CSC8325 : An Introduction to Bioinformatics Theory and Practice
- Offered for Year: 2022/23
- Module Leader(s): Dr Katherine James
- Lecturer: Dr Simon Cockell
- Owning School: Computing
- Teaching Location: Newcastle City Campus
Semesters
| Semester 1 Credit Value: | 10 |
| ECTS Credits: | 5.0 |
Aims
To introduce the data that arises from studies in molecular biology. To reinforce the theory underlying the concepts and techniques of sequence analysis and post-genomic bioinformatics. An understanding of the distributed and available resources for bioinformatics analyses.
This module provides an introductory understanding of the basic theory behind bioinformatics analyses and experience in practically applying that theory. The module introduces basic concepts of molecule biology, sequence analysis and genomic era biology. It introduces a number of many different tools and their usage, and touches on analysis algorithms behind some of them. The basics of protein motifs, structure and families, and phylogenetics are introduced.
Outline Of Syllabus
Basic concepts of molecular biology: genomes, transcriptomes, proteomes.
Database searching tools.
Sequence analysis: genome annotation, sequence alignment, multiple sequence alignment.
Basic phylogenetic analysis and molecular evolution.
Protein families.
Post genomic analysis: Basic gene and genomic comparison, protein structure, proteomics.
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 30’ sessions, non-synchronous online |
| Guided Independent Study | Assessment preparation and completion | 12 | 1:00 | 12:00 | coursework for Essay |
| Guided Independent Study | Assessment preparation and completion | 21 | 1:00 | 21:00 | coursework for practical/ lab report |
| 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 sessions, if available. Otherwise additional synchronous online sessions |
| Scheduled Learning And Teaching Activities | Drop-in/surgery | 4 | 1:30 | 6:00 | Synchronous PIP sessions, if available. Otherwise additional synchronous online sessions- Qs re lecs |
| Guided Independent Study | Independent study | 21 | 1:00 | 21:00 | 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 materials for 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 |
|---|---|---|---|---|
| Essay | 1 | M | 25 | Low stakes summative assessment: An essay on the bioinformatics approaches for a given biological problem. Max 1000 words |
| Practical/lab report | 1 | M | 75 | Summative assessment: A practical report on a bioinformatics analysis exercise. Max 2,000 words. |
Assessment Rationale And Relationship
The low stakes summative assessment will assess the student’s growing knowledge of the field. The summative coursework will assess the student’s ability to apply theory in a practical setting and will be assessed as an essay and practical report, which are suitable methods for assessing the use of bioinformatics software.
Reading Lists
Timetable
- Timetable Website: www.ncl.ac.uk/timetable/
- CSC8325's Timetable