Merge pull request #1307 from virtualcell/help_7_6

First Pass at updating help for VCell 7.6

vcell-client/UserDocumentation/originalXML/TOC.xml

@@ -6,6 +6,7 @@
       		<tocitem target="RuleBasedOverview" text="Rule-Based Features"/>  		
     		<tocitem target="GeneralNavAndWinSetup" text="General Navigation and Window Setup"/>
     		<tocitem target="TopMenu" text="Top Menu"/>
+			<tocitem target="Login" text="User Login"/>
     		<tocitem target="File" text="File Menu">
 	    		<tocitem target="New" text="File->New Menu"/>
     			<tocitem target="Open" text="File->Open Menu"/>
@@ -18,16 +19,20 @@
     			<tocitem target="Export" text="File->Export Menu"/>
     		</tocitem>
     		<tocitem target="Account" text="Account Menu">
-    			<tocitem target="Login" text="User Login"/>
-    			<tocitem target="ChangeUser" text="Change User Menu"/>
+				<tocitem target="Auth0Overview" text="Website Login">
+					<tocitem target="Auth0ProfilePage" text="Website Profile Page">
+						<tocitem target="Auth0ExistingUserAccountLinking" text="Existing Users Profile Help"/>
+						<tocitem target="Auth0ReturningUserAccountLinking" text="Returning Users Profile Help"/>
+						<tocitem target="Auth0NewUserAccountCreation" text="New Users Profile Help"/>
+					</tocitem>
+				</tocitem>
     			<tocitem target="SetProxy" text= "Set Proxy Window"/>
-    			<tocitem target="UpdateRegistrationInfo" text="Update Registration Information Menu"/>
-    			<tocitem target="NewUserRegistration" text="New User Registration"/>
     			<tocitem target="ViewSimStatus" text="View Simulation Jobs"/>
     		</tocitem>	
     		<tocitem target="Window" text="Window Menu"/>
     		<tocitem target="Tools" text="Tools Menu">
     			<tocitem target="LaunchVirtualFRAP" text="Launch Virtual FRAP Menu"/>
+				<tocitem target="ExportedDataViewer" text="Exported Data Viewer"/>
  				<tocitem target="TransformToStochCapable" text="Transform to Stochastic Capable Menu"/>
     		</tocitem>
     		<tocitem target="Help" text="Help Menu"/>
@@ -36,8 +41,10 @@
     	    <tocitem target="RuleBasedTheory" text="Introduction to Rule-Based Modeling"/> 
        		<tocitem target="RBCreate" text="How to create a rule-based model"/> 		
     		<tocitem target="RBSimulate" text="How to simulate a rule-based model"/> 
-    		<tocitem target="NFSimApp" text="Network-Free Application"/>		
-    	</tocitem>
+    		<tocitem target="NFSimApp" text="Network-Free Application"/>
+<!--			<tocitem target="SpringSaLaDTheory" text="Introduction to SpringSaLaD Modeling"/>
+			<tocitem target="LangevinApp" text="SpringSaLaD Application"/> -->
+		</tocitem>
     	<tocitem target="PhysOverview" text="Physiology">
     		<tocitem target="ReactDiagView" text="Reaction Diagram"/>
     		<tocitem target="ReactTabView" text="Reactions Table">
@@ -74,9 +81,12 @@
     		</tocitem>
     		<tocitem target="SpecificationsOverview" text="Specifications">
     	   		<tocitem target="SpeciesSpecifications" text="Species">
-    			     <tocitem target="fieldData" text="Field Data"/>
+					<tocitem target="fieldData" text="Field Data"/>
+<!--					<tocitem target="SSSpeciesSpecifications" text="SpringSaLaD Species"/> -->
     			</tocitem>
-   	 	  		<tocitem target="ReactionsSpecifications" text="Reactions"/>
+   	 	  		<tocitem target="ReactionsSpecifications" text="Reactions">
+<!--					<tocitem target="SSReactionsSpecifications" text="SpringSaLaD Reactions"/> -->
+				</tocitem>
    	 	  		<tocitem target="NetworkSpecifications" text="Network"/>
    	 	  		<tocitem target="NetworkFreeSpecifications" text="Network-Free"/>  	 	  		
     		</tocitem>
@@ -88,7 +98,9 @@
    	 	  		<tocitem target= "AssignmentRules" text ="Assignment Rules"/>
    	 	  	</tocitem>
     		<tocitem target="simulations_overview" text="Simulations">
-    	   		<tocitem target="simulations" text="Simulations"/>
+    	   		<tocitem target="simulations" text="Simulations">
+					<tocitem target="BatchSimulations" text="Batch Simulations"/>
+				</tocitem>
     	   		<tocitem target="simulationEditor" text="Simulation Editor"/>
     	   		<tocitem target="NFSimSimulationEditor" text="NFSim Simulation Editor"/>
    	 	  		<tocitem target="output_functions" text="Output Functions"/>
@@ -104,6 +116,7 @@
 					<tocitem target="PostProcessingStats" text="Post Processing Statistics Data"/>
 					<tocitem target="PostProcessingImage" text="Post Processing Image Data"/>
 					<tocitem target="ExportingSpatialSimResults" text="Exporting Spatial Simulation Results"/>
+					<tocitem target="ImageJDataViewerPlugin" text="FIJI/ImageJ VCell Simulation Results Viewer Plugin"/>
 					<tocitem target="OpenHDF5ImageJ" text="Importing HDF5 files into FIJI/ImageJ"/>		
 					<tocitem target="SpecificFormatSettings" text="Specific Format Settings"/>
    		        </tocitem>

