An Introduction to Solving Biological Problems with PERL

BeginnersPrerequisites

This course is aimed at those new to programming and provides an introduction to programming using Perl.

During this course you will learn the basics of the Perl programming language, including how to store data in Perl’s standard data structures such as arrays and hashes, and how to process data using loops, functions, and many of Perl’s built in operators. You will learn how to write and run your own Perl scripts and how to pass options and files to them. The course also covers sorting, regular expressions, references and multi-dimensional data structures.

The course will be taught using the online Learning Perl materials created by Sofia Robb of the University of California Riverside.

The course website providing links to the course materials is here.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

• Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
• Further details regarding eligibility criteria are available here
• Further details regarding the charging policy are available here

• No prior programming experience is required
• Ability to use a plain text editor
• Very basic knowledge of UNIX would be an advantage

Number of sessions: 2

• Lesson 01 - Perl script skeleton
• Lesson 02 - Variables: scalars, arrays, and hashes
• Lesson 03 - Assigning Values to Scalar Variables
• Lesson 04 - Array Assignment
• Lesson 05 - Accessing elements of an array
• Lesson 06 - Reassigning elements of an array
• Lesson 07 - Hash Assignment
• Lesson 08 - Accessing elements of a hash
• Lesson 09 - Reassigning elements of a hash
• Lesson 10 - String functions and operators
• Lesson 11 - Numeric Operators and functions
• Lesson 12 - Truth and conditional statements
• Lesson 13 - Loops
• Lesson 14 - Loop Control
• Lesson 15 - Array Functions
• Lesson 16 - Hash Functions
• Lesson 17 - Sort with arrays and hashes
• Lesson 18 - User/Command-line input
• Lesson 19 - Sanity checks and testing
• Lesson 20 - Files and File handles
• Lesson 21 - References and multidimensional data structures
• Lesson 22 - Regular Expressions
• Lesson 23 - Subroutines or Custom functions
• Lesson 24 - System Calls

After this course you should be able to:

• write simple Perl programs to process biological data
• understand Perl programs written by others
• use core Perl modules in your own programs
• know how to develop your skills in Perl after the course

• To enable bench scientists with no previous programming background to write simple PERL scripts and to understand and edit slightly more complex scripts

Presentations, demonstrations and practicals

2

A number of times per year