ci>
+                    </apply>
+                  </apply>
+                </piece>
+                <otherwise>
+                  <cn> 0 </cn>
+                </otherwise>
+              </piecewise>
+              <apply>
+                <minus/>
+                <apply>
+                  <times/>
+                  <ci> cw </ci>
+                  <ci> w </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+          <listOfLocalParameters>
+            <localParameter id="W" value="0.5" units="uM_s_1"/>
+            <localParameter id="c7" value="0.016" units="s_1"/>
+            <localParameter id="c8" value="-0.03" units="s_1"/>
+            <localParameter id="c9" value="0.24" units="uM_s_1"/>
+            <localParameter id="cw" value="0.06" units="s_1"/>
+          </listOfLocalParameters>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+    <spatial:geometry spatial:coordinateSystem="Cartesian">
+      <spatial:listOfCoordinateComponents>
+        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
+          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="100"/>
+        </spatial:coordinateComponent>
+        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
+          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="100"/>
+        </spatial:coordinateComponent>
+      </spatial:listOfCoordinateComponents>
+      <spatial:listOfDomainTypes>
+        <spatial:domainType spatial:spatialId="fish_eye" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="fish_body" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="outside" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="fish_body_outside_membrane" spatial:spatialDimensions="2"/>
+        <spatial:domainType spatial:spatialId="fish_body_fish_eye_membrane" spatial:spatialDimensions="2"/>
+      </spatial:listOfDomainTypes>
+      <spatial:listOfDomains>
+        <spatial:domain spatial:spatialId="outside0" spatial:domainType="outside">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="fish_body1" spatial:domainType="fish_body">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="89" spatial:coord2="22" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="fish_eye2" spatial:domainType="fish_eye">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="22" spatial:coord2="38" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="membrane_outside0_fish_body1" spatial:domainType="fish_body_outside_membrane"/>
+        <spatial:domain spatial:spatialId="membrane_fish_body1_fish_eye2" spatial:domainType="fish_body_fish_eye_membrane"/>
+      </spatial:listOfDomains>
+      <spatial:listOfAdjacentDomains>
+        <spatial:adjacentDomains spatial:spatialId="membrane_outside0_fish_body1_fish_body1" spatial:domain1="membrane_outside0_fish_body1" spatial:domain2="fish_body1"/>
+        <spatial:adjacentDomains spatial:spatialId="membrane_outside0_fish_body1_outside0" spatial:domain1="membrane_outside0_fish_body1" spatial:domain2="outside0"/>
+        <spatial:adjacentDomains spatial:spatialId="membrane_fish_body1_fish_eye2_fish_eye2" spatial:domain1="membrane_fish_body1_fish_eye2" spatial:domain2="fish_eye2"/>
+        <spatial:adjacentDomains spatial:spatialId="membrane_fish_body1_fish_eye2_fish_body1" spatial:domain1="membrane_fish_body1_fish_eye2" spatial:domain2="fish_body1"/>
+      </spatial:listOfAdjacentDomains>
+      <spatial:listOfGeometryDefinitions>
+        <spatial:analyticGeometry spatial:spatialId="Geometry225509093">
+          <spatial:listOfAnalyticVolumes>
+            <spatial:analyticVolume spatial:spatialId="fish_eye" spatial:domainType="fish_eye" spatial:functionType="layered" spatial:ordinal="2">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <piecewise>
+                  <piece>
+                    <cn type="integer"> 1 </cn>
+                    <apply>
+                      <lt/>
+                      <apply>
+                        <plus/>
+                        <apply>
+                          <power/>
+                          <apply>
+                            <plus/>
+                            <cn type="integer"> -24 </cn>
+                            <ci> x </ci>
+                          </apply>
+                          <cn type="integer"> 2 </cn>
+                        </apply>
+                        <apply>
+                          <power/>
+                          <apply>
+                            <plus/>
+                            <cn type="integer"> -58 </cn>
+                            <ci> y </ci>
+                          </apply>
+                          <cn type="integer"> 2 </cn>
+                        </apply>
+                      </apply>
+                      <cn type="integer"> 25 </cn>
+                    </apply>
+                  </piece>
+                  <otherwise>
+                    <cn type="integer"> 0 </cn>
+                  </otherwise>
+                </piecewise>
+              </math>
+            </spatial:analyticVolume>
+            <spatial:analyticVolume spatial:spatialId="fish_body" spatial:domainType="fish_body" spatial:functionType="layered" spatial:ordinal="1">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <piecewise>
+                  <piece>
+                    <cn type="integer"> 1 </cn>
+                    <apply>
+                      <or/>
+                      <apply>
+                        <lt/>
+                        <apply>
+                          <plus/>
+                          <apply>
+                            <power/>
+                            <apply>
+                              <times/>
+                              <cn> 0.27 </cn>
+                              <apply>
+                                <plus/>
+                                <cn type="integer"> -42 </cn>
+                                <ci> x </ci>
+                              </apply>
+                            </apply>
+                            <cn type="integer"> 2 </cn>
+                          </apply>
+                          <apply>
+                            <power/>
+                            <apply>
+                              <times/>
+                              <cn> 0.1 </cn>
+                              <apply>
+                                <plus/>
+                                <cn type="integer"> -50 </cn>
+                                <ci> y </ci>
+                              </apply>
+                            </apply>
+                            <cn type="integer"> 2 </cn>
+                          </apply>
+                        </apply>
+                        <cn type="integer"> 100 </cn>
+                      </apply>
+                      <apply>
+                        <and/>
+                        <apply>
+                          <lt/>
+                          <ci> y </ci>
+                          <apply>
+                            <plus/>
+                            <cn type="integer"> -10 </cn>
+                            <ci> x </ci>
+                          </apply>
+                        </apply>
+                        <apply>
+                          <gt/>
+                          <ci> y </ci>
+                          <apply>
+                            <plus/>
+                            <cn type="integer"> 110 </cn>
+                            <apply>
+                              <minus/>
+                              <ci> x </ci>
+                            </apply>
+                          </apply>
+                        </apply>
+                        <apply>
+                          <lt/>
+                          <ci> x </ci>
+                          <cn type="integer"> 90 </cn>
+                        </apply>
+                      </apply>
+                    </apply>
+                  </piece>
+                  <otherwise>
+                    <cn type="integer"> 0 </cn>
+                  </otherwise>
+                </piecewise>
+              </math>
+            </spatial:analyticVolume>
+            <spatial:analyticVolume spatial:spatialId="outside" spatial:domainType="outside" spatial:functionType="layered" spatial:ordinal="0">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <cn type="integer"> 1 </cn>
+              </math>
+            </spatial:analyticVolume>
+          </spatial:listOfAnalyticVolumes>
+        </spatial:analyticGeometry>
+      </spatial:listOfGeometryDefinitions>
+    </spatial:geometry>
+  </model>
+</sbml>
diff --git a/examples/v0.84/no_spatial.xml b/examples/v0.84/no_spatial.xml
new file mode 100644
index 0000000..0fa2775
--- /dev/null
+++ b/examples/v0.84/no_spatial.xml
@@ -0,0 +1,168 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" 
+level="3" version="1">
+  <model metaid="COPASI1" id="New_Model_Application0" name="New Model_Application0">
+    <listOfUnitDefinitions>
+      <unitDefinition id="substance">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="volume">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="area">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="molecules">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="umol_um3_litre_1">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um3">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um2">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_um3_molecules_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_zero__001_m3_mol_1_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one__0E_6">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one_000000_0">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000000"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one_000_0_m_3_mol_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="M">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="compartment_1" name="compartment_1" spatialDimensions="3" size="1" constant="true"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="species_1" initialConcentration="6" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" />
+      <species id="species_2" initialConcentration="0.1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" />
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="v1" value="0.06" constant="true"/>
+      <parameter id="v2" value="0.12" constant="true"/>
+      <parameter id="V" value="0.5" constant="true"/>
+      <parameter id="Km" value="0.1" constant="true"/>
+      <parameter id="k1" value="1" constant="true"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false">
+        <listOfReactants>
+          <speciesReference species="species_1" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> k1 </ci>
+              <ci> species_1 </ci>
+              <ci> species_2 </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false">
+        <listOfProducts>
+          <speciesReference species="species_1" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <ci> v2 </ci>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false">
+        <listOfProducts>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <ci> v1 </ci>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false">
+        <listOfReactants>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> V </ci>
