1. Introduction to computers and
programming

2. 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

3. The computer

4. Internally

5. The connections

6. 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

7. Information coding
• Binary • How to count
 0 or 1 128 64 32 16 8 4 2 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

8. 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

9. RAM/ROM
Memory mapping
Address Values
10111001
• Size reminder:
0000
00001111
• Kilobyte Kb 210 ~103
0001
0002 11100011 • Megabyte Mb 220 ~106
.. • Gigabyte Gb 230 ~109
.. • Terabyte Tb 240 ~1012
..
• Petabyte Pb 250 ~1015
• …
..
FFFF 00100100

10. HD/DVD
trac
k
sector
hea
d

11. 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

12. 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.

13. ASCII & Unicode
• ASCII 7/8 bits
• Unicode •
 UTF-8/16/32 bits
 ISO-8859 (Latin)
• od -c od -h

14. Software layers
Files Data (.doc, .mp3)
Software Word, scripts, mail, web browser…
User Interface Quartz CLI, X-Windows Windows
Operating MacOSX Linux Windows
System
ROM Firmware BIOS
Hardware CPU, RAM, HD, DVD

15. 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…

16. 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

17. 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
filename
path

18. 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)

19. 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

20. 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

21. 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

22. 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

23. Packets
The data travels within
units called packets

24. Packet breakout
Usual TCP/IP payload per packet: 512 bytes

25. Introduction to programming

26. What is a program?
• How to cook?
• The algorithm
• Are you a programmer?

27. Pseudocode
• This is the pseudocode for a game of Monopoly

28. Flowcharts

29. Flowcharts details

30. 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…

31. 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…

32. Source code
• Instructions • Data structures
 Statement, blocks  Variable
 Affectation  List
 Operators  Array
 Loops  Hash
 Tests  Pointers
 Subroutines  Objects
 Comments

33. 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

34. 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…

35. 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

36. 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

37. Flowchart

38. 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’nn";
@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

39. 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

40. 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

41. Unix
• Next presentation…