Notebook Sessions

bioAF provides managed notebook sessions for interactive 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.

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