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Part 1 of 'Introduction to Linux for bioinformatics': Introduction


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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

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Part 1 of 'Introduction to Linux for bioinformatics': Introduction

  1. 1. This presentation is available under the Creative Commons Attribution-ShareAlike 3.0 Unported License. Please refer to if you use this presentation or parts hereof. Introduction to Linux for bioinformatics Getting Linux Joachim Jacob 5 and 12 May 2014
  2. 2. 22 of 38 Mixing exercises and theory This training will introduce you to Linux in a broad range of concepts. ● Exercises ● Graphical >>> command line ● Terminology
  3. 3. 33 of 38 Linux ... Can somebody tell me what they think about when hearing 'Linux' ?
  4. 4. 44 of 38 A bunch of hardware: a computer!
  5. 5. 55 of 38 They use different signals to communicate Hallo BonjourOla Hello Ni Hao Buenos dias Guten tag
  6. 6. 66 of 38 An operating system translates
  7. 7. 77 of 38 An operating system translates
  8. 8. 88 of 38 An OS is stored on the hard disk Oempf
  9. 9. 99 of 38 Linux drives the computer hardware Get me that file! OK The linux kernel
  10. 10. 1010 of 38 Linux drives the computer hardware Get me that file! OK The linux kernel
  11. 11. 1111 of 38 Linux drives the computer hardware Get me that file! OK The linux kernel Here you are: Thank you
  12. 12. 1212 of 38 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
  13. 13. 1313 of 38 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 ...
  14. 14. 1414 of 38 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.
  15. 15. 1515 of 38 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, ….
  16. 16. 1616 of 38 Why Linux?
  17. 17. 1717 of 38 Why Linux? ● Stable ● Safe ● Adjustable
  18. 18. 1818 of 38 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,...
  19. 19. 1919 of 38 But, the teacher's computer runs not 'linux'
  20. 20. 2020 of 38 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.
  21. 21. 2121 of 38 So – who of you is using Linux already? Graphics:
  22. 22. 2222 of 38 So – who of you is using Linux already?
  23. 23. 2323 of 38 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...
  24. 24. 2424 of 38 Linux for the desktop Dozens Linux distributions to run on your desktop exist. A top 10 on urce=major
  25. 25. 2525 of 38 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,...
  26. 26. 2626 of 38 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:
  27. 27. 2727 of 38 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.
  28. 28. 2828 of 38 They differ in 'desktop environment' Unity KDE Gnome Cinnamon
  29. 29. 2929 of 38 They differ in file managers Thunar Dolphin Nautilus Krusader
  30. 30. 3030 of 38 How do I choose?
  31. 31. 3131 of 38 Quickly and easy try them out! Oempf
  32. 32. 3232 of 38 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.
  33. 33. 3333 of 38 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)
  34. 34. 3434 of 38 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 Linux Windows Choose during boot which OS you want to launch. : level of difficulty
  35. 35. 3535 of 38 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
  36. 36. 3636 of 38 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
  37. 37. 3737 of 38
  38. 38. 3838 of 38 Break