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title BioShell
description A guide to accessing and using BioShell, a preconfigured cloud bioinformatics environment available on NCI Nirin and ARDC Nectar Research Cloud.
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Introduction

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.

BioShell is available through NCI Nirin and ARDC Nectar Research Cloud and is designed for researchers and learners at all stages. Whether you are a higher degree student running your first bioinformatics analysis, a trainer delivering a national workshop, or a researcher who needs a consistent and reproducible environment to share with collaborators, BioShell removes the technical overhead so you can focus on your 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.

Quick start guide

  1. Check you are eligible — confirm your project is life-science related and aligns with the five ABLeS principles.
  2. Identify your access pathway — most users apply through ABLeS; training organisers contact the BioCommons Training Team.
  3. Submit your access request — submit via the appropriate pathway and wait for your infrastructure placement to be confirmed.
  4. Accept your terms and conditions — accept the terms for your assigned infrastructure before access is granted.
  5. Connect to your BioShell environment via SSH — use the connection details provided in your provisioning notification.
  6. Choose your flavour — select the preconfigured environment profile that matches your task.
  7. Load a tool and run your analysis — use Bio-Shelley or module load to access tools from the BioShell tool library.
  8. 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.

How to cite

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.