Australian BioCommons Workflow Commons
VISION
Australian life scientists can discover, understand, and execute priority workflows that underpin their research programs.
CHALLENGES
Molecular analyses methods are continuously evolving, as new instrument types are rolled out, and more data is generated with existing instruments. These changes mean that researchers increasingly need to analyse larger and more complex datasets.
Using computational workflows to encode data analysis allows methods to be discovered, shared, validated, executed and reused across the life sciences community - lowering the barrier to accessing new analysis methods.
However, it is difficult for research communities to keep up with the constant evolution of computational workflows. One of the most frequent requests from researchers is: how do we apply this new workflow to our data?
These challenges call for an ecosystem of services and platforms that allow Australian life scientists to discover, understand, and execute priority workflows that underpin their research programs.
APPROACH
Australian BioCommons has established the Workflow Commons in response to the above challenges.
The Workflow Commons aims to:
Address challenges in workflow discovery, creation, sharing, validation, execution, and reuse in collaboration with workflow developers, users and infrastructure providers
Develop and deploy priority workflows that address emerging data analysis requirements in consultation with the life science community
Improve the FAIRness of workflows via an ecosystem of services, training and support.
Australian BioCommons is collaborating with our partners at Sydney Informatics Hub, the National Computational Infrastructure (NCI), and the Queensland Cyber Infrastructure Foundation (QCIF) to deliver the Workflow Commons. We consult with the BioCommons bioinformatics workflows community to understand their ongoing challenges and identify gaps in existing community scale digital infrastructure.
PROJECT TIMELINE
January 2024 - December 2026
PROJECT OUTPUTS
JULY 2025 - DECEMBER 2025
TAXODACTYL
High-confidence, evidence-based taxonomic assignment of DNA sequences.
Nextflow workflow for the conservative taxonomy assignment to DNA sequences, designed for high-confidence, auditable results in biosecurity and biodiversity contexts.
This project was developed in collaboration between QCIF and the Department of Agriculture, Fisheries and Forestry, delivering a Workflow in the field of Biosecurity.
JANUARY 2025 - JUNE 2025
ONTViSc (ONT-based Viral Screening for Biosecurity)
A new bioinformatics workflow that facilitates the detection of viruses and viroids from both amplicon and metagenomic Oxford Nanopore (ONT) data using different analytical strategies. The ONTViSc workflow is now available for anyone to deploy or adapt.
This project was developed in collaboration between QCIF and the Department of Agriculture, Fisheries and Forestry, delivering a Workflow in the field of Biosecurity.
Pipeface
NCI have worked with the Garvan Institute to develop Pipeface, a Nextflow workflow that aligns the variant calling phase and can annotate long read ONT and/or PacBio HiFi data. The DeepVariant stage in the workflow is optimised using deepvariant-nextflow, to improve both runtime efficiency and service unit usage.
This project was developed in collaboration between NCI Australia and the Garvan Institute of Medical Research, delivering a Workflow in the field of Variant Calling.
Deepvariant-nextflow
CI have worked with the Garvan Institute to develop deepvariant-nextflow, a Nextflow workflow to run different steps of Google's DeepVariant as independent jobs on Gadi, optimising both service unit usage and performance.
This project was developed in collaboration between NCI Australia and the Garvan Institute of Medical Research, delivering a Workflow in the field of Variant Calling.
JULY 2024 - DECEMBER 2024
Nextflow workflow template generator
The SIH team developed a template that can be used to structure custom Nextflow workflows, develop understanding and Nextflow skills to support upskilling Australian researchers.
This project was a key collaboration with the Sydney Informatics Hub at the University of Sydney, delivering a Guidance resource in the field of Bioinformatics.
JANUARY 2024 - JUNE 2024
Parabricks-Genomics-nf
The team created a scalable CLI implementation of NVIDIA’s GPU accelerated genomics workflow for Illumina short read sequencing data.
This project was a key collaboration with the Sydney Informatics Hub at the University of Sydney, NCI Australia and the Northcott Neuroscience Laboratory, ANZAC Research Institute, delivering a Workflow resource in the field of Variant Calling.
scRNAseq Processing Workflows
Collection of Galaxy workflows that produces an ‘AnnData’ object, which can then be used as a base for downstream analysis of Single Cell RNASeq data.
This project was a key collaboration with QCIF, delivering a Workflow in the field of Single-cell Sequencing.
Pre-Alphafold workflow to create list of target-candidate pairs
Developed a workflow in Galaxy Australia that restructures input data into target-candidate pairs to enable researchers in Structural Biology to more easily set up large AlphaFold2 analyses. Testing of this approach using real data has provided information about computational requirements and potential optimisations.
This project was developed in collaboration with the University of Melbourne and the Australian Structural Biology Computing Community, delivering a Workflow in the field of Structural Biology.
Building the future of bioinformatics with Nextflow: Technical innovation, community engagement, and career development opportunities
Explore the technical advantages of Nextflow, highlight ways to engage with a thriving global community, and provide valuable insights into career growth opportunities within this ecosystem.
This project was a key collaboration between Australian BioCommons and Nextflow Seqera, delivering Training in the field of Bioinformatics.
Genome assembly workflow for nanopore reads
Development of a genome assembly Galaxy workflow for Threatened Species Initiative (TSI) researchers, using Oxford nanopore’s sequence data. This is to complement existing Galaxy workflows developed for TSI to assemble PacBio HiFi data.
This project was developed in collaboration with the University of Melbourne and the Threatened Species Initiative, delivering a Workflow in the field of Genome Assembly.
Making sense of gene and protein lists with functional enrichment analysis
Discover how to use functional enrichment analysis combined with gene ontology and pathway information to highlight the underlying biology in your data.
This project was developed in collaboration with the Sydney Informatics Hub at the University of Sydney, delivering Training in the field of Pathway Analysis.
PROJECT PARTNERS