+              <ci> species_2 </ci>
+              <apply>
+                <divide/>
+                <cn> 1 </cn>
+                <apply>
+                  <plus/>
+                  <ci> Km </ci>
+                  <ci> species_2 </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>
diff --git a/examples/v0.84/transport.xml b/examples/v0.84/transport.xml
new file mode 100644
index 0000000..7098d28
--- /dev/null
+++ b/examples/v0.84/transport.xml
@@ -0,0 +1,338 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
+  <model id="simple_transport_simulation" name="simple_transport_simulation">
+    <annotation>
+        <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+        <update step="1" freq="50"/>
+        <items>
+          <item sbmlId="s1" palette="black-blue.txt" max="6"/>
+          <item sbmlId="s0" palette="black-green.txt" max="6"/>
+        </items>
+      </spatialInfo>
+
+      <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+        <vcell:VCMLSpecific>
+          <vcell:BioModel Name="simple_transport" KeyValue="60099072"/>
+          <vcell:SimulationSpec Name="simulation" KeyValue="60099056"/>
+        </vcell:VCMLSpecific>
+      </vcell:VCellInfo>
+    </annotation>
+    <listOfUnitDefinitions>
+      <unitDefinition id="substance">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="volume">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="area">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="molecules">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="umol_um3_litre_1">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um3">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um2">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_um3_molecules_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="molecules_um_2_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000000000000"/>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="metre" exponent="-2" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="pA_um_2">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="ampere" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="metre" exponent="-2" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="extracellular" name="extracellular" spatialDimensions="3" units="um3" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain0extracellular" spatial:compartment="extracellular" spatial:domainType="subdomain0" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="cytosol" name="cytosol" spatialDimensions="3" units="um3" constant="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:OutsideCompartment Name="membrane0"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <spatial:compartmentMapping spatial:spatialId="subdomain2cytosol" spatial:compartment="cytosol" spatial:domainType="subdomain2" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="nucleus" name="nucleus" spatialDimensions="3" units="um3" constant="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:OutsideCompartment Name="membrane1"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <spatial:compartmentMapping spatial:spatialId="subdomain1nucleus" spatial:compartment="nucleus" spatial:domainType="subdomain1" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="membrane0" name="membrane0" spatialDimensions="2" units="um2" constant="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:OutsideCompartment Name="extracellular"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <spatial:compartmentMapping spatial:spatialId="subdomain0_subdomain2_membranemembrane0" spatial:compartment="membrane0" spatial:domainType="subdomain0_subdomain2_membrane" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="membrane1" name="membrane1" spatialDimensions="2" units="um2" constant="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:OutsideCompartment Name="cytosol"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <spatial:compartmentMapping spatial:spatialId="subdomain1_subdomain2_membranemembrane1" spatial:compartment="membrane1" spatial:domainType="subdomain1_subdomain2_membrane" spatial:unitSize="1"/>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="s1" compartment="nucleus" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:Compound Name="s1"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+      </species>
+      <species id="s0" compartment="cytosol" initialConcentration="3010" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:Compound Name="s0"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+      </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="s1_diff" value="0.1" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="s1"/>
+      </parameter>
+      <parameter id="s1_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="s1" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="s1_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="s1" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="s1_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="s1" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="s1_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="s1" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="s0_diff" value="0.1" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="s0"/>
+      </parameter>
+      <parameter id="s0_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="s0" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="s0_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="s0" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="s0_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="s0" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="s0_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="s0" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="x" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="y" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      </parameter>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction id="transport0" name="transport0" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <annotation>
+          <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+            <vcell:VCMLSpecific>
+              <vcell:SimpleReaction Structure="membrane1"/>
+              <vcell:ReactionRate Name="J"/>
+            </vcell:VCMLSpecific>
+          </vcell:VCellInfo>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="s0" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="s1" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <cn> 1 </cn>
+              <ci> membrane1 </ci>
+            </apply>
+          </math>
+          <listOfLocalParameters>
+            <localParameter id="I" value="0" units="pA_um_2"/>
+          </listOfLocalParameters>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+    <spatial:geometry spatial:coordinateSystem="Cartesian">
+      <spatial:listOfCoordinateComponents>
+        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
+          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="100"/>
+        </spatial:coordinateComponent>
+        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
+          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="100"/>
+        </spatial:coordinateComponent>
+      </spatial:listOfCoordinateComponents>
+      <spatial:listOfDomainTypes>
+        <spatial:domainType spatial:spatialId="subdomain1" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain2" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain0" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain0_subdomain2_membrane" spatial:spatialDimensions="2"/>
+        <spatial:domainType spatial:spatialId="subdomain1_subdomain2_membrane" spatial:spatialDimensions="2"/>
+      </spatial:listOfDomainTypes>
+      <spatial:listOfDomains>
+        <spatial:domain spatial:spatialId="subdomain00" spatial:domainType="subdomain0">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="subdomain21" spatial:domainType="subdomain2">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="16" spatial:coord2="16" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="subdomain12" spatial:domainType="subdomain1">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="24" spatial:coord2="24" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="membrane_subdomain00_subdomain21" spatial:domainType="subdomain0_subdomain2_membrane"/>
+        <spatial:domain spatial:spatialId="membrane_subdomain21_subdomain12" spatial:domainType="subdomain1_subdomain2_membrane"/>
+      </spatial:listOfDomains>
+      <spatial:listOfAdjacentDomains>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain00_subdomain21_subdomain21" spatial:domain1="membrane_subdomain00_subdomain21" spatial:domain2="subdomain21"/>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain00_subdomain21_subdomain00" spatial:domain1="membrane_subdomain00_subdomain21" spatial:domain2="subdomain00"/>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain21_subdomain12_subdomain12" spatial:domain1="membrane_subdomain21_subdomain12" spatial:domain2="subdomain12"/>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain21_subdomain12_subdomain21" spatial:domain1="membrane_subdomain21_subdomain12" spatial:domain2="subdomain21"/>
+      </spatial:listOfAdjacentDomains>
+      <spatial:listOfGeometryDefinitions>
+        <spatial:analyticGeometry spatial:spatialId="spatial2d8sq">
+          <spatial:listOfAnalyticVolumes>
+            <spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="2">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <piecewise>
+                  <piece>
+                    <cn type="integer"> 1 </cn>
+                    <apply>
+                      <and/>
+                      <apply>
+                        <geq/>
+                        <ci> x </ci>
+                        <cn type="integer"> 24 </cn>
+                      </apply>
+                      <apply>
+                        <leq/>
+                        <ci> x </ci>
+                        <cn type="integer"> 76 </cn>
+                      </apply>
+                      <apply>
+                        <geq/>
+                        <ci> y </ci>
+                        <cn type="integer"> 24 </cn>
+                      </apply>
+                      <apply>
+                        <leq/>
+                        <ci> y </ci>
+                        <cn type="integer"> 76 </cn>
+                      </apply>
+                    </apply>
+                  </piece>
+                  <otherwise>
+                    <cn type="integer"> 0 </cn>
+                  </otherwise>
+                </piecewise>
+              </math>
+            </spatial:analyticVolume>
+            <spatial:analyticVolume spatial:spatialId="subdomain2" spatial:domainType="subdomain2" spatial:functionType="layered" spatial:ordinal="1">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <piecewise>
+                  <piece>
+                    <cn type="integer"> 1 </cn>
+                    <apply>
+                      <and/>
+                      <apply>
+                        <geq/>
+                        <ci> x </ci>
+                        <cn type="integer"> 16 </cn>
+                      </apply>
+                      <apply>
