2024/25 Taught Postgraduate Module Catalogue

BIOL5126M Practical Bioinformatics

15 creditsClass Size: 75

Module manager: Dr Sergei Krivov
Email: s.krivov@leeds.ac.uk

Taught: Semester 1 (Sep to Jan) View Timetable

Year running 2024/25

Pre-requisite qualifications

Undergraduate degree in biological sciences

Module replaces

BIOL5172M - Practical Bioinformatics

This module is not approved as an Elective

Module summary

An overview of the practical problems that bioinformatics tools can be applied to investigate. Give hands-on experience with the bioinformatics tools. Teach students how to acquire new skills/learn new tools. Develop critical thinking, creative problem solving and paper writing skills.

Objectives

- To train students in the use of a range of bioinformatics tools
- To provide an overview of the practical problems that bioinformatic tools can be used to solve in academic and industrial biological research
- To work on a defined research problem as part of a team and to describe the investigation and results in written and verbal form

Learning outcomes
On completion of this module, students should be able to:
1. Describe the types of practical problems to which bioinformatics tools can be applied.
2. Use the most important primary and secondary bioinformatics databases and software;
3. Understand the problem of sequence alignments, how bio-molecular sequences and structures evolve, the notion of protein families and the principles and problems of phylogenetic tree construction.
4. Use databases associated with bio-molecular structures and tools for structural analysis and visualisation; structure alignment and classification;
5. Understand the protein folding problem and the principles of protein structure prediction. Explain the relationship between microscopic dynamics and macroscopic properties of proteins and the relationship between sequence, structure and dynamics in proteins.
6. Investigate an unknown sequence and present the results of the investigation in a form of a research paper/executive summary.

Skills outcomes
The problem based learning aspect of assessment 1 requires:
- teamwork;
- communication with the team;
- creative problem solving; and
- critical thinking.

There is also a peer assessment aspect that requires self-awareness.

Syllabus

An overview of the practical problems that bioinformatics tools can be applied to investigate; bioinformatics databases, software and web-based tools; molecular evolution; sequence alignment; dynamic programming and substitution matrices; sequence database searching, methods and statistics; multiple sequence alignment, protein domain families, iterative searching and PSI-BLAST; phylogenetic tree estimation; protein structure analysis; structural alignment and classification; protein structure prediction, secondary structure prediction, comparative modelling, fold recognition, ab initio; whole genome databases and analyses; gene prediction; Machine Learning and longitudinal data analysis.

Teaching methods

Delivery type	Number	Length hours	Student hours
Lecture	4	3.00	12.00
Practical	5	3.00	15.00
Private study hours			123.00
Total Contact hours			27.00
Total hours (100hr per 10 credits)			150.00

Opportunities for Formative Feedback

Progress will be monitored in the practical classes and problem-based learning sessions. Students will be given feedback during group presentations.

Methods of assessment

Coursework

Assessment type	Notes	% of formal assessment
Assignment	Structure prediction: Problem-based learning group work	30.00
Assignment	Sequence analysis : Analyse a mystery protein sequence and interpret and evaluate the results in the form of Scientific journal paper	70.00
Presentation	Group presentations of important bioinformatics tools/website.	0.00
Total percentage (Assessment Coursework)		100.00

Assessment 1/ Problem Based Learning is a group-based exercise. Students as a group a given a specific problem, which they don’t know how to solve yet. Using the help from the demonstrators during the two CBL session the students, first formulate learning questions, then attack the learning questions independently and finally develop the solution and writeup the answer as a group (500 words + Appendices). The group work is marked and then students divide the marks between themselves according to group’s assessment of each individual contribution to the final solution. Assessment 2 is an individual assessment when the students are required to analyse an unknown sequence of a protein, for example, it possible structure or function, etc, and present the results in the form of a scientific journal paper of 2500-3000 words. It is an open-ended exercise, to find as much as possible about the sequence, and students may use all the tools learned in the module. Students are encouraged to select/find the sequence for the project themselves but can also be given a sequence. Assessment in the form of group work will be an individual resit.

Reading list

The reading list is available from the Library website

Last updated: 31/07/2024

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