Introduction to computers and

programming
 Content

• Hardware • Network
• Information storage  Protocols
 RAM, ROM  Packets
 HD, DVD • Programming
• Display  Algorithm
 Images  Pseudocode
 Characters (fonts)  Flowchart
• File system/type • Languages
 Encryption • Source code
 Compression  Example
The computer
Internally
The connections
 Information storage

• 1 bit • bit (1 or 0)
• 8 bits • byte (octet) (28)
• 16 bits • word (216)
• 32 bits • double (232)
• 64 bits • long double (264)

Encoding information on a fixed element of length n with a

base b gives bn non-redundant possibilities
 Information coding

• Binary • How to count

128 64 32 16 8 4 2 1
 0 or 1
1 0 1 1 0 1 0 1
• Octal
 0-7 • 128+32+16+4+1=
• Hexadecimal  181 (decimal)
 265 (octal)
 0-9+A-F
 B5 (hexadecimal)
• Decimal
 0-9 • Signed vs unsigned
 0 to 255
 -127 to +127
 Operations on bits

• Booleans: • Example tables

 0 = false = no AND 0 1
0 0 0
 1 = true = yes
1 0 1
• Operators:
OR 0 1
 AND 0 0 1

 OR 1 1 1

 XOR XOR 0 1

 NOT 0 0 1
1 1 0
 RAM/ROM
Memory mapping
Address Values
1 0 1 1 1 0 0 1
• Size reminder:
0000
0 0 0 0 1 1 1 1 • Kilobyte Kb 210 ~103
0001
0002 1 1 1 0 0 0 1 1 • Megabyte Mb 220 ~106
.. • Gigabyte Gb 230 ~109
.. • Terabyte Tb 240 ~1012
..
• Petabyte Pb 250 ~1015
• …

..
FFFF 0 0 1 0 0 1 0 0
HD/DVD

track

sector

head
 Display
QuickTime™ et un
décompresseur TIFF (non compressé)
sont requis pour visionner cette image.

• Screen pixel or dots

• Fonts
• Color coding: 32 bits
• 1 pixel = 3 bytes of color (RGB)+1  Bitmap
byte alpha channel (transparency)  Vectors
• 1600x1200x4bytes=7,5 Mb!
 TrueType, OpenType,
PostScript
 Keyboard/Mouse

• Each key (or combination • The mouse movements

of keys) of the keyboard  1 to 4 bytes (vertical &
sends a code to the horizontal)
computer. • Buttons
• The code is interpreted and  Clicked, pressed, rolled
converted to the
corresponding ASCII or buttons
Unicode number.
 ASCII & Unicode

• ASCII 7/8 bits

• Unicode •
 UTF-8/16/32 bits
 ISO-8859 (Latin)

• od -c od -h
 Software layers

Files Data (.doc, .mp3)

Software Word, scripts, mail, web browser…
User Interface Quartz CLI, X-Windows Windows
Operating System MacOSX Linux Windows
ROM Firmware BIOS
Hardware CPU, RAM, HD, DVD
 File systems

• Method the OS uses to store information

 Storage unit, directories, subdirectories (Windows,
VMS)
 Single arborescence (Linux, MacOSX, all Unix)
• What exactly is a file?
 a piece of information (text, graphic, data, music
program, script)
 it is identified by a name and an logical address (or
path)
 other informations: date, size, type, creator,
ownership, physical address…
 File system organisation

Disk 1 Disk 2 Disk 2

C: D: /

DOCS PROGS CONFIG DATA Directories /usr /home

Disk 1
WORD EXCEL EXPT1 EXPT2 Subdirectories local phil john

bin lib

emacs X11

Windows Unix
 Path

• The path is the logical address used by

the system or the user to locate a file.
• Example:
/bd_du_Palais/35/etage/4/appart/12/Dupont_ Jean.txt

suffix
path filename
 File types

• Executable • Special cases in Unix

 .exe  STDIN
 .app  STDOUT
 Unix requires « x »  STDERR

• Data
 Text (.txt)
 Music (.mp3)
 Image (.jpg, .gif)
 Movie (.mpg, .mov)
 Binary (.bin)
 Encryption / compression

• Compression
 Reducing the size of files
 E.g., .mp3, .gz, .jpg, .zip
• Encryption
 Protecting your privacy
 E.g., .pgp
• Packing
 Grouping the files
 E.g., .tar
 Networks

• Direct
 USB 11Mb-480Mb
 Ethernet 10Mb-1Gb

• Wired
 Modem 56Kb
 ADSL 600Kb-8Mb
 LAN 10Mb-10Gb

• Wireless
 Bluetooth 1Mb-20Mb
 WIFI (AirPort) 11Mb-54Mb
 Network (ethernet or wireless)

• Computer talk to each • Handshaking

other via network • Transmission
protocols • Ackowledgement
 ip, tcp, http, ftp, …

• TCP/IP • DNS
 Domain Name Server
 transmission control
protocol/internet protocol • URL
 Universal Resource
Locator
• IP addess
 192.42.197.51
 DNS reminder

2 Root DNS 3
*.org

5 4
Local DNS Primary DNS
dns.anywhere.net www.expasy.org

1 6
www.expasy.org ??

