This is part 1 of the training session 'Introduction to Linux for bioinformatics'. We explain in very general terms what Linux is and stands for, and how we can get access to it. Interested in following this training session? Please contact me at http://www.jakonix.be/contact.html

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Introduction to Linux
for bioinformatics
Getting Linux
Joachim Jacob
5 and 12 May 2014

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Mixing exercises and theory
This training will introduce you to Linux in a
broad range of concepts.
● Exercises
● Graphical >>> command line
● Terminology

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Linux ...
Can somebody tell me what they think
about when hearing 'Linux' ?

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A bunch of hardware: a computer!

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They use different signals to communicate
Hallo
BonjourOla
Hello
Ni Hao
Buenos dias
Guten tag

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An operating system translates

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An operating system translates

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An OS is stored on the hard disk
Oempf

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Linux drives the computer hardware
Get me that file!
OK
The linux
kernel

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Linux drives the computer hardware
Get me that file!
OK
The linux
kernel

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Linux drives the computer hardware
Get me that file!
OK
The linux
kernel
Here you are:
Thank you

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Who's asking? GNU!
Get me that file!
OK
The linux
kernel
Here you are:
Thank you
The operating
system
GNU
Provides the
low level
commands
to commu-
nicate with
the hardware
through Linux

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There's a lot of chatter
The linux
kernel
The operating
system
GNU
What's in that directory?
('ls' in GNU language)
3 files: reads.fastq,
pe_aln.sam, README
Show me the content of
that file reads.fastq
(e.g. 'head')
I read:
>HS:0012541
ATCGAATATACGATG
...

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GNU/Linux goes along very well
The linux
kernel
The operating
system
GNU
While the linux kernel
takes care of managing
the computer resources
(CPU, disks, file system,
RAM, networkcards, …),
GNU provides the
means of commu-
nication with the linux
kernel through the well-
known commands and
programs (bash, ls,
mkdir,...).
GNU is usually the first
layer of user interaction.
http://www.gnu.org/software/

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But who cares?
The linux
kernel
The operating
system
GNUGNU/Linux
The goal of linux
is to be as
invisible as
possible, doing
the heavy lifting
on the
background.
This GNU/Linux
operating system
is a solid core for
a lot of computers
and devices.
Other OSes: Windows,
Mac OS x, Solaris, ….http://coe.uncc.edu/mosaic/mosaic-linux/linux-basics/linux-kernel.html
https://www.dlitz.net/go/sticker/linuxstk800.jpg

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Why Linux?

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Why Linux?
● Stable
● Safe
● Adjustable

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Why Linux?
● Open source: the kernel code is viewable by
anyone.
● Open development: anybody can propose
enhancements /change it to their needs.
● Free-to-use: anybody can use the kernel to
drive their own computer or device (always interesting in
academics: a lot of development here)
● Stable: it is one of the most stable OS you can
find.
* since so many people use the linux kernel for their projects, and because of the many
eyes watching it, debugging happens at an astonishing rate.
** all this is protected (to remain open) by powerful licenses such as GPL, Apache
license, creative commons,...

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But, the teacher's computer runs not 'linux'

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This is the Ubuntu flavour of Linux
The rock solid Linux kernel
Ubuntu's applications and graphical interface
Many different organisations use the Linux kernel.
Some, such as Canonical, to create the Ubuntu Linux
distribution, adding their graphical sauce to it.

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So – who of you is using Linux already?
http://www.linuxfoundation.org/
Graphics: http://thenakedhero.com
http://www.youtube.com/watch?v=yVpbFMhOAwE

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So – who of you is using Linux already?

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Linux for your computer
Different distributions
● They all use the Linux OS kernel
● They add their graphical user interface
● They add tools and applications (backup, texteditor,...)
● They provide a software package manager
● initialization & configuration scripts
● commercial support
There are many distributions (600+), but perhaps only a
few that really matter...
http://www.distrowatch.com
http://www.linuxtoday.com/

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Linux for the desktop
Dozens Linux distributions to run on
your desktop exist.
A top 10 on
http://distrowatch.com/dwres.php?reso
urce=major

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Guide to choosing your distribution
● Server
● Commercial support (company driven)
– SUSE Linux ES, Red Hat EL, Ubuntu Server
● Free and community driven
– Debian, CentOS, Scientific Linux
● Personal computer
● Old hardware, slow:
– Puppy Linux, Crunchbang, Lubuntu, ...
● New hardware, fast:
– For home use: Linux Mint, Ubuntu ...
– For work use: Crunchbang, OpenSuse, Ubuntu,...
http://www.linux.org/threads/selecting-a-linux-distribution.4087/
http://distrowatch.com/dwres.php?resource=major

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Guide to choosing your distribution
Perhaps it's easier to define the opposite
● Want stability? Don't choose Fedora.
● Want the latest and hottest? Don't choose CentOS
● Want a lightweight distro? Don't choose Ubuntu
● Want classic look? Don't choose Elementary OS
● Want to do bioinformatics? Don't choose CentOS,
go for the latest actively developed.
● ...
(guess I can keep going)
Thread: Distro best for bioinformatics: http://www.biostars.org/p/16778/

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Linux in different disguises
Linux kernel
Desktop environment
Filemanager
Browser
Emailclient
Systemsettings
...
The philosophy is to have the choice of several
exchangeable components to customize your
experience.

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They differ in 'desktop environment'
http://en.wikipedia.org/wiki/Desktop_environmen
Unity
KDE
Gnome
Cinnamon

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They differ in file managers
Thunar
Dolphin
http://en.wikipedia.org/wiki/File_manager
Nautilus
Krusader

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How do I choose?
http://fedoraproject.org http://www.ubuntu.com
http://pinguyos.com/http://linuxmint.com/

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Quickly and easy try them out!
Oempf

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Run Linux in 'live modus'
Put Linux on a USB stick, and tell your computer to
start up from the USB stick, instead of the hard drive.

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How to create a live USB
Live modus!
1. Grab a USB key or CD
2. Download an ISO file: pick the 64-bit version
3. Put the ISO image to the USB key or CD, e.g. with Unetbootin
4. Boot your computer from the USB key or CD (press F2 during boot)
http://unetbootin.sourceforge.net/

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Notes about installing Linux
Straight forward
Give your complete hard disk to Linux.
The current installers are very user friendly.
If you want access to other OSes on your computer (Windows,...): 2 options
VIRTUALISATION DUAL BOOT
http://www.virtualbox.org
Linux
Windows
Choose during boot which OS you
want to launch.
http://www.gnu.org/software/grub/
: level of difficulty

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Keywords
operating system
linux
GNU
open source
distribution
desktop environment
live CD
virtual machine
dual boot
Write in your own words what the terms mean

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Exercise: let's play!
To complete the exercises, you will find .iso images
of different distributions in the Downloads folder.
Pick one of those 2 exercises (click on the link):
A: Create a bootable live USB
or
B: Install Linux as a virtual machine

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Break