Notebook Sessions & Work Nodes

bioAF provides managed notebook sessions and interactive Work Nodes for analysis, no need to install anything locally or manage servers.

JupyterHub and RStudio

Choose the environment that fits your workflow:

  • JupyterHub: Python-based analysis with Jupyter notebooks
  • RStudio Server: R-based analysis with the full RStudio IDE

Both run in your browser. Your files are saved to cloud storage, so your work persists across sessions.

Work Nodes

When a browser notebook isn’t enough, launch a Work Node: a full Linux virtual machine you can SSH into and use like your own workstation.

  • SSH access, with conda environments and your GitHub repositories pre-cloned
  • Bring your own command-line tools, not just Python or R
  • Ideal for prototyping a custom pipeline before promoting it to the catalog

Work Nodes use the same versioned environments and the same idle auto-stop as notebook sessions.

Automatic output persistence

Whether you use a notebook session or a Work Node, your outputs are saved to cloud storage automatically. Your files survive idle auto-stop and restarts, so nothing is lost when a session shuts down: you pick up exactly where you left off when you return.

Versioned environments

Every notebook session runs in a versioned environment, a specific set of packages and tools. This means:

  • Your analysis is reproducible: the same environment produces the same results
  • You can update packages without breaking existing work
  • You can always go back to a previous environment version

Create environments by uploading a Dockerfile or conda specification. bioAF builds the image and makes it available for sessions.

Notebook session environment selection RStudio Server running in browser within a bioAF notebook session

Idle auto-stop

To manage costs, sessions automatically stop after a configurable idle period. When you come back, restart the session and pick up where you left off, your files are still there.

i How does idle detection work?
bioAF monitors your session for activity (keyboard input, running computations). If there's no activity for the configured timeout period (default: 60 minutes), the session shuts down gracefully, saving your work to cloud storage.

Terminal access

Need a command line? Click the Terminal button on any running session to open a browser-based terminal directly into the session container. This is useful for:

  • Installing one-off packages
  • Running quick shell commands
  • Debugging environment issues