Bioinformatics 2

Note: these pages are continuously being revised for the 2014 session, please check back often.

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.

This course builds on basic knowledge acquired in Bioinformatics 1, and will introduce advanced and modern concepts used in functional genomics and modelling.

As Bioinformatics 1, the course will involve group-based practical work on using and developing bioinformatics solutions.

Course catalogue entry

Summary of Intended Learning Outcomes:

Course Discussion Forum

https://www.forums.ed.ac.uk/viewforum.php?f=1461

Classes

All lectures are in Room AT4.12 in Appleton Tower.

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 on level 4 in Appleton Tower to collect your passwords. Let them know you are from another school but registered for Bioinformatics 2. Any problems should be fixed there.

Schedule

15 Jan: Introduction
22 Jan: Probabilistic Modelling 1
29 Jan: Probabilistic Modelling 2
05 Feb: Gene Features and Protein Models
12 Feb: ChIP Seq (Dr Gabriele Schweikert)
19 Feb: IWL - no lecture
26 Feb: GeneNetwork tutorial (Prof Rob Williams)
05 Mar: Project cycles and research methods in Bioinformatics
12 Mar: Concepts in Molecular Modelling
19 Mar: Spatial Modelling in Kappa (Dr Oksana Sorokina)
26 Mar:

more to be announced.

Assessment

The course will have a mini project, which will be set following the first session. This will be worth 30%. The rest of the marks will come from an end of semester exam.

Assignment for 2014

Assignments Deadline:

21 March 2014, 4pm.

Feedback

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.

Staff

Course Staff are:
Guest Lecturers:
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.

Resources

Basic concepts are well explained in the following book, which 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.

A good textbook covering basic and advanced concepts is:
Jones N.C. and Pevzner P. (2004) An Introduction to Bioinformatics Algorithms, MIT Press


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