Merge pull request #1310 from virtualcell/FixingImageSuffixBug

Fixing image suffix bug

vcell-client/UserDocumentation/originalXML/topics/ch_1/Introduction/ChangeUser.xml

@@ -6,7 +6,7 @@
 	</introduction>
 
 	<appearance>
-		<imgReference target = "LoginDialog.PNG"/>
+		<imgReference target = "LoginDialog.png"/>
 	</appearance>
 
 	<comments>  </comments>

vcell-client/UserDocumentation/originalXML/topics/ch_1/Introduction/Export.xml

@@ -29,7 +29,7 @@
 	</introduction>
 
 	<appearance>
-		<imgReference target = "FileExport.PNG"/>
+		<imgReference target = "FileExport.png"/>
 	</appearance>
 
 	<operations>

vcell-client/UserDocumentation/originalXML/topics/ch_1/Introduction/File.xml

@@ -7,7 +7,7 @@
 	</introduction>
 
 	<appearance>
-		<imgReference target = "FileMenu.PNG"/>
+		<imgReference target = "FileMenu.png"/>
 	</appearance>
 
 	<operations> 
@@ -32,7 +32,7 @@
 	</list>
 		<para>
  	  	</para>
-	  	<imgReference target = "FileSaveWarning.PNG"/>
+	  	<imgReference target = "FileSaveWarning.png"/>
  		<para>
  	  <list>
 	  <item>		

vcell-client/UserDocumentation/originalXML/topics/ch_1/Introduction/Help.xml

@@ -7,7 +7,7 @@
 	</introduction>
 
 	<appearance>
-	<imgReference target = "HelpMenu.PNG"/>
+	<imgReference target = "HelpMenu.png"/>
 	</appearance>
 
 	<operations> 
@@ -33,11 +33,11 @@
 	  <bold>VCell Properties</bold> - displays locations for local files including the Installation Directory and VCell Home Directory.
 	  </item>
 	  <item>           
-         <bold> Virtual Cell License Information</bold> - shows a dialog that displays the license information for the Virtual Cell. <imgReference target = "VCellLicense.PNG"/>
+         <bold> Virtual Cell License Information</bold> - shows a dialog that displays the license information for the Virtual Cell. <imgReference target = "VCellLicense.png"/>
 	  </item>
 	  <para></para>
 	  <item>   
-         <bold> About The Virtual Cell</bold> - pops up a dialog that displays the Version and edition of the currently launched VCell. <imgReference target = "AboutVCell.PNG"/>
+         <bold> About The Virtual Cell</bold> - pops up a dialog that displays the Version and edition of the currently launched VCell. <imgReference target = "AboutVCell.png"/>
 	  </item>
 	  <para></para>
 	  <item>

vcell-client/UserDocumentation/originalXML/topics/ch_1/Introduction/LaunchVirtualFRAP.xml

@@ -10,7 +10,7 @@
 	</introduction>
 
 	<appearance>
-		<imgReference target = "VirtualFRAP.PNG"/>	
+		<imgReference target = "VirtualFRAP.png"/>
 	</appearance>
 
 	<operations> </operations>

vcell-client/UserDocumentation/originalXML/topics/ch_1/Introduction/ManageDBCompareWith.xml

@@ -16,7 +16,7 @@
 	At the level where that item is, it will be marked with a <bold>"?"</bold>. Items that are only in the modified model are marked with an <bold>"N"</bold> for <bold>new</bold>. 
 	Items that are only in the baseline model are marked with an <bold>"R"</bold> for <bold>removed</bold>; they are considered to be removed from the modified model.
 	</para>
-	<imgReference target = "ManageDBCompareWith.PNG"/>
+	<imgReference target = "ManageDBCompareWith.png"/>
 	<para>
 	When any of these items are selected, the value in the baseline model and the modified model are displayed in the text area below. 
 	If the user is aware that any two similar items (for example., 2 species in the models being compared) represent the same entity, the two items can be selected and the <bold>Associate</bold> button can be clicked to associate the two items.

vcell-client/UserDocumentation/originalXML/topics/ch_1/Introduction/New.xml

@@ -8,7 +8,7 @@
 	</introduction>
 
 	<appearance>
-		<imgReference target = "FileNewMathModelMenuItem.PNG"/>
+		<imgReference target = "FileNewMathModelMenuItem.png"/>
 	</appearance>
 
