Wiki source code of Getting Started with HDC

Version 6.1 by Dennis Segebarth on 2024/12/20 15:00

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1.1	1	{{box cssClass="floatinginfobox" title="Table of Contents"}}
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	5	= Accessing HealthDataCloud (HDC) =
	6
	7	== Creating a User Account ==
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4.1	9	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>>url:https://ebrains.eu/register/]] to obtain one.
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	11	To create an HDC user account:
	12
	13	* Visit the HDC Portal at [[https:~~/~~/hdc.humanbrainproject.eu/>>url:https://hdc.humanbrainproject.eu/]] and click the Login button.
	14	* (((
	15	Click the EBRAINS button and enter your EBRAINS username and password.
	16	)))
	17	* (((
	18	Review and familiarize yourself with the Terms of Use, then click Accept to finalize your registration.
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4.1	20	* 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>>url:https://hdc.humanbrainproject.eu]] or at the bottom left corner (“Terms of Use”) of each page after logging into the HDC.
1.1	21	)))
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	23	Your personal information is collected to provide a user account and access to HDC services in accordance with the [[HDC Privacy Policy>>url:https://object.hdc.humanbrainproject.eu/public-resources/HDC-Privacy-Policy.pdf]].
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6.1	25	== Discovering the HDC - a Quick Start Guide ==
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6.1	27	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!
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	29	(% class="box warningmessage" %)
	30	(((
6.1	31	Important: Please note that the HDC central node platform has not yet undergone a GDPR audit and you are, therefore, not allowed to upload any sensitive data to the platform.
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	33
	34	=== Join the HealthDataCloud Test Project ===
	35
6.1	36	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:
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	38	1. Go to the Projects page using the the top-level navigation bar:
5.1	39	\\[[image:Projects_navigation_bar.png\|\|height="80" width="839"]]
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	41	1. Click on the Join Starting Project button:
5.1	42	[[image:Join_starting_project.png\|\|height="291" width="827"]]
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	44	1. 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>>https://xwiki.hdc.humanbrainproject.eu/bin/view/userguide/Managing%20HDC%20Projects/#HProjectRoles]] 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:
5.1	45	\\[[image:Screenshot 2024-11-25 104224.png\|\|height="294" width="458"]]
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	47	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:
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5.1	49	[[image:HDC_test_project_on_Projects_page.png\|\|height="283" width="869"]]
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	51
	52	The landing page of the HealthDataCloud Test Project will look like this (please refer to [[this section>>https://xwiki.hdc.humanbrainproject.eu/bin/view/userguide/HDC%20Portal%20Navigation/#HProjectsInterface]] of our User Guide article to learn more about the Projects Interface):
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	54	[[image:Landing_page_HDC_test_project.png\|\|height="430" width="872"]]
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	56
	57	(% class="box infomessage" %)
	58	(((
	59	Access permissions within the HDC are tied to your EBRAINS account and setting of new permissions may sometimes take a while to be updated. This can sometimes cause an "Access denied" error, when you try to access the HealthDataCloud Test Project after completing the steps above. To enforce an update of your permissions in your EBRAINS Account, simply logout and log back in to the HDC central node platform. The associated permissions of your EBRAINS account are now refreshed and you will be able to access the HealthDataCloud Test Project.
	60	)))
	61
6.1	62	=== Learn about Zone Restrictions ===
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6.1	64	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>>https://xwiki.hdc.humanbrainproject.eu/bin/view/userguide/Working%20with%20HDC%20Project%20Files%20in%20the%20Portal/]]), which introduce many additional features we won´t touch upon here.
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6.1	66	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>>https://xwiki.hdc.humanbrainproject.eu/bin/view/userguide/Managing%20HDC%20Projects/#HProjectRoles]] 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>>https://xwiki.hdc.humanbrainproject.eu/bin/view/userguide/Working%20with%20HDC%20Datasets/]] of our User Guide for more information about Datasets).
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6.1	68	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.
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6.1	70	=== Upload Data ===
4.1	71
6.1	72	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:
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6.1	74	1. Go to the File Explorer// //of the HealthDataCloud Test Project:
	75	\\[Screenshot]
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	77	1. 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:
	78	\\[Screenshot]
	79	\\
	80	1. 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.