vcell-client/UserDocumentation/originalXML/topics/Auth0/Auth0ExistingUserAccountLinking.xml

@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<vcelldoc>
+    <page title="Auth0 Existing User Account Linking">
+
+        <introduction>
+            Users who remember their existing VCell account login can easily access their old account by providing the username
+            and password of their old VCell account. All the user's existing models, permissions, and old VCell Username will
+            immediately become available to the user, once the old credentials are input.
+        </introduction>
+
+        <appearance>
+            <imgReference target = "ProfileOldLogin.png"/>
+        </appearance>
+
+        <operations>
+            If the user has forgotten their credentials, they will need to follow the instructions
+            <link target="Auth0ReturningUserAccountLinking">Here</link>
+        </operations>
+
+    </page>
+
+</vcelldoc>

vcell-client/UserDocumentation/originalXML/topics/Auth0/Auth0LinkAccount.xml

@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<vcelldoc>
+    <page title="Auth0 Profile Page">
+
+        <introduction>
+            After logging into Auth0 for the first time, the user will be redirected to the <bold>Profile</bold> page
+            in Auth0. There, the user will complete the final step to creating an Auth0 account.
+        </introduction>
+
+        <appearance>
+            <imgReference target = "userLoginReg.png"/>
+        </appearance>
+
+        <operations>
+            The <bold>Virtual Cell User Registration</bold> dialog prompts the user to choose a 'login id' (user name, case sensitive) and password.
+            In order to complete the registration, the user needs to provide other information such as a valid email address (for VCell software notifications and to retrieve forgotten passwords), first and last name of user, job title, organization and address.
+            The user can choose to decline receiving emails regarding VCell notifications by clicking on the checkbox at the bottom of the registration dialog.
+        </operations>
+
+        <comments>  </comments>
+
+    </page>
+
+</vcelldoc>

vcell-client/UserDocumentation/originalXML/topics/Auth0/Auth0NewUserAccountCreation.xml

@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<vcelldoc>
+    <page title="Auth0 New User Account Creation">
+
+        <introduction>
+            New users (or those who simply wish to make a fresh new VCell account) simply need to fill out the bottom
+            section of the profile page
+        </introduction>
+
+        <appearance>
+            <imgReference target = "ProfileCreateNew.png"/>
+        </appearance>
+
+        <operations>
+            If a message saying "Failed to map new user, please try again", the likely cause is the VCell username
+            already exists. Pick a new one and try again.
+        </operations>
+
+        <comments>  </comments>
+
+    </page>
+
+</vcelldoc>

vcell-client/UserDocumentation/originalXML/topics/Auth0/Auth0Overview.xml

@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<vcelldoc>
+    <page title="Auth0 Overview">
+
+        <introduction>
+            Auth0 is a browser and web-based authentication service that allows (in the context of VCell) users to login
+            to VCell in a secure and modern way. Some benefits include:
+            <list>
+                <item>Modern and secure login</item>
+                <item>Ability to login with Google accounts</item>
+                <item>Ability to remember login upon opening VCell, while providing a multiple ways to logout</item>
+            </list>
+        </introduction>
+
+        <appearance>
+            <imgReference target = "MainPageWithLogin.png"/>
+        </appearance>
+
+        <operations>
+        </operations>
+
+        <comments>  </comments>
+
+    </page>
+
+</vcelldoc>

