Changes for page Using JupyterHub in HDC

Last modified by Dennis Segebarth on 2026/02/26 12:16

From 6.1 to 5.1

From version 21.1

edited by Dennis Segebarth
on 2026/02/26 12:16

Change comment: There is no comment for this version

To version 6.1

edited by Dennis Segebarth
on 2024/03/01 09:14

Change comment: There is no comment for this version

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  {{toc depth="2"/}}
  {{/box}}
--{{warning}}
--**Disclaimer:** This article may contain screenshots from other Pilot-based deployments. Differences only apply to variations in branding and color schemes, not the functionalities covered in this article, though.
--{{/warning}}
--
  JupyterHub is an open-source, multi-user version of Jupyter Notebook for performing analysis of Project files in the Core. More information can be found in the application documentation [[https:~~/~~/jupyter.org/>>https://jupyter.org/]].
--[[image:1723798240534-407.png||height="189" width="291"]]
++[[image:Jupyterhub-Logo-300x100px cropped.png||height="13%" width="20%"]]
  = How it Works =
@@ -29,13 +29,9 @@
  JupyterHub is configured at the time of Project Setup. If you launch JupyterHub and receive a notice that it hasn’t been deployed for your project, please contact your Platform Administrator.
--{{info}}
--If you access JupyterHub of the HealthDataCloud Test Project, please be aware that the resources are limited for each user to: 2 GB of persistent storage volume, 4 GB memory, and a single CPU. These limitations can easily be adjusted for new Projects.
--{{/info}}
--
  = Launching JupyterHub =
--[[image:1723798257792-201.png||height="121" width="349"]]
++[[image:HDC Project Workspace tool navigation Jupyterhub v1.0.0 2023-05-25.png||height="9%" width="25%"]]
 . Launch your Project and click the **JupyterHub icon** in the left menu bar.
 . Click **Sign in with Keycloak** to initiate your session. JupyterHub automatically authenticates with your existing username and password and launches your session - no additional sign-in is required.
@@ -50,7 +50,7 @@
 . In the Launcher, click the **Python 3 Notebook **icon, or click **File > New > Notebook**.
 . Create your Notebook.
--[[image:1723798278604-114.png||height="376" width="865"]]
++[[image:Project Workspace Jupyter Create Python Notebook v2.1.6 2023-02-07.png||height="22%" width="50%"]]
  = Launching the Terminal =
@@ -59,7 +59,7 @@
 . In the Launcher, click the **Terminal **icon, or click **File > New > Terminal**.
 . The terminal window opens.
--[[image:1723798293872-992.png||height="162" width="863"]]
++[[image:Project Workspace Jupyter Launch Terminal v2.1.6 2023-02-07.png||height="9%" width="50%"]]
  Ubuntu is used to host Jupyter Notebook. Use the command cat /etc/os-release to determine to current version of Ubuntu:
@@ -196,12 +196,12 @@
  Afterwards, the environment will be listed when you open the Launcher to open a new Jupyter Notebook:
--[[image:1723798325144-485.png||height="436" width="867"]]
++[[image:Project Workspace Jupyter view new Kernel 2023-07-11.png||height="25%" width="50%"]]
  and also from each opened Notebook, e.g., via **Kernel > Change Kernel…** :
--[[image:1723798338447-469.png||height="317" width="247"]]
++[[image:Project Workspace Jupyter Kernel change Kernel dropdown 2023-07-11.png||height="32%" width="25%"]]
  = Installing New Python Packages =
@@ -291,9 +291,9 @@
  * Open the login window and enter your HDC username and password (i.e. your EBRAINS account credentials).
  * Grant access by clicking **Yes**.
--[[image:1723798355215-434.png||height="352" width="379"]]
++[[image:Pilotcli Jupyter user login Grant Access window v2.4.0 2023-05-25.png||height="28%" width="30%"]]
--[[image:1723798365454-527.png||height="123" width="376"]]
++[[image:Pilotcli Jupyter user login Device Login Successful v2.4.0 2023-05-25.png||height="10%" width="30%"]]
  * After successful confirmation, return to the terminal in your JupyterHub browser tab.
@@ -376,7 +376,7 @@
  The file “Chemical Tracking Data.csv” can be viewed in the JupyterHub graphical user interface:
--[[image:1723798383409-873.png||height="267" width="874"]]
++[[image:Jupyter downloaded file in Home folder v2.4.11 2023-05-25 1850.png||height="15%" width="50%"]]
  == Uploading Project Data from JupyterHub using the Pilot Command Line Interface ==
@@ -417,10 +417,12 @@
  Chemical Tracking Data rev.csv  Chemical Tracking Data.csv
  {{/code}}
--[[image:1723798397694-530.png||height="217" width="863"]]
++[[image:Jupyterhub file upload back to core v2.4.11 2023-05-25 1926.png||height="13%" width="50%"]]
  ----
--Copyright © 2023-2026 [[Indoc Systems>>url:https://www.indocsystems.com]].
++Copyright © 2023-2024 [[Indoc Systems>>url:https://www.indocsystems.com]].
  HealthDataCloud is powered by Pilot technology, a product of [[Indoc Systems>>url:https://www.indocsystems.com]].
++
++

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