	81	\\[Screenshot]
	82	\\
	83	1. You can check the progress of the upload by clicking on the File Status Icon. Please refer to [[this article>>https://xwiki.hdc.humanbrainproject.eu/bin/view/userguide/Working%20with%20HDC%20Project%20Files%20in%20the%20Portal/]] in our User Guide for many more features that are available when uploading data to the HDC, including the [[//Resumable Upload//>>https://xwiki.hdc.humanbrainproject.eu/bin/view/userguide/Working%20with%20HDC%20Project%20Files%20in%20the%20Portal/#HResumingFailedUploads]] feature that allows you to continue previous uploads that got interrupted, e.g. due to unstable network connections.
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6.1	85
	86	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>>https://xwiki.hdc.humanbrainproject.eu/bin/view/userguide/Working%20with%20HDC%20Project%20Files%20in%20the%20Portal/#HRequestingFileCopyfromtheGreenRoomtotheCore]] 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.
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	88	=== Working with Data in the //Core// ===
	89
	90	.. currently in prepartion ..
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1.1	97	== Obtaining your own HDC Project ==
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	99	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>>url:https://object.hdc.humanbrainproject.eu/public-resources/HDC-Access-Policy.pdf]].
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	101	== Joining a Project ==
	102
	103	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.
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	105	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.
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	107	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.
	108
	109	== Changing your Password or Forgot Password ==
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	111	Your HDC password is your EBRAINS password.
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	113	* To change your EBRAINS password, sign into [[EBRAINS>>url:https://www.ebrains.eu]] and click Manage Account in the upper right corner.
	114	* If you forgot your EBRAINS password, click Forgot Password from the EBRAINS Login window and follow the prompts to create a new password.
	115
	116	== Logging into the HDC Portal ==
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	118	* (((
	119	Open the [[HDC Portal>>url:https://hdc.humanbrainproject.eu/]] in a supported web browser.
	120
	121	* 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.
	122	)))
	123	* Click the Login button
	124	* (((
	125	Click the EBRAINS button and enter your EBRAINS username and password.
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	127	* If you don’t already have a valid EBRAINS account, please visit the [[EBRAINS registration page>>url:https://ebrains.eu/register/]] to obtain one, then return to the [[HDC Portal>>url:https://hdc.humanbrainproject.eu]] and log in with your EBRAINS username and password.
	128	)))
	129
	130	== Viewing your User Profile ==
	131
	132	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.
	133
	134	== Logging out of the HDC Portal ==
	135
	136	It’s recommended to always log out of the Portal whenever you finish using the platform or step away from your workstation.
	137
	138	* To log out of your session manually, click your username in the top right of the page and select Logout.
	139	* 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.
	140
	141	= How to get help =
	142
	143	== Consult the User Guide ==
	144
	145	This guide provides information on how to use the features of the HDC platform.
	146
	147	== Submit a Support Inquiry ==
	148
	149	* 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.
	150	* Anyone can submit an inquiry to the [[EBRAINS support team>>url:https://www.ebrains.eu/contact]].
	151
	152	== Watch for Upcoming Maintenance updates ==
	153
	154	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.
	155
	156	== Contact us ==
	157
	158	* Log in and submit a Support inquiry from the Portal Support section.
	159	* Submit a support inquiry to the [[EBRAINS Support Team>>url:https://www.ebrains.eu/contact]].
	160
	161	= HDC Portal organization =
	162
	163	The Portal consists of the following areas:
	164
	165	* Main Menu (common to all pages)
	166	* Dashboard
	167	* Projects Landing Page
	168	* Projects Interface
	169	* Datasets
	170	* Platform Management (for Platform Administrators only)
	171
	172	Detailed information on these components is offered in dedicated sections of the User Guide.
	173
	174	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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	177	----
	178
3.1	179	Copyright © 2023-2024 [[Indoc Systems>>url:https://www.indocsystems.com]].
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2.1	181	HealthDataCloud is powered by Pilot technology, a product of [[Indoc Systems>>url:https://www.indocsystems.com]].