Merge branch 'help_7_6_Logan' into help_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"/>
@@ -18,11 +19,14 @@
     			<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"/>

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/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>

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

@@ -3,32 +3,26 @@
 <page title="Introduction" target="GeneralOverview">
 
 	<introduction>
-The Virtual Cell Modeling and Simulation Framework (VCell) 
+The Virtual Cell Modeling and Simulation Framework (<bold>VCell</bold>)
 was developed by the National Resource for Cell Analysis and 
 Modeling. This unique software platform has been designed to model cell
-biological processes. Biochemical and electrophysiological data describing
-individual reactions are associated with experimental microscopic 
-image data describing their subcellular locations. Cell physiological events 
+biological processes, through describing and processing biochemical and electrophysiological data of
+individual reactions; commonly, the model is built based off of associated experimental microscopic
+image data that describes the model's subcellular locations. Cell physiological events
 can then be simulated within the empirically derived geometries, thus facilitating 
 the direct comparison of model predictions with experiment.
 <para></para>
-VCell consists of a biological and mathematical framework. As described in the <link target="General">Overview</link>, users can create 
-biological models from which the software will generate the mathematical code 
+VCell consists of a biological and mathematical framework. As described in the <link target="General">Overview</link>,
+		users can create biological models from which the software will generate the mathematical code
 needed to run simulations.  Mathematicians may opt to use the math framework, 
-based on the Virtual Cell Markup Language, for creating their own mathematical descriptions. 
+based on the Virtual Cell Markup Language (<bold>VCML</bold>), for creating their own mathematical descriptions.
 <para></para>
 Models can be reused, updated, and made available to the scientific community. In
 addition, models may also be privately shared amongst collaborating groups. The data from
 simulations are stored on the Virtual Cell database server and are easily exported in a variety of formats.
-Access to the Virtual Cell modeling software is available via the internet using a JAVA based interface.
+Access to the Virtual Cell modeling software is available a desktop application written in java, with certain features
+		available through a REST API.
 The Virtual Cell has been developed using the latest supported Java technology.
-<para></para>
-Virtual Cell also supports 
-<link target="RuleBasedOverview">rule-based modeling</link>, which allows the representation 
-of species as structured objects consisting of <link target="Molecules">molecules</link> 
-and uses  <def target = "def_ReactionRules">reaction rules</def> to define molecular interactions that transform the attributes of species. 
-The rule-based approach allows one to systematically incorporate site-specific details of
-molecular interactions into a model.
 	</introduction>
 
 </page>

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

@@ -3,31 +3,26 @@
 <page title="User Login">
 
 	<introduction> 
-	The <bold>Login</bold> dialog allows a user to log in to his/her VCell user account to access and manipulate his/her VCell models.
+	When VCell is launched, a dialog window will pop up, welcoming the user and asking how they would like to proceed
+		with login. There are three options:
+	<list>
+		<item>
+			<bold>Login</bold> - Redirect to the default browser of the computer, to authenticate through Auth0.
+		</item>
+		<item>
+			<bold>Guest</bold> - Immediately login as the VCell Guest User, allowing limited access to VCell features.
+		</item>
+		<item>
+			<bold>Skip</bold> - Dismisses the dialog, placing VCell in a "offline" state. Should the user wish to login
+			at a future time, it is possible through the `Account` menu.
+		</item>
+	</list>
+		For more information about what happens after clicking <bold>Login</bold>, see <link target="Auth0Overview">Auth0 Overview</link>
 	</introduction>
 
 	<appearance>
-		<imgReference target = "LoginDialog.PNG"/>
+		<imgReference target = "VCellLoginPopup.png"/>
 	</appearance>
-
-	<operations>
-	<para>
-	The <bold>Login</bold> dialog prompts user to provide a 'login ID' (User Name, case sensitive) and password. Clicking <bold>OK</bold> authenticates the user name and password and if successful, the user is logged in and can proceed with editing/creating models. 
-	Clicking <bold>Cancel</bold> cancels the login process. The user can still create models, but cannot save or run simulations.
-	</para>
-
-	<para>
-	If the user has forgotten his/her password, clicking on the <bold>Forgot Login Password...</bold> button displays a message to the user saying that the password will be sent via email to the user's currently registered email address.
-	The user can choose to accept or cancel the operation. 
-	</para>
-	<imgReference target = "LoginForgotPswd.PNG"/>. 
-
- 	<para>
- 	First time users should register with VCell to enable interaction with the VCell Database and access to VCell simulation servers. Clicking on the <link target = "NewUserRegistration">New User Registration</link> allows a user to register and use the Virtual Cell.
- 	</para>
- 	<para><bold>Login as Guest</bold>allows an individual to open public models and to build models and run simulations on their local machine.  Guests cannot save models to the database or use VCell simulation servers.
- 	</para>
-	</operations>
 	<comments>  </comments>
 
 </page>