Accessing HealthDataCloud (HDC)

Creating a User Account

All active EBRAINS users can use their EBRAINS credentials to create a user account in the HealthDataCloud central node platform. If you don’t already have a valid EBRAINS account, please visit the EBRAINS registration page to obtain one.

To create an HDC user account:

• Visit the HDC Portal at https://hdc.humanbrainproject.eu/ and click the Login button.

• Click the EBRAINS button and enter your EBRAINS username and password.

• Review and familiarize yourself with the Terms of Use, then click Accept to finalize your registration.

  • Note, the Accept button isn’t activated until you scroll down to the end of the document. You may export the Terms of Use as a PDF file or review them at any time from both the HDC website or at the bottom left corner (“Terms of Use”) of each page after logging into the HDC.

Your personal information is collected to provide a user account and access to HDC services in accordance with the HDC Privacy Policy.

Discovering the HDC - a Quick Start Guide

With the release of Pilot-HDC v1.3, you can now discover all features of the HealthDataCloud central node platform on a self-serve basis. Here, we prepared a quick start guide that you can follow along, or explore the platform on your own - it´s now easier than ever!

Join the HealthDataCloud Test Project

Before being able to test the platforms features, you have to join one of its Projects. A Project is an isolated, access-controlled data management unit in HDC that holds all of the data and computational resources relating to a research project. Projects are owned by a Project Administrator, a role analogous to an academic Principal Investigator. Usually, joining a Project requires the corresponding Project Admin to invite you to join. However, for testing and discovering of the HDC features, we created the HealthDataCloud Test Project, which you can join yourself at any moment by the click of a button. To do so:

1. Go to the Projects page using the the top-level navigation bar:
   
   
    
2. Click on the Join Starting Project button:
   
    
3. A pop-out window will open and confirm that you successfully joined the HealthDataCloud Test Project with the role of a Project Collaborator (see this section of our User Guide for more information about the different roles and associated permissions) and remind you again to not upload any sensitive information or data to this Project:
   
   

You can now proceed to the landing page of the HealthDataCloud Test Project, either by clicking on the Go to Project button in the pop-out, or via the Projects page using the navigation bar, where the HealthDataCloud Test Project will now be listed:

The landing page of the HealthDataCloud Test Project will look like this (please refer to this section of our User Guide article to learn more about the Projects Interface):

Learn about Zone Restrictions

As a Research Data Management Platform, the central features of the HDC evolve around data flows, and how compliance with data privacy regulations can be ensured by default and by design. In this quick start guide, we´ll help you gain a general understanding of the Platforms design and access restrictions that apply in it´s different zones. Once you complete this guide, however, we highly recommend you have a look at our in-depth articles about the respective topics (for instance, see Working with Project Files in the Portal), which introduce many additional features we won´t touch upon here.

Any data that is uploaded to the platform first lands in the Green Room zone of the respective Project. The Green Room is a dedicated and highly isolated storage area within each Project, where only the Project Administrator(s) and the user who uploaded the data have access to it. This allows the Project Administrator(s) to verify that the data are compliant with the respective Project’s data management plan before being copied to the Core zone of the Project. This is important, as data in the Core automatically becomes accessible to all members who have at least the Project Collaborator role (see this section of our User Guide for more information about the different roles and associated permissions). Data that was transferred into the Core zone of a Project can then also be organized into Datasets. In brief, Datasets are collections of related Project files, folders, and detailed metadata. The Dataset feature allows users to organize Project files, enrich with annotations, validate data structures, and publish controlled versions for sharing (see this article of our User Guide for more information about Datasets).

The HDC also offers Workspace Tools, i.e. direct integration of computational tools like JupyterHub that allow you to view, process, analyze, or annotate and describe your data. In general, Workspace Tools can be deployed in both Green Room and Core zones, depending on the Projects needs. In the HealthDataCloud Test Project, however, all Workspace Tools (the virtual programming environment JupyterHub, the business intelligence tool Superset, the Virtual Machine interface Guacamole, and the documentation tool XWiki) are deployed in the Core zone.