+                        <leq/>
+                        <ci> x </ci>
+                        <cn type="integer"> 84 </cn>
+                      </apply>
+                      <apply>
+                        <geq/>
+                        <ci> y </ci>
+                        <cn type="integer"> 16 </cn>
+                      </apply>
+                      <apply>
+                        <leq/>
+                        <ci> y </ci>
+                        <cn type="integer"> 84 </cn>
+                      </apply>
+                    </apply>
+                  </piece>
+                  <otherwise>
+                    <cn type="integer"> 0 </cn>
+                  </otherwise>
+                </piecewise>
+              </math>
+            </spatial:analyticVolume>
+            <spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="0">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <cn type="integer"> 1 </cn>
+              </math>
+            </spatial:analyticVolume>
+          </spatial:listOfAnalyticVolumes>
+        </spatial:analyticGeometry>
+      </spatial:listOfGeometryDefinitions>
+    </spatial:geometry>
+  </model>
+</sbml>
diff --git a/examples/v0.84/turing.xml b/examples/v0.84/turing.xml
new file mode 100644
index 0000000..a478d21
--- /dev/null
+++ b/examples/v0.84/turing.xml
@@ -0,0 +1,354 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
+  <model metaid="COPASI1" id="New_Model_Application0" name="New Model_Application0">
+    <annotation>
+      <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+        <update step="0.07" freq="50"/>
+        <items>
+          <item sbmlId="species_1" palette="black-blue.txt" max="2"/>
+          <item sbmlId="species_2" palette="black-green.txt" max="2"/>
+        </items>
+      </spatialInfo>
+    </annotation>
+    <listOfUnitDefinitions>
+      <unitDefinition id="substance">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="volume">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="area">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="molecules">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="umol_um3_litre_1">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um3">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um2">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_um3_molecules_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_zero__001_m3_mol_1_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one__0E_6">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one_000000_0">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000000"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one_000_0_m_3_mol_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="M">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="compartment_1" name="compartment_1" spatialDimensions="3" size="1" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain0compartment_1" spatial:compartment="compartment_1" spatial:domainType="subdomain0" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="c2" name="c2" spatialDimensions="3" size="1" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain1c2" spatial:compartment="c2" spatial:domainType="subdomain1" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="Membrane2" name="Membrane2" spatialDimensions="2" size="1" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain0_subdomain1_membraneMembrane2" spatial:compartment="Membrane2" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="species_1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
+      <species id="species_2" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="x" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="y" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="species_1_diff" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="species_1_diff_Y" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="species_1_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_1_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_1_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_1_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_diff" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="species_2_diff_y" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="species_2_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="v1" value="0.06" constant="true"/>
+      <parameter id="v2" value="0.12" constant="true"/>
+      <parameter id="V" value="0.5" constant="true"/>
+      <parameter id="Km" value="0.1" constant="true"/>
+      <parameter id="k1" value="1" constant="true"/>
+    </listOfParameters>
+    <listOfInitialAssignments>
+      <initialAssignment symbol="species_1">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <piecewise>
+            <piece>
+              <cn> 20 </cn>
+              <apply>
+                <and/>
+                <apply>
+                  <and/>
+                  <apply>
+                    <gt/>
+                    <ci> x </ci>
+                    <cn> 20 </cn>
+                  </apply>
+                  <apply>
+                    <lt/>
+                    <ci> x </ci>
+                    <cn> 25 </cn>
+                  </apply>
+                </apply>
+                <apply>
+                  <and/>
+                  <apply>
+                    <gt/>
+                    <ci> y </ci>
+                    <cn> 70 </cn>
+                  </apply>
+                  <apply>
+                    <lt/>
+                    <ci> y </ci>
+                    <cn> 85 </cn>
+                  </apply>
+                </apply>
+              </apply>
+            </piece>
+            <otherwise>
+              <cn> 0.5 </cn>
+            </otherwise>
+          </piecewise>
+        </math>
+      </initialAssignment>
+      <initialAssignment symbol="species_2">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <cn> 0.1 </cn>
+        </math>
+      </initialAssignment>
+    </listOfInitialAssignments>
+    <listOfReactions>
+      <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfReactants>
+          <speciesReference species="species_1" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <cn> 1 </cn>
+              <ci> species_1 </ci>
+              <ci> species_2 </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfProducts>
+          <speciesReference species="species_1" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <cn> 0.12 </cn>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfProducts>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <cn> 0.06 </cn>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfReactants>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <cn> 0.5 </cn>
+              <ci> species_2 </ci>
+              <apply>
+                <divide/>
+                <cn> 1 </cn>
+                <apply>
+                  <plus/>
+                  <cn> 0.1 </cn>
+                  <ci> species_2 </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+    <spatial:geometry spatial:coordinateSystem="Cartesian">
+      <spatial:listOfCoordinateComponents>
+        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
+          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="100"/>
+        </spatial:coordinateComponent>
+        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
+          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="100"/>
+        </spatial:coordinateComponent>
+      </spatial:listOfCoordinateComponents>
+      <spatial:listOfDomainTypes>
+        <spatial:domainType spatial:spatialId="subdomain1" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain0" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
+      </spatial:listOfDomainTypes>
+      <spatial:listOfDomains>
+        <spatial:domain spatial:spatialId="subdomain10" spatial:domainType="subdomain1">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="subdomain01" spatial:domainType="subdomain0">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="1" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="membrane_subdomain10_subdomain01" spatial:domainType="subdomain0_subdomain1_membrane"/>
+      </spatial:listOfDomains>
+      <spatial:listOfAdjacentDomains>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain01" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain01"/>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain10" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain10"/>
+      </spatial:listOfAdjacentDomains>
+      <spatial:listOfGeometryDefinitions>
+        <spatial:analyticGeometry spatial:spatialId="Geometry4">
+          <spatial:listOfAnalyticVolumes>
+            <spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="1">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <piecewise>
+                  <piece>
+                    <cn type="integer"> 1 </cn>
+                    <apply>
+                      <and/>
+                      <apply>
+                        <geq/>
+                        <ci> x </ci>
+                        <cn type="integer"> 1 </cn>
+                      </apply>
+                      <apply>
+                        <leq/>
+                        <ci> x </ci>
+                        <cn type="integer"> 99 </cn>
+                      </apply>
+                      <apply>
+                        <geq/>
+                        <ci> y </ci>
+                        <cn type="integer"> 1 </cn>
+                      </apply>
+                      <apply>
+                        <leq/>
+                        <ci> y </ci>
+                        <cn type="integer"> 99 </cn>
+                      </apply>
+                    </apply>
+                  </piece>
+                  <otherwise>
+                    <cn type="integer"> 0 </cn>
+                  </otherwise>
+                </piecewise>
+              </math>
+            </spatial:analyticVolume>
+            <spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="0">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <cn type="integer"> 1 </cn>
+              </math>
+            </spatial:analyticVolume>
+          </spatial:listOfAnalyticVolumes>
+        </spatial:analyticGeometry>
+      </spatial:listOfGeometryDefinitions>
+    </spatial:geometry>
+  </model>
+</sbml>
diff --git a/examples/v0.84/turing_300x300.xml b/examples/v0.84/turing_300x300.xml
new file mode 100644
index 0000000..cdd9075
--- /dev/null
+++ b/examples/v0.84/turing_300x300.xml
@@ -0,0 +1,354 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
+  <model metaid="COPASI1" id="New_Model_Application0" name="New Model_Application0">
+    <annotation>
+      <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+        <update step="0.07" freq="500"/>
+        <items>
+          <item sbmlId="species_1" palette="black-blue.txt" max="2"/>
+          <item sbmlId="species_2" palette="black-green.txt" max="2"/>
+        </items>
+      </spatialInfo>
+    </annotation>
+    <listOfUnitDefinitions>
