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Module

CSC8326 : Advanced Bioinformatics Theory and Practice

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

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
Scheduled Learning And Teaching ActivitiesLecture51:005:00Coursework for formative assessment
Scheduled Learning And Teaching ActivitiesLecture240:3012:00Material for lectures, split in 30min sessions, non-sync online
Guided Independent StudyDirected research and reading240:3012:00Lecture follow up
Scheduled Learning And Teaching ActivitiesPractical31:304:30Three 1h30m PiP sessions for Q&A on practicals and coursework
Scheduled Learning And Teaching ActivitiesPractical63:0018:00Practicals, split in 3h sessions, non-sync online
Guided Independent StudyProject work241:0024:00Coursework for Summative assessment
Guided Independent StudyIndependent study201:0020:00Background reading
Scheduled Learning And Teaching ActivitiesScheduled on-line contact time31:304:30Three 1h30m synchronous online sessions for Q&A on the lectures.
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
Practical/lab report1M100A practical report on an advanced bioinformatics exercise. Max 2,500 words. Summative assessment.
Formative Assessments
Description Semester When Set Comment
Report1MCompulsory formative assessment: design of computational approach for bioinformatics analysis problem. 500 words max
Assessment Rationale And Relationship

The formative assessment in coursework 1 will assess the students growing knowledge of bioinformatics algorithm design applied to the problem set in coursework 2, providing feedback. The summative assessment, coursework 2, will assess the students’ ability to understand and apply the concepts of a range of a bioinformatics analytical techniques, including those described in coursework1, and also their ability to design new approaches.

Reading Lists

Timetable