IDC306: Biocomputing

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Following content will be taught in biological context.

Introduction to Computation: history of computation, need of computation in modern biology.
The types of biological data and databases: sequence, structure, expression, interaction, enzyme activity, genomic and population data-sets.
Common data formats used in biology: separator delimited text files and their relevance, fasta sequence format, alignment files, tree representation, HTML/XML files, bed/gff files etc.
Working with text editors and spreadsheets.
Data compression: Huffman encoding, Burrows wheeler transformation, Gif, Jpeg, Png, Zip, Tar etc.
Command-line programming: working with Linux/Cygwin shell, regular expressions, installing software in Linux, vi editor, shell scripting, working with MS DOS
Introduction to relational databases: MySQL
Basic computer programming: elements of programming, PERL or Python.
Advanced computer programming : writing functions/packages, writing images, working with databases through programs, connecting to servers/WWW, developing user interfaces with HTML/CGI and Tk
Statistical computing using R: basic R functions, statistical tests of significance, working with advanced packages
Graphics: working with Gimp, Photoshop, Illustrator and MS powerpoint for basic imaging.