Introduction to Linux for bioinformatics

Trainer Christof De Bo
BITS Courses TRAINING AT VIB

Goal

After this training you will

  • feel comfortable using Linux
  • know how software works on Linux and how to use it
  • use bash to execute commands in Linux and know your way around the file system
  • have an overview of Linux tools that are extremely useful for bioinformatics

Summary

This training is intended for all Linux novices who want to learn the basics of Linux without getting too much technical details.

This hands-on training will show you how to effectively use Linux, a free operating system. Bioinformatics depends heavily on Linux-based computers and software. A lot of good scientific software is written specifically for Linux/Unix. Additionally, Linux has most popular programming languages (e.g.Python, Perl, C) already installed and ready to use! Data management happens swiftly with the dedicated text manipulation tools and file system properties. This training will teach you all you need to know to swiftly start using Linux, be it on the server of your department, or on your own computer (even if you're already running Windows or Mac OS).


Prior to the training session, you will receive a poll to ask you your personal goals by following this training sesion. Depending on the outcome, the schedule will be adjusted.

Prerequisites

No skills required.

Schedule

See the TRAINING AT VIB website for a detailed schedule of this training.

Training material

Links

Quick Reference Cards:

Selected beginner's manuals and tutorials:

  • Linux' grep commands explained in simple examples from the Geek Stuff
  • Manipulating Data on Linux: get data to and from Linux, examine and slice files, view and manipulate data, data visualization, binary data storage, databases, mathematical modeling
  • Linux fundamentals beginners' manual:  install, command line, shell expansion, pipes and commands, vi, scripting, local user management, file security
  • A funny overview of Linux filesystem, as a guided tour!
  • Graphical overview of the Linux file structure
  • GNU/Linux command-line tools summary for beginners: shell, help, directing input/output, file system, find system information, control the system, manage users, text tools, mathematical tools, graphic tools, network commands, security, archive files, work with MS-DOS files, schedule commands
  • Linux basics manual: help, find things, permissions, commands, process management, text viewing and editing, shell, shell scripts, Perl scripts, remote copy, archive and compress, screen, devices, environment variables

Advanced guides:

Looking for a good distro to start with?

  • PinguyOS: a Linux OS for everyone, not just geeks. It is based on Ubuntu and comes with all everyday tools you need
  • Linux Mint: a powerful easy to use Linux OS, also based on Ubuntu
  • Guide to buying a Linux computer
  • Novice guide to buying a Linux laptop: CPU, video card, X server, RAM, hard disk, optical disk, power management, wireless, fingerprint scanner, Fn key support, ports, sound, docking station, ethernet, Linux distributions, vendors

Books

linuxpocket  PerlAndUnix  linux in depth  developbioinfo  sysadmin  runninglinux

Scientific topics Linux, Command-line interface, Shell
Target audience Life Science Researchers, PhD students, post-docs, beginner bioinformaticians