MSc Bioinformatics and Systems Biology / Course details

This unit aims to introduce basic programming skills to the non-expert, including the Unix environment, command line driven computing and 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 a particular problem in genomics/proteomics. Labs 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 aims to: • Develop relevant programming skills for, including the Unix environment. • Develop skills in writing programs to solve biological data handling problems, both as individuals and as a group.

• 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 software for individual tasks, and working in small groups to link together programs to form an analysis pipeline. • 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 Unix environment and command line driven computing, including basic commands for files, folders and management, pipes and redirection. • 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. • Development of individual standalone programs, that can also be run as a pipeline in a project group setting. Code, coupled with a short group report are assessed as one of the projects. • Labs 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 from demonstrators and lecturers.

• Lectures: 12 hours.• Practicals: 24 hours. • Online tutorials: 12 hours.• Project work: three programming projects will be completed during Semester 1, in the practical classes and in the students' own time.

Three short project reports, software and demonstration of software resulting from the second project. 20% project 1, 30% project 2 and 50% project 3 (10% group component).

Detailed written feedback on projects and reports is provided for each student and group, as well as verbal feedback during labs on scripts and programs as they are written.

• 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.