Using BioShell: Interactive environments

BioShell supports two browser-based interactive environments for notebook and script-based work. Both run on your BioShell instance and are accessible through your browser once you have connected via SSH.

Important: You must have an active SSH connection to your BioShell instance before opening either environment in your browser. See Connecting to BioShell.

JupyterLab

JupyterLab is a browser-based environment for writing and running Python, R, and shell notebooks. It is well suited to exploratory analysis, visualisation, and combining code with documentation.

Open your browser and go to:

http://<your-bioshell-ip>:8888

Fig 4. JupyterLab open in a browser connected to a BioShell instance.

RStudio

RStudio is a browser-based environment for R-based analysis. If you are familiar with the RStudio desktop application, the browser version works in exactly the same way.

Open your browser and go to:

http://<your-bioshell-ip>:8787

Fig 5. RStudio open in a browser connected to a BioShell instance.

Tip: Your SSH terminal and browser environments connect to the same BioShell instance. Any tool you have loaded with module load in your terminal is also available inside JupyterLab and RStudio.

Note: If you cannot reach JupyterLab or RStudio in your browser, check that your SSH connection is still active. If you are connecting from outside your institution’s network, you may need an SSH tunnel. Contact your local IT support for help with this.