| title | |
|---|---|
| description | A guide to accessing and using BioShell, a preconfigured cloud bioinformatics environment available on NCI Nirin and ARDC Nectar Research Cloud. |
| sidebar | false |
BioShell is a ready-to-use cloud bioinformatics environment designed to get you from data to results with as little setup as possible. Rather than spending time configuring software on your own machine, you connect to BioShell and find a fully equipped workspace already waiting for you — with the tools, compute power, and interactive environments you need to run analyses that would be impractical on a laptop.
Whether you are a higher degree student running your first bioinformatics analysis or a trainer delivering a national workshop, BioShell removes the technical overhead so you can focus on delivering science.
This guide walks you through requesting access, choosing the right environment for your work, and using BioShell's built-in tools and support features. It assumes you are comfortable with basic command-line navigation, but no prior experience with cloud infrastructure, containers, or software installation is needed. BioShell is developed by Australian BioCommons as part of the ABLeS programme and supports the BioCommons Training cooperative and Bioinformatics ToolFinder.
Note: This guide does not cover how to provision a virtual machine on Nectar or NCI, or how to build a BioShell instance from scratch. See the BioShell GitHub repository and the infrastructure documentation for those topics.
Tip: New to cloud computing or virtual machines? Read Why use a cloud workspace? first — it explains what BioShell is, how it compares to HPC, and whether it is right for your work.
- Check you are eligible — confirm your project is life-science related and aligns with the five ABLeS principles or Australian BioCommons Co-hosted Event standards.
- Submit your access request — submit via the appropriate pathway and wait for your infrastructure placement to be confirmed.
- Understand Acceptable use policy and service terms — accept the terms for your assigned infrastructure before access is granted.
- Connect to your BioShell environment via SSH — use the connection details provided in your provisioning notification.
- Find data and tools to run your analysis — use Bio-Shelley or
module loadto access tools from the BioShell tool library. - Launch an interactive environment — open JupyterLab or RStudio directly in your browser for notebook-based work.
Tip: Not sure which tools are available or how to load them? Run
shelley-bio search "<what you want to do>"for instant suggestions.
If you use BioShell in your research or training, please cite it as:
O'Brien M, Jaya F, Samaha G, Xue W, Al Bkhetan Z, Botting A, Gustafsson J. (2026). BioShell how-to guide. Australian BioCommons. [AUTHOR TO SUPPLY — Zenodo DOI once minted]
Fig 1. Overview of the BioShell access and use flow: from submitting an access request through to connecting, choosing a flavour, loading tools, and launching interactive environments.
BioShell is delivered through a collaboration between Australian BioCommons, the Sydney Informatics Hub at the University of Sydney, ARDC Nectar Research Cloud, and the National Computational Infrastructure.
