- added sensible defaults to example models

fbergmann · Jun 24, 2014 · 5f32c8d · 5f32c8d
1 parent fc4e8ac
commit 5f32c8d
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Showing 16 changed files with 130 additions and 5 deletions.
diff --git a/.gitignore b/.gitignore
@@ -163,3 +163,4 @@ pip-log.txt
 
 # Mac crap
 .DS_Store
+/examples/private
diff --git a/SpatialUI/spatialmainwidget.cpp b/SpatialUI/spatialmainwidget.cpp
@@ -9,7 +9,6 @@
 
 #include <SpatialSBML/datahelper.hh>
 
-
 #include <QApplication>
 #include <QtGui>
 #include <QObject>
@@ -24,7 +23,6 @@
 #include <QStatusBar>
 
 
-
 #include <sbml/SBMLTypes.h>
 #include <sbml/packages/spatial/extension/SpatialSpeciesRxnPlugin.h>
 #include <sbml/packages/spatial/extension/SpatialModelPlugin.h>
@@ -37,6 +35,7 @@
 #include <stdlib.h>
 #endif // USE_SBW_INTEGRATION
 
+#define SPATIAL_ANNOTATION_URL "http://fbergmann.github.io/spatial-sbml/settings"
 
 
 using namespace std;
@@ -653,8 +652,6 @@ XMLNode* getAnnotationNode(Model* model, const std::string& ns)
   return NULL;
 }
 
-#define SPATIAL_ANNOTATION_URL "http://spatial-sbml/settings"
-
 void SpatialMainWindow::initializeDisplay(Model* model)
 {
 

diff --git a/examples/The_Brusselator.xml b/examples/The_Brusselator.xml
@@ -1,6 +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">
   <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" name="black-blue.txt" max="6"/>
+          <item sbmlId="Y" name="black-green.txt" max="6"/>
+        </items>
+      </spatialInfo>
+	</annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
         <listOfUnits>

diff --git a/examples/The_Brusselator_300x300.xml b/examples/The_Brusselator_300x300.xml
@@ -1,7 +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">
   <model id="The_Brusselator_Application0" name="The Brusselator_Application0">
-    <listOfUnitDefinitions>
+	<annotation>
+        <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
+        <update step="0.1" freq="500"/>
+        <items>
+          <item sbmlId="X" name="black-blue.txt" max="6"/>
+          <item sbmlId="Y" name="black-green.txt" max="6"/>
+        </items>
+      </spatialInfo>
+	</annotation>
+	<listOfUnitDefinitions>
       <unitDefinition id="substance">
         <listOfUnits>
           <unit kind="item" exponent="1" scale="0" multiplier="1"/>

diff --git a/examples/advection.xml b/examples/advection.xml
@@ -2,6 +2,14 @@
 <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" name="black-blue.txt" max="6"/>
+          <item sbmlId="C_cytosol" name="black-green.txt" max="1000"/>
+          <item sbmlId="A_cytosol" name="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"/>

diff --git a/examples/fish.xml b/examples/fish.xml
@@ -1,6 +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">
   <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" name="black-blue.txt" max="6"/>
+          <item sbmlId="v" name="black-green.txt" max="6"/>
+          <item sbmlId="w" name="black-red.txt" max="6"/>
+        </items>
+      </spatialInfo>
+	</annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
         <listOfUnits>

diff --git a/examples/fish_300x300.xml b/examples/fish_300x300.xml
@@ -1,6 +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">
   <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" name="black-blue.txt" max="6"/>
+          <item sbmlId="v" name="black-green.txt" max="6"/>
+          <item sbmlId="w" name="black-red.txt" max="6"/>
+        </items>
+      </spatialInfo>
+	</annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
         <listOfUnits>

diff --git a/examples/fish_big.xml b/examples/fish_big.xml
@@ -1,6 +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">
   <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" name="black-blue.txt" max="6"/>
+          <item sbmlId="v" name="black-green.txt" max="6"/>
+          <item sbmlId="w" name="black-red.txt" max="6"/>
+        </items>
+      </spatialInfo>
+	</annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
         <listOfUnits>

diff --git a/examples/transport.xml b/examples/transport.xml
@@ -2,6 +2,14 @@
 <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" name="black-blue.txt" max="6"/>
+          <item sbmlId="s0" name="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"/>

diff --git a/examples/turing.xml b/examples/turing.xml
@@ -1,6 +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="true" 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" name="black-blue.txt" max="2"/>
+          <item sbmlId="species_2" name="black-green.txt" max="2"/>
+        </items>
+      </spatialInfo>
+    </annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
         <listOfUnits>

diff --git a/examples/turing_300x300.xml b/examples/turing_300x300.xml
@@ -1,6 +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="true" 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" name="black-blue.txt" max="2"/>
+          <item sbmlId="species_2" name="black-green.txt" max="2"/>
+        </items>
+      </spatialInfo>
+    </annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
         <listOfUnits>

diff --git a/examples/turing_parameters-stripe.xml b/examples/turing_parameters-stripe.xml
@@ -1,6 +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="true" 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" name="black-blue.txt" max="2"/>
+          <item sbmlId="species_2" name="black-green.txt" max="2"/>
+        </items>
+      </spatialInfo>
+    </annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
         <listOfUnits>

diff --git a/examples/turing_parameters.xml b/examples/turing_parameters.xml
@@ -1,6 +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="true" 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" name="black-blue.txt" max="2"/>
+          <item sbmlId="species_2" name="black-green.txt" max="2"/>
+        </items>
+      </spatialInfo>
+    </annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
         <listOfUnits>

diff --git a/examples/turing_parameters_50x50.xml b/examples/turing_parameters_50x50.xml
@@ -1,6 +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="true" 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" name="black-blue.txt" max="2"/>
+          <item sbmlId="species_2" name="black-green.txt" max="2"/>
+        </items>
+      </spatialInfo>
+    </annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
         <listOfUnits>

diff --git a/examples/turing_parameters_tiny.xml b/examples/turing_parameters_tiny.xml
@@ -1,6 +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="true" 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" name="black-blue.txt" max="2"/>
+          <item sbmlId="species_2" name="black-green.txt" max="2"/>
+        </items>
+      </spatialInfo>
+    </annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
         <listOfUnits>

diff --git a/examples/turing_uniform.xml b/examples/turing_uniform.xml
@@ -1,6 +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="true" 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" name="black-blue.txt" max="2"/>
+          <item sbmlId="species_2" name="black-green.txt" max="2"/>
+        </items>
+      </spatialInfo>
+    </annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="substance">
         <listOfUnits>
Original file line number	Diff line number	Diff line change
Expand Up		@@ -163,3 +163,4 @@ pip-log.txt

		# Mac crap
		.DS_Store
		/examples/private