Wenjing Xue1, Dr Mitchell O'Brien2,3, Dr Matthew Downton1, Dr Georgina Samaha2,3
1NCI Australia, Australia, 2Sydney Informatics Hub, University of Sydney, 3Australian BioCommons,
Biography:
Wenjing Xue is HPC Specialist (Life and Health Sciences) at NCI Australia. Wenjing supports users across NCI's HPC and cloud systems helping them conduct novel research efficiently and at scale.
Mitchell O'Brien is committed to making bioinformatics more accessible by developing scalable infrastructure and innovative pipelines that empower researchers. Through his work with SIH and the Australian BioCommons, Mitchell focuses on advancing the bioinformatics community by creating reproducible workflows and building collaborative partnerships to drive scientific discovery and accessibility in the life sciences.
Abstract:
Powerful bioinformatics tools are transforming life sciences, but these tools are hard to install and configure, especially for researchers without deep technical expertise. As a result, many scientists feel overwhelmed or hesitant to engage with modern computational methods. To address these barriers, the Bioimage project provides a ready-to-use interface to high performance computing environments that is reproducible, user-friendly and designed to make bioinformatics tools and training more accessible to researchers at all skill levels.
The Bioimage is a lightweight, pre-configured virtual machine image designed to simplify access to key bioinformatics tools, automated pipelines, and reference datasets. Leveraging Singularity HPC (SHPC) and CVMFS, the Bioimage automates software setup and access to reference datasets, eliminating the need for complex installation and data management. Automated workflows are supported through Nextflow, while researchers have access to familiar tools for interactive data visualisation and analysis.
The Bioimage project also offers scripts for setup and instance management. Trainers and users can build the image, boot and shut down VMs, and manage access, whether for single-users or shared instances. Tasks like IP allocation, credential setup, and user separation are handled with simple commands. This approach provides a repeatable and scalable way to deliver consistent environments for workshops and collaborative projects, greatly simplifying preparation and software deployment. Participants can start using the environment immediately, without needing to install anything locally.
The Bioimage project streamlines bioinformatics by linking powerful tools with seamless automation and smart access controls. Making advanced workflows faster, easier, and more accessible to researchers.