This organisation develops a genomic breeding pipeline in Julia covering data I/O, modelling, visualisation, and application layers. Current capabilities include genomic prediction assessment (e.g., repeated k-fold CV) and allele effect extraction; GWAS, mating/crossing designs, breeding simulations, and high-dimensional selection indices are under development.

Library	Description	Status	Docs
GenomicBreeding.jl	Orchestrates the entire genomic breeding workflow (pipelines, and integration across modules)
GenomicBreedingCore.jl	Core data structures, utilities, and shared abstractions
GenomicBreedingIO.jl	Data input and output
GenomicBreedingModels.jl	Genomic prediction models
GenomicBreedingPlots.jl	Static plotting functions
GenomicBreedingDB.jl	Database connectivity and persistence for genotypes/phenotypes, results, and metadata
GenomicBreedingApp.jl	User-facing application layer that surfaces workflows and visualisations
GenomicBreedingInteractivePlots.jl	Interactive visualisations for dynamic exploration of results

flowchart TB
    Workflow[GenomicBreeding.jl] --> Core[GenomicBreedingCore.jl]
    Workflow --> IO[GenomicBreedingIO.jl]
    Workflow --> Models[GenomicBreedingModels.jl]
    Workflow --> Plots[GenomicBreedingPlots.jl]
    Core --> IO
    Core --> Models
    Core --> Plots
    Core --> DB[GenomicBreedingDB.jl]
    IO --> DB
    Plots --> IPlots[GenomicBreedingInteractivePlots.jl]
    DB --> App[GenomicBreedingApp.jl]

• Core: finalise data structures for genotypes/phenotypes; define common interfaces.
• Models: complete repeated k-fold CV, allele effect extraction; add benchmarking harness.
• IO: standardise loaders (VCF, CSV/TSV, JLD2) and schema validation.
• Plots: deliver model evaluation plots (CV metrics, residuals, feature importance).
• .github: CI for Julia versions, unit tests, and documentation builds.

• Models: implement GWAS pipeline (linear/mixed models), p-value correction, Manhattan/Q-Q plots.
• IO/DB: support GWAS input tables and result storage; indexing for fast retrieval.
• InteractivePlots: interactive Manhattan/QQ with hover details and region zoom.
• Workflow: end-to-end GWAS run configuration and reproducible reports.

• Models/Core: utilities for mating plans (e.g., optimal contribution, diversity constraints).
• App: UI for proposing/validating crossing designs; export to breeding operations.
• Plots: pedigree and cross outcome visualisation.

• Models: stochastic/forward simulations with selection strategies; track genetic gain and inbreeding.
• DB: store simulation scenarios and outcomes; comparison dashboards.
• InteractivePlots: time-series and scenario comparison widgets.

• Models: multi-trait indices (economic weights, sparsity/regularisation); sensitivity analyses.
• Workflow/App: templated runs and interactive tuning.