+      <unitDefinition id="substance">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="volume">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="area">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="molecules">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="umol_um3_litre_1">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um3">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um2">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_um3_molecules_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_zero__001_m3_mol_1_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one__0E_6">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one_000000_0">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000000"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one_000_0_m_3_mol_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="M">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="compartment_1" name="compartment_1" spatialDimensions="3" size="1" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain0compartment_1" spatial:compartment="compartment_1" spatial:domainType="subdomain0" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="c2" name="c2" spatialDimensions="3" size="1" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain1c2" spatial:compartment="c2" spatial:domainType="subdomain1" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="Membrane2" name="Membrane2" spatialDimensions="2" size="1" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain0_subdomain1_membraneMembrane2" spatial:compartment="Membrane2" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="species_1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
+      <species id="species_2" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="x" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="y" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="species_1_diff" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="species_1_diff_Y" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="species_1_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_1_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_1_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_1_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_diff" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="species_2_diff_y" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="species_2_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="v1" value="0.06" constant="true"/>
+      <parameter id="v2" value="0.12" constant="true"/>
+      <parameter id="V" value="0.5" constant="true"/>
+      <parameter id="Km" value="0.1" constant="true"/>
+      <parameter id="k1" value="1" constant="true"/>
+    </listOfParameters>
+    <listOfInitialAssignments>
+      <initialAssignment symbol="species_1">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <piecewise>
+            <piece>
+              <cn> 20 </cn>
+              <apply>
+                <and/>
+                <apply>
+                  <and/>
+                  <apply>
+                    <gt/>
+                    <ci> x </ci>
+                    <cn> 20 </cn>
+                  </apply>
+                  <apply>
+                    <lt/>
+                    <ci> x </ci>
+                    <cn> 25 </cn>
+                  </apply>
+                </apply>
+                <apply>
+                  <and/>
+                  <apply>
+                    <gt/>
+                    <ci> y </ci>
+                    <cn> 70 </cn>
+                  </apply>
+                  <apply>
+                    <lt/>
+                    <ci> y </ci>
+                    <cn> 85 </cn>
+                  </apply>
+                </apply>
+              </apply>
+            </piece>
+            <otherwise>
+              <cn> 0.5 </cn>
+            </otherwise>
+          </piecewise>
+        </math>
+      </initialAssignment>
+      <initialAssignment symbol="species_2">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <cn> 0.1 </cn>
+        </math>
+      </initialAssignment>
+    </listOfInitialAssignments>
+    <listOfReactions>
+      <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfReactants>
+          <speciesReference species="species_1" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <cn> 1 </cn>
+              <ci> species_1 </ci>
+              <ci> species_2 </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfProducts>
+          <speciesReference species="species_1" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <cn> 0.12 </cn>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfProducts>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <cn> 0.06 </cn>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfReactants>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <cn> 0.5 </cn>
+              <ci> species_2 </ci>
+              <apply>
+                <divide/>
+                <cn> 1 </cn>
+                <apply>
+                  <plus/>
+                  <cn> 0.1 </cn>
+                  <ci> species_2 </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+    <spatial:geometry spatial:coordinateSystem="Cartesian">
+      <spatial:listOfCoordinateComponents>
+        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
+          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="300"/>
+        </spatial:coordinateComponent>
+        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
+          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="300"/>
+        </spatial:coordinateComponent>
+      </spatial:listOfCoordinateComponents>
+      <spatial:listOfDomainTypes>
+        <spatial:domainType spatial:spatialId="subdomain1" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain0" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
+      </spatial:listOfDomainTypes>
+      <spatial:listOfDomains>
+        <spatial:domain spatial:spatialId="subdomain10" spatial:domainType="subdomain1">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="subdomain01" spatial:domainType="subdomain0">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="1" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="membrane_subdomain10_subdomain01" spatial:domainType="subdomain0_subdomain1_membrane"/>
+      </spatial:listOfDomains>
+      <spatial:listOfAdjacentDomains>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain01" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain01"/>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain10" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain10"/>
+      </spatial:listOfAdjacentDomains>
+      <spatial:listOfGeometryDefinitions>
+        <spatial:analyticGeometry spatial:spatialId="Geometry4">
+          <spatial:listOfAnalyticVolumes>
+            <spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="1">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <piecewise>
+                  <piece>
+                    <cn type="integer"> 1 </cn>
+                    <apply>
+                      <and/>
+                      <apply>
+                        <geq/>
+                        <ci> x </ci>
+                        <cn type="integer"> 1 </cn>
+                      </apply>
+                      <apply>
+                        <leq/>
+                        <ci> x </ci>
+                        <cn type="integer"> 299 </cn>
+                      </apply>
+                      <apply>
+                        <geq/>
+                        <ci> y </ci>
+                        <cn type="integer"> 1 </cn>
+                      </apply>
+                      <apply>
+                        <leq/>
+                        <ci> y </ci>
+                        <cn type="integer"> 299 </cn>
+                      </apply>
+                    </apply>
+                  </piece>
+                  <otherwise>
+                    <cn type="integer"> 0 </cn>
+                  </otherwise>
+                </piecewise>
+              </math>
+            </spatial:analyticVolume>
+            <spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="0">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <cn type="integer"> 1 </cn>
+              </math>
+            </spatial:analyticVolume>
+          </spatial:listOfAnalyticVolumes>
+        </spatial:analyticGeometry>
+      </spatial:listOfGeometryDefinitions>
+    </spatial:geometry>
+  </model>
+</sbml>
diff --git a/examples/v0.84/turing_parameters-stripe.xml b/examples/v0.84/turing_parameters-stripe.xml
new file mode 100644
index 0000000..7b89f8f
--- /dev/null
+++ b/examples/v0.84/turing_parameters-stripe.xml
@@ -0,0 +1,354 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
+  <model metaid="COPASI1" id="New_Model_Application0" name="New Model_Application0">
+      <annotation>
+      <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+        <update step="0.05" freq="50"/>
+        <items>
+          <item sbmlId="species_1" palette="black-blue.txt" max="2"/>
+          <item sbmlId="species_2" palette="black-green.txt" max="2"/>
+        </items>
+      </spatialInfo>
+    </annotation>
+    <listOfUnitDefinitions>
+      <unitDefinition id="substance">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="volume">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="area">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="molecules">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="umol_um3_litre_1">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um3">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um2">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_um3_molecules_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_zero__001_m3_mol_1_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one__0E_6">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one_000000_0">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000000"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one_000_0_m_3_mol_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="M">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="compartment_1" name="compartment_1" spatialDimensions="3" size="1" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain0compartment_1" spatial:compartment="compartment_1" spatial:domainType="subdomain0" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="c2" name="c2" spatialDimensions="3" size="1" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain1c2" spatial:compartment="c2" spatial:domainType="subdomain1" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="Membrane2" name="Membrane2" spatialDimensions="2" size="1" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain0_subdomain1_membraneMembrane2" spatial:compartment="Membrane2" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="species_1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
+      <species id="species_2" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="x" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="y" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="species_1_diff" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="species_1_diff_Y" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="species_1_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_1_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_1_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_1_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_diff" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="species_2_diff_y" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="species_2_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="v1" value="0.06" constant="true"/>
