VCell Help Updates

vcell-client/UserDocumentation/originalXML/TOC.xml

@@ -5,35 +5,29 @@
     		<tocitem target="General" text="Overview"/>
 <!--      		<tocitem target="RuleBasedOverview" text="Rule-Based Features"/>  		-->
     		<tocitem target="GeneralNavAndWinSetup" text="General Navigation and Window Setup"/>
+			<tocitem target="Login" text="Logging into VCell"/>
     		<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"/>
     			<tocitem target="SaveAs" text="File->Save As Menu"/>
     			<tocitem target="RevertToSaved" text="File->Revert to Saved Menu"/>
+				<tocitem target="CompareWithSaved" text="Compare With Saved"/>
     			<tocitem target="Permissions" text="File->Permissions Menu"/> 			 
     			<tocitem target="FieldData" text="File->Field Data Menu"/>
     			<tocitem target="Import" text="File->Import Menu (SBML files)"/>
     			<tocitem target="ImportBNGL" text="File->Import Menu (BNGL files)"/>
     			<tocitem target="Export" text="File->Export Menu"/>
     		</tocitem>
     		<tocitem target="Account" text="Account 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="Auth0ProfilePage" text="Login"/>
     			<tocitem target="SetProxy" text= "Set Proxy Window"/>
     			<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"/>
     	</tocitem>
@@ -62,8 +56,8 @@
     			<tocitem target="PathLink" text="Edit Pathway Links"/> 	
     		</tocitem>
     		<tocitem target="Molecules" text="Molecules Table">
-    			<tocitem target="PP_Molecules" text="Edit Molecule"/>
-      		</tocitem>	  			    	
+    			<tocitem target="PP_Molecules" text="Specify Molecular Details"/>
+      		</tocitem>
     		<tocitem target="Observables" text="Observables Table">
     			   <tocitem target="PP_Observables" text="Edit Observable"/>
     		</tocitem>	   

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

@@ -3,27 +3,26 @@
 <page title="Account">
 
 	<introduction>
-	The <bold>Account</bold> menu bar option allows the user to change the account settings for the current user of VCell.
+	The <bold>Account</bold> menu bar option allows the user to change the login status the current user of VCell, and to manage account settings using the VCell Auth0 app.
 	</introduction>
 
 	<appearance>
 		<imgReference target = "AccountMenu.png"/>
 	</appearance>
 
 	<operations> 
-	Clicking the Account menu displays the following selections 
-	<list>
+		<list>
 		<item>
-			<bold>Login</bold> - allows user to login if they have not do so already.
+			<bold>Login</bold> directs the user to the <link target = "Auth0ProfilePage">VCell Auth0 Profile page</link> to login to VCell if they are not currently logged in.
 		</item>
 		<item>
-			<bold>Login as Guest</bold> - allows user to login as guest if they are not logged in already.
+			<bold>Login as Guest</bold> allows user to login as a "guest" if they are not logged in already.  Guest login can only access public models and cannot be used to save a model to the database.
 		</item>
 		<item>
-			<bold>Logout</bold> - allows user to logout if they are logged in.
+			<bold>Logout</bold> allows user to logout if they are logged in. The user will be directed to the VCell Auth0 site to complete the logout. Once logged out the user can only use VCell in an offline mode, with no connection to the VCell database or servers.
 		</item>
 		<item>
-			<link target = "Auth0ProfilePage">Manage User</link> - takes the user to the Auth0 profile page.
+			<link target = "Auth0ProfilePage">Manage User</link> - takes the user to their Auth0 profile web page to manage VCell credentials.
 		</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.
@@ -32,7 +31,7 @@
 		<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.
+		<link target = "ViewSimStatus">View Simulation Jobs</link> provides a way to view and currently running, stopped or failed simulation jobs and to stop any jobs currently running.
 		</item>
 	</list>
 	</operations>

vcell-client/UserDocumentation/originalXML/topics/ch_1/Introduction/Auth0ProfilePage.xml