 	<operations>
@@ -25,7 +25,7 @@
 		<bold>Spatial from database geometry</bold> - creates a spatial MathModel where the spatial geometry is
 			selected from VCell geometries stored in the VCell database (any geometry that belongs to the current user
 			or that is shared by other users).
-		<imgReference target = "FileNewMathModelDBGeom.PNG"/>
+		<imgReference target = "FileNewMathModelDBGeom.png"/>
 		</item>
 		<item>
 		<para>
@@ -36,7 +36,7 @@
 			VCell database; or created from scratch.
 		For further information on creating geometries, refer to the section on <link target = "GeometryOverview">Geometry</link>.
 		</para>
-		<imgReference target = "FileNewMathModelNewGeom.PNG"/>
+		<imgReference target = "FileNewMathModelNewGeom.png"/>
 		</item>
 		<item>
 		<para>
@@ -46,8 +46,8 @@
 			in the BioModel that should be converted to a MathModel.
 		<bold>Note:</bold> Each application has a separate MathModel associated with it.  
 		</para>
-		<imgReference target = "FileNewMathFromBio.PNG"/>
-		<imgReference target = "FileNewMathFromBioAppln.PNG"/>
+		<imgReference target = "FileNewMathFromBio.png"/>
+		<imgReference target = "FileNewMathFromBioAppln.png"/>
 		</item>
 	</list>
 	</operations>

vcell-client/UserDocumentation/originalXML/topics/ch_1/Introduction/Open.xml

@@ -17,7 +17,7 @@
 	For example, clicking on 'File->Open->BioModel' will open a dialog that lists all BioModels accessible to current user.
 	Additionally, <bold>Local...</bold> displays a local file chooser to select VCell documents saved on the user's own computer (using 'File->Export...' or 'File->Save As Local...').
 	</para>
-	<imgReference target = "FileNewMathFromBio.PNG"/>
+	<imgReference target = "FileNewMathFromBio.png"/>
 	</operations>
 	<comments>  </comments>
 

vcell-client/UserDocumentation/originalXML/topics/ch_1/Introduction/Permissions.xml

@@ -9,7 +9,7 @@
 	</introduction>
 
 	<appearance>
-		<imgReference target = "FilePermission.PNG"/>
+		<imgReference target = "FilePermission.png"/>
 	</appearance>
 
 	<operations>

vcell-client/UserDocumentation/originalXML/topics/ch_1/Introduction/RevertToSaved.xml

@@ -6,7 +6,7 @@
 	</introduction>
 
 	<appearance>
-		<imgReference target = "FileRevertToSaved.PNG"/>
+		<imgReference target = "FileRevertToSaved.png"/>
 	</appearance>
 
 	<operations>

vcell-client/UserDocumentation/originalXML/topics/ch_1/Introduction/SetProxy.xml

@@ -8,7 +8,7 @@ Set Proxy allows a user to define a proxy to enable connection through a firewal
 	</introduction>
 
 	<appearance>  
-<imgReference target = "SetProxy.PNG"/>
+<imgReference target = "SetProxy.png"/>
 	</appearance>
 
 	<operations>

vcell-client/UserDocumentation/originalXML/topics/ch_1/Introduction/TransformToStochCapable.xml

@@ -17,7 +17,7 @@
 	<para>
 	Clicking on <bold>Tools -> Transform to Stochastic Capable</bold> menu option brings up a warning to the user about potential changes to the model if the tool is used.
 	</para>
-	<imgReference target = "TransformToStochWarning.PNG"/>
+	<imgReference target = "TransformToStochWarning.png"/>
 	<para>
 	Clicking <bold>Cancel</bold> will cancel the transform operation. Clicking <bold>OK</bold> will open the "Transform to Stochastic Capable Model" dialog. 
 	This dialog displays a table of all the reactions in the model.

vcell-client/UserDocumentation/originalXML/topics/ch_1/Introduction/ViewSimStatus.xml

@@ -8,7 +8,7 @@ View Simulation Jobs opens a window that allows the user to search for VCell sim
 	</introduction>
 
 	<appearance>  
-<imgReference target = "ViewSimStatus.PNG"/>
+<imgReference target = "ViewSimStatus.png"/>
 	</appearance>
 
