Nine pre-selected Exemplar Use Cases (EUCs) act as co-creators, stress-testers and early adopters. Each embeds a real research problem into the development of the Methods Commons and helps seed the BioFAIR Workflow Collection.
| # | Focus | Institution(s) | Technologies | Objective |
|---|---|---|---|---|
| 1 | Bioimaging | Dundee / Bioimaging UK | Galaxy, WorkflowHub, OME-Zarr, RO-Crate, BioImage Model Zoo | FAIR, domain-agnostic imaging workflows; streaming multi-terabyte datasets and democratising AI image-analysis models |
| 2 | Single-cell genomics (livestock) | Roslin Institute | Nextflow, StarSolo, CellBender, Parse, 10X Genomics | Standardised pipelines for non-model species (fish, birds, livestock) with complex genomes |
| 3 | Single-cell workflow training | Open University | Galaxy, Intergalactic Workflow Commission, WorkflowHub | Adaptable workflows and live training for researchers at under-resourced institutions |
| 4 | Spatial transcriptomics (plants) | John Innes Centre, Earlham, QIB | Nextflow, Galaxy | Pipelines for plant spatial transcriptomics |
| 5 | Single-cell analysis | Oxford, John Radcliffe Hospital | Nextflow, EDAM, Bioconductor, nf-core, Galaxy, WorkflowHub | Packaging, registering and reusing R-based analyses in Galaxy |
| 6 | Bacterial genomics & epidemiology | Cambridge Veterinary Medicine | Nextflow, phylogeny tools | Short/long-read WGS mapping for variant calling and phylogeny, applied to M. bovis transmission studies |
| 7 | Microbiome & metavirome | Quadram Institute | Nextflow, Galaxy, federated cloud/HPC | Porting internal microbiome/viral pipelines to reliable, federated workflows |
| 8 | Fungal genomics (agri-ecology) | UCL (Eco-flow), RBG Kew | Eco-flow, Nextflow, Seqera, nf-core | Scalable pipelines for analysing degraded historical fungal specimens at scale (Fungarium Sequencing Project) |
| 9 | Metagenomics & spatial omics (microbiome) | UK Centre for Ecology & Hydrology | Snakemake, Jupyter, Python, RStudio, Isambard-AI | High-throughput eDNA/microbiome pipelines integrated with GIS for national biodiversity and soil-health monitoring |
Selection criteria
Use cases are selected for readiness, generalisability and impact, technical capability, diversity (region, domain and task type), feasibility and extensibility. The set is cycled or extended over time as new needs emerge from BioFAIR Fellows, Pathfinder projects and the wider community.