more updates, new navigation structure

_sidebar.md

@@ -5,9 +5,17 @@
 * [Overview](/docs/overview/platform.md)
     * [Landing Page](/docs/overview/landing_page.md)
     * [Dashboard](/docs/overview/dashboard/dashboard.md)
-        * [Project Management](/docs/overview/dashboard/new_project.md)
+        * [Projects](/docs/overview/dashboard/projects.md)
         * [Tutorials](/docs/overview/dashboard/tutorials.md)
+        * [Services](/docs/overview/dashboard/services.md)
+        * [Data](/docs/overview/dashboard/data.md)
+    * Workflow
+        * [Creating a Project](/docs/overview/dashboard/new_project.md)
         * [Sharing and Publishing](/docs/overview/dashboard/share.md)
+        * [Adding, Deleting and Updating Services](/docs/overview/dashboard/addservices.md)
+        * [Connecting Services](/docs/overview/dashboard/connectservices.md)
+        * [Running a Pipeline](/docs/overview/dashboard/runpipeline.md)
+        * [Loading Data](/docs/overview/dashboard/loaddata.md)
     * [**Sim4Life** Manual](/docs/overview/sim4life.md)
 * [License Agreements](/docs/licensing/license.md)
     * [Sim4Life](/docs/licensing/copyright_Sim4Life.md)

docs/overview/dashboard/data.md

@@ -1 +1,16 @@
+## Data
 
+```DATA``` tab allows you to browse the output files of all of your active pipelines in one place. This is most useful for downloading the data created on the online platform to your local computer. In this tab, you will find a file tree with ``simcore.s3``. Expanding ``simcore.s3`` will display a folder for each of your projects with the title of that project. Expanding the folder of each project will allow you to access the data (outputs or notebooks) belonging to each Service within that project.
+
+For JupyterLab Services, ``work.zip`` is a zip file containing everything in your directory including notebooks, inputs and outputs while the ``output_1.zip`` contains only the files you have placed inside the ``outputs/output_1`` folder.
+
+### Downloading Data
+ - Select the file you would like to download,
+ - Click the download button at the very bottom of the window.
+
+### Cloud Storage Types
+   To embed your data into Services and Studies, and to store, retrieve and maintain your data, we currently offer Sim-Core S3. This is accessible using the *File Picker* or the *Data* tab in the Dashboard. Files can be selected from there to be used within *Services*. Moreover, files can be added (e.g., from your local disk), deleted, or downloaded from one of the cloud storages to your computer.
+
+FIGURE
+
+   File access through the Data tab. 

docs/overview/dashboard/projects.md

@@ -1 +1,46 @@
 
+## Projects Tab
+
+Each card listed in the ```PROJECTS``` tab represents a simulation project that belongs to you or is shared with you. The user needs to click on the card and then click the ```OPEN``` button on the project details window to open the project. 
+
+### Project Details
+
+When you click on a project an overview page will be shown. This page shows more details on the project (e.g., the project description, creation date, etc...) and allows you to perform actions (e.g., opening it, sharing, etc...). Depending on the access rights, you will able to modify the Project details (e.g., description and thumbnail, add tags, etc.), by using the pencil icons.
+
+In addition, by clicking on the left-most icons, you will able to perform more operations on the project.
+
+FIGURE
+
+The Project Details.
+
+
+### Project Workbench
+
+After you open a project, click the ```Restore``` button at the right corner to open the *Interactive* view of the project workbench. You can select *Workbench* to create and edit your flow chart, see your *Services*, debug and run your project .
+
+FIGURE
+
+   The Project Workbench.
+
+
+(1) Primary Column
+ - In the Nodes list tab, you can see the list of Services that are included in the project and rename or delete them. To delete a Service, select the Service and then click the Delete button on the menu bar. You can also rename a Service by selecting a Service and clicking the rename button on the menu bar.
+ - In the Storage tab, you can browse all the data from any project you have created.
+
+(2) Secondary Column
+ - When no Service is selected, this tab will show the Project metadata.
+ - When a Service is selected as in the case of the image above, the inputs and output parameters of that service will be shown in separate tabs.
+
+(3) Workbench Views
+ - **Pipeline:** This is the default view of the pipeline, showing Services and their connections
+ - **Interactive:** When an Interactive Service is selected in the pipeline view or in the primary column, this tab will show the GUI for the Interactive Service
+ - **Logger:** This tab will display all messages pertinent to the running of your project. These messages can be filtered by keywords/keyphrases entered into the *Filter* field.
+
+(4) Run/Stop: For pipelines containing Computational Services, the Run button is used to execute the pipeline while the Stop button can abort a running pipeline.
+
+(5) Pipeline Workspace: When viewing the Pipeline tab, this is where you can create and edit the Project by adding new services, deleting services, and linking them together.
+
+(6) Service: Each Service is visible in the Pipeline workspace as a box with a name, input port, and/or an output port.
+
+(7) Dashboard: When you have finished working on your Project, click on the ```Dashboard``` button to go back to your Dashboard. While doing so, any changes you made to your project will be saved.
+

