Last modified: 20 Jan 2023 16:21
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 then 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, its metabolic and environmental responses, growth constraints and regulation, cell surface markers and antibiotic resistance, producing a full inventory of genes and their presumptive functions. Overall, the course prepares a student for future employment in a biosciences workplace, where genome sequencing and annotation is becoming an everyday tool of modern biotechnology.
| Study Type | Postgraduate | Level | 5 |
|---|---|---|---|
| Term | Second Term | Credit Points | 15 credits (7.5 ECTS credits) |
| Campus | Aberdeen | Sustained Study | No |
| Co-ordinators |
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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.
Information on contact teaching time is available from the course guide.
| Assessment Type | Summative | Weighting | 10 | |
|---|---|---|---|---|
| Assessment Weeks | 28,29,31,33 | Feedback Weeks | 28,29,31,33 | |
| Feedback |
Submission of relevant computer programming output file and short answer questions at the end of each topic. Students must complete this assessment to demonstrate they have completed the course at the required standard. Students cannot elect to omit this element since the whole course is based on completion of these advanced bioinformatics activities. Submission of requested output file and related questions confirmed. Any students failing to complete at first attempt given additional support with late or second submission accepted for marking. |
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| Knowledge Level | Thinking Skill | Outcome |
|---|---|---|
| Procedural | Apply | Develop skills in Unix and the command line within a HPC infrastructure. |
| Procedural | Create | Apply 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. |
| Assessment Type | Summative | Weighting | 15 | |
|---|---|---|---|---|
| Assessment Weeks | 34 | Feedback Weeks | 39 | |
| Feedback |
1 hour exam. Feedback per question with marking. |
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| Knowledge Level | Thinking Skill | Outcome |
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| Assessment Type | Summative | Weighting | 50 | |
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| Assessment Weeks | 35 | Feedback Weeks | 38 | |
| Feedback | ||||
| Knowledge Level | Thinking Skill | Outcome |
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| Assessment Type | Summative | Weighting | 25 | |
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| Assessment Weeks | 32 | Feedback Weeks | 35 | |
| Feedback |
2 hour exam. Feedback per question with marking. |
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| Knowledge Level | Thinking Skill | Outcome |
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| Assessment Type | Formative | Weighting | 0 | |
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| Assessment Weeks | 27,28,29,30,31,32,33 | Feedback Weeks | 27,28,29,30,31,32,33 | |
| Feedback |
Tutor answers to questions and feedback to comments, as relevant. |
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| Knowledge Level | Thinking Skill | Outcome |
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| Assessment Type | Formative | Weighting | ||
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| Assessment Weeks | 27,28,30,32 | Feedback Weeks | 27,28,29,30,31,32 | |
| Feedback |
Four formative Multiple Choice Question tests. |
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| Knowledge Level | Thinking Skill | Outcome |
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| Assessment Type | Summative | Weighting | 100 | |
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| Assessment Weeks | Feedback Weeks | |||
| Feedback |
Oral resit examination will assess understanding of the learning outcomes of the course, does not cover individual assignments. |
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| Knowledge Level | Thinking Skill | Outcome |
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| Knowledge Level | Thinking Skill | Outcome |
|---|---|---|
| Conceptual | Analyse | Explain the underlying principles of the tools used and analyse your outputs to determine the validity and limitations of the approach and/ or data. |
| Procedural | Apply | Develop skills in Unix and the command line within a HPC infrastructure. |
| Conceptual | Evaluate | Critically evaluate your findings in the context of the field of microbial genomics and the global health challenge of antimicrobial drug resistance. |
| Procedural | Create | Apply 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. |
| Conceptual | Evaluate | Demonstrate knowledge by explaining and critically appraising through written presentation appropriate to specialists in the field of genomics. |
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