Upload Data

Now that you have a high-level understanding of the different zones within the HDC, let´s start by uploading some test data to the platform via the it´s web interface, i.e. the Portal. Please be reminded again, however, to abide by the Platform Terms of Use and any Project-specific restrictions when using the Portal, and - specifcally - that you are not allowed to upload any sensitive data to the HealthDataCloud Test Project. To upload data:

1. Go to the File Explorer of the HealthDataCloud Test Project:
   
   
    
2. You automatically land in your home directory within the Green Room zone, which is also indicated in the UI. Feel free to create a new folder and, once you selected the destination folder to which you´d like to upload, please click on Upload:
   
   
    
3. A pop-out window will open and prompt you to specify the file(s) or folder(s) you´d like to upload. Once you selected data to upload, click on Upload to start the upload, or click on Cancel to abort. Once more: Please remember that you are not allowed to upload sensitive data to the HealthDataCloud Test Project.
   
   
    
4. You can check the progress of the upload by clicking on the File Status Icon. Please refer to this article in our User Guide for many more features that are available when uploading data to the HDC, including the Resumable Upload feature that allows you to continue previous uploads that got interrupted, e.g. due to unstable network connections.

Congratulations - you now know about the most important and basic functionality of the HDC. As a next step, you´d usually want to copy the newly uploaded data from the Green Room to the Core of the Project, in order to work on them collaboratively with your team. If you are not a Project Administrator, though, you do not have the permissions to directly copy data between zones. Instead, you will have to open a Copy to Core Request, which needs to be approved by a Project Administrator - giving them the chance to validate that the data complies with the Projects Data Management plan (see this section in our User Guide for a more detailed description of this process). In our Quick Start Guide, we´ll instead continue with working on some data that already resides in the Core of the Project and can be accessed collaboratively.

Working with Data in the Core

As outlined in above section Learn about Zone Restrictions, data in the Core zone of a Project is shared with all Project members that have at least the Project Collaborator role to foster collaboration. You can browse all accessible data by using again the File Explorer, click on Core, and then navigate to the folder of interest. In this Quick Start Guide, we will now introduce how you can leverage Workspace Tools like JupyterHub to process, analyze, and visualize your data. For this, 

1. Click on the JupyterHub icon to launch your own server within the HealthDataCloud Test Project:
   
   
    
2. If prompted, select to "Sign in with Keycloak" which allows you to continue using single sign-on (SSO). Next, make sure to select the Datascience Environment which will launch your instance of JupyterHub with all the required packages preinstalled. After clicking on start, you can see the status of your server launch indicated by a progress bar:
   
   
    
3. Once your server has launched, you can use JupyterHub as you´re used to in order to create Jupyter Notebooks or write scripts. For this Quick Start Guide, we´ll continue to use the Terminal in order to leverage the platform´s command line interface (CLI), pilotcli to move data between your Project and the Workspace Tools:
   
   
    
4. Now you´ll authenticate your session with the pilotcli by executing the command pilotcli user login to initiate the login process. This will output a link:
   
   
    
5. Please use a new browser tab or window to access the link from step 4. Then grant the requested permission to complete your login process:
   
   
    
6. Back in JupyterHub, the Terminal will confirm your successful login, which allows you to perform the final step of this section, which is to copy a demo Juypter Notebook that guides you through the entire remaining process by executing the following command in the JupyterHub Terminal: pilotcli file sync hdctestproject/dsegebarth/tabula_muris_facs/tabula_muris_demo.ipynb .
   
   
    
7. This will download a demo Jupyter Notebook with rich annotations and explanations, guiding you through the process of how a typical analysis workflow within HDC using Jupyter Notebooks could look like. Please feel free to follow along and execute the cells of the notebook, which will download the remaining data as needed.
   
