Y7q3 (#67)

* Added new tutorial

* refactor instructions to submit new services: point users to the cookiecutters

* update intro about SPARC/SPARC cores

* Update to study 3-dots button

* update to animations/screenshots for creating studies

* update retrieving_files with new design

* updates to data doc, user menu and study

* update support sections

* typos and minor improvements

* changes to codeowners

.github/CODEOWNERS

@@ -1,8 +1,8 @@
 *.py         @pcrespov
-*.md         @drniiken
+*.md         @elisabettai
 Makefile     @pcrespov
 
 /tools/      @pcrespov
-/docs/       @drniiken
-/docs/welcome/ @KZzizzle
+/docs/       @elisabettai
+/docs/welcome/ @elisabettai
 /docs/codeathon-2022.md @elisabettai

docs/platform_introduction/Data.md

@@ -3,7 +3,7 @@ The data tab allows you to browse the output files of all of your active pipelin
 
 In this tab, you will find a file tree with ```My Data/simcore.s3```. Expanding ```simcore.s3``` will display a folder for each of your Studies with the title of that Study. Expanding the folder of each Study will allow you to access the data (outputs or notebooks) belonging to each Service within that Study. 
 
-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.
+For JupyterLab and other Interactive Services, clicking on the folder corresponding to the Study will show the `workspace` folder. This folder contains all the files that you created in the `workspace` folder of you Service, including notebooks.
 
 ## Downloading Data
 To download files:

docs/platform_introduction/profile.md

@@ -4,36 +4,29 @@ In the right top corner (clicking on the user icon/avatar), the user and platfor
 
 Clicking on the icon provides:
 
-* the user preferences dialog
+* the user account dialog: username and password
+* user preferences
 * organizations dialog, see more information [here](/docs/study_setup/sharestudy.md#organization).
+* the light/dark theme switch
 * information about the current platform and versions of essential parts
 * licence information
 * logout from the platform
 
-![user_menu](https://user-images.githubusercontent.com/18575092/223439622-ca90f973-29dc-4317-8a90-3b7eeac075e3.png ':size=200%')
+![image](https://github.com/ITISFoundation/osparc-manual/assets/18575092/292f5541-d2db-4af8-a2c5-35ac93c241fc)
 
 ## Preferences
 Entering the preferences dialog, a separate window pops up which allows the user to define and modify settings and preferences as follows:
 
-* __Profile Settings__ <br/>
-  Information like name and profile picture - the picture is based on your [gravatar](https://en.gravatar.com/).
-
-* __Security Settings__ <br/>
-  Here the user can set/change the password to their account.
+* __Confirmation Settings__ <br/>
+  Here, the User can toggle confirmation pop-ups throughout the platform, such as the confirmations when deleting a Study or a Service. We urge caution when disabling these alerts as we cannot retrieve deleted studies.
 
-* __API Settings__ <br/>
+* __API Keys/Tokens__ <br/>
   Here the user can generate API key and secret pairs for use with the API (see [here](https://itisfoundation.github.io/osparc-simcore-clients/#/) for more API documentation). Users can also specify access tokens for the DAT-Core/Pennsieve platform - for automated access of files (storage, retrieval) on Pennsieve.
 
-* __Additional (and Experimental) Settings__ <br/>
-  Here, e.g., the UI Theme can be set (light vs dark) and input/output ports can be set to map automatically. More details about this feature can be found [here](docs/study_setup/connecting_services?id=auto-connect-option).
+* __Create/Edit Tags__ <br/>
+  Here you may define custom tags, or labels, for your Studies, that are only visible to you. See [here](/docs/platform_introduction/user_setup/annotations.md#tags) more information on how you can use them.
 
-  ![prefs](https://user-images.githubusercontent.com/18575092/223441101-19c2b0d1-8fe9-438e-934a-cee9fd745289.png ':size=600') <br/>
 
-* __Confirmation Settings__ <br/>
-  Here, the User can toggle confirmation pop-ups throughout the platform, such as the confirmations when deleting a Study or a Service. We urge caution when disabling these alerts as we cannot retrieve deleted studies.
+![image](https://github.com/ITISFoundation/osparc-manual/assets/18575092/f076bbcc-655b-4148-b253-48610d6996f3)
 
-* __Tags__ <br/>
-  Here you may define custom tags, or labels, for your Studies, that are only visible to you. See [here](/docs/platform_introduction/user_setup/annotations.md#tags) more information on how you can use them.
 
