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Module

BIO8076 : Applied Bioinformatics

  • Offered for Year: 2022/23
  • Module Leader(s): Dr Martin Edwards
  • Lecturer: Dr James Stach
  • Owning School: Natural and Environmental Sciences
  • Teaching Location: Newcastle City Campus
Semesters
Semester 2 Credit Value: 20
ECTS Credits: 10.0

Aims

Module introduces the basic concepts of bioinformatics for the study of DNA and proteins. The module is devised such that students from a range of backgrounds can understand the theory and practice of applying computer-based analysis to the field of molecular biology. The module is hands-on and will train as well as educate the students. The module is divided into lectures and workshops to ensure that lecture information is transferred to practical teaching. The students will become competent in the use of molecular biology databases hosting nucleic acid and protein sequence information and bioinformatics tools including those aimed at investigating: sequence similarity, sequence analysis, protein structure, phylogeny, and genome browsing. The series of workshops will present students with actual problem solving exercises ensuring that students are able to apply what they learn, particularly during their research projects.

Outline Of Syllabus

Lectures/Workshops

An introduction to bioinformatics (1)
Sequence prediction and genome browsing (1)
Sequence databases (2)
Sequence similarity (2)
Sequence analysis (2)
Structural prediction (2)


Practical workshops (5)

As above - aligned with lectures. Each workshop will be used to give students data to analyse using the different bioinformatics tools that they have been introduced to. Students will submit their results at the end of each session for feedback.

Teaching Methods

Teaching Activities
Category Activity Number Length Student Hours Comment
Guided Independent StudyAssessment preparation and completion160:0060:00In course assessment (60%) - Short answer assessment based on tasks completed in the practicals.
Structured Guided LearningStructured research and reading activities35:0015:00Reading, reviewing online materials to prepare for laboratory sessions
Scheduled Learning And Teaching ActivitiesWorkshops153:0045:00Student led practical sessions
Scheduled Learning And Teaching ActivitiesDrop-in/surgery14:004:00Module leader will be available to answer general student queries.
Guided Independent StudyIndependent study155:0075:00Follow up on workshops
Scheduled Learning And Teaching ActivitiesModule talk11:001:00Introduction to module sections
Total200:00
Teaching Rationale And Relationship

The module aims to provide both theory and practice in bioinformatics. This is achieved using the lecture/workshop model; students are given theory and demonstrations, guided to online tutorials and practice, and then set problems to work through in a workshop. The module will make strong use of online materials, such that students can attempt problems prior to lectures and workshops, giving the students an opportunity to direct the teaching to their needs.

Assessment Methods

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

Other Assessment
Description Semester When Set Percentage Comment
Prof skill assessmnt2M100Students will apply knowledge gained from the training workshops to a biological challenge closely aligned to contributors research.
Formative Assessments
Description Semester When Set Comment
Written exercise2MIndividual & class feedback provided during each of 15 scheduled workshops to insure understanding of each technique and/or theory
Assessment Rationale And Relationship

The practical components are designed such that students will be solving problems relevant to molecular biology. This will provide them with the skills required to apply bioinformatics to their research. The assessments will ensure that the students are fully able to conduct basic bioinformatics to the level required for postgraduate research.

Students will be provided with verbal formative feedback during the workshop/breakout sessions so they can make immediate corrections to analyses and improve practice.

Study Abroad students may request to take their exam before the semester 2 exam period, in which case the format of the paper may differ from that shown in the MOF. Study Abroad students should contact the school to discuss this.

Reading Lists

Timetable