+      <parameter id="v2" value="0.12" constant="true"/>
+      <parameter id="V" value="0.5" constant="true"/>
+      <parameter id="Km" value="0.1" constant="true"/>
+      <parameter id="k1" value="1" constant="true"/>
+    </listOfParameters>
+    <listOfInitialAssignments>
+      <initialAssignment symbol="species_1">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <piecewise>
+            <piece>
+              <cn> 20 </cn>
+              <apply>
+                <and/>
+                <apply>
+                  <and/>
+                  <apply>
+                    <gt/>
+                    <ci> x </ci>
+                    <cn> 15 </cn>
+                  </apply>
+                  <apply>
+                    <lt/>
+                    <ci> x </ci>
+                    <cn> 25 </cn>
+                  </apply>
+                </apply>
+                <apply>
+                  <and/>
+                  <apply>
+                    <gt/>
+                    <ci> y </ci>
+                    <cn> 65 </cn>
+                  </apply>
+                  <apply>
+                    <lt/>
+                    <ci> y </ci>
+                    <cn> 85 </cn>
+                  </apply>
+                </apply>
+              </apply>
+            </piece>
+            <otherwise>
+              <cn> 2 </cn>
+            </otherwise>
+          </piecewise>
+        </math>
+      </initialAssignment>
+      <initialAssignment symbol="species_2">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <cn> 0.08 </cn>
+        </math>
+      </initialAssignment>
+    </listOfInitialAssignments>
+    <listOfReactions>
+      <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfReactants>
+          <speciesReference species="species_1" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> k1 </ci>
+              <ci> species_1 </ci>
+              <ci> species_2 </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfProducts>
+          <speciesReference species="species_1" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <ci> v2 </ci>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfProducts>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <ci> v1 </ci>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfReactants>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> V </ci>
+              <ci> species_2 </ci>
+              <apply>
+                <divide/>
+                <cn> 1 </cn>
+                <apply>
+                  <plus/>
+                  <ci> Km </ci>
+                  <ci> species_2 </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+    <spatial:geometry spatial:coordinateSystem="Cartesian">
+      <spatial:listOfCoordinateComponents>
+        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
+          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="100"/>
+        </spatial:coordinateComponent>
+        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
+          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="100"/>
+        </spatial:coordinateComponent>
+      </spatial:listOfCoordinateComponents>
+      <spatial:listOfDomainTypes>
+        <spatial:domainType spatial:spatialId="subdomain1" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain0" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
+      </spatial:listOfDomainTypes>
+      <spatial:listOfDomains>
+        <spatial:domain spatial:spatialId="subdomain10" spatial:domainType="subdomain1">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="subdomain01" spatial:domainType="subdomain0">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="1" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="membrane_subdomain10_subdomain01" spatial:domainType="subdomain0_subdomain1_membrane"/>
+      </spatial:listOfDomains>
+      <spatial:listOfAdjacentDomains>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain01" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain01"/>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain10" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain10"/>
+      </spatial:listOfAdjacentDomains>
+      <spatial:listOfGeometryDefinitions>
+        <spatial:analyticGeometry spatial:spatialId="Geometry4">
+          <spatial:listOfAnalyticVolumes>
+            <spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="1">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <piecewise>
+                  <piece>
+                    <cn type="integer"> 1 </cn>
+                    <apply>
+                      <and/>
+                      <apply>
+                        <geq/>
+                        <ci> x </ci>
+                        <cn type="integer"> 1 </cn>
+                      </apply>
+                      <apply>
+                        <leq/>
+                        <ci> x </ci>
+                        <cn type="integer"> 99 </cn>
+                      </apply>
+                      <apply>
+                        <geq/>
+                        <ci> y </ci>
+                        <cn type="integer"> 1 </cn>
+                      </apply>
+                      <apply>
+                        <leq/>
+                        <ci> y </ci>
+                        <cn type="integer"> 99 </cn>
+                      </apply>
+                    </apply>
+                  </piece>
+                  <otherwise>
+                    <cn type="integer"> 0 </cn>
+                  </otherwise>
+                </piecewise>
+              </math>
+            </spatial:analyticVolume>
+            <spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="0">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <cn type="integer"> 1 </cn>
+              </math>
+            </spatial:analyticVolume>
+          </spatial:listOfAnalyticVolumes>
+        </spatial:analyticGeometry>
+      </spatial:listOfGeometryDefinitions>
+    </spatial:geometry>
+  </model>
+</sbml>
diff --git a/examples/v0.84/turing_parameters.xml b/examples/v0.84/turing_parameters.xml
new file mode 100644
index 0000000..b2600ea
--- /dev/null
+++ b/examples/v0.84/turing_parameters.xml
@@ -0,0 +1,354 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
+  <model metaid="COPASI1" id="New_Model_Application0" name="New Model_Application0">
+      <annotation>
+      <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+        <update step="0.07" freq="50"/>
+        <items>
+          <item sbmlId="species_1" palette="black-blue.txt" max="2"/>
+          <item sbmlId="species_2" palette="black-green.txt" max="2"/>
+        </items>
+      </spatialInfo>
+    </annotation>
+    <listOfUnitDefinitions>
+      <unitDefinition id="substance">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="volume">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="area">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="molecules">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="umol_um3_litre_1">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um3">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um2">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_um3_molecules_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_zero__001_m3_mol_1_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one__0E_6">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one_000000_0">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000000"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one_000_0_m_3_mol_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="M">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="compartment_1" name="compartment_1" spatialDimensions="3" size="1" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain0compartment_1" spatial:compartment="compartment_1" spatial:domainType="subdomain0" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="c2" name="c2" spatialDimensions="3" size="1" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain1c2" spatial:compartment="c2" spatial:domainType="subdomain1" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="Membrane2" name="Membrane2" spatialDimensions="2" size="1" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain0_subdomain1_membraneMembrane2" spatial:compartment="Membrane2" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="species_1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
+      <species id="species_2" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="x" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="y" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="species_1_diff" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="species_1_diff_Y" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="species_1_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_1_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_1_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_1_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_diff" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="species_2_diff_y" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="species_2_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="v1" value="0.06" constant="true"/>
+      <parameter id="v2" value="0.12" constant="true"/>
+      <parameter id="V" value="0.5" constant="true"/>
+      <parameter id="Km" value="0.1" constant="true"/>
+      <parameter id="k1" value="1" constant="true"/>
+    </listOfParameters>
+    <listOfInitialAssignments>
+      <initialAssignment symbol="species_1">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <piecewise>
+            <piece>
+              <cn> 20 </cn>
+              <apply>
+                <and/>
+                <apply>
+                  <and/>
+                  <apply>
+                    <gt/>
+                    <ci> x </ci>
+                    <cn> 20 </cn>
+                  </apply>
+                  <apply>
+                    <lt/>
+                    <ci> x </ci>
+                    <cn> 25 </cn>
+                  </apply>
+                </apply>
+                <apply>
+                  <and/>
+                  <apply>
+                    <gt/>
+                    <ci> y </ci>
+                    <cn> 70 </cn>
+                  </apply>
+                  <apply>
+                    <lt/>
+                    <ci> y </ci>
+                    <cn> 85 </cn>
+                  </apply>
+                </apply>
+              </apply>
+            </piece>
+            <otherwise>
+              <cn> 0.5 </cn>
+            </otherwise>
+          </piecewise>
+        </math>
+      </initialAssignment>
+      <initialAssignment symbol="species_2">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <cn> 0.1 </cn>
+        </math>
+      </initialAssignment>
+    </listOfInitialAssignments>
+    <listOfReactions>
+      <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfReactants>
+          <speciesReference species="species_1" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> k1 </ci>
+              <ci> species_1 </ci>
