Introduction to Bioinformatics 320-ERS-1ITBL

Main goal of the course is to prepare students for efficient work in unix (Linux) environment using command line tools. Students will also learn easy ways to automatize their multiple task work with simple scripts, even on remote servers. Large part of the course will focus on practical manipulation of text files including pattern recognition as an easy guide to prepare input files for multiple applications.

1. Introduction to Linux: GUI, documentation, file system organization, command structure in terminal.
(2 hours)

2. Terminal commands every user should know. Build-in text editors (gedit, nano). Useful operators. How to connect and work on remote servers.
(3 hours)

3. How to work with text files: easy way for identification of complex patterns and their modification/replacement with powerful language of regular expressions (regex).
(4 hours)

4. How to create and execute a bash script. Futher automatization of scripts using loops (for, while, until).
(4 hours)

5. Main molecular biology databases.
(2 hours)