-* __Organizations Settings__ <br/>
-  Here you may review the organizations you are a part of, create new organizations, or manage the membership and access rights of organizations where you are a maintainer. See [Sharing](/docs/study_setup/sharestudy.md) for more information about Organization settings. 

docs/platform_introduction/studies.md

@@ -15,44 +15,44 @@ In addition, by clicking on the left-most icons, you will able to perform many m
 
 There are a number of operations that are specific to Studies, accessible by the three dots button at the upper right hand corner of each Study or from the Study Details window.
 
-![studyoptions](https://user-images.githubusercontent.com/18575092/267010897-fe6f4de4-415f-450c-8d7b-e7c8d2dd3a8f.png ':size=200')
+![studyoptions](https://github.com/ITISFoundation/osparc-manual/assets/18575092/3f9ecd5d-9396-4e9a-b0b6-2c963d76e792)
 
 
 These operations are:
-1. **Open:** it will open the Study and bring you to the [Study Workbench](#study-workbench). Depending on the amount of data in the Study, this operation may take few seconds-minutes
-2. **Title:** allows you to rename the Study. You can do the same from the Study details page
-3. **Study Files:** allows you to download [data](/docs/platform_introduction/Data.md) produced by your Study
-4. **Sharing:** allows you to [share](/docs/study_setup/sharestudy.md) your study with other users of the platform
-5. **Tags:** you can add custom [tags](/docs/platform_introduction/user_setup/annotations.md#tags) to your Study/Template to help you classifying and filtering them
-6. **Duplicate** allows you to create a copy of that Study (which will have the same name of the original study + "Copy")
-7. **Export cMIS**: this will download various Excel files that you need to adhere to the [SPARC Dataset Structure (SDS)](https://docs.sparc.science/docs/overview-of-sparc-dataset-format) and publish your computational Study on the [SPARC Portal](sparc.science). In addition, if you have provided a [Quality](/docs/platform_introduction/user_setup/annotations.md#quality) assessment by filling in the Ten Simple Rules (TSRs) rating rubric, the rating values will be also exported.
-8. **Delete:** as you may guess, this will delete the particular Study, with a confirmation popup. This will be allowed only if you are the [Owner](/docs/study_setup/sharestudy.md#user-roles) of a Study. Warning: deleting a Study cannot be undone!
+1. **Open**: it will open the Study and bring you to the [Study Workbench](#study-workbench). Depending on the amount of data in the Study, this operation may take few seconds-minutes
+2. **Rename**: allows you to rename the Study. You can do the same from the Study details page
+3. **Thumbnail**: by clicking here, you can add a thumbnail to your Study. This requires being the owner of the Study or having write access*
+4. **Duplicate**: allows you to create a copy of that Study (which will have the same name of the original study + "Copy")
+5. **Export cMIS**: this will download various Excel files that you need to adhere to the [SPARC Dataset Structure (SDS)](https://docs.sparc.science/docs/overview-of-sparc-dataset-format) and publish your computational Study on the [SPARC Portal](sparc.science). In addition, if you have provided a [Quality](/docs/platform_introduction/user_setup/annotations.md#quality) assessment by filling in the Ten Simple Rules (TSRs) rating rubric, the rating values will be also exported.
+6. **Share**: allows you to [share](/docs/study_setup/sharestudy.md) your study with other users of the platform*
+7. **Tags**: you can add custom [tags](/docs/platform_introduction/user_setup/annotations.md#tags) to your Study/Template to help you classifying and filtering them
+8. **Study Files**: allows you to download [data](/docs/platform_introduction/Data.md) produced by your Study
+9. **Delete**: as you may guess, this will delete the particular Study, with a confirmation popup. This will be allowed only if you are the [Owner](/docs/study_setup/sharestudy.md#user-roles) of a Study. Warning: deleting a Study cannot be undone!
 
-This is just a list of the most important operations, feel free to click on the other tabs and discover more.
 
