Lecture GK-1

Introduction; Perl (1); Working with Linux

Aims

• To place bioinformatics in a wider context.
• To introduce the Perl programming language.
• To introduce some basic Linux commands (for students who are not already proficient with the Linux operating system).

Objectives

After this lecture you will be able to:

• discuss a range of experimental methods, the kinds of data that these generate, and examples of biological questions that these can help to address;
• write and execute a simple Perl script;
• use scalar variables in Perl programs, including the default variable $_;
• use loops and conditional statements in Perl programs;
• use simple numeric and string operators in Perl programs;
• use the standard input and output file handles (<STDIN> and <STDOUT >) and file handles for external files;
• access command line arguments from within Perl programs;
• use the Linux shell to perform some basic operations.

Supplementary Material

The lecture handout, featuring some of the lecture slides, is available on-line (one per page, four per page).

Links to Wikipedia pages describing some experimental methods:

• DNA sequencing
• Protein sequencing
• X-ray crystallography
• Nuclear magnetic resonance (NMR) spectroscopy
• Cryo-electron microscopy
• Small-angle X-ray scattering
• DNA microarray
• RNA-Seq
• Two-dimensional gel electrophoresis
• Mass spectrometry
• In situ hybridization

Programs from the lecture: /chalmers/users/kemp/MVE360/lecture1/

The article "Scripting: Higher Level Programming for the 21st Century" by John K. Ousterhout (designer/developer of the Tcl scripting languages) contains some interesting opinions on the growth of scripting languages and their relationship to system programming languages like C, C++ and Java.

The value of Perl and Unix pipelines in Bioinformatics is illustrated in the article "How Perl Saved the Human Genome Project" by Lincoln Stein.