A ready-to-use cloud bioinformatics environment for life-science researchers, trainers, and developers.
Getting started
Why use a cloud workspace for bioinformatics?
An introduction to virtual machines, cloud computing, and why BioShell is a great starting point for life-science researchers and workshop participants.
Check out the community
See the training workshops and research outcomes supported by BioShell, and how you can get involved.
Using BioShell
Accessing BioShell
How to check your eligibility, request access to BioShell, and connect to your environment for the first time.
Connecting to BioShell
How to connect to your BioShell environment via SSH and what to expect on first login.
Choosing the right environment size
How to choose the right number of CPUs, memory, and storage for your BioShell environment.
Interactive environments
How to use JupyterLab and RStudio browser-based coding environments in BioShell.
Using Nextflow with CVMFS
How to run Nextflow workflows on BioShell using containers already available in CVMFS instead of downloading them.
How to use Shelley
A collection of guides for finding, building, and installing bioinformatics tools with Shelley
Tools and reference data
How to find, install, and load bioinformatics tools and reference datasets in BioShell using CVMFS, Shelley, and sHPC.
Support
Project support
Get help with your BioShell project from the Australian BioCommons team.
Submit a requestSource code
BioShell is open source. Browse the VM image build scripts and configuration.
View repositoryAcknowledging BioShell
As part of the acceptable use policy and service terms for accessing BioShell, you need to acknowledge use of BioShell in relevant research, training, and innovation outputs using the format:
“This work is supported by BioShell, a service provided by Australian BioCommons and its partners. The service receives NCRIS funding through Bioplatforms Australia as well as The University of Sydney”
How to cite
If you use BioShell in your research or training, please cite it as:
O’Brien MJ, Jaya F, Xue W, Al Bkhetan Z, Botting A, Ward N, Gustafsson J, Samaha G. (2026). BioShell how-to guide. Australian BioCommons. [AUTHOR TO SUPPLY — Zenodo DOI once minted]
Operational partners
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.
