Introduction to GNU/Linux, Free/Libre Open Source Software, comparing the OS with Mac OSX and Microsoft Windows, and a few other infos and pointers. Content partially reused from a Masters Degree at VHIR where I had to tech that introduction prior to using GNU/Linux tools for Bioinformatics in that master of traslational medicine: https://www.vhir.org

1. Vall d’Hebron Institut
de Recerca
Introduction to GNU/Linux
Xavier de Pedro Puente, Ph.D.

2. Introduction to GNU/Linux
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Xavier de Pedro Puente, Ph.D.
xavier.depedro@vhir.org
Academics:

Degree in Biology
(University of Barcelona - UB)

Ph.D. in Biology
(University of Barcelona - UB)

Postgraduate in Bioinformatics
(Open University of Catalonia – UOC)
Current Work:

Bioinformatics technician (UEB, VHIR)

Systems administrator (UEB, VHIR)

Professor of Sustainability (IES Abroad Barcelona)

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• GNU/Linux OS (a.k.a. “Linux”)
- GNU/Linux “Distributions”
- Your USBDISKs (et al.)
• Basic Differences between:
- GNU/Linux and Windows
- GNU/Linux and MacOSX
• Command line runs
Introduction to GNU/Linux
(for VHIR Master students)
By: Xavier de Pedro

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GNU/Linux OS (a.k.a. “Linux”)
●
End User
Applications:
●
Operating
System:
●
Computer:
(Harware)
"Windows" "Mac" "Linux”

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Operating System (OS): GNU progs. + Linux kernel

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GNU/Linux "Distribution”

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GNU/Linux "Distribution”

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Your USBDISKs (et al.): Option A
USBDISK BioLinux8 on local VirtualBox (VT-x in BIOS)
BioLinux: Dawn Field et al. (2006) "Open software for biologists: from famine to feast". Nature
Biotechnology 24, 801 - 803 (2006). doi:10.1038/nbt0706-801

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Your USBDISKs (et al.): Option B
USBDISK Lubuntu on VirtualBox (no VT-x, BIOS?)
Lubuntu: Lightweidht Desktop on a Ubuntu GNU/Linux Distribution. http://lubuntu.net

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Your USBDISKs (et al.: "X2Go"): Option C
Connection to remote VBox (on ueb.vhir.org port 2201-5)
X2Go: Program to connect to a remote computer through GUI (Graphical User Interface)

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Your USBDISKs (et al.: "X2Go"): Option C
Connection to remote VBox (on ueb.vhir.org port xxx1-5)
X2Go: http://wiki.x2go.org

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Your USBDISKs (et al.): Option D
LiveUSB (Lubuntu-based; BIOS to boot from USB)
LXLE: A Lubuntu-based GNU/Distribution with improved desktop http://www.lxle.net

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Basic Differences between: GNU/Linux & Windows
●
Technical differences
– User: root vs. administrator
– Case sensitive vs. Case insensitive
●
"MyFile != myfile" vs. "MyFile = myfile"
– "Symbolic or Hard Links" vs. "Shortcuts"
– Paths: Slash ("/") vs. Backslash ("")
– Main harddrive/partition: "/" vs. "C:"
– Partition formats: ext2, ext3, ext4, ... vs. fat16/fat32/ntfs
– User default folder: /home/username vs. "C:Documents and Settings" or
"c:UsersusernameMyDocuments"
– USBdisk default folder: "/media/username/usbdiskname" vs. "X:usbdiskname"
– Secure (Viruses???) vs. Insecure (viruses, bots, worms, trojans, backdoors, ...)
– It can extend computer useful life vs. Planned & perceived obsolescence
– Performance, with same hardware: Faster vs. Slower (Antivirus, antispyware,...)
– normal user: "sudo program" in console vs. "Run program as administrator"

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Basic Differences between: GNU/Linux & Windows
●
Phylosophical differences
– Freedom: "Free/Libre Open Source Software
(FLOSS)" vs. "Closed Source/Propietary software"
●
Software Sustainability: High vs. Low
– Usually: product given for free (at no Cost) vs.
product for (excessive?) profit
– Money comes through: customizations and
training vs. Selling Software
– FLOSS Fosters local economies as well as big
companies vs. Big & remote Corporations growth.

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Basic Differences between: GNU/Linux & MacOSX
●
Technical differences
– Users:
– Case:
– Links:
– Paths:
– Main harddrive/partition
– Partition formats: ext2, ext3, ext4, ... vs. HFS+
– User default folder: /home/username vs. "/Users/Username"
– USBdisk default folder:
– Secure (Viruses???) vs. Secure (Viruses?)
– It can extend computer useful life vs. Planned & perceived obsolescence
– Performance, with same hardware: Faster??? vs. Extremely Fast
– normal user:

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Basic Differences between: GNU/Linux & MacOSX
●
Phylosophical differences
– Freedom: "Free/Libre Open Source Software
(FLOSS)" vs. "Closed Source/Propietary software"
●
Software Sustainability: High vs. Low
– Usually: product given for free (at no Cost) vs.
product for (excessive?) profit
– Money comes through: customizations and
training vs. Selling Software & Hardware
– FLOSS Fosters local economies as well as big
companies vs. Big & remote Corporations growth.

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Command line runs (i)
●
Serial vs. Parallel tasks
●
Shell = Terminal = Console ("Black" text screen
to run commands)s
– Secure Shell = ssh = a safe way to connect to
remote computers or servers (encrypted)
– ftp: File Transfer Protocol
●
to transfer files between computers or servers
●
you can NOT run commands (other than listings)
– sftp: like FTP but "secure" (best: using ssh libraries)

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Command line runs (ii)
●
Example of simple local commands:
– ps -e
– ls -l
– df -h
– top
●
Example of bioinformatics shell programs:
– fastqc
– fastx
– blast*
– …

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Command line runs (iii)
●
Example of network commands:
– ping google.com
– ifconfig
– ftp manager@ueb.vhir.org
– sftp manager@ueb.vhir.org
– sftp -p 2200 manager@ueb.vhir.org
– ssh manager@ueb.vhir.org
– ssh -p 2200 manager@ueb.vhir.org
●
Example of shell-based programs:
– nano (simple editor: press "Ctrl + X" to eXit)
– htop (type "q" to quit/exit)
– mc (Midnight Commander). Click on F10 (with mouse or trackpad) to quit
– R ( Type "q()" to quit)

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More information
●
Ubuntu GNU/Linux:
– http://www.ubuntu.com
●
Linkat (Ubuntu):
– Manual Installation with custom partitions (advanced, or for servers):
http://linkat.xtec.cat/portal_linkat/wikilinkat/index.php/Wiki_Linkat_edu
_14.04
– Desktop installation (easy):
http://linkat.xtec.cat/portal_linkat/wikilinkat/index.php/Linkat_edu_14.
04_Autònom
●
Forums for help and support:
– VHIR:
http://forums.vhir.org
– Ubuntu (Catalan LoCo Team):
http://ubuntuforums.org/forumdisplay.php?f=206