BioCLI: Improving command-line infrastructure for life scientists

Australian life scientists are set to be empowered with the resources, skills, and knowledge required to access command-line infrastructure for bioinformatics research through the newly established BioCLI Project. 

Data analysis in the life sciences is constantly evolving, as new instrument types are rolled out and larger amounts of data are generated. The flexibility, scalability, and control uniquely afforded by the command-line interface (CLI) gives users powerful capabilities to interrogate their data, meaning that coding skills can sometimes be essential to particularly complex data analyses. However, the sheer number and diversity of bioinformatics data, tools, and working scales presents a significant entry barrier to using the CLI for life scientists.

Australian BioCommons has established the BioCLI Project to uplift life scientists and help tackle the challenges of working at the CLI, offering environments and services that will reduce friction for processing and analysis of molecular data at scale. Working with our partners at Sydney Informatics Hub, the National Computational Infrastructure (NCI), and the Pawsey Supercomputing Research Centre, BioCLI will:

  • Develop key CLI infrastructure such as public virtual machine images that come preconfigured with all the essentials for life sciences research (eg. the BioImage)

  • Accelerate command-line job throughput by configuring key tools and workflows to run efficiently on specialised hardware or queuing systems (eg. configuration of Parabricks for NCI’s Gadi supercomputer)

  • Provide clear documentation for accessing and configuring all BioCLI outputs

  • Have a strong focus on empowering researchers through a dedicated training program

Keep up to date with the latest BioCLI project developments on our website, and be sure to register for our upcoming entry-level webinar “What exactly is bioinformatics?” delivered by Dr Georgie Samaha, Product Owner of BioCLI and Bioinformatics Group Lead at the Sydney Informatics Hub, The University of Sydney.

Patrick Capon2024, BioCLI