@@ -0,0 +1,31 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<vcelldoc>
+    <page title="Auth0 Profile Page">
+
+        <introduction>
+            When <bold>Login</bold> is selected at first use, the user is redirected to the <bold>AuthO Profile</bold> page to create a user profile and complete creating an Auth0 account. A VCell username is required to access all the functionality of VCell. The VCell username will then be mapped to an Auth0 login account.
+            <para></para>
+        </introduction>
+        <appearance>
+        </appearance>
+
+        <operations>
+        <bold>Existing Users</bold> need to provide the username
+        and password of their existing VCell account.
+        <imgReference target = "ProfileOldLogin.png"/>
+        <para>
+        <bold>Select Forgot my password</bold> if you have forgotten your password. Provide the username and associated email of the account and an email will be sent with a link that will immediately approve linking the VCell account to an Auth0 account. If you do not remember both old username and email, contact VCell Support
+         <imgReference target = "ProfileRecoverAccount.png"/>
+        </para>
+        <para>
+        <bold>New VCell Users</bold> need to create a username and provide a valid email address.  VCell usernames are case-sensitive. Click the checkbox at the bottom of the registration dialog if you wish to decline receiving VCell notification emails.
+       <imgReference target = "ProfileCreateNew.png"/>
+        </para>
+        <para>
+        Once a unique VCell Username is applied, a new Auth0 account is created and you are directed to a Success Auth0 profile page.  Simply close the page and return to VCell. A message saying Failed to map new user, please try again will appear if the username provided is already in use. Pick a new one and try again.
+        </para>
+        <imgReference target = "ProfileUserMapped.PNG"/>
+
+        </operations>
+    </page>
+</vcelldoc>

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

@@ -1,31 +1,31 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<vcelldoc>
-<page title="Compare With">
-	
-	<introduction>
-	<para>It is difficult to compare models by simply visually inspecting the different components. 
-	Instead, the best way to compare models is with the Compare Models feature which automatically performs a side-by-side comparison of all the different components of the model.
-	</para>
-	</introduction>
-		
-	<operations>
-
-	<para>
-	The models are compared and the user is presented with a composite model in a <bold>Compare Models</bold> dialog, shown above, where only differences are indicated. An <bold>"X"</bold> will indicate which part of the model is different. 
-	The <bold>"X"</bold> will originate at the parent level in the tree and travel down the tree wherever there is a difference between the two models. 
-	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"/>
-	<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.
-	Similarly, <bold>Disassociate</bold> button will dissociate two similar items in the two models being compared. This will not alter the original models in any way.
-	</para>
-	</operations>
-	
-	<comments>  </comments>
-
-</page>
-
+<?xml version="1.0" encoding="UTF-8"?>
+<vcelldoc>
+<page title="Compare With Saved">
+
+	<introduction>
+	<para>It is difficult to compare models by simply visually inspecting the different components. 
+	Instead, the best way to compare models is with the Compare Models feature which automatically performs a side-by-side comparison of all the different components of the model.
+	</para>
+	</introduction>
+
+	<operations>
+
+	<para>
+	The models are compared and the user is presented with a composite model in a <bold>Compare Models</bold> dialog, shown above, where only differences are indicated. An <bold>"X"</bold> will indicate which part of the model is different. 
+	The <bold>"X"</bold> will originate at the parent level in the tree and travel down the tree wherever there is a difference between the two models. 
+	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"/>
+	<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.
+	Similarly, <bold>Disassociate</bold> button will dissociate two similar items in the two models being compared. This will not alter the original models in any way.
+	</para>
+	</operations>
+
+	<comments>  </comments>
+
+</page>
+
 </vcelldoc>

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

@@ -49,7 +49,7 @@
 	  </item>
 	  <item>
 		<bold>Compare With Saved</bold> - compares the currently open document with its latest saved version in the database and displays the result in a separate window. 
-		Refer to the section on <link target = "ManageDBCompareWith">Compare With</link> for further information. 
+		Refer to the section on <link target = "CompareWithSaved">Compare With Saved</link> for further information.
 	  </item>
 	  <item>
 		<link target = "Permissions">Permissions...</link>