| CODE | MMB3002 | ||||||||
| TITLE | Introduction to Bioinformatics | ||||||||
| UM LEVEL | 03 - Years 2, 3, 4 in Modular Undergraduate Course | ||||||||
| MQF LEVEL | 6 | ||||||||
| ECTS CREDITS | 4 | ||||||||
| DEPARTMENT | Centre for Molecular Medicine and Biobanking | ||||||||
| DESCRIPTION | The vast amount of data generated by biological experiments critically require the use of computational tools for analysis and, hence, the discovery of novel insights. Bioinformatics is a data-intensive interdisciplinary field, involving molecular biology, genetics, computer science, mathematics, and statistics, which aims to provide these tools. Bioinformatics has many practical uses and applications which we will explore during the unit. These include (but are not limited to) genome assembly, gene function, gene prediction and annotation, RNA and protein expression, sequence alignment, comparative genomics, biological networks (e.g. signalling, metabolic, protein-protein interaction networks, etc.), protein structure prediction, systems biology, phylogeny (and evolution), and drug discovery. This study-unit will offer topics from two parallel streams: molecular biology and computer science. Popular bioinformatics tools will be described, including their underlying algorithms. Moreover, biological implications of results will be explained. Throughout the unit the student will be guided using practical, real-world examples. This study-unit focuses on the clinical perspective of bioinformatics. Study-unit Aims: This unit aims to take the student through a number of practical scenarios which may be encountered in a clinical setting. The term "clinical bioinformatics" is defined as "clinical application of bioinformatics-associated sciences and technologies to understand molecular mechanisms and potential therapies for human diseases". We will use bioinformatics tools to analyse sequence and structural data for genes and proteins. The theoretical underpinnings of these tools will be explained (e.g. what the result scores mean, how they are calculated etc.). Its focus is on using bioinformatics tools rather than building new ones programmatically. Each student will be assessed with a relevant bioinformatics project (independent home activity) - this will expose the student to a practical scenario. Learning Outcomes: 1. Knowledge & Understanding: By the end of the study-unit the student will be able to: - Execute an analysis on patient data using computational tools; - List computational tools available to execute genomic and proteomic analysis; - Explain the differences between local and global sequence alignment; - Align DNA and protein sequences (to a reference) and find variants/mutations; - Evaluate whether the underlying theoretical assumptions of specific bioinformatics tools apply to the data at hand; - Use (and query) of sequence and structure databases to support findings. 2. Skills: By the end of the study-unit the student will be able to: - Use BLAST family of tools to search for similar sequences; - Use Clustal family of tools to align multiple sequences; - Use of Galaxy platform for bioinformatics analysis; - Use of GeneCards database for gene annotation; - Use PDB to search for protein structures. Main Text/s and any supplementary readings: Clinical Bioinformatics (2014, second edition) Ronald J. A. Trent ISBN-10: 1493947001 Bioinformatics for Beginners (2014) Supratim Choudhuri ISBN-10: 0124104711 Bioinformatics for Biologists 1st Edition (2011) Pavel Pevzner, Ron Shamir ISBN-10: 1107648874 Understanding Bioinformatics (2006) Marketa Zvelebil, Jeremy Baum ISBN-10: 0815340249 Introduction to Bioinformatics (4th Edition, 2014) Arthur Lesk ISBN-10: 0199651566 |
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| STUDY-UNIT TYPE | Lecture, Independent Study, Project and Tutorial | ||||||||
| METHOD OF ASSESSMENT |
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| LECTURER/S | Panagiotis Alexiou Byron Baron Joseph Bonello Jean Paul Ebejer (Co-ord.) Brendon Scicluna |
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The University makes every effort to ensure that the published Courses Plans, Programmes of Study and Study-Unit information are complete and up-to-date at the time of publication. The University reserves the right to make changes in case errors are detected after publication.
The availability of optional units may be subject to timetabling constraints. Units not attracting a sufficient number of registrations may be withdrawn without notice. It should be noted that all the information in the description above applies to study-units available during the academic year 2024/5. It may be subject to change in subsequent years. |
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