Your learning pathway

Start with a biological question, establish what was measured, and only then choose the analysis. This guide identifies a manageable shared core and shows where the two courses branch. The course map retains the full curriculum and formal assessment schemes.

Before you start

You should be able to explain DNA → RNA → protein, distinguish a sample from a biological replicate, interpret a mean and confidence interval, and import a table in R. You do not need to know every assay or analysis package.

Readiness check	If you need a refresher
Describe what a molecular measurement represents	B01: Questions and measurements
Read a CSV, select columns and join by an identifier	B04, then P14: Data handling
Explain a linear-model coefficient and uncertainty	B12: Statistics; optional Bayesian linear regression background
Identify the independently allocated treatment unit	B02: Design, then P15

Try the linked practical before deciding you are ready. A script that runs is only one part of readiness: explain its rows, units and comparison in words.

Shared core: six stages

The estimates below are suggested student study time, including reading and exercises. They are planning estimates, not contact hours or credit allocations. Beginners may need longer. Completing all six stages takes about 24–32 hours, before pathway branches and real-data cases.

Stage	Essential reading and work	Time	Evidence that you are ready to move on
1. Question and design	B01/B02; P15	3–4 h	State the question, treatment/observation unit, sampling time and confounders
2. Identity and provenance	B03/B04; P14	3–4 h	Join two shuffled tables by identifiers and explain unmatched samples
3. Measurement and quality	B05/B06 plus the assay you need; P08, P16	5–6 h	Distinguish raw measurement, transformed value and biological abundance
4. Model and contrast	B12; P09, P19	5–7 h	Write the design and contrast; explain normalization, uncertainty and multiplicity
5. Integration and evidence	B14/B15; P10, P21	5–7 h	Justify sample matching, scaling, eligible background and an integration strategy
6. Interpretation and report	B17/B18; P25, P13	3–4 h	Separate observation, inference, causal claim and next validation step

Keep a one-page analysis record throughout: question; observations and units; source; exclusion rules; model; diagnostic; conclusion; limitation. Carry that record into a real-data case and the synthesis assignment.

Depth labels for every module

Core means the named part is essential to the shared pathway. Extension means a course branch or question may require it. Advanced means it assumes the core and is not a hidden prerequisite. A core module can still contain optional mathematical or computational sections.

Block	Shared entry level	Prerequisites	Suggested first pass
B01: Foundations	Core	Molecular biology	1 h: question, layers, measurement
B02: Design	Core	B01, introductory statistics	1.5 h: allocation, sampling, confounding
B03: Databases	Core	B01	1 h: identifiers, versions, provenance
B04: Programming	Core	Basic R	1.5 h: import, join, reproducibility
B05: Genomics	Core survey; sequence-method extension	B03/B04	1.5 h: reads, variants and reference dependence
B06: Transcriptomics	Core	B02/B04; B12 for models	2 h: counts, normalization and contrasts
B07: Epigenomics	Extension; core survey for Multi-Omics	B02/B05/B06	1 h: assay evidence and regulatory limits
B08: Proteomics	Extension; core survey for Multi-Omics	B02/B03/B04	1.5 h: identification, abundance, missingness
B09: Metabolomics	Extension; core survey for Multi-Omics	B02/B04	1.5 h: features, annotation and quantification
B10: Microbiomics	Extension; core survey for Multi-Omics	B02/B05/B12	1 h: composition and host associations
B11: Phenomics	Extension; core survey for Multi-Omics	B02/B04	1 h: repeated measurements and decision time
B12: Statistics	Core	Introductory statistics, B02/B04	2 h: contrasts, uncertainty and validation
B13: Association	Extension; core for GSB association branch	B05/B12	1.5 h: structure, prediction and regulatory evidence
B14: Networks	Core interpretation; dynamic models advanced	B03/B06/B12	1.5 h: backgrounds, edges and evidence
B15: Integration	Core	B02/B04/B12 and two assay modules	2 h: matching, scaling and strategy
B16: Emerging methods	Advanced	B02/B06/B12/B15	1.5 h: single-cell/spatial assumptions
B17: Integrity	Core throughout	None beyond the current task	1 h: provenance, reporting and responsible reuse
B18: Synthesis	Core	Shared stages 1–5	1.5 h: production question and defensible conclusion

These labels guide navigation; they do not remove material from either supplied outline. The original module mapping remains in the course map.

Choose your course branch

Genomics, Systems Biology and Bioinformatics

After stages 1–2, follow the sequence branch through P01–P06 and B05. Allow 6–9 additional hours for retrieval, similarity, alignment and phylogeny. Add P07: Structure if protein structure is part of your question. Return to stages 3–5, develop B13 with P29, and compare networks with P11.

Use Case 1 for a real count-model analysis. For a computational project, extend P20 or P23 with a justified validation design. Dynamic networks and B16 are advanced choices after the essential analysis has been explained.

Multi-Omics Technology in Animal Production

At stage 3, survey B05–B11 and complete P17: Metabolomics, P18: Proteomics and the relevant P27/P28. Allow 7–10 additional hours for assay comparisons and exercises. The aim is to choose technologies and sampling, not to master every specialized software pipeline.

Use Case 2 to reason about missing protein measurements, then Case 3 to join actual cattle assays and examine confounding. Finish with P26: Research proposal, explaining what a new study would need to distinguish disease consequences from prospective risk markers.

Use the supporting resources

The visual guide explains six concepts that recur across modules. The media guide provides optional viewing with a question to answer afterwards. The assessment guide shows what a successful piece of work demonstrates. Attempt the exercises before revealing suggested answers; a different justified method can be acceptable when its assumptions match the question.