VRE Lab

Description

This VRE Lab workspace hosts a JupyterLab environment that provides Jupyter notebooks alongside a number of useful applications accessible through the browser. This catalog item can easily be extended with additional applications to suit your research needs.

The workspace includes Python environment management with uv.

You can automatically install environments and dependencies for Python, R, Julia, and Conda using the Custom Packages Optional Component provided in this workspace.

If you wish to customise this workspace further by installing system packages or need additional help, you can contact us

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.

Optional Components

VRE Lab allows you to customise your workspace by selecting additional optional components during workspace creation. This lets you pre-install tools for your research needs.

During workspace creation, you’ll see an Optional components section where you can check the components you want to install.

Available components:

Open VSCode Server: Web-based integrated development environment (IDE) for coding directly in your browser.
OpenRefine UU: Data cleaning and transformation tool accessible from JupyterLab.
Python tools: Additional tools for managing Python environments (includes uv, poetry, and conda).
Custom Packages UU: Automatically install dependencies for Python, R, Julia, or Conda projects from Git repositories, Zenodo, Dataverse, or DOI links.

Custom Packages UU

If you select “Custom Packages UU”, you can provide a comma-separated list of project identifiers (e.g., GitHub URLs, Zenodo links, or DOIs) in the workspace parameters. These projects will be saved to /local-share with their dependencies installed in separate environments.

Simply check the boxes for the components you need, then continue with workspace creation. You can always install additional software later using sudo rights from the terminal.

Access

Accessing the Workspace

Open your SURF Research Cloud portal.
When choosing your catalog item, simply search for VRE Lab and click the yellow “Access” button.
Log in with your institutional credentials (Solis ID for UU users).

Since you’re already signed in to access SURF Research Cloud, you may not need to authenticate again.

Requesting Access to the Catalog Item Collection

Most Utrecht University users already have access to this catalog item. If you cannot find VRE Lab when creating a workspace:

You need to request access to the Utrecht University Catalog Item Collection.
Follow these steps to request access.
Once approved, you’ll be able to create VRE Lab workspaces.

Usage

After logging in, you’ll have access to the JupyterLab interface which includes:

Jupyter notebooks for interactive coding
Additional browser-based applications
Integrated terminal access

Data transfer options

See our data transfer manuals.

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)

You can upload data directly to the workspace using the Upload Files button in the JupyterLab interface.

For larger data transfers, the recommended iBridges client for Yoda and iRODS is preinstalled.

Sudo rights

Sudo rights can be obtained by adding collaboration members to the src_co_admin group in SRAM.

Members with sudo rights can install system-level packages and perform administrative tasks on the workspace.

Tips

This workspace includes uv for Python environment management. See the Python environment manual for best practices and getting started.

Workspace security

Please take a moment to read the security recommendations for VREs.