Bioinformatics: Introduction to PERL

Beginners

This course takes students from having no knowledge of how to program, to being able to write useful applications. Students will come away with an application framework that they can easily adapt and extend to suit their own particular needs. Each course topic is introduced and placed in context, and then complete example code is provided to illustrate the subject under discussion, which is gone through line by line and then implemented by the students. For more advanced students related challenges are provided without solutions, although training staff are happy to provide help and guidance. Throughout the course, the emphasis is on making sure that each student understands and appreciates what is going on, and therefore the course handbook provides plenty of room for the students’ own notes, while the provision of comprehensive answers to class questions is a top priority.

• Postgraduates
• Researchers
• Further details regarding Graduate School of Life Sciences' eligibility criteria are available

Number of sessions: 3

• What is Perl and where can I get it?
• What is programming?
• Getting a Perl program to run
• Getting Perl to check our code for us
• Simple mathematical functions
• Scalar variables
• Using strict
• Loops
• Lists
• Writing to files
• Reading from files
• Pattern matching
• Reading in sequence data
• Subroutines
• Looking for motifs in DNA sequence
• Reading in structure data
• Image analysis
• Grid-type data: simple analysis of 2D graphical images; modules; CPAN; computer images; object orientation.

The course begins with the fundamental aspects of the language – variables, functions, loops and control flow. It goes on to explore input and output, error handling, and data analysis using pattern matching with regular expressions. During the course, we will focus on using the core aspects of Perl to perform the basic tasks of almost any program – reading data in, processing it, and writing out results.

Presentations and practicals

This course will be taught by Paul Weston, author of ‘Bioinformatics Software Engineering: Delivering Effective Applications’, published by John Wiley and Sons. With 20 years experience in application development, and a background that includes sequence assembly pipelining, distributed computing, and online gaming, he still enjoys writing Perl. He is a Senior Computer Programmer in the Variation Informatics Group at the Wellcome Trust Sanger Institute.

3

A number of times per year