CSC8326 : Advanced Bioinformatics Theory and Practice (Inactive)
- Inactive for Year: 2023/24
- Module Leader(s): Miss Katherine James
- Other Staff: Dr Simon Cockell
- Owning School: Computing
- Teaching Location: Newcastle City Campus
Semesters
| Semester 1 Credit Value: | 10 |
| ECTS Credits: | 5.0 |
Aims
To introduce more advanced concepts in bioinformatics, especially the computational and algorithmic approaches underpinning modern bioinformatics approaches.
The module covers the theoretical aspects a number of many different tools and their usage, as well as the analysis algorithms behind some of them including BLAST and dynamic programming. The module introduces the concepts behind modern postgenomic bioinformatics including material of biological pathways and networks. Later parts of the module introduces the concepts behind modern postgenomic bioinformatics including material of biological pathways and networks. More advanced approaches to biological sequence analysis, assembly, comparison and annotation are also introduced, including comparative genomics.
Outline Of Syllabus
• Sequencing algorithms
• Genome sequence assembly and annotation
• Sequence analysis and comparison algorithms.
• Advanced phylogenetics and genome comparison.
• Transcriptomics and proteomics analysis including single-cell data analysis
• Analysis of other -omics data
• Advanced protein structure prediction
• Biological pathway analysis.
• Biological network analysis, including gene networks.
Teaching Methods
Teaching Activities
| Category | Activity | Number | Length | Student Hours | Comment |
|---|---|---|---|---|---|
| Structured Guided Learning | Lecture materials | 24 | 0:30 | 12:00 | Material for lectures, split in 30min sessions, non-sync online |
| Scheduled Learning And Teaching Activities | Lecture | 8 | 1:00 | 8:00 | Coursework for formative assessment |
| Guided Independent Study | Directed research and reading | 24 | 0:30 | 12:00 | Lecture follow up |
| Scheduled Learning And Teaching Activities | Practical | 8 | 2:00 | 16:00 | Synchronous PIP. To develop practical work |
| Guided Independent Study | Project work | 30 | 1:00 | 30:00 | Coursework for Summative assessment |
| Scheduled Learning And Teaching Activities | Drop-in/surgery | 4 | 1:30 | 6:00 | Synchronous PIP sessions. Ask Qs re lecs |
| Guided Independent Study | Independent study | 16 | 1:00 | 16:00 | Background reading |
| Total | 100:00 |
Teaching Rationale And Relationship
Lectures will be used to introduce the learning material and for demonstrating the key concepts by example. Students are expected to follow-up lectures within a few days by re-reading and annotating lecture notes to aid deep learning.
Practical sessions will be used to emphasise the learning material and its application to the solution of problems and exercises set as coursework, during which students will analyse problems as individuals and in teams. Students are expected to spend time on coursework outside timetabled practical classes.
Students aiming for 1st class marks are expected to widen their knowledge beyond the content of lecture notes through background reading.
Assessment Methods
The format of resits will be determined by the Board of Examiners
Other Assessment
| Description | Semester | When Set | Percentage | Comment |
|---|---|---|---|---|
| Practical/lab report | 1 | M | 100 | A practical report on an advanced bioinformatics exercise. Max 2,500 words. Summative assessment. |
Formative Assessments
| Description | Semester | When Set | Comment |
|---|---|---|---|
| Report | 1 | M | Compulsory formative assessment: design of computational approach for bioinformatics analysis problem. 500 words max |
Assessment Rationale And Relationship
The formative assessment will assess the students growing knowledge of bioinformatics algorithm design applied to the problem set in the summative assessment, providing feedback. The summative assessment will assess the students’ ability to understand and apply the concepts of a range of a bioinformatics analytical techniques, including those described in the formative piece, and also their ability to design new approaches.
The practical reports are not typical essays. Where the word count is a good proxy for effort, the report should collect the results of the practical experiments that the students have performed, using the techniques covered throughout the module, contain a description of design decisions, an experimental plan and a report of experimental results, hence the requested 2500 word limit.
Reading Lists
Timetable
- Timetable Website: www.ncl.ac.uk/timetable/
- CSC8326's Timetable