+              <ci> species_2 </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfProducts>
+          <speciesReference species="species_1" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <ci> v2 </ci>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfProducts>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <ci> v1 </ci>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfReactants>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> V </ci>
+              <ci> species_2 </ci>
+              <apply>
+                <divide/>
+                <cn> 1 </cn>
+                <apply>
+                  <plus/>
+                  <ci> Km </ci>
+                  <ci> species_2 </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+    <spatial:geometry spatial:coordinateSystem="Cartesian">
+      <spatial:listOfCoordinateComponents>
+        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
+          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="100"/>
+        </spatial:coordinateComponent>
+        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
+          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="100"/>
+        </spatial:coordinateComponent>
+      </spatial:listOfCoordinateComponents>
+      <spatial:listOfDomainTypes>
+        <spatial:domainType spatial:spatialId="subdomain1" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain0" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
+      </spatial:listOfDomainTypes>
+      <spatial:listOfDomains>
+        <spatial:domain spatial:spatialId="subdomain10" spatial:domainType="subdomain1">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="subdomain01" spatial:domainType="subdomain0">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="1" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="membrane_subdomain10_subdomain01" spatial:domainType="subdomain0_subdomain1_membrane"/>
+      </spatial:listOfDomains>
+      <spatial:listOfAdjacentDomains>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain01" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain01"/>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain10" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain10"/>
+      </spatial:listOfAdjacentDomains>
+      <spatial:listOfGeometryDefinitions>
+        <spatial:analyticGeometry spatial:spatialId="Geometry4">
+          <spatial:listOfAnalyticVolumes>
+            <spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="1">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <piecewise>
+                  <piece>
+                    <cn type="integer"> 1 </cn>
+                    <apply>
+                      <and/>
+                      <apply>
+                        <geq/>
+                        <ci> x </ci>
+                        <cn type="integer"> 1 </cn>
+                      </apply>
+                      <apply>
+                        <leq/>
+                        <ci> x </ci>
+                        <cn type="integer"> 99 </cn>
+                      </apply>
+                      <apply>
+                        <geq/>
+                        <ci> y </ci>
+                        <cn type="integer"> 1 </cn>
+                      </apply>
+                      <apply>
+                        <leq/>
+                        <ci> y </ci>
+                        <cn type="integer"> 99 </cn>
+                      </apply>
+                    </apply>
+                  </piece>
+                  <otherwise>
+                    <cn type="integer"> 0 </cn>
+                  </otherwise>
+                </piecewise>
+              </math>
+            </spatial:analyticVolume>
+            <spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="0">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <cn type="integer"> 1 </cn>
+              </math>
+            </spatial:analyticVolume>
+          </spatial:listOfAnalyticVolumes>
+        </spatial:analyticGeometry>
+      </spatial:listOfGeometryDefinitions>
+    </spatial:geometry>
+  </model>
+</sbml>
diff --git a/examples/v0.84/turing_parameters_50x50.xml b/examples/v0.84/turing_parameters_50x50.xml
new file mode 100644
index 0000000..612028c
--- /dev/null
+++ b/examples/v0.84/turing_parameters_50x50.xml
@@ -0,0 +1,354 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
+  <model metaid="COPASI1" id="New_Model_Application0" name="New Model_Application0">
+      <annotation>
+      <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+        <update step="0.07" freq="50"/>
+        <items>
+          <item sbmlId="species_1" palette="black-blue.txt" max="2"/>
+          <item sbmlId="species_2" palette="black-green.txt" max="2"/>
+        </items>
+      </spatialInfo>
+    </annotation>
+    <listOfUnitDefinitions>
+      <unitDefinition id="substance">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="volume">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="area">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="molecules">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="umol_um3_litre_1">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um3">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um2">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_um3_molecules_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_zero__001_m3_mol_1_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one__0E_6">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one_000000_0">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000000"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one_000_0_m_3_mol_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="M">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="compartment_1" name="compartment_1" spatialDimensions="3" size="1" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain0compartment_1" spatial:compartment="compartment_1" spatial:domainType="subdomain0" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="c2" name="c2" spatialDimensions="3" size="1" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain1c2" spatial:compartment="c2" spatial:domainType="subdomain1" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="Membrane2" name="Membrane2" spatialDimensions="2" size="1" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain0_subdomain1_membraneMembrane2" spatial:compartment="Membrane2" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="species_1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
+      <species id="species_2" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="x" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="y" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="species_1_diff" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="species_1_diff_Y" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="species_1_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_1_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_1_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_1_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_diff" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="species_2_diff_y" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="species_2_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="v1" value="0.06" constant="true"/>
+      <parameter id="v2" value="0.12" constant="true"/>
+      <parameter id="V" value="0.5" constant="true"/>
+      <parameter id="Km" value="0.1" constant="true"/>
+      <parameter id="k1" value="1" constant="true"/>
+    </listOfParameters>
+    <listOfInitialAssignments>
+      <initialAssignment symbol="species_1">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <piecewise>
+            <piece>
+              <cn> 20 </cn>
+              <apply>
+                <and/>
+                <apply>
+                  <and/>
+                  <apply>
+                    <gt/>
+                    <ci> x </ci>
+                    <cn> 20 </cn>
+                  </apply>
+                  <apply>
+                    <lt/>
+                    <ci> x </ci>
+                    <cn> 25 </cn>
+                  </apply>
+                </apply>
+                <apply>
+                  <and/>
+                  <apply>
+                    <gt/>
+                    <ci> y </ci>
+                    <cn> 20 </cn>
+                  </apply>
+                  <apply>
+                    <lt/>
+                    <ci> y </ci>
+                    <cn> 25 </cn>
+                  </apply>
+                </apply>
+              </apply>
+            </piece>
+            <otherwise>
+              <cn> 0.5 </cn>
+            </otherwise>
+          </piecewise>
+        </math>
+      </initialAssignment>
+      <initialAssignment symbol="species_2">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <cn> 0.1 </cn>
+        </math>
+      </initialAssignment>
+    </listOfInitialAssignments>
+    <listOfReactions>
+      <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfReactants>
+          <speciesReference species="species_1" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> k1 </ci>
+              <ci> species_1 </ci>
+              <ci> species_2 </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfProducts>
+          <speciesReference species="species_1" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <ci> v2 </ci>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfProducts>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <ci> v1 </ci>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfReactants>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> V </ci>
+              <ci> species_2 </ci>
+              <apply>
+                <divide/>
+                <cn> 1 </cn>
+                <apply>
+                  <plus/>
+                  <ci> Km </ci>
+                  <ci> species_2 </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+    <spatial:geometry spatial:coordinateSystem="Cartesian">
+      <spatial:listOfCoordinateComponents>
+        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
+          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="50"/>
+        </spatial:coordinateComponent>
+        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
+          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="50"/>
+        </spatial:coordinateComponent>
+      </spatial:listOfCoordinateComponents>
+      <spatial:listOfDomainTypes>
+        <spatial:domainType spatial:spatialId="subdomain1" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain0" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
+      </spatial:listOfDomainTypes>
+      <spatial:listOfDomains>
+        <spatial:domain spatial:spatialId="subdomain10" spatial:domainType="subdomain1">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="subdomain01" spatial:domainType="subdomain0">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="1" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="membrane_subdomain10_subdomain01" spatial:domainType="subdomain0_subdomain1_membrane"/>
+      </spatial:listOfDomains>