 	<operations>

vcell-client/UserDocumentation/originalXML/topics/ch_1/Introduction/Window.xml

@@ -7,7 +7,7 @@
 	</introduction>
 
 	<appearance>
-		<imgReference target = "WindowMenu.PNG"/>
+		<imgReference target = "WindowMenu.png"/>
 	</appearance>
 
 </page>

vcell-client/UserDocumentation/originalXML/topics/ch_10/RuleBasedChapter/RuleBasedTheory.xml

@@ -25,9 +25,9 @@
 	by the ligand–receptor interaction rule requires just two rate constants: on and
 	off rates.</para>
 	<para> The rule below depicts the EGF receptor with a binding site for egf (l), a second unspecified site (r) and two phosphorylation sites (Y1068 and Y11848) that can be phosphorylated, unphosphorylated, bound or unbound, combining with an EGF molecule with a receptor binding site (r):</para>
-	<imgReference target = "rule1.PNG"/>
+	<imgReference target = "rule1.png"/>
 	<para>Some of the possible reactions generated by this rule are:</para>
-	<imgReference target = "reac-combined.PNG"/>
+	<imgReference target = "reac-combined.png"/>
 	</introduction>
 
 	<appearance>  

vcell-client/UserDocumentation/originalXML/topics/ch_10/RuleBasedChapter/SpringSaLaDTheory.xml

@@ -7,9 +7,9 @@
 
 	<para>Another paragraph</para>
 	<para>Yet another paragraph...</para>
-	<imgReference target = "rule1.PNG"/>
+	<imgReference target = "rule1.png"/>
 	<para>...with images inserted between paragraphs...</para>
-	<imgReference target = "reac-combined.PNG"/>
+	<imgReference target = "reac-combined.png"/>
 	</introduction>
 
 	<appearance>  

vcell-client/UserDocumentation/originalXML/topics/ch_2/Physiology/Observables.xml

@@ -19,7 +19,7 @@
 	</introduction>
 
 	<appearance>
-		<imgReference target = "observables.PNG"/>
+		<imgReference target = "observables.png"/>
 		<para></para>The Observables Table displays 
 		<list>
 			<item>The <bold>Name</bold> of Observable (can be edited).</item>

vcell-client/UserDocumentation/originalXML/topics/ch_2/Physiology/ReactTabView.xml

@@ -8,7 +8,7 @@
 	</introduction>
 
 	<appearance>
-		<imgReference target = "Mix_Rules.PNG"/>
+		<imgReference target = "Mix_Rules.png"/>
 
 	The Reactions table has several columns:
 	<list> 

vcell-client/UserDocumentation/originalXML/topics/ch_2/Physiology/SpeciesTabView.xml

@@ -16,7 +16,7 @@
 	(using <def target= "def_NFSim">NFSim</def> solver).</para>
  	</introduction>
 	<appearance>
-	<imgReference target = "Mix_Species.PNG"/>
+	<imgReference target = "Mix_Species.png"/>
 	<para>The Species Tab has several columns:</para>
 	<list> 
 		<item>The species <bold>Name</bold>.  New species are automatically named s_number. When a BNGL file is imported species names are automatically generated. 

vcell-client/UserDocumentation/originalXML/topics/ch_3/BioModelApplications/Geometry/geom_spatial_mapping.xml

@@ -19,7 +19,7 @@
 	</introduction>
 
 	<appearance>
-	<imgReference target = "Structure_Mapping.PNG"/>
+	<imgReference target = "Structure_Mapping.png"/>
 	<para>
 	From a selected application click on "Geometry and click the "Structure Mapping" tab.
 	The left panel depicts the "physiology (structures)", the right depicts the "Geometry (subdomains)" and the bottom displays a table of the structure mapping assignments.  

vcell-client/UserDocumentation/originalXML/topics/ch_3/BioModelApplications/Simulations/NFSimSimulationEditor.xml

@@ -11,7 +11,7 @@
 		A user can set end simulation time, output interval N (simulations results are outputted every N seconds)
 		 and Advanced Solver Options.
 	</introduction>
-	<appearance><imgReference target="NFSimSolver.PNG"/></appearance>
+	<appearance><imgReference target="NFSimSolver.png"/></appearance>
 
