Bioinformatics 1

Assignment 2 deadline Thursday 23 Nov 4pm. Get in touch if you have problems submitting. Late submissions get marks deducted.

Course Details

Course Concept and Aims

A primary requisite for relevant, and efficient, research in Bioinformatics is that scientists from both fields (biology and informatics) are involved, or consulted. Team work can only be successful if all parties have a basic ground knowledge of the respective other field and, most importantly, that they can communicate with each other.

The aims of the course are to help you overcome both of these difficulties in your future careers. The course will cover topics that include core biology concepts that relate to bioinformatics, biological data and their source and structure as well as common tools for their analysis.

The course will also involve group-based practical work on using and developing bioinformatics solutions.

Course catalogue entry

Summary of Intended Learning Outcomes:

Course Discussion Forum

If the class is interested, we can use NB as a discussion forum.


All lectures are in Appleton Tower room 5.05 (West Lab).

This is a computing lab since we aim to use examples and media based walkthroughs in the class. Each session will have a mix of lecture style material with tutorial and lab type events used where appropriate. Please ask questions during the class.

For those without DICE login accounts, please go to the ITO office in Forrest Hill to collect your passwords. Let them know you are from another school but registered for Bioinformatics 1. Any problems should be fixed there.


Course materials

22 Sept: Introduction, basic molecular biology, computer set-up (Armstrong/Hennig)
29 Sept: Basic operations on DNA (Hennig)
06 Oct: Sequencing and sequence alignment I (Hennig)
13 Oct: Sequence alignment algorithms (Armstrong)
17 Nov: Functional genomics and RNA-Seq (Dr Owen Dando, Edinburgh)
20 Oct: MSA and Phylogenetics (Hennig)
27 Oct: Databases and sequence alignment (Dr Lysimachos Zografos, Parkure Ltd.)
03 Nov: Poteomics (Armstrong)
10 Nov: Mutations (Armstrong)
24 Nov: Summary and outlook
tbd: Q&A session, we will run this about a week before the exam date.


The course will have two homework assignments which we will set as soon as possible and are available below on this website. These will be worth 30% (15% each). The rest of the marks will come from an end of semester exam.

Assignments and deadlines:

Assignments should be submitted via the DICE submit command, or to the ITO collection box in case of problems with the former.

Assignment 1: Deadline 4pm on 26 October 2017.

Assignment 2: Deadline 4pm on 23 November 2017.


We will give written feedback on the submitted coursework, and have scheduled two Q&A and feedback sessions after the assignments. Since most lectures will have a practical component, we will also provide direct feedback during these sessions. We encourage everyone to actively participate and to ask questions whenever they arise. Course staff can always be contacted by email to ask questions and/or arrange a meeting. Please let us know if you have any constructive criticism about the course, or if you are interested in learning more about particular areas.


Course Staff are:
Guest Lecturer: We have a mix of wet-lab and computational activities so can be hard to find. Always best to drop an email with the question and we'll meet or mail you asap.


Basic concepts are well explained in the following book chapter, which can be read in preparation for te course. It is available online on campus:
Julia E. Richards , R. Scott Hawley Chapter 3 - The Central Dogma of Molecular Biology : How Cells Orchestrate the Use of Genetic Information The Human Genome A User's Guide, 2011

Apart from this, we will not be using a specific text book. All material required for the course will be linked from the course web pages. For looking up specific concepts we recommend the use of Pubmed's bookshelf system. For a more interactive introduction to many concepts we recommend the excellent Dolan DNA Learning Centre websites.

2016 lecture notes
2015 lecture notes
2014 lecture notes
2013 lecture notes
2012 lecture notes
2011 lecture notes

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