+      <spatial:listOfAdjacentDomains>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain01" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain01"/>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain10" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain10"/>
+      </spatial:listOfAdjacentDomains>
+      <spatial:listOfGeometryDefinitions>
+        <spatial:analyticGeometry spatial:spatialId="Geometry4">
+          <spatial:listOfAnalyticVolumes>
+            <spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="1">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <piecewise>
+                  <piece>
+                    <cn type="integer"> 1 </cn>
+                    <apply>
+                      <and/>
+                      <apply>
+                        <geq/>
+                        <ci> x </ci>
+                        <cn type="integer"> 1 </cn>
+                      </apply>
+                      <apply>
+                        <leq/>
+                        <ci> x </ci>
+                        <cn type="integer"> 49 </cn>
+                      </apply>
+                      <apply>
+                        <geq/>
+                        <ci> y </ci>
+                        <cn type="integer"> 1 </cn>
+                      </apply>
+                      <apply>
+                        <leq/>
+                        <ci> y </ci>
+                        <cn type="integer"> 49 </cn>
+                      </apply>
+                    </apply>
+                  </piece>
+                  <otherwise>
+                    <cn type="integer"> 0 </cn>
+                  </otherwise>
+                </piecewise>
+              </math>
+            </spatial:analyticVolume>
+            <spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="0">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <cn type="integer"> 1 </cn>
+              </math>
+            </spatial:analyticVolume>
+          </spatial:listOfAnalyticVolumes>
+        </spatial:analyticGeometry>
+      </spatial:listOfGeometryDefinitions>
+    </spatial:geometry>
+  </model>
+</sbml>
diff --git a/examples/v0.84/turing_parameters_tiny.xml b/examples/v0.84/turing_parameters_tiny.xml
new file mode 100644
index 0000000..0ddcc46
--- /dev/null
+++ b/examples/v0.84/turing_parameters_tiny.xml
@@ -0,0 +1,354 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
+  <model metaid="COPASI1" id="New_Model_Application0" name="New Model_Application0">
+      <annotation>
+      <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+        <update step="0.07" freq="30"/>
+        <items>
+          <item sbmlId="species_1" palette="black-blue.txt" max="2"/>
+          <item sbmlId="species_2" palette="black-green.txt" max="2"/>
+        </items>
+      </spatialInfo>
+    </annotation>
+    <listOfUnitDefinitions>
+      <unitDefinition id="substance">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="volume">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="area">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="molecules">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="umol_um3_litre_1">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um3">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um2">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_um3_molecules_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_zero__001_m3_mol_1_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one__0E_6">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one_000000_0">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000000"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one_000_0_m_3_mol_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="M">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="compartment_1" name="compartment_1" spatialDimensions="3" size="1" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain0compartment_1" spatial:compartment="compartment_1" spatial:domainType="subdomain0" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="c2" name="c2" spatialDimensions="3" size="1" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain1c2" spatial:compartment="c2" spatial:domainType="subdomain1" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="Membrane2" name="Membrane2" spatialDimensions="2" size="1" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain0_subdomain1_membraneMembrane2" spatial:compartment="Membrane2" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="species_1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
+      <species id="species_2" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="x" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="y" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="species_1_diff" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="species_1_diff_Y" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="species_1_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_1_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_1_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_1_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_diff" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="species_2_diff_y" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="species_2_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="v1" value="0.06" constant="true"/>
+      <parameter id="v2" value="0.12" constant="true"/>
+      <parameter id="V" value="0.5" constant="true"/>
+      <parameter id="Km" value="0.1" constant="true"/>
+      <parameter id="k1" value="1" constant="true"/>
+    </listOfParameters>
+    <listOfInitialAssignments>
+      <initialAssignment symbol="species_1">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <piecewise>
+            <piece>
+              <cn> 20 </cn>
+              <apply>
+                <and/>
+                <apply>
+                  <and/>
+                  <apply>
+                    <gt/>
+                    <ci> x </ci>
+                    <cn> 20 </cn>
+                  </apply>
+                  <apply>
+                    <lt/>
+                    <ci> x </ci>
+                    <cn> 25 </cn>
+                  </apply>
+                </apply>
+                <apply>
+                  <and/>
+                  <apply>
+                    <gt/>
+                    <ci> y </ci>
+                    <cn> 70 </cn>
+                  </apply>
+                  <apply>
+                    <lt/>
+                    <ci> y </ci>
+                    <cn> 85 </cn>
+                  </apply>
+                </apply>
+              </apply>
+            </piece>
+            <otherwise>
+              <cn> 0.5 </cn>
+            </otherwise>
+          </piecewise>
+        </math>
+      </initialAssignment>
+      <initialAssignment symbol="species_2">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <cn> 0.1 </cn>
+        </math>
+      </initialAssignment>
+    </listOfInitialAssignments>
+    <listOfReactions>
+      <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfReactants>
+          <speciesReference species="species_1" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> k1 </ci>
+              <ci> species_1 </ci>
+              <ci> species_2 </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfProducts>
+          <speciesReference species="species_1" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <ci> v2 </ci>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfProducts>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <ci> v1 </ci>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfReactants>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> V </ci>
+              <ci> species_2 </ci>
+              <apply>
+                <divide/>
+                <cn> 1 </cn>
+                <apply>
+                  <plus/>
+                  <ci> Km </ci>
+                  <ci> species_2 </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+    <spatial:geometry spatial:coordinateSystem="Cartesian">
+      <spatial:listOfCoordinateComponents>
+        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
+          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="21"/>
+        </spatial:coordinateComponent>
+        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
+          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="21"/>
+        </spatial:coordinateComponent>
+      </spatial:listOfCoordinateComponents>
+      <spatial:listOfDomainTypes>
+        <spatial:domainType spatial:spatialId="subdomain1" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain0" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
+      </spatial:listOfDomainTypes>
+      <spatial:listOfDomains>
+        <spatial:domain spatial:spatialId="subdomain10" spatial:domainType="subdomain1">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="subdomain01" spatial:domainType="subdomain0">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="1" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="membrane_subdomain10_subdomain01" spatial:domainType="subdomain0_subdomain1_membrane"/>
+      </spatial:listOfDomains>
+      <spatial:listOfAdjacentDomains>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain01" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain01"/>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain10" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain10"/>
+      </spatial:listOfAdjacentDomains>
+      <spatial:listOfGeometryDefinitions>
+        <spatial:analyticGeometry spatial:spatialId="Geometry4">
+          <spatial:listOfAnalyticVolumes>
+            <spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="1">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <piecewise>
+                  <piece>
+                    <cn type="integer"> 1 </cn>
+                    <apply>
+                      <and/>
+                      <apply>
+                        <geq/>
+                        <ci> x </ci>
+                        <cn type="integer"> 1 </cn>
+                      </apply>
+                      <apply>
+                        <leq/>
+                        <ci> x </ci>
+                        <cn type="integer"> 20 </cn>
+                      </apply>
+                      <apply>
+                        <geq/>
+                        <ci> y </ci>
+                        <cn type="integer"> 1 </cn>
+                      </apply>
+                      <apply>
+                        <leq/>
+                        <ci> y </ci>
+                        <cn type="integer"> 20 </cn>
+                      </apply>
+                    </apply>
+                  </piece>
+                  <otherwise>
+                    <cn type="integer"> 0 </cn>
+                  </otherwise>
+                </piecewise>
+              </math>
+            </spatial:analyticVolume>
+            <spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="0">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <cn type="integer"> 1 </cn>
+              </math>
+            </spatial:analyticVolume>
+          </spatial:listOfAnalyticVolumes>
+        </spatial:analyticGeometry>
+      </spatial:listOfGeometryDefinitions>
+    </spatial:geometry>
+  </model>
+</sbml>
diff --git a/examples/v0.84/turing_uniform.xml b/examples/v0.84/turing_uniform.xml