docs/overview/dashboard/services.md

@@ -1 +1,24 @@
+## Services
 
+Every Project is composed of one or more ```Services```. Services are building blocks for projects and can provide data/files, visualize results (2D, 3D), implement code in Jupyter notebooks or perform computations to execute simulations within a project. The computational backend involves all services needed to handle the actual computational workload. A computational workflow is described as a pipeline that sequentially processes a stream of data. Every pipeline consists of multiple algorithms, each one expecting specific input data and providing specific output data.
+
+All these services can be already provided within a project or can be set up from scratch by the user by selecting options in the Service catalog.
+
+FIGURE
+
+   Connected Services as well as selection of Services via the Service Catalog in the Workbench.
+
+### Service Types:
+
+ * **Computational**: Computational Services such as a ```Python Runner``` will allow the setting of some parameters (e.g., input files) and will perform a computation with no user interaction required. Interactive Services only perform tasks with user interaction, as is the case for services such as the ```JupyterLab```. JupyterLab services will allow you to write and execute code within the JupyterLab GUI, but as with all interactive Services, will not run automatically when a project pipeline is launched. Computational Services, on the other hand, will automatically read all input parameters at runtime and execute the static code embedded inside them.
+ * **Interactive:** In terms of viewing, Interactive Services will have a special view in the Workbench through the Interactive View tab. You may occasionally want to maximize this view to have a larger working area. To do this, you can click on the maximize button in the upper right-hand corner of the Interactive View.
+
+FIGURE
+
+   *Restore* button to get into the Interactive Mode.
+
+FIGURE
+
+   *Maximize* button in the Interactive Mode.
+
+This section functions very similarly in the ```TUTORIALS``` tab. To add services to an existing project, you may access the ```Service Catalog``` directly within a project workspace without going through the ```SERVICES``` tab.

docs/overview/dashboard/tutorials.md

@@ -1,9 +1,17 @@
 ## Tutorials
 
-A set of several tutorials will help you to get familiar with **_S4L_<sup>_lite_</sup>**.
+A set of several tutorials available in The ```TUTORIALS``` tab of the ```Dashboard``` will help you to get familiar with **Sim4Life**.
 
 <p align="center">
   <img width="90%" src="assets/dashboard/tutorials.png">
 </p>
 
-Clicking on any of the cards will create a copy of the tutorial in Projects so that you can continue working with the simulation file or results without changing the original tutorial project.
+Clicking on a tutorial project will create a copy of that project, which will appear in your own ```PROJECTS``` tab with the same name as the tutorial. Any changes you make to this copy will not affect the original tutorial. This is extremely useful, for example, if your team uses the same analysis pipeline but you may want to change an input file.
+
+### Grouping Tutorials
+
+By default, the tutorials will be displayed with a flat list. Alternatively, you can organize them by clicking on the ```Group``` button. For instance, you can group them by ```Tags```. Other grouping options are available, such as ```Shared with``` will group them by ```Organization```.
+
+
+
+