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Module

CSC8325 : An Introduction to Bioinformatics Theory and Practice

  • Offered for Year: 2020/21
  • Module Leader(s): Dr Jaume Bacardit
  • Other Staff: Dr Harold Fellermann, 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

Please note that module leaders are reviewing the module teaching and assessment methods for Semester 2 modules, in light of the Covid-19 restrictions. There may also be a few further changes to Semester 1 modules. Final information will be available by the end of August 2020 in for Semester 1 modules and the end of October 2020 for Semester 2 modules.

Teaching Activities
Category Activity Number Length Student Hours Comment
Guided Independent StudyAssessment preparation and completion151:0015:00coursework for practical/ lab report
Guided Independent StudyAssessment preparation and completion91:009:00coursework for Essay
Scheduled Learning And Teaching ActivitiesLecture240:3012:00Material for lectures, split in 30’ sessions, non-synchronous online
Guided Independent StudyDirected research and reading240:3012:00lecture follow up
Scheduled Learning And Teaching ActivitiesPractical63:0018:00Practicals, split in 3h sessions, non-synchronous online
Scheduled Learning And Teaching ActivitiesDrop-in/surgery31:304:30Three 1h30’ PiP sessions (can also be followed online) to ask questions on practicals & coursework
Scheduled Learning And Teaching ActivitiesDrop-in/surgery31:304:30Three 1h30’ synchronous online sessions to ask questions on the lectures
Guided Independent StudyIndependent study251:0025:00Background reading
Total100:00
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

Please note that module leaders are reviewing the module teaching and assessment methods for Semester 2 modules, in light of the Covid-19 restrictions. There may also be a few further changes to Semester 1 modules. Final information will be available by the end of August 2020 in for Semester 1 modules and the end of October 2020 for Semester 2 modules.

The format of resits will be determined by the Board of Examiners

Other Assessment
Description Semester When Set Percentage Comment
Essay1M25Low stakes summative assessment: An essay on the bioinformatics approaches for a given biological problem. Max 1000 words
Practical/lab report1M75Summative 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