Client query Target server

client.anywhere.net 129.194.8.64
 Packets

The data travels within

units called packets
 Packet breakout

Usual TCP/IP payload per packet: 512 bytes

Introduction to programming
 What is a program?

• How to cook?
• The algorithm
• Are you a programmer?
 Pseudocode

• This is the pseudocode for a game of Monopoly

Flowcharts
Flowcharts details
 Languages

• Low level (processor dependent)

 Machine code, assembler
• High level: structured, procedural
 Fortran, C, Pascal…
• High level: object oriented
 C++, Java, C#, Perl, Objective-C…
• Virtual machines
 Java, C#…
• Scripting
 Perl, Python, JavaScript…
 Source code -> Object code

• Compiler+linker • Compiler+linker
 Fortran, C, Pascal, C++…  Fast to execute, but slow
to debug
• Interpreter • Interpreter
 Basic, Perl…  Slow to execute, but fast
to debug (no need to
recompile)
• Intermediate • Intermediate
 Java  Slow…
 Source code

• Instructions • Data structures

 Statement, blocks  Variable
 Affectation  List
 Operators  Array
 Loops  Hash
 Tests  Pointers
 Subroutines  Objects
 Comments
 Source code (2)

• Statement, blocks • Variable

 One or more  A region in memory
instructions for the that can be modified
processor
 Exists in different
• Affectation types
 Change to a variable  Scalar, char, numeric,
• Operator boolean
 affect one or more  List, array
variable  Hash
 + * - / AND OR NOT…  Combination->data
structure
 Source code (3)

• Loops • Pointers
 Allow the computer to  Reference to region in
repeat blocks memory (address)
• Tests • Objects
 Decide what to do
 Combination of data
• Subroutines and code
 Programs frequently
called (functions)
• Comments
 The most important
lines of the source
code…
 Example: a text to treat

« Noon rings out. A wasp, making an ominous sound, a sound akin to a klaxon or a
tocsin, flits about. Augustus, who has had a bad night, sits up blinking and purblind. Oh
what was that word (is his thought) that ran through my brain all night, that idiotic word
that, hard as I'd try to pun it down, was always just an inch or two out of my grasp - fowl
or foul or Vow or Voyal? - a word in a quizz which, by association, brought into play an
incongruous mass and magma of nouns, idioms, slogans and sayings, a confusing,
amorphous outpouring which I sought in vain to control or turn off but which wound
around my mind a whirlwind of a cord, a whiplash of a cord, a cord that would split again
and again, would knit again and again, of words without communication or any possibility
of combination, words without pronunciation, signification or transcription but out of
which, notwithstanding, was brought forth a flux, a continuous, compact and lucid flow: an
intuition, a vacillating frisson of illumination as if caught in a flash of lightning or in a mist
abruptly rising to unshroud an obvious sign - but a sign, alas, that would last an instant
only to vanish for good. »

Gilbert Adair
 Result…

a=97 n=91
b=15 o=104 Do you see any problem??
c=26 p=15
d=35 q=1
f=23 r=43
g=32 s=59
h=44 t=77
Try with this:
i=90 u=52
j=1 v=4 « The quick brown fox, jumps
k=5 w=31 over the lazy dog. »
l=33 x=2
m=17 y=13
z=2
Flowchart
 Source code example

#!/usr/bin/perl -w # essential line of all perl scripts

$filename = "avoid.txt"; # affect « avoid.txt » to the variable $filename

# open the file, or exit

open(FILE, $filename) || die "Cannot open file ‘$filename’\n\n";
@text = <FILE>; # add each line of the file to an array
close FILE;

foreach $line (@text) { # read one line from the array into $line and repeat for each line
@table = split(//,$line); # read each character of the line in an array
while ($char=pop(@table)) { # read one character of the array 'table' and repeat for all
$char =~ s/[^a-z]//; # keep only the alphabetical character a to z
if ($char) { # check if the character exists and execute the block
$count{$char}++; # if yes, increment by one the hash 'count'
}
}
}

# print each character and its number of occurence one per line
foreach $c (keys %count) {
print "$c=$count{$c}\n";
}
exit; # quit the program
 Tips

• Think about your • Test the code

problem  For all the possible
• Create a flowchart functions or cases (if
possible)
• Create the  Give it to users as a
pseudocode beta (if not possibe)
• Verify the memory  Sell it (if you work for
used by your Microsoft©… ;-)
variables • Debug
• Write the code
 Summary of the week

• Monday • Wednesday
 Intro computers &  Object Oriented
programming programming
 BioPerl
 Intro Unix
 EMBOSS
 Tutorial Unix
• Thursday
• Tuesday  Database indexing
 Intro Perl  BLAST
 Regexp & Perl In-liners  HTML & cgi-bin
• Friday
 Finish exercises
 Users questions
 Unix

• Next presentation…

Vassilios
alias
UnixMan!!!