A computer with coloured lines arranged to look like code

BioCLI: Improving command-line infrastructure for life scientists

Vision

A collection of command-line environments and services, tailored to the needs of Australian life science researchers, deployed at the compute infrastructures they use, supporting both research and training.

Challenges

Data Complexity: Handling the growing scale and complexity of ‘omics data and complex analyses requires the flexibility, scalability, and control uniquely afforded by the command-line interface (CLI). 

Varied methods and expertise: The diversity of bioinformatics data, scale of work, available tools presents significant challenges when configuring CLI environments. Most life scientists do not have the expertise required, and need to be empowered with the resources, skills, and knowledge to navigate CL environments and handle substantial workloads confidently and efficiently.

Approach

Australian BioCommons has established the BioCLI Project to address the above challenges.

The BioCLI Project aims to empower life scientists with user-focused CLI environments and services that reduce friction for processing and analysis of molecular data at scale. Our offerings will: 

  • Provide a training program that empowers users to tackle the challenges of working at the CLI

  • Develop public, preconfigured virtual machine images containing essential bioinformatics-specific tools, libraries, and datasets, and testing them on national, institutional, and commercial infrastructures 

  • Streamline access to, and execution of, bioinformatics software and workflows via the CLI across institutional and national computational infrastructures

  • Facilitate wide access to the specialised hardware required to run bioinformatics tools in an accelerated environment

  • Enable access to curated reference datasets that are needed for standard processing and analysis

  • Provide clear documentation for accessing and configuring all BioCLI outputs.

Australian BioCommons is collaborating with our partners at Sydney Informatics Hub, the National Computational Infrastructure (NCI), and the Pawsey Supercomputing Research Centre to deliver the BioCLI Project.

Project timeline

January 2024 - December 2026

Project partners