Jupyter Notebooks
Description
This catalog item starts a JupyterLab environment in which you can work with Jupyter notebooks.
Jupyter is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning, and much more.
All users in your Collaborative Organisation can login to the workspace and will then be presented with their own notebook environment.
If needed, we can help you to automatically install certain packages when the workspace is created, so that these are available from inside the Jupyter environment immediately. Please contact us for this. However, you can of course also install your own dependencies from with the Notebook.
Creation
Create a storage volume
If desired, first create a storage volume before creating the workspace.
See the Getting started page for more info about how and why to create a storage volume.
Create a workspace
In the Research Cloud portal click the ‘Create a new workspace’ button and follow the steps in the wizzard.
See the workspace creation manual page for more guidance.
Access
You can login to the workspace in your browser, via your ResearchCloud time-based password.
Usage
When logged in you are immediately presented with a JupyterLab environment in which you can work with different notebooks.
Data Transfer Jupyter Notebook
Use this table to find the appropriate data transfer method for your situation:
| Data Source | Recommended Tool | Best For | Skill Level |
|---|---|---|---|
| Your PC/laptop | JupyterLab Upload button | Small files, quick uploads | Beginner (GUI) |
| Yoda/iRODS | iBridges | All file sizes, CLI access | Beginner to Intermediate |
| Yoda/iRODS | iCommands | Large datasets, transfer automation, CLI | Intermediate (CLI) |
| SURFdrive, ResearchDrive, OneDrive | rclone | Cloud storage sync, scheduled transfers | Intermediate (CLI) |
| Your PC/laptop | scp | Direct one-time transfers | Intermediate (CLI) |
| Your PC/laptop | rsync | Sync or repeated transfers | Intermediate (CLI) |
| Your PC/laptop (Windows only) | MobaXterm | Graphical SSH/SFTP client | Intermediate |
| Your PC/laptop | Cyberduck | Graphical SFTP client | Intermediate |
| GitHub/GitLab | git clone | Code repositories, version control | Intermediate (CLI) |
All command-line tools (iBridges CLI, iCommands, rclone, scp/rsync, Git) must be run from the JupyterLab terminal.
See our data transfer manuals for detailed step-by-step guides.
Installing additional software
The user has admin rights to install additional software on the system from the Jupyter terminal (use sudo <command>).
Tips
Workspace security
Please take a moment to read the security recommendations for VREs.