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Genomics and Introductory Bioinformatics

Module description

Genomics has revolutionised biological research in recent years. Determining the complete genome sequence of almost any organism is now within the reach of most research bioscientists. Recent technological advances in next-generation sequencing make it possible to study gene expression and epigenetic modifications on a genome-wide scale. Reaping the benefits from these advances requires new approaches to biological and biomedical research and an increasing role for computational analysis of biological sequence data (bioinformatics). In this module, you will learn about the technologies that are driving advances in our understanding of genomes. You will study cutting-edge research that uses these methods to address health and disease as well as fundamental biology of animals, plants and microbes. During the computer-based practical exercises and coursework task, you will explore some of the freely available sequence data and computational tools on which modern genomics research relies and make new discoveries.  This module provides an exciting learning opportunity at the forefront of modern biology and will lay some of the foundations for more advanced bioinformatics studies in Stage 3. 

Module aims - intentions of the module

This module aims to discuss concepts, techniques and applications of genomics and introduces the bioinformatics methods that support them. The module will focus on state-of-the-art technology for analysis of genomes and gene expression and critically discuss their use in biological research. Computer-based practical activities will consolidate use of internet-based bioinformatics tools and databases through individual and group work, and a coursework research project will provide a platform to engage in bioinformatics-based research.

Module content is updated every year to explore topical research areas, including those carried out by the lecturers, that are of global relevance. For example, students were provided with genome sequence data recently generated at Exeter from several related pathogenic bacteria; students were asked to independently explore the data and discover and interpret genetic differences among these bacterial genomes in the light of their ability to cause disease on important crop plants. This approach is deliberately open-ended, dependent on students’ creative researching of the unknown rather than regurgitating text-book knowledge. You will learn about the computational tools by doing rather than only reading and explore how genomic science can inform policy and practice in medicine, biotechnology and/or agriculture.

Through the computer-based practical activities and assessments, you will develop skills relevant to future employment:

• You will develop your ability to identify key demands of tasks, manage your time effectively, work collaboratively in small groups.
• You will be encouraged to present your ideas clearly and concisely within the constraints of the stipulated medium, e.g. a single-page poster with limited space. This will require you to use good judgement around prioritising what to include and what to omit and the balance of space devoted to each component of your presentation.
• You will actively contribute to the content and delivery of the module through the questions and answers that you post and read via the discussion forum and the discoveries that you make during computer practicals and coursework.
• You will be encouraged to use your creativity and initiative in driving the direction of your coursework project and in the practicals rather than following a prescriptive set of instructions or answering specifically defined questions.

Intended Learning Outcomes (ILOs)

ILO: Module-specific skills

On successfully completing the module you will be able to...

• 1. Discuss the theoretical basis of genomics
• 2. Describe the application and impact of genomics in research and medicine
• 3. Explain the challenges and impact of genome-wide approaches in research and medicine
• 4. Relate the outputs from applying genomics to modern bioscience

ILO: Discipline-specific skills

On successfully completing the module you will be able to...

• 5. Describe and evaluate approaches to the application of genomics in modern biosciences with reference to primary literature, reviews and research articles
• 6. Describe in some detail essential facts and theory across a subdiscipline of the biosciences
• 7. Identify critical questions from the literature and synthesise research-informed examples from the literature into written work
• 8. With some guidance, deploy established techniques of bioinformatic analysis to make new discoveries

ILO: Personal and key skills

On successfully completing the module you will be able to...

• 9. Communicate ideas, principles and theories fluently by written and visual means in a manner appropriate to the intended audience
• 10. Collect and interpret appropriate data, drawing on a range of sources, with limited guidance
• 11. Work in a small team and deal proficiently with the issues that teamwork requires (i.e. communication, motivation, decision-making, awareness, responsibility, and management skills, including setting and working to deadlines)

Syllabus plan

Whilst the module’s precise content may vary from year to year, it is envisaged that the syllabus will cover some or all of the following topics:

• Theoretical basis of genomes, genome sequencing and analysis using next generation sequencing technologies, including transcriptomics and epigenomics.
• Theoretical basis of bioinformatics, including sequence assembly and identifying sequence similarity.
• Example research studies illustrating the applications of these technologies.
• Question and answer sessions (e.g. through online forum), discussion and feedback around coursework and preparation for exam.

Accessibility statement:

As part of this module you will undertake sessions in the computing laboratory (of up to 80 students) that are typically 2 hrs in duration. Breaks are possible and students are welcome to leave the laboratory for short periods. In the event of unavoidable absence, it is possible to complete the computer practical tasks remotely.

Learning activities and teaching methods (given in hours of study time)

Details of learning activities and teaching methods

Formative assessment

Summative assessment (% of credit)

Details of summative assessment

Details of re-assessment (where required by referral or deferral)

Re-assessment notes

Deferral – if you miss an assessment for certificated reasons that are approved by the Mitigation Committee, you will normally be either deferred in the assessment or an extension may be granted. If deferred, the format and timing of the re-assessment for each of the summative assessments is detailed in the table above ('Details of re-assessment'). The mark given for a deferred assessment will not be capped and will be treated as it would be if it were your first attempt at the assessment.

Referral - if you have failed the module (i.e. a final overall module mark of less than 40%) and the module cannot be condoned, you will be required to complete a re-assessment for each of the failed components on the module. The format and timing of the re-assessment for each of the summative assessments is detailed in the table above ('Details of re-assessment'). If you pass the module following re-assessment, your module mark will be capped at 40%.

Indicative learning resources - Basic reading

Snyder M. 2016. Genomics and personalized medicine: what everyone needs to know. Oxford University Press. ISBN 9780190234768. http://encore.exeter.ac.uk/iii/encore/record/C__Rb3509950

Indicative learning resources - Web based and electronic resources

ELE page: https://vle.exeter.ac.uk/course/view.php?id=10207 (A list of book chapters, scientific literature and approved websites will be provided during each lecture and via ELE. Due to the fast-moving nature of this field, some of the lecture material will be based on recent review articles and primary scientific articles, which will be provided via ELE.)

Key words search

Genomes, transcriptomes, sequencing, epigenomics, bioinformatics