Appendix

Published

Jun 2026

This appendix summarizes shared principles, reproducibility expectations, and technical conventions used across CDI Omics Systems.

Reproducibility

CDI Omics Systems emphasizes reproducible workflows through transparent analytical pipelines, version-controlled environments, structured reporting, and clearly documented analytical decisions.

Across all builds, reproducibility means that another analyst should be able to understand:

  • what data were used
  • how inputs were prepared
  • which quality checks were performed
  • which scripts or tools were applied
  • how outputs were generated
  • how biological conclusions were reached
  • how the analysis can be repeated or extended

Reproducibility is therefore treated as a system-level responsibility, not only a final reporting step.

Environments

Typical environments across CDI Omics Systems may include:

  • Quarto
  • R
  • Python
  • Bioconductor
  • GitHub Pages
  • renv
  • Conda
  • virtual environments
  • containers where appropriate

The specific environment depends on the omics domain, but each system should document the computational context used to generate results.

Shared File Organization

Although individual Omics System Builds may differ, a typical project structure may include:

project/
├── _quarto.yml
├── index.qmd
├── chapters/
├── data/
│   ├── example/
│   ├── input/
│   ├── metadata/
│   ├── results/
│   └── reports/
├── scripts/
│   ├── bash/
│   ├── R/
│   └── python/
├── figures/
├── logs/
├── README.md
└── references.bib

This structure helps separate source data, generated outputs, analysis scripts, reports, and supporting documentation.

Common Analytical Layers

Across Omics System Builds, the following analytical layers are commonly represented:

Biological Question
        ↓
Experimental Design
        ↓
Data Generation
        ↓
Omics Data Processing
        ↓
Quality Control
        ↓
Feature Generation or Feature Validation
        ↓
Domain-Specific Analysis
        ↓
Statistical Inference
        ↓
Biological Interpretation
        ↓
Reproducible Reporting

Each system adapts these layers to its own data type and biological focus.

Expected System Outputs

A mature Omics System should produce more than a final table or plot.

Expected outputs may include:

  • validated input summaries
  • metadata checks
  • quality control reports
  • analysis-ready feature tables
  • statistical result tables
  • interpretation evidence tables
  • biological interpretation summaries
  • figures and visual summaries
  • reproducible reports
  • version-controlled project documentation

These outputs support transparency, reuse, and scientific defensibility.

Workflow Philosophy

CDI Omics Systems focuses on:

  • systems over isolated outputs
  • interpretation-first analysis
  • reproducible reporting
  • transparent analytical reasoning
  • documentation as part of analysis
  • biological meaning over tool execution
  • extensible workflows over one-time scripts

The goal is to help analysts move from scattered analysis steps toward structured systems that can be understood, reproduced, communicated, and trusted.

References

References and supplementary technical resources will continue expanding as individual system builds mature.

Each Omics System Build may include domain-specific references, including software documentation, statistical methods, biological interpretation resources, and reproducibility guidance.