vcell-client/UserDocumentation/originalXML/topics/Auth0/Auth0ProfilePage.xml

@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<vcelldoc>
+    <page title="Auth0 Profile Page">
+
+        <introduction>
+            After logging into Auth0 for the first time, the user will be redirected to the <bold>Profile</bold> page
+            in Auth0. There, the user will complete the final step to creating an Auth0 account.
+        </introduction>
+        <appearance>
+            <imgReference target = "ProfileUsernameExplanation.png"/>
+        </appearance>
+        <operations>
+            In order to properly use VCell, users must have a VCell Username. There are three ways to link a VCell
+            username to an Auth0 login:
+            <list>
+                <item>Existing Users - <link target="Auth0ExistingUserAccountLinking">Use old VCell login</link></item>
+                <item>Forgot your password? - <link target="Auth0ReturningUserAccountLinking">Recover old VCell Account</link></item>
+                <item>New VCell Users - <link target="Auth0NewUserAccountCreation">Create new Username</link></item>
+            </list>
+
+            Once a VCell Username is applied, a new Auth0 account has been successfully created, as indicated by seeing
+            a new Auth0 profile page layout, similar to the image below:
+            <para></para>
+            <imgReference target = "ProfileUserMapped.png"/>
+        </operations>
+        <comments> </comments>
+    </page>
+</vcelldoc>

vcell-client/UserDocumentation/originalXML/topics/Auth0/Auth0ReturningUserAccountLinking.xml

@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<vcelldoc>
+    <page title="Auth0 Returning User (Forgot Password) Account Linking">
+
+        <introduction>
+            Users who have forgotten their password are still able to recover their account, by providing the username
+            and associated email of their old VCell account.
+        </introduction>
+
+        <appearance>
+            <imgReference target = "ProfileRecoverAccount.png"/>
+        </appearance>
+
+        <operations>
+            If the correct combination was input, an email will be sent to the old account's email address, with a link
+            to immediately approve the linking of the VCell account to the Auth0 account.
+        </operations>
+
+        <comments> Note that if you do not remember both old username and email, you will have to contact VCell Support
+        at [email protected]</comments>
+
+    </page>
+
+</vcelldoc>

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

@@ -14,16 +14,22 @@
 	Clicking the Account menu displays the following selections 
 	<list>
 		<item>
-		<link target = "ChangeUser">Change User...</link> - allows user to change the user of the currently open VCell document by providing a different user name and password.
+			<bold>Login</bold> - allows user to login if they have not do so already.
 		</item>
 		<item>
-		<link target = "SetProxy">Set Proxy...</link> - allows the user to set a Proxy if local policy prevents direct connection to the VCell server.
+			<bold>Login as Guest</bold> - allows user to login as guest if they are not logged in already.
+		</item>
+		<item>
+			<bold>Logout</bold> - allows user to logout if they are logged in.
 		</item>
 		<item>
-		<link target = "UpdateRegistrationInfo">Update Registration Info...</link> - allows user to update his/her registration information.
+			<link target = "Auth0ProfilePage">Manage User</link> - takes the user to the Auth0 profile page.
+		</item>
+		<item>
+		<link target = "SetProxy">Set Proxy...</link> - allows the user to set a Proxy if local policy prevents direct connection to the VCell server.
 		</item>
 		<item>
-		<bold>Reconnect</bold> - allows user to reconnect to the server. The status bar displays the connecting status.
+		<bold>Reconnect (Refresh)</bold> - allows user to reconnect to the server. The status bar displays the connecting status.
 		</item>
 		<item>
 		<link target = "ViewSimStatus">View Simulation Jobs</link> - provides a way to view and stop simulation jobs.

