Genomics and Introductory Bioinformatics

Module titleGenomics and Introductory Bioinformatics
Module codeBIO2092
Academic year2020/1
Credits15
Module staff

Dr David Studholme (Convenor)

Duration: Term123
Duration: Weeks

11

Number students taking module (anticipated)

90

Description - summary of the module content

Module description

The analysis of whole genomes 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. Furthermore, recent technological advances such as next-generation sequencing make it possible to study gene expression and epigenetic modifications on a genome-wide scale. To gain the maximum benefit from these advances now 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 increase our understanding of health and disease as well as fundamental biology of animals, plants and microbes. During the computer-based practicals 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 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. Practical classes 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 research.

Module content is updated every year to explore topical research areas, including those carried out by the lecturers, and 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 practicals 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

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.
  • Case Studies illustrating the applications of these technologies.
  • Question and answer sessions, discussion and feedback around coursework and preparation for exam.

Learning and teaching

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

Scheduled Learning and Teaching ActivitiesGuided independent studyPlacement / study abroad
371130

Details of learning activities and teaching methods

CategoryHours of study timeDescription
Scheduled Learning and Teaching21Computer practicals
Scheduled Learning and Teaching16Lectures
Guided Independent Study87Reading the literature recommended as essential reading and further reading and revision for assessments
Guided Independent Study26Preparing and writing the research project coursework assessment

Assessment

Formative assessment

Form of assessmentSize of the assessment (eg length / duration)ILOs assessedFeedback method
Lecturer and demonstrator feedback during practicals7 x 3 hours1-8Oral

Summative assessment (% of credit)

CourseworkWritten examsPractical exams
40600

Details of summative assessment

Form of assessment% of creditSize of the assessment (eg length / duration)ILOs assessedFeedback method
Essay examination601 hour1-7, 9, 10Written
Poster presenting findings of bioinformatics coursework research project40One page A34, 8-11Written

Re-assessment

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

Original form of assessmentForm of re-assessmentILOs re-assessedTimescale for re-assessment
Essay examinationEssay examination1-7, 9, 10August Ref/Def
PosterPoster4, 8-11August Ref/Def

Re-assessment notes

Deferral – if you miss an assessment for certificated reasons judged acceptable by the Mitigation Committee, you will normally be either deferred in the assessment or an extension may be granted. The mark given for a re-assessment taken as a result of deferral 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 overall (i.e. a final overall module mark of less than 40%) you will be required to sit a further examination. The mark given for a re-assessment taken as a result of referral will count for 100% of the final mark and will be capped at 40%.

Resources

Indicative learning resources - Basic reading

  • Lesk, Arthur M. Introduction to Genomics. 2017. Third edition. ISBN: 9780198754831

Indicative learning resources - Web based and electronic resources

  • ELE page: http://vle.exeter.ac.uk/course/view.php?id=4041 (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.)
  • Gawad C, Koh W, Quake SR. 2016. Single-cell genome sequencing: current state of the science. Nat Rev Genet. 17:175-88. Available online: https://doi.org/10.1038/nrg.2015.16 via the ELE.

Module has an active ELE page

Key words search

Genomes, transcriptomes, sequencing, epigenomics, bioinformatics

Credit value15
Module ECTS

7.5

Module pre-requisites

BIO1334 Genetics or NSC1003 Foundations in Natural Science

Module co-requisites

None

NQF level (module)

5

Available as distance learning?

No

Origin date

11/02/2013

Last revision date

04/03/2019