 	<operations>
 	<bold>Advanced Solver Options</bold>	

vcell-client/UserDocumentation/originalXML/topics/ch_3/BioModelApplications/Simulations/Results/Spatial/OpenHDF5ImageJ.xml

@@ -9,7 +9,7 @@
 	</introduction>
 		S
 	<appearance>
-	<imgReference target = "ImageJImportHDF5.PNG"/>
+	<imgReference target = "ImageJImportHDF5.png"/>
 	</appearance>
 
 
@@ -22,7 +22,7 @@
 	<para>
 	<bold>Select</bold> all of the datasets ending in ".../DataValues (XYZT)" to be imported. If you exported data for multiple variables in a single HDF5 file, the data for each variable appears as a separate data set path in the table.
 	</para>
-	<imgReference target = "ImageJHDF5Table.PNG"/>
+	<imgReference target = "ImageJHDF5Table.png"/>
 	<para>
 	<bold>Click "Individual Hyperstacks (custom layout)"</bold> and <bold>enter "xyzt"</bold> in the text box. (Note that it is not yet possible to use the "Combine to..." functions with the exported VCell HDF5 files.)  Then <bold>select "Load"</bold>
 	</para>

vcell-client/UserDocumentation/originalXML/topics/ch_3/BioModelApplications/Simulations/Results/Spatial/PostProcessingImage.xml

@@ -9,7 +9,7 @@
 	(Note: The panel will indicate "No Data" if data you are viewing was generated from a simulation run on a version of VCell earlier then 5.2 or if flourescence functions were not specified prior to the simulation run)
 	</introduction>
 
-	<appearance> 		<imgReference target = "PostProcessingImageData.PNG"/> </appearance>
+	<appearance> 		<imgReference target = "PostProcessingImageData.png"/> </appearance>
 
 	<operations>
 	<para>

vcell-client/UserDocumentation/originalXML/topics/ch_3/BioModelApplications/Simulations/Results/Spatial/PostProcessingStats.xml

@@ -9,7 +9,7 @@
 	(Note: A No Data message will appear if the data you are viewing was generated from a simulation run on a version of VCell earlier then 5.2)
 	</introduction>
 
-	<appearance> 	<imgReference target = "PostProcessingDataGraph.PNG"/> </appearance>
+	<appearance> 	<imgReference target = "PostProcessingDataGraph.png"/> </appearance>
 
 	<operations><para> <bold>Post Processing Variable Statistics:</bold> To view one or more compartmental average values of variables, select the variable names in the list and a graph of values over time will appear in the right hand pane. The data in tabular form can be accessed by clicking the spreadsheet icon at the lower right of the graph pane, and toggled back to graphical form with the adjacent graph icon.  Note, to select multiple variables, press the Control key while clicking on variable name of interest.
 	</para>

vcell-client/UserDocumentation/originalXML/topics/ch_3/BioModelApplications/Simulations/generated_math.xml

@@ -19,7 +19,7 @@
 	</introduction>
 
 	<appearance>
-	<imgReference target = "generated_math_main.PNG"/>
+	<imgReference target = "generated_math_main.png"/>
 	</appearance>
 
 	<operations>

vcell-client/UserDocumentation/originalXML/topics/ch_3/BioModelApplications/Simulations/simulations_overview.xml

@@ -44,7 +44,7 @@
 	<para></para>
 	<para>
 	<bold>Right-clicking</bold> on a simulation row will reveal a drop down submenu providing a way to edit End Time and Output Option (frequency of saved data points).
-	<imgReference target="SimulationsMenuRightClick.PNG"/>
+	<imgReference target="SimulationsMenuRightClick.png"/>
 	</para>
 	 </operations>
 

vcell-client/UserDocumentation/originalXML/topics/ch_3/BioModelApplications/Specifications/NetworkFreeSpecifications.xml

@@ -12,7 +12,7 @@
 	</appearance>
 
 	<operations>
-	<imgReference target = "NetworkFreeTab.PNG"/>
+	<imgReference target = "NetworkFreeTab.png"/>
 	<para>	
 <bold>Create New Rule-Based VCell BioModel</bold> from the original physiology. A new BioModel is created and opened in a new window. A rule based model can be created only for models with a single compartment and if all reactions have mass action kinetics.  Molecules, observables, species with molecular details, and reaction rules are transferred to a new
 BioModel without changes. Species without molecular details and reactions are converted into rule-based physiology by generating a molecule for each species, and converting reactions to fully-defined reaction rules.</para>

vcell-client/UserDocumentation/originalXML/topics/ch_3/BioModelApplications/Specifications/NetworkSpecifications.xml

