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MB5522: ADVANCED BIOINFORMATICS AND GENOME SEQUENCING (2023-2024)

Last modified: 12 Jan 2024 15:16


Course Overview

An exciting course that brings a student right up to date with bioinformatics, genome assembly and annotation technology. You, the student, will analyse the genome of an unknown bacterium from the environment. The genome of this isolate has been extracted and whole genome sequenced. You will assemble your own bacterial genome and functionally annotate it, taught by expert bioinformaticians from our Centre for Genome-Enabled Biology and Medicine. Your analysis will enable you to identify the species you have isolated, produce a full inventory of genes and their presumptive functions, allowing an exploration of the antibiotic resistance potential of the bacteria. Overall, the course prepares a student for future employment in a biosciences' workplace, where genome sequencing, assembly and annotation is becoming an everyday tool of modern biotechnology. 

Course Details

Study Type Postgraduate Level 5
Session Second Sub Session Credit Points 15 credits (7.5 ECTS credits)
Campus Aberdeen Sustained Study No
Co-ordinators
  • Dr E Collie-duguid

What courses & programmes must have been taken before this course?

What other courses must be taken with this course?

None.

What courses cannot be taken with this course?

None.

Are there a limited number of places available?

No

Course Description

This course will take students through the exciting and challenging process of analysing the sequence of a bacterial genome from an environmental isolate. The course will teach students how to quality filter and trim raw sequencing data, assemble a genome, quality control the output, annotate genes, and carry out functional gene analysis using modern bioinformatics, to produce an assembled genome and full inventory of the genes of a novel bacterial isolate. This course will develop your knowledge and skills in bioinformatics analysis of genomic data, and you will learn how to use scripting via the command line and the Galaxy interface.


Contact Teaching Time

Information on contact teaching time is available from the course guide.

Teaching Breakdown

  • 1 Computer Practical during University weeks 27, 29 - 30, 34
  • 2 Computer Practicals during University weeks 28, 31 - 33
  • 1 Support Tutorial during University weeks 26, 29
  • 1 Tutorial during University weeks 26, 34

More Information about Week Numbers


Details, including assessments, may be subject to change until 31 August 2023 for 1st half-session courses and 22 December 2023 for 2nd half-session courses.

Summative Assessments

Short Answer Test

Assessment Type Summative Weighting 15
Assessment Weeks 37 Feedback Weeks 39

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Feedback

1-hour exam held on campus. Feedback per question with marking.

Learning Outcomes
Knowledge LevelThinking SkillOutcome
Sorry, we don't have this information available just now. Please check the course guide on MyAberdeen or with the Course Coordinator

Report: Individual

Assessment Type Summative Weighting 15
Assessment Weeks 35 Feedback Weeks 38

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Feedback
Learning Outcomes
Knowledge LevelThinking SkillOutcome
Sorry, we don't have this information available just now. Please check the course guide on MyAberdeen or with the Course Coordinator

Coding Test

Assessment Type Summative Weighting 25
Assessment Weeks 33 Feedback Weeks 36

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Feedback

2-hour exam held on campus. Feedback per question with marking.

Learning Outcomes
Knowledge LevelThinking SkillOutcome
Sorry, we don't have this information available just now. Please check the course guide on MyAberdeen or with the Course Coordinator

Topic-specific Computer Coding Activities

Assessment Type Summative Weighting 45
Assessment Weeks 28,30,32,34 Feedback Weeks 30,32,34,36

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Feedback

Submission of relevant computer programming output files with short answer questions and summary methods and interpretation at the end of each topic.

 

Learning Outcomes
Knowledge LevelThinking SkillOutcome
ProceduralApplyDevelop skills in Unix and the command line within a HPC infrastructure.
ProceduralCreateApply and enhance these informatics skills to perform analysis of a genomics dataset (next generation sequencing data) using bioinformatics software to assemble a bacterial genome and identify ARGs.

Formative Assessment

Class Test - Multiple Choice Questions

Assessment Type Formative Weighting
Assessment Weeks 27,28,30,32 Feedback Weeks 27,28,29,30,31,32

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Feedback

Four formative Multiple Choice Question tests.

Learning Outcomes
Knowledge LevelThinking SkillOutcome
Sorry, we don't have this information available just now. Please check the course guide on MyAberdeen or with the Course Coordinator

Resit Assessments

Oral Exam

Assessment Type Summative Weighting 100
Assessment Weeks Feedback Weeks

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Feedback

Oral resit examination (approximately 1 hour duration) will assess understanding of the learning outcomes of the course, does not cover individual assignments.

Learning Outcomes
Knowledge LevelThinking SkillOutcome
Sorry, we don't have this information available just now. Please check the course guide on MyAberdeen or with the Course Coordinator

Course Learning Outcomes

Knowledge LevelThinking SkillOutcome
ConceptualEvaluateCritically evaluate your findings in the context of the field of microbial genomics and the global health challenge of antimicrobial drug resistance.
ProceduralApplyDevelop skills in Unix and the command line within a HPC infrastructure.
ConceptualAnalyseExplain the underlying principles of the tools used and analyse your outputs to determine the validity and limitations of the approach and/ or data.
ConceptualEvaluateDemonstrate knowledge by explaining and critically appraising through written presentation appropriate to specialists in the field of genomics.
ProceduralCreateApply and enhance these informatics skills to perform analysis of a genomics dataset (next generation sequencing data) using bioinformatics software to assemble a bacterial genome and identify ARGs.

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