BMS5021 - Introductory Bioinformatics Manual

Dr Lochlan Fennell

01/03/2024

Chapter 1 Welcome to BMS5021 - Introductory Bioinformatics

Welcome to the beginning of the bioinformatics component of BMS5021 - Introductory Bioinformatics. Over the past four weeks, you have taken a crash course in the fundamentals of molecular biology. These concepts underpin the analyses we do in bioinformatics. Bioinformatics combines the strengths of computer science, statistics, and biology in order to analyse and interpret large-scale biological data, ultimately leading to new discoveries and understandings.

In the past decade, advances in high-throughput technologies have generated a vast quantity of biological data, including genomic sequences, gene expression profiles, and protein structures. Bioinformatics plays a crucial role in making meaning of this wealth of information by providing the necessary tools and methodologies for data analysis, interpretation, and visualisation.

The objective of this course is to provide you with the knowledge and skills necessary to navigate the bioinformatics landscape and apply computational techniques to solve real-world biological problems. Data derived biological systems it is inherently “messy”. Over the coming four weeks, you will come to appreciate the varied nature of bioinformatic data, and apply tools and algorithms to glean insight from large and complex bioinformatic datasets.

1.1 Navigating the course manual

This book will serve as your course manual. On the left hand side of the screen you will notice that the book is broken into several chapters. Each chapter represents a weeks worth of practical activities. These are to be completed in class. Complete these at your leisure to improve your bioinformatic ability. Clicking these links will help you navigate between different activities. There is also a search bar to search the entire book.

1.2 Learning programming

In class, you are to work independently and in small groups to solve the workshop exercises. We have designed this course in a way that will teach you Bash syntax and also programming logic. Learning programming can be tough and will require a degree of critical thinking and deep engagement with the content and resources. In some exercises we will provide example code and others you will be expected to use manuals and other guides to design the code yourself. When you are completing these exercises we strongly encourage you to avoid simply copying and pasting code from this manual or other sources. You will learn best by working through the exercises yourself and making mistakes! We are here to guide you through this process.

Solutions to the problems in the workshop manual will be available at the conclusion of the week. These will be cleared denoted in the workshop manual.