MSc Bioinformatics and Systems Biology

This unit aims to introduce basic programming skills to the non-expert, using the Python programming language. Using an online environment, accessible directly from any browser, we will introduce the basics of Python, which is a powerful scripting language that is now ubiquitous throughout bioinformatics and scientific computing. You will test your developing skills on series of assessed project including one that aims to develop a "pipeline" of simple Python programs to address particular problems in biology. Practical sessions are coupled to all the lectures where you will be able to test out your new skills, tackle exercises, and work on your project code where demonstrators and lecturers are able to help you design and debug your code. 

This unit aim is to:  

Develop relevant programming skills using the Python programming language to solve biological data handling problems.  

Students will become familiar with use of a range of programming skills useful for writing bioinformatics software and developing biological data analysis solutions in Python.  

They will gain experience of writing usable bioinformatic tools to solve tasks relevant to biological problems.  

Students will be aware of issues of usability and will know how to deliver a bioinformatics project with a specific brief.     

Introduction to CoCalc as an online learning environment.

Introduction to the Python programming language. This will cover language syntax essentials, variables, conditional and loops, file input and output, functions, regular expressions and modules. All will be illustrated with examples, mostly centred on biological data types.  

Introduction to the Unix environment and command line driven computing, including basic commands for files, folders and management, pipes and redirection.  

Development of individual standalone programs, that can also be run as a pipeline in a project group setting.  

Lectures: 12 hours.

Practicals: 24 hours.  

Online question and answer sessions: 12 hours.

Project work: three programming projects will be completed during Semester 1, in the practical classes and in the students' own time.  

Three projects will be assessed with the following weighting based on complexity:

20% project 1, 30% project 2 and 50% project 3. 

Practical sessions are coupled to lectures where you will be able to test out your new skills, tackle exercises and work on your project code with guidance and verbal feedback from demonstrators and lecturers. 

Learning Python, Second Edition, Lutz and Ascher. O'Reilly Media ISBN: 978- 1-4493-5573-9 | ISBN 10: 1-4493-5573-0.  

Python for Biologists: A complete programming course for beginners. Martin Jones. ISBN-10: 1492346136 - ISBN-13: 978-1492346135 - better for complete beginners.