101. Introductory Unix for Bioinformatics

The basic 101 level course teaches the applications of Unix tools and utilities to perform routine sequence analysis tasks. This is an introductory course for those who want to obtain a basic understanding of the Unix OS and can be completed in 2-3 months. All commands are customized for the Tcsh shell.

Unix for Bioinformatics 101 covers the following topics:

    § The Bioinformatics working environment
    § Navigating the Unix file system
    § Creating and manipulating sequence files
    § Downloading and manipulating sequences from Entrez
    § Unix commands and utilities (piping, redirection)
    § Editing files in Unix with the Emacs editor

201. Advanced Unix for Bioinformatics

Unix is the platform of choice for large-scale Bioinformatics operations. Among other things, 201 describes work-flow operations in a typical high-throughput sequencing center - a fundamental aspect of large-scale sequencing that controls how sequence data is stored, distributed and processed in these centers - and, the biology of the sequencing process itself. Unix 201 can be taken in combination with Perl 201.

Unix for Bioinformatics 201 covers the following topics:

    § Editing and manipulating sequence files with the vi editor
    § FTP and downloading databases from NCBI
    § Unix commands and utilities for sequence analysis
    § Using wild cards with commands
    § File compression and uncompression
    § Process control

 

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