This module will equip the learner with a fundamental understanding of the structure, organisation, and function of the genome: knowledge necessary to generate, organise, analyse, and interpret high-volume genomic data. This will include: 1) fundamental structure of DNA, genes, RNA, inheritance, and the genetic code; 2) genomic organisation; 3) transcription and translation and their regulation; 4) epigenomics; and 5) metagenomics.

1. Appraise the evidence for the mechanisms of genetic inheritance, evolution, and how variation arises in individual genome sequences.
2. Differentiate among the genomic organisation of eukaryotes, prokaryotes, and viruses.
3. Differentiate between transcription and translation: their molecular bases and regulation.
4. Critique the role of epigenetics in the regulation of gene expression.
5. Appraise the role of metagenomics in human biology and environmental science.

This module will equip the learner with an understanding of the current next-generation DNA sequencing technology used to generate modern large scale genomic sequence data and introduce the learner to the databanks and archives (public databases) into which sequence data are deposited, accessed, and searched/mined. This will include: 1) the basic principles of DNA sequencing and their development to the current next-generation high-throughput sequencing technology; 2) key reactions in used in sequencing technology; 3) genome assembly; 4) use of genomic databases; and 5) ethical and legal considerations surrounding the use of genomic data repositories.

1. Catalogue the development of DNA sequencing from early-stage techniques to the current next generation sequencing technologies- incl. implications for cost, logistics, and technical difficulty.
2. Relate the key reactions and technologies harnessed by sequencing technologies.
3. Organise a sequencing project- genome assembly from fragments.
4. Analyse public genomic databases to perform core bioinformatics tasks.
5. Evaluate the legal, ethical, and social concerns associated with using public genomic sequence databases.

This project-based module will equip the learner with the skills required to perform an array of core bioinformatics operations using a web-based graphical user interface software platform (e.g. GALAXY) while establishing a solid understanding of their theoretical underpinnings. Platforms like GALAXY offer web-based bioinformatics software with a graphical user interface that enables completion of complex bioinformatics problems without the use of a computer programming language. Learnings in this module will enable the student to plan, design, organise, perform, and interpret the results of core bioinformatics analysis routines without the added complexities of learning code. Students will accrue a comprehensive understanding of the foundational methodologies of bioinformatics by performing complete (end-to-end) analyses and solving a real-world problem in a project. Students will gain the confidence to appraise common bioinformatics tasks, select appropriate analyses, and interpret the results. This foundation will serve as a springboard to further abilities to perform bioinformatics analyses using command line code in a future module (see Bioinformatics Analysis on the Command Line). Skills taught will include: 1) genomic data retrieval from public NCBI databases; 2) quality control and mapping reads to genomes (global alignment, reassembly, and annotation); 3) phylogenetics and evolutionary signatures; 4) gene regulatory modules and transcriptomics; 5) epigenetic feature inspection using ChIP-seq; 6) single nucleotide variant calling.

1. Design & build a workflow to fetch genomic sequences, perform quality assessments, map to a reference genome, and identify coding regions.
2. Construct (assemble) a microbial genome using sequences from the short read archive.
3. Design & build a workflow to perform variant calling.
4. Design & build a workflow to perform a phylogenetic analysis.
5. Investigate the presence of epigenetic sites in a genomic sequence.