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


JULY 2025 - DECEMBER 2025

Spatial Sampler

How-to guides and code-snippets for asking questions of single-cell spatial datasets. They include worked examples on real datasets.

How-to guide
View on GitHub

scRNAvigator

A collection of R notebooks for interactive exploration, processing, and analysis of your single cell RNA sequencing data.

WORKFLOW

View R notebooks
View on GitHub

Spatial omics workshop

A hands-on workshop demonstrating in situ spatial experiments with Seurat in R, covering quality control, visualisation, and best practices.

TRAINING

View event details

Spatial omics webinar

A webinar navigating the spatial omics landscape, featuring method comparisons, analysis considerations, and bioinformatics theory explainers.

TRAINING

Watch recording

TAXODACTYL

Nextflow workflow for the conservative taxonomy assignment to DNA sequences, designed for high-confidence, auditable results in biosecurity and biodiversity context.

WORKFLOW

View on WorkflowHub

JANUARY 2025 - JUNE 2025

ONTViSc

Nextflow-based bioinformatics pipeline designed to help diagnostics of viruses and viroid pathogens for biosecurity.

Developed in collaboration with the Department of Agriculture, Fisheries and Forestry.

WORKFLOW

View on GitHub
How-to guide
Read more

Pipeface

Nextflow workflow that aligns the variant calling phase and can annotate long read ONT and/or PacBio HiFi data.

Developed in collaboration with Garvan Institute for Medical Research.

WORKFLOW

View on GitHub

Deepvariant-nextflow

Nextflow workflow to run different steps of Google's DeepVariant as independent jobs on Gadi, optimising service unit usage and performance.

Developed in collaboration with Garvan Institute for Medical Research.

WORKFLOW

View on WorkflowHub
View on GitHub

JULY 2024 - DECEMBER 2024

Pre-Alphafold workflow

Creates a list of target-candidate pairs that can be used as input into Alphafold2.

Developed in collaboration with Community for Structural Biology Computing in Australia.

WORKFLOW

View on Galaxy Australia

Genome assembly workflow

Galaxy workflow to assemble genomes from Nanopore reads for Threatened Species Initiative.

Developed in collaboration with Threatened Species Initiative.

WORKFLOW

View on WorkflowHub

Making sense of gene protein lists

Discover how to use functional enrichment analysis combined with gene ontology and pathway information to highlight the underlying biology in your data.

TRAINING

View event details

Building the future of bioinformatics with Nextflow

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.

TRAINING

View event details

Template to aid beginners in learning how to develop best practice Nextflow workflows. 

WORKFLOW

Nextflow workflow template generator

View on GitHub
How-to guide

JANUARY 2024 - JUNE 2024

Parabricks-Genomics-nf

GPU-enabled Nextflow pipeline for alignment and germline short variant calling for short read sequencing data. 

WORKFLOW

View on GitHub
View on WorkflowHub

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.

GUIDANCE

scRNAseq Processing Workflows

How-to guide
View on WorkflowHub