 *To learn about Study sharing and publishing, see [Sharing and Publishing Studies](/docs/study_setup/sharestudy.md)*
 
 ## Study Workbench
 
-Double-clicking on a Study from the **Dashboard** will bring you to the Study's workbench. This is where you will create and edit your flow chart, see your Services, debug and run your Study.
+Clicking on a Study from the **Dashboard** and then on the `Open` button will bring you to the Study's workbench. This is where you will create and edit your Study, see your Services, debug and run your Study.
 
-![image](https://github.com/ITISFoundation/osparc-manual/assets/18575092/0eed1a66-822c-4efb-be43-945db69e72cc)
+![image](https://github.com/ITISFoundation/osparc-manual/assets/18575092/baf3dd2c-0505-4aac-b6fa-506b0c22cb0d)
 
 The **Workbench** consists of four main windows, shown in the image below:
 1. **Primary Column:** 
     * In Nodes List tab, you can see the list of Services that are included in the Study 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 Study you have created.
 2. **Secondary Column:** 
-    * When no Service is selected, this tab will show the Study 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.
+    * When no Service is selected, this tab will show the Study metadata, [App Mode](./appmode.md) settings and Annotations (or "sticky-notes")
+    * When a Service is selected as in the case of the image above, the inputs and output parameters of that service will be shown.
 3. **Workbench Views:** 
     * **Pipeline**: this is the default view of the pipeline, showing Services and their connections
     * **Interactive**: when an [Interactive Service](/docs/platform_introduction/services.md#service-types) 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 Study. These messages can be filtered by keywords/keyphrases entered into the “Filter” field.
 4. **Run/Stop** for pipelines containing [Computational Services](/docs/platform_introduction/services.md#service-types), 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 are able to create and edit the Study 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 with your Study, click on the **Dashboard** button to go back to your Homepages. While doing so, any changes you made to your study will be saved.
+7. **Dashboard:** when you have finished working with your Study, click on the **Dashboard** button to go back to your Homepage. While doing so, any changes you made to your study will be saved.
 
 <!-- 3. **Sharing** allows you view who the Study is shared with and to add collaborators to the Study. See [Sharing Studies](/docs/study_setup/sharestudy.md) for more details.
 4. **Quality:** allows you to view (and edit depending on your permissions) the quality of a Study according to the [Ten Simple Rules](https://www.imagwiki.nibib.nih.gov/content/10-simple-rules-conformance-rubric) for computational modeling.

docs/study_setup/add_service.md

@@ -38,10 +38,9 @@ You can also open the same window by clicking on the Study card and then selecti
 
 
 ### Update a Service from inside the Study
-It is also possible to update a Service from inside the Study Workbench (Secondary Column). When you click on a node (Service) that can be updated, you will find the *Update Service* function after clicking on the gears icon (see image below). To update the Service, just follow the instructions (Stop the Service, this will also trigger the saving of the data inside the service, update it, and restart it).
-
-![boot-options-workbench](https://github.com/ITISFoundation/osparc-manual/assets/18575092/12de41da-a76d-4255-91e8-85848fb9f6f3)
+It is also possible to update a Service from inside the Study Workbench (Secondary Column). When you click on a node (Service) that can be updated, you will find the *Update Service* function under the "Options" section in the Secondary Column. To update the Service, just follow the instructions (Stop the Service, this will also trigger the saving of the data inside the service, update it, and restart it).
 
+![image](https://github.com/ITISFoundation/osparc-manual/assets/18575092/f4ad2fd4-3fbb-4eb2-8d1d-a8c76ffab36f)
 **Items of note:**
 - It is only possible to update to the latest version
 - All settings and data will be preserved when updating

docs/study_setup/create_study.md

@@ -3,19 +3,22 @@
 ## Study From Scratch
 You may choose to create a Study (*o²S²PARC* project) from scratch or based on an existing Template. To create an empty Study with no Services inside, navigate to the **Studies** tab of the **Dashboard** and click on the ```Empty Study``` button, which will take you directly to the **Study Workspace** of your new Study.
 
-![emptystudy](../../_media/emptystudy.png)
+![image](https://github.com/ITISFoundation/osparc-manual/assets/18575092/885508bc-4e7a-4b8f-a1b9-0ed1647dc6af)
 
 ## Study From Template
 
 You may also create the Study from an existing Template, navigate to the **Templates** tab of the **Dashboard** and click on an existing card. This will create a copy of the Template Study which will from this point on, be accessible from the **Studies** tab of the **Dashboard**. This Study will be private unless you decide to share it an any changes you make to the resulting Study will not affect the Template you have copied from. 
 