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

@@ -0,0 +1,42 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<vcelldoc>
+<page title="Exported Data Viewer">
+
+	<introduction>
+	The <bold>Exported Data Viewer</bold> lists exported spatial simulation results that can be accessed or viewed by the user.
+	</introduction>
+
+	<appearance>	
+	<imgReference target = "ExportedDataViewer.png"/>
+	</appearance>
+
+	<operations> 
+	The table lists all exported spatial simulation result sets that were exported using the current local computer.  For each 	exported dataset, the table reports the associated BioModel Name (BM Name), Application Name (App Name), Simulation Name (Sim Name), Time Slice exported (first/last), file Format, and Date Exported.
+	<para>
+	<bold>Filter</bold> by selecting or deselecting the checkbox for Export file Type or Time Interval since the data was exported.
+	</para>
+	<para>	
+	<bold>Copy Link</bold> copies a link to the selected dataset stored on VCell servers.  The link will allow other analysis or viewing software (e.g. Fiji/ImageJ, Excel) access to the data.  The link can be shared with others and provides access only to the specific exported dataset.
+	</para>
+	<para>
+	<bold>Delete Export</bold> deletes any selected exported datasets from the servers.
+	</para>
+	<para>
+	<bold>Search</bold> any information in each of the columns to filter the table.
+	</para>
+	<para>
+	<bold>Export Details</bold> describe the variables exported, simulation ID and Name, and the link itself and can be selected and copied using "ctrl-c"
+	</para>
+	<para>
+	A <bold>Parameters</bold> table lists any Application parameters overwritten from default values for the Simulation that was exported; this distinguishes among different simulations when scanning parameter values.
+	</para>
+
+	</operations>
+
+	<comments>
+	Exported N5 files can be viewed directly from the server using Fiji/ImageJ.  A VCell Dataviewer plugin to FIJI/ImageJ can be 	installed from https://sites.imagej.net/VCell-Simulations-Result-Viewer/
+ 	</comments>
+
+</page>
+
+</vcelldoc>

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> 

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

@@ -1,31 +1,46 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <vcelldoc>
-<page title="Overview" target="General">
-
-	<introduction> 
-The Virtual Cell Software provides 2 environments for defining computational models.  
-<bold>BioModels</bold> and <bold>MathModels</bold> allow the user to create models using the tool that best suits their experience.  
-A BioModel consists of a model description (<link target = "PhysOverview">Physiology</link>), and one or more <link target = "ApplicationOverview">Applications</link> generated using a graphical interface to define model elements.  
-A MathModel is a document defined using the VCell Markup Language (VCML) and is created using VCML 'code'.
-<para><bold>BioModel</bold></para>
-The <link target = "PhysOverview">BioModel Physiology</link> 
-includes what is known about the biological system in terms of cellular structures, species and biochemical reactions. 
-
-Each <link target = "ApplicationOverview">BioModel Application</link> 
-allows the user to define the  quantitative conditions needed to define, run and visualize a Virtual Experiment, i.e. numerical simulation.  Thus, an Application includes the <link target = "GeometryOverview">Geometry</link>, the <link target = "SpecificationsOverview">Specifications</link> (species, 
-reactions), <link target = "ProtocolsOverview">Protocols</link> (events, electrical mapping), <link target = "simulations_overview">Simulations</link> and <link target = "PEOverview">Parameter Estimation</link> (if applicable).
-
-A single BioModel may have numerous 
-Applications, in which geometries and/or parameters have been changed.  Each
-Application, in turn can have multiple Simulations, in which different numerical
-methods or conditions are used.
-
-<para><bold>MathModel</bold></para>
-MathModels define Virtual Experiments using VCell Markup Language.
-
-
-	</introduction>
-
-</page>
+    <page title="Overview" target="General">
+
+        <introduction>
+            VCell provides two styles of developing computational models:
+			<list>
+                <item><bold>BioModels</bold></item>
+                <item><bold>MathModels</bold></item>
+            </list>
+            Each uses a different methodology of model creation that best suits a given user's experience.
+
+            <para><bold>BioModel</bold></para>
+            A BioModel is a computational model defined and built through defining biological concepts within
+            a graphical interface.
+
+            BioModels consist of:
+            <list>
+                <item>a model's biological system, including cellular structures, species and biochemical reactions ("<link target="PhysOverview">Physiology</link>")</item>
+                <item>one or more sets of constraints and conditions imposed on the model ("<link target="ApplicationOverview">Application</link>")</item>
+            </list>
+
+            Each <link target="ApplicationOverview">Application</link>
+            allows the user to define the quantitative values needed to define, run and visualize a Virtual
+            Experiment (i.e. numerical simulation). Thus, an <bold>Application</bold> includes:
+            <list>
+                <item><link target="GeometryOverview">Geometry</link></item>
+                <item><link target="SpecificationsOverview">Specifications</link> (e.g. species, reactions)</item>
+                <item><link target="ProtocolsOverview">Protocols</link> (e.g. events, electrical mapping)</item>
+                <item>one or more <link target="simulations_overview">Simulations</link></item>
+                <item><link target="PEOverview">Parameter Estimation</link> (if applicable)</item>
+			</list>
+
+            <para><bold>MathModel</bold></para>
+            MathModels define Virtual Experiments using the <bold>Virtual Cell Markup Language</bold> (<bold>VCML</bold>).
+            A MathModel consists of:
+            <list>
+                <item></item>
+            </list>
+
+
+        </introduction>
+
+    </page>
 
 </vcelldoc>