The document provides an introduction to key concepts in computers and programming, including hardware components, information storage, displays, file systems, networks, and programming languages. It discusses topics like RAM, hard drives, pixels, file types, protocols, algorithms, pseudocode, and languages from low-level to high-level. Examples of binary counting, Boolean logic operators, and a source code sample in Perl are also provided.

1. Introduction to computers and
programming

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

3. The computer

4. Internally

5. The connections

6. Information storage
• 1 bit
• 8 bits
• 16 bits
• 32 bits
• 64 bits
• bit (1 or 0)
• byte (octet) (28)
• word (216)
• double (232)
• 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
 0 or 1
• Octal
 0-7
• Hexadecimal
 0-9+A-F
• Decimal
 0-9
• How to count
128 64 32 16 8 4 2 1
1 0 1 1 0 1 0 1
• 128+32+16+4+1=
 181 (decimal)
 265 (octal)
 B5 (hexadecimal)
• Signed vs unsigned
 0 to 255
 -127 to +127

8. Operations on bits
• Booleans:
 0 = false = no
 1 = true = yes
• Operators:
 AND
 OR
 XOR
 NOT
• Example tables
AN
D
0 1
0 0 0
1 0 1
OR 0 1
0 0 1
1 1 1
XO
R
0 1
0 0 1
1 1 0

9. RAM/ROM
Memory mapping
Address Values
0000
0001
0002
..
..
..
..
FFFF
• Size reminder:
• Kilobyte Kb 210 ~103
• Megabyte Mb 220 ~106
• Gigabyte Gb 230 ~109
• Terabyte Tb 240 ~1012
• Petabyte Pb 250 ~1015
• …
1 0 1 1 1 0 0 1
0 0 0 0 1 1 1 1
1 1 1 0 0 0 1 1
0 0 1 0 0 1 0 0

10. HD/DVD
track
sector
head

11. Display
• Screen pixel or dots
• Color coding: 32 bits
• 1 pixel = 3 bytes of color (RGB)+1
byte alpha channel (transparency)
• 1600x1200x4bytes=7,5 Mb!
• Fonts
 Bitmap
 Vectors
 TrueType, OpenType,
PostScript
QuickTime™ et un
décompresseur TIFF (non compressé)
sont requis pour visionner cette image.

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

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

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

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
Directories
Subdirectories
DOCS PROGS
WORD EXCEL
CONFIG DATA
EXPT1 EXPT2
Windows
/
/usr /home
local phil john
bin lib
emacs X11
Unix
C: D:
Disk 1
Disk 2

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
filename
suffix
path

18. File types
• Executable
 .exe
 .app
 Unix requires « x »
• Data
 Text (.txt)
 Music (.mp3)
 Image (.jpg, .gif)
 Movie (.mpg, .mov)
 Binary (.bin)
• Special cases in Unix
 STDIN
 STDOUT
 STDERR

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
other via network
protocols
 ip, tcp, http, ftp, …
• TCP/IP
 transmission control
protocol/internet protocol
• Handshaking
• Transmission
• Ackowledgement
• DNS
 Domain Name Server
• URL
 Universal Resource
Locator
• IP addess
 192.42.197.51

22. DNS reminder
2 3
Primary DNS
Root DNS
Local DNS
1
5 4
6
www.expasy.org
Client query Target server
129.194.8.64
*.org
dns.anywhere.net
client.anywhere.net
www.expasy.org ??

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

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

33. Source code (2)
• Statement, blocks
 One or more
instructions for the
processor
• Affectation
 Change to a variable
• Operator
 affect one or more
variable
 + * - / AND OR NOT…
• Variable
 A region in memory
that can be modified
 Exists in different
types
 Scalar, char, numeric,
boolean
 List, array
 Hash
 Combination->data
structure

34. Source code (3)
• Loops
 Allow the computer to
repeat blocks
• Tests
 Decide what to do
• Subroutines
 Programs frequently
called (functions)
• Comments
 The most important
lines of the source
code…
• Pointers
 Reference to region in
memory (address)
• Objects
 Combination of data
and 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
b=15
c=26
d=35
f=23
g=32
h=44
i=90
j=1
k=5
l=33
m=17
n=91
o=104
p=15
q=1
r=43
s=59
t=77
u=52
v=4
w=31
x=2
y=13
z=2
Do you see any problem??
Try with this:
« The quick brown fox, jumps
over the lazy dog. »

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

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

41. Unix
• Next presentation…
VVaassssiilliiooss aalliiaass
UUnniixxMMaann!!!!!!