-![template](https://user-images.githubusercontent.com/28002886/153609911-f50dcbeb-103b-42a8-ba65-0db312803586.gif)
+![study_from_template](https://github.com/ITISFoundation/osparc-manual/assets/18575092/27f1cecb-4d52-49f0-8a95-209bf5571e8f)
 
 ## Copying a Study
 You may choose to create a Study from an existing one by creating a copy of it. To create a copy of a Study go to the **Studies** tab of the **Dashboard**, click on the ```More options``` (3-dots) button on the Study card and select ```Duplicate```.
 
 If the study is small (it contains few MB of data) the copy will take few seconds, while it might take longer for larger Studies. In those cases, you will be informed about the progress (see animation below). The copying process works similar to [Publishing a Study as a Template](../study_setup/sharestudy.md#publishing-a-study-as-a-template).
 
-![copy_studies](https://user-images.githubusercontent.com/18575092/207315848-7c049250-96d1-42f0-bc30-409186f9b6ec.gif)
+![duplicate_study](https://github.com/ITISFoundation/osparc-manual/assets/18575092/9ef0d194-eedb-4a8b-8f9d-b38f83563bea)
 
 **Note**: copying is limited to Studies that are smaller than 100 GiB. Please [**contact us**](../support/support.md) if you cannot reduce the size and you need to copy a large Study. 
+
+## Study from a Service
+When you go to the o²S²PARC Dashboard, click on the Services tab and then open a new Service, a new Study will be created that contains that Service. Once you close the Study, it will appear on your Studies tab in the Dashboard.

docs/study_setup/loading_data/retrieving_files.md

@@ -1,12 +1,13 @@
 # Retrieving Files
 
-Some Services will provide you with output files. To access these files, click on the Service which supplies output. This action will show the Service parameters in the *Secondary Column* of the **Workbench** with the Service's inputs shown by default. To access the Service outputs, click on the the outputs icon. The Service's computed outputs will be shown and if files have been generated, they will appear as clickable links. Clicking on a file link will either download it to your local computer or, in specific cases (such as for PDF files), will open a new browser tab where you can preview the file. You may also access output files by clicking on the ```Artifacts``` button on the lower part of the Service outputs window. 
+Some Services will provide you with output files. To access these files, click on the Service which supplies output. This action will select the Service parameters and show its Inputs and Outputs in the *Secondary Column* of the **Workbench**.
 
-![Outputs](https://user-images.githubusercontent.com/28002886/153729409-31dfdb29-70be-4ee0-8b98-2ad91999decd.png)
+ The Service's computed outputs will be shown and if files have been generated, they will appear as clickable links. Clicking on a file link will either download it to your local computer or, in specific cases (such as for PDF files), will open a new browser tab where you can preview the file. You may also access output files by clicking on the ```Service data``` button on the lower part of the Service outputs section. 
 
-When the ```Artifacts``` button is clicked, a popup will show the output folder for this Service. You may then download these files locally by clicking the ```Download``` button with the cloud icon in the lower left hand corner. For Computational Services that have run, you will also find a log file under ```Artifacts``` to help you debug runtime errors or to keep as a record. This file is not show in the Service Outputs because it is not a true output parameter of the Computational Service.
+![Outputs](https://github.com/ITISFoundation/osparc-manual/assets/18575092/e142ac23-05f4-46f7-b72d-bf4a8765dc79)
+
+When the ```Service data``` button is clicked, a popup will show the output folder for this Service. You may then download these files locally by clicking the ```Download``` button with the cloud icon in the lower left hand corner. For Computational Services that have run, you will also find a log file under ```logs.zip``` to help you debug runtime errors or to keep as a record. This file is not show in the Service Outputs because it is not a true output parameter of the Computational Service.
 
-![Screenshot 2019-07-18 at 22 35 57](https://user-images.githubusercontent.com/28002886/153730102-2f4020c6-98ce-4296-8bcf-f49a0b01bb23.png)
 
 ## Other Files