new file mode 100644
index 0000000..fa8ae90
--- /dev/null
+++ b/examples/v0.84/turing_uniform.xml
@@ -0,0 +1,318 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/requiredElements/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="false" spatial:required="true">
+  <model metaid="COPASI1" id="New_Model_Application0" name="New Model_Application0">
+      <annotation>
+      <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+        <update step="0.07" freq="50"/>
+        <items>
+          <item sbmlId="species_1" palette="black-blue.txt" max="2"/>
+          <item sbmlId="species_2" palette="black-green.txt" max="2"/>
+        </items>
+      </spatialInfo>
+    </annotation>
+    <listOfUnitDefinitions>
+      <unitDefinition id="substance">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="volume">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="area">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="molecules">
+        <listOfUnits>
+          <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="umol_um3_litre_1">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1e-021"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um3">
+        <listOfUnits>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="um2">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_um3_molecules_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-021"/>
+          <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="uM_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_zero__001_m3_mol_1_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="0.001"/>
+          <unit kind="metre" exponent="3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one__0E_6">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-006"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one_000000_0">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000000"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="_one_000_0_m_3_mol_s_1">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="M">
+        <listOfUnits>
+          <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000"/>
+          <unit kind="metre" exponent="-3" scale="0" multiplier="1"/>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="compartment_1" name="compartment_1" spatialDimensions="3" size="1" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain0compartment_1" spatial:compartment="compartment_1" spatial:domainType="subdomain0" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="c2" name="c2" spatialDimensions="3" size="1" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain1c2" spatial:compartment="c2" spatial:domainType="subdomain1" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="Membrane2" name="Membrane2" spatialDimensions="2" size="1" constant="true">
+        <spatial:compartmentMapping spatial:spatialId="subdomain0_subdomain1_membraneMembrane2" spatial:compartment="Membrane2" spatial:domainType="subdomain0_subdomain1_membrane" spatial:unitSize="1"/>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="species_1" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
+      <species id="species_2" compartment="compartment_1" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isSpatial="true"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="x" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="x" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="y" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="false">
+        <spatial:spatialSymbolReference spatial:spatialId="y" spatial:type="coordinateComponent"/>
+      </parameter>
+      <parameter id="species_1_diff" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="species_1_diff_Y" value="4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_1" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="species_1_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_1_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_1_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_1_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_1" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_diff" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="0"/>
+      </parameter>
+      <parameter id="species_2_diff_y" value="0.4" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:diffusionCoefficient spatial:variable="species_2" spatial:coordinateIndex="1"/>
+      </parameter>
+      <parameter id="species_2_BC_Xm" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_BC_Xp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Xmax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_BC_Ym" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymin" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="species_2_BC_Yp" value="0" constant="true" req:mathOverridden="spatial" req:coreHasAlternateMath="true">
+        <spatial:boundaryCondition spatial:variable="species_2" spatial:coordinateBoundary="Ymax" spatial:type="Flux"/>
+      </parameter>
+      <parameter id="v1" value="0.06" constant="true"/>
+      <parameter id="v2" value="0.12" constant="true"/>
+      <parameter id="V" value="0.5" constant="true"/>
+      <parameter id="Km" value="0.1" constant="true"/>
+      <parameter id="k1" value="1" constant="true"/>
+    </listOfParameters>
+    <listOfInitialAssignments>
+      <initialAssignment symbol="species_1">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <cn> 2 </cn>
+        </math>
+      </initialAssignment>
+      <initialAssignment symbol="species_2">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <cn> 0.1 </cn>
+        </math>
+      </initialAssignment>
+    </listOfInitialAssignments>
+    <listOfReactions>
+      <reaction metaid="COPASI2" id="reaction_1" name="reaction_1" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfReactants>
+          <speciesReference species="species_1" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <cn> 1 </cn>
+              <ci> species_1 </ci>
+              <ci> species_2 </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI3" id="reaction_2" name="reaction_2" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfProducts>
+          <speciesReference species="species_1" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <cn> 0.12 </cn>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI4" id="reaction_3" name="reaction_3" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfProducts>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <cn> 0.06 </cn>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction metaid="COPASI5" id="reaction_4" name="reaction_4" reversible="false" fast="false" req:mathOverridden="spatial" req:coreHasAlternateMath="true" spatial:isLocal="true">
+        <listOfReactants>
+          <speciesReference species="species_2" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <cn> 0.5 </cn>
+              <ci> species_2 </ci>
+              <apply>
+                <divide/>
+                <cn> 1 </cn>
+                <apply>
+                  <plus/>
+                  <cn> 0.1 </cn>
+                  <ci> species_2 </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+    <spatial:geometry spatial:coordinateSystem="Cartesian">
+      <spatial:listOfCoordinateComponents>
+        <spatial:coordinateComponent spatial:spatialId="x" spatial:componentType="cartesianX" spatial:sbmlUnit="um" spatial:index="0">
+          <spatial:boundaryMin spatial:spatialId="Xmin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Xmax" spatial:value="100"/>
+        </spatial:coordinateComponent>
+        <spatial:coordinateComponent spatial:spatialId="y" spatial:componentType="cartesianY" spatial:sbmlUnit="um" spatial:index="1">
+          <spatial:boundaryMin spatial:spatialId="Ymin" spatial:value="0"/>
+          <spatial:boundaryMax spatial:spatialId="Ymax" spatial:value="100"/>
+        </spatial:coordinateComponent>
+      </spatial:listOfCoordinateComponents>
+      <spatial:listOfDomainTypes>
+        <spatial:domainType spatial:spatialId="subdomain1" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain0" spatial:spatialDimensions="3"/>
+        <spatial:domainType spatial:spatialId="subdomain0_subdomain1_membrane" spatial:spatialDimensions="2"/>
+      </spatial:listOfDomainTypes>
+      <spatial:listOfDomains>
+        <spatial:domain spatial:spatialId="subdomain10" spatial:domainType="subdomain1">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="subdomain01" spatial:domainType="subdomain0">
+          <spatial:listOfInteriorPoints>
+            <spatial:interiorPoint spatial:coord1="1" spatial:coord2="0" spatial:coord3="5"/>
+          </spatial:listOfInteriorPoints>
+        </spatial:domain>
+        <spatial:domain spatial:spatialId="membrane_subdomain10_subdomain01" spatial:domainType="subdomain0_subdomain1_membrane"/>
+      </spatial:listOfDomains>
+      <spatial:listOfAdjacentDomains>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain01" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain01"/>
+        <spatial:adjacentDomains spatial:spatialId="membrane_subdomain10_subdomain01_subdomain10" spatial:domain1="membrane_subdomain10_subdomain01" spatial:domain2="subdomain10"/>
+      </spatial:listOfAdjacentDomains>
+      <spatial:listOfGeometryDefinitions>
+        <spatial:analyticGeometry spatial:spatialId="Geometry4">
+          <spatial:listOfAnalyticVolumes>
+            <spatial:analyticVolume spatial:spatialId="subdomain0" spatial:domainType="subdomain0" spatial:functionType="layered" spatial:ordinal="1">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <piecewise>
+                  <piece>
+                    <cn type="integer"> 1 </cn>
+                    <apply>
+                      <and/>
+                      <apply>
+                        <geq/>
+                        <ci> x </ci>
+                        <cn type="integer"> 1 </cn>
+                      </apply>
+                      <apply>
+                        <leq/>
+                        <ci> x </ci>
+                        <cn type="integer"> 99 </cn>
+                      </apply>
+                      <apply>
+                        <geq/>
+                        <ci> y </ci>
+                        <cn type="integer"> 1 </cn>
+                      </apply>
+                      <apply>
+                        <leq/>
+                        <ci> y </ci>
+                        <cn type="integer"> 99 </cn>
+                      </apply>
+                    </apply>
+                  </piece>
+                  <otherwise>
+                    <cn type="integer"> 0 </cn>
+                  </otherwise>
+                </piecewise>
+              </math>
+            </spatial:analyticVolume>
+            <spatial:analyticVolume spatial:spatialId="subdomain1" spatial:domainType="subdomain1" spatial:functionType="layered" spatial:ordinal="0">
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
+                <cn type="integer"> 1 </cn>
+              </math>
+            </spatial:analyticVolume>
+          </spatial:listOfAnalyticVolumes>
+        </spatial:analyticGeometry>
+      </spatial:listOfGeometryDefinitions>
+    </spatial:geometry>
+  </model>
+</sbml>