Computing tools for bioinformatics: UNIX, regular expressions and shell script

Main contents

  • Introduction to UNIX and GNU/Linux.
  • Servers: Connection and data exchange.
  • Navigation: paths, permissions, edition and search.
  • Regular expressions: grep, sed, awk
  • Shell scripting on bash.

Type: Mandatory
PDF sheet: Download.


Rodrigo Santamaría (


The student will familiarice with basic concepts from UNIX operating systems, the most used systems for computing servers and for most cutting edge bioinformatic tools. The student will obtain the required skills to connect, to share information and to navigate through a UNIX-like server. He will also learn the basic commands for text editing, search and run programs, with especial emphasis on text pattern searches (regular expressions) and the development of programs (shell scripts), which serves also as an introduction to programming on the posterior subjects (Python and R).