@@ -8,7 +8,7 @@
 	</introduction>
 
 	<appearance>
-	<imgReference target = "NetworkTab.PNG"/>
+	<imgReference target = "NetworkTab.png"/>
 	<list>
 		<item><bold>Max Iterations</bold> - how many times the rules are applied to the set of 
 		<def target = "def_SeedSpecies">seed species</def> to generate new species and reactions.</item>
@@ -23,7 +23,7 @@
 
 	<operations>
 Clicking the "Edit/Test Constraints" button presents a window to specify new constraints. 	
-<imgReference target = "NetworkConstraints.PNG"/>	
+<imgReference target = "NetworkConstraints.png"/>
 <list>	
 	<item><bold>Test/Run</bold> to attempt to generate a reaction network using the specified constraints.</item>
 	<item><bold>Apply</bold> the constraints without generating a network;  a <link target="simulations_overview">simulation</link> will be performed sequentially after generating the network.</item>
@@ -33,12 +33,12 @@ Warnings may be generated when specifying or applying the constraints:
 <list>
 	<item>
 		<bold>Max iterations number may be insufficient</bold> suggests that the network may be not exaustively generated. In this case the <bold>Network Generation Status</bold> pane displaying the number of species will show that the number of species during the last two iterations is different.  Generation of the network is generally considered complete when the last iteration does not produce new species and thus		the number of species at the last two iterations is the same.
-		<imgReference target = "MaxIterNumber.PNG"/> 
+		<imgReference target = "MaxIterNumber.png"/>
 	</item>
 
 	<item>
 		<bold>Max Molecules/Species number may be not sufficient</bold> indicates that a species with aspecified number of molecules is a subject of a rule applied in the last interation.  This indicates that the network is truncated because of the limits set for the number of molecules of that species in the network.
-		<imgReference target = "MaxMolec.PNG"/>
+		<imgReference target = "MaxMolec.png"/>
 
 			<para><bold>Note:</bold> When the warning is displayed, the network is truncated, so a simulation using NFSim is likely to produce different results compared to deterministic or stochastic simulations that use this network.</para></item>
 
@@ -47,7 +47,7 @@ Warnings may be generated when specifying or applying the constraints:
 
 	<item>
 		<bold>View Generated Species/View Generated Reactions</bold> after constraints are applied. The pop-up window shows the species name, depiction and searchable BNGL code. Species names are the same as seen  "Generated Species" is checked in the "Simulation Results" window.
-		<imgReference target = "View_species.PNG"/> 
+		<imgReference target = "View_species.png"/>
 	</item>
 
 	<item>

vcell-client/UserDocumentation/originalXML/topics/ch_8/PropertiesPanes/PP_Annotations.xml

@@ -7,7 +7,7 @@ Each element in a VCell BioModel, as well as the BioModel itself, can be annotat
  	</introduction>
 
 	<appearance>
-		<imgReference target = "PP_Annotations.PNG"/>
+		<imgReference target = "PP_Annotations.png"/>
 	</appearance>
 
 	<operations>
@@ -17,15 +17,15 @@ Each element in a VCell BioModel, as well as the BioModel itself, can be annotat
 		</item>
 		<item>
 		Follow the <bold>annotation link</bold> by double click on the underlined link portion of the annotation.
-		<imgReference target = "PP_Annotate_links.PNG"/>
+		<imgReference target = "PP_Annotate_links.png"/>
 		</item>
 		</list>
 		<para>
 		<list>
 		<item>
 <bold>Add</bold> new unique identifiers using the drop down menu to select a supported provider.  Double click the provider link to go to the provider web site to search for the appropriate provider.  Add the identifier to the annotation pane using the exact format shown in the example. Supported identity providers are listed in the <link target="AnnotationProviders">Appendix</link>
 		</item>
-		<imgReference target = "PP_AddAnnotations.PNG"/>
+		<imgReference target = "PP_AddAnnotations.png"/>
 		</list>
 		</para>
 		<para>