Week 1 - An Introduction to Bioinformatics

This week we will take a tour of Bioinformatics as an inter-disciplinary subject. This will help you to understand the vast range of application areas that Bioinformatians work in and some of the key tools and resources that you will encounter in more detail throughout the course.

We will also give you more detailed information about how to use the course website and learning tools. Finally we will describe the common structure we will be using each week so that you know what you have to do and when.

Welcome & Overview

Welcome to the first week of Bioinformatics 1. This course has been designed to give you all a good foundation to the discipline no matter where you start from.

For some of you some parts of what we will cover will be familiar, but for others you will be encountering these for the first time. We have already put up on our GitHub repository an optional micro-course called "Introduction to Programming in Python" that introduces you to the core basics of the language. We will be using Python Notebooks in this course, these are explained and worked through in the tutorials and are written with explanations embedded. These are also supported by the teaching team and indeed between you and your peers in discussion groups.

As we have mentioned, you are not expected to be an expert Biologist or Programmer, there are other courses specifically aimed to develop your expertise and knowledge in these; they simply wouldn't fit into this course on top of teaching you the fundamentals of Bioinformatics in 10-weeks. We provide you with what you need to follow the course and enable you to make informed decisions about which skills you would like to further develop in your future learning.

So, once again welcome to the course and the first week. This week will be focussed on getting you oriented in the course and the various tools we will be using, we will also take a look at what Bioinformatics actually is by looking at its history and its place in modern biological and biomedical research. We will then take a little time to introduce you to 'Noteable' which is the University of Edinburgh's web-browser based executable scripting environment. We will be using Noteable to run the scripts in this course, meaning you do not need to install your own software (though you can if you would like to). Finally we will be sharing our thoughts about how it is to be a Bioinformatician working at many interfaces between disciplines with the challenges and opportunities that come with that.

The course team will be monitoring the discussion boards regularly and stimulating discussion in the various topic areas so please do feel free to get started whenever you have a moment.

Reading Lists & Resources

Each week we will have an accompanying reading list with some articles & web-sites for self study to support the course. You can find the course "Resource List" - here. We will continue to curate the list throughout the course especially if things pop up in the lectures and practicals that we want to add a reference or link to so do please check back in on the list from time to time.

We have generally tried to identify resources as "Essential", "Recommended" or "Further Reading" in an attempt to help you prioritise your reading during the course.

Finally a very important time to draw your attention to what you can consider the "core text" for the course, which is the excellent "Bioinformatics & Functional Genomics" Third Edition by Jonathan Pevsner. You will be pleased to know that this text-book is available free online as part of the University's subscription portfolio. You can find it right at the top of the resource list. If you have any problems accessing or using any of the above please do drop us a comment in the Piazza Discussion Forum and we will try to get things resolved as soon as possible.

Lecture 1 - An Introduction to Bioinformatics

The lecture slides for Week 1 - "An Introduction to Bioinformatics" can be found here.

The video of the lecture can be found here. You can also click the image below to view it directly on YouTube:

As well as the optional Python mini-course we have prepared two Python Notebooks for you to explore if you would like to:-

Quick introduction to Python/Notebooks & BioPython - notebook 
Basic Sequence Retrieval & Manipulation - notebook

There are also two challenges at the end of the second notebook if you would like to have a go at these. Please feel free to post in the Piazza Discussion board in the relevant section if you have any queries and/or comments. Please refrain from posting your solutions on there until we've had a chance to go through these.

Please don't worry if you don't have time to look at these, they will be part of the computing lab in week 2 where we will guide you through them as well as some additional notebooks on pairwise sequence alignment.