   

There are obviously many more features that the HDC has to offer, which are explained in great detail in other sections of this User Guide. We hope this Quick Start Guide allowed you to gain a good understanding of the core features and functionalities of the HDC and how they can support your collaborative day to day work. For more information on how to request the creation of your own HDC Project that allows you to on-board your team and specify the computational resources needed, please have a look at the following sections.

Obtaining your own HDC Project

A Project is an isolated, access-controlled data management unit in HDC that holds all of the data and computational resources relating to a research project. Projects are owned by a Project Administrator, a role analogous to an academic Principal Investigator. If you’re interested in starting up your own HDC Project, please contact the HDC team (see Contact Us). Access to HDC is governed by the HDC Access Policy.

Joining a Project

If a Project Administrator has invited you to join an HDC Project and you already have an HDC user account, you’ll receive an email informing you of your new Project membership and role. You’ll be able to access the Project the next time you log in.

If you received an invitation to join an HDC Project but don’t already have a user account, you can complete your account registration following the instructions in the invitation email (see Creating a User Account) and then log in to the Portal and access your Project.

If you’re a Project Administrator, the Platform Administrator will invite you to your new Project. Consult the article Managing HDC Projects for more information.

Changing your Password or Forgot Password

Your HDC password is your EBRAINS password.

• To change your EBRAINS password, sign into EBRAINS and click Manage Account in the upper right corner.
• If you forgot your EBRAINS password, click Forgot Password from the EBRAINS Login window and follow the prompts to create a new password.

Logging into the HDC Portal

• Open the HDC Portal in a supported web browser.

  • Popular browsers like Google Chrome, Mozilla Firefox, Microsoft Edge, and Apple Safari are supported. Some older browser versions as well as other browsers like Internet Explorer may not be supported.
• Click the Login button

• Click the EBRAINS button and enter your EBRAINS username and password.

  • If you don’t already have a valid EBRAINS account, please visit the EBRAINS registration page to obtain one, then return to the HDC Portal and log in with your EBRAINS username and password.

Viewing your User Profile

Click your username in the top right corner of any page and click Account to open your account profile page. The account page displays your user profile information, Project membership, and recent activities relating to your account.

Logging out of the HDC Portal

It’s recommended to always log out of the Portal whenever you finish using the platform or step away from your workstation.

• To log out of your session manually, click your username in the top right of the page and select Logout.
• Idle sessions are logged out for added security. After a period of inactivity, a warning reminds you that your session is about to expire. If no further action is performed and no active processes are running, your session will be logged out automatically.

How to get help

Consult the User Guide

This guide provides information on how to use the features of the HDC platform.

Submit a Support Inquiry

• Users logged into the HDC portal can view the Support panel by clicking Support from the top right of any page. Here, you will find Frequently Asked Questions (FAQs) and, after scrolling to the bottom of the support panel, a form to submit a Support inquiry.
• Anyone can submit an inquiry to the EBRAINS support team.

Watch for Upcoming Maintenance updates

The support team announces planned maintenance with notifications displayed after logging into the portal. If you see an Upcoming Maintenance notice, take note of future downtime periods and plan your platform use to minimize the impact on your work.

Contact us

• Log in and submit a Support inquiry from the Portal Support section.
• Submit a support inquiry to the EBRAINS Support Team.

HDC Portal organization

The Portal consists of the following areas:

• Main Menu (common to all pages)
• Dashboard
• Projects Landing Page
• Projects Interface
• Datasets
• Platform Management (for Platform Administrators only)

Detailed information on these components is offered in dedicated sections of the User Guide.

HDC also offers a full-featured Command Line Interface, pilotcli, a binary executable program that provides advanced users with convenient tools for performing file actions and platform-related tasks programmatically. For more information on the Command Line Interface, see Working with HDC Project Files in the Command Line Interface.

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HealthDataCloud is powered by Pilot technology, a product of Indoc Systems.