O'Brien M1,2, Xue W3, Jaya F1,2, Botting A4, Downton M3, Ward N2, Phippard L2, Samaha G1,2
1Sydney Informatics Hub, The University of Sydney, , Australia, 2Australian BioCommons, , Australia, 3National Computational Infrastructure (NCI), Canberra, Australia, 4Australian Research Data Commons (ARDC), Melbourne, Australia
Biography:
Mitchell O'Brien is a bioinformatician at the Sydney Informatics Hub and Australian BioCommons, where he is the Product Owner of BioShell. With a PhD in genomics and experience spanning clinical genomics, conservation biology, and machine learning, Mitchell focuses on building scalable, reproducible infrastructure that lowers barriers to bioinformatics for researchers at all levels. He has extensive experience deploying workflows across HPC and cloud platforms, and is committed to building the tools, environments, and community partnerships that make computational life science more accessible across Australia.
Abstract:
Bioinformatics has become increasingly computationally intensive. Large datasets, complex analyses, and growing expectations for reproducibility are pushing researchers toward high-performance computing (HPC), yet many lack the training to navigate systems, complex dependencies, and inconsistent environments. The gap between local workflows and HPC remains a barrier to productive and reproducible research, highlighting the need for a safe, accessible entry point into bioinformatics practice.
BioShell is Australian BioCommons’ response to this gap. It is available as a public codebase and a managed service for scalable research and training. It is an open source, portable, virtual machine service that provides a versioned, reproducible Linux environment with R, Python, RStudio, JupyterLab, and Lua-based module system (Lmod) pre-installed. It is cloud-based and built with Ansible and Packer to ensure consistency across deployments. Users can begin in familiar interfaces while building confidence with the command line.
BioShell is a supported workspace, providing integrated access to Galaxy Project’s tools and reference datasets via CernVM-File System (CVMFS). This gives users an extensive, curated software ecosystem without manual installation or dependency management. Findability within this ecosystem is facilitated by Shelley, a command-line agent that locates and builds tools from CVMFS, manages container execution via Singularity and Singularity-HPC, and exposes software as standard Lmod modules, delivering a consistent HPC-like experience without requiring systems administration expertise.
BioShell was developed to run across Australian Research Data Commons Nectar and National Computational Infrastructure Nirin cloud platforms. It was co-developed by bioinformaticians, engineers, and infrastructure specialists to lower the barriers to bioinformatics.
