Practicals and exercises

The 31 practicals provide a complete initial teaching collection for both harmonized outlines. Each includes a biological question, assumptions, runnable examples, interpretation, exercises and suggested answers. The P01–P31 numerical inputs are hypothetical; they require no biological downloads or additional analysis packages. The separate three real-data cases use local public extracts; Cases 1–2 require DESeq2/limma as documented. The examples teach the methods and their limits rather than claiming production-pipeline qualification.

The 26 original sessions map to 24 shared practicals. Seven additional practicals strengthen sample identity, regularized prediction, microbiomics, phenomics, association, epigenomics and advanced-method reasoning.

Follow the learning pathway to select essential work, use the visual guide for recurring concepts, and consult the assessment guide for case assignments and a shared rubric.

Work through a practical

Start by stating the biological question and the observation unit. Predict the result of the worked calculation before running it, then investigate the sensitivity or diagnostic extension. Use the interpretation challenge to distinguish the numerical evidence from the biological claim. Keep a short analysis record with units, denominators, assumptions and the follow-up needed.

Run the practicals

Download or clone the course repository and open genomics-systems-bioinfo.Rproj. Quarto uses R with knitr/rmarkdown to render the practicals. In the RStudio Terminal, for example:

quarto render tutorials/p09_rnaseq.qmd

You can also run the displayed chunks in order in a clean R session, starting in either the repository root or its tutorials/ folder. The code locates the local teaching helpers in R/. These helpers and their hypothetical data model are part of the repository; a copied code fragment still needs those files. No biological download is required. Use the code folds to inspect each calculation and attempt exercises before revealing suggested answers.

Genomics, Systems Biology and Bioinformatics pathway

  1. Biological Databases and Sequence Retrieval
  2. Basic Sequence Analysis and Manipulation
  3. Command-Line Bioinformatics
  4. Sequence Similarity and Homology Analysis
  5. Multiple Sequence Alignment and Conserved-Region Analysis
  6. Phylogenetic Analysis
  7. Protein Structure and Structural Bioinformatics
  8. Sequencing Data Quality Assessment
  9. RNA-Seq Data Analysis
  10. Functional Annotation and Pathway Analysis
  11. Biological Network Analysis
  12. Biological Data Visualization
  13. Integrated Bioinformatics Data Analysis
  14. Scientific Reporting and Presentation

Multi-Omics Technology in Animal Production pathway

  1. Multi-Omics Experimental Design in Animal Production
  2. Quality Assessment and Preprocessing of Multi-Omics Data
  3. Transcriptome Data Analysis
  4. Metabolomics Data Processing and Analysis
  5. Proteomics Data Analysis
  6. Exploratory Analysis of Multi-Omics Data
  7. Functional Enrichment and Pathway Analysis
  8. Multi-Omics Data Integration
  9. Multi-Omics Association with Animal Production Traits
  10. Multi-Omics Network and Biomarker Analysis
  11. Integrated Multi-Omics Interpretation
  12. Multi-Omics Research Proposal and Scientific Reporting

Both pathways reuse Practical 9 for RNA-seq and Practical 10 for enrichment. Assign the relevant extensions rather than requiring the same exercise twice.

Complete practical library

Choose prerequisite blocks in the module index and see formal module numbering and assessment weights in the unified map.