An introduction to bioinformatics

Computers, networks and

operating systems
Why biocomputing ?
 services for biologists/biochemists
 databases (sequences raw and annotated,
2D gels, 3D structures, biological images,
profiles)
 tools (sequence analysis and manipulation,
prediction, identification, phylogeny)
 simulations (in silico biology)
The tremendous increase of nucleotide sequences

 EMBL data…

 In 1998...  Now...
What is a computer?
 Physical: processor, memory, data storage,
keyboard, screen, network connection
 Logical: collection of programs designed
for particular tasks
 Virtual: user interface that presents a view
of the computer and its surroundings
 Caution! The user interface often hides
underlying complexities.
 From hardware to software

PC system Macintosh system UNIX system

Application Netscape Netscape Netscape

}
GUI Windows95 X-windows + window
manager
MacOS
OS linux, HP-UX, Solaris,
MS-DOS
Irix, A/UX, MacOSX...

Hardware PC compatible Macintosh Sun, Silicon Graphics,

HP, PC, Macintosh...
Properties of the OS
 Methods of communication: “shells”,
graphical user interfaces (GUI)
 Multitasking: multiple programs can run
simultaneously
 Multi-user: multiple users can use the
computer simultaneously
 Multi-processing: the OS can distribute
the work among multiple processors
User interfaces
 Command line: VMS, Unix, DOS
 Local graphical user interface (GUI):
MacOS, Windows (various flavors)
 Distributed GUI: X-Windows (Unix, VMS)
 OS-independent GUI: Web browsers, Java
What is a file ?
 a piece of information (text, graphic, data)
 it is identified by a name and an logical
address (or path)
 other informations: date, size, type,
creator, ownership, physical address...
File names
 DOS: 8 char., a dot, 3 char. extension
(determines file type), case insensitive
 MacOS: 32 char., anything goes, file type
determined from hidden attributes
 Unix: no limit on size, but avoid spaces and
most special characters; customary to use
file name extension to determine type;
case sensitive!
 What is a path ?
 The path is the logical address used by the
system or the user to locate a file
 Ex:
/bd_du_Palais/35/etage/4/appart/12/Dupont/
path Jean.txt

suffix
filename
File systems
 Method the OS uses to store information
 File = unit of data storage
 Types: programs, data, configuration, system,
I/O (Unix, DOS)
 File organization
 Storage unit, directories, subdirectories
(MacOS, DOS/Windows, VMS)
 Single arborescence (Unix)
 File system organization

Disk 1 Disk 2
/
C: D:

/usr /home
DOCS PROGS CONFIG DATA Directories
local phil john
WORD EXCEL EXPT1 EXPT2

bin lib
Subdirectories
emacs X11

DOS, MacOS
Unix
What is Unix?
 Multitasking, multi-user OS
 Derived from a common ancestor, many
varieties today
 Examples: Solaris (Sun), Digital Unix (DEC),
Irix (Silicon Graphics), HP-UX (Hewlett
Packard), AIX (IBM), Linux (freeware), A/UX
(Apple) (move to Mac OS X in spring 2001)
 Versions for almost every hardware
platform (including PC and Mac)
Why use Unix?
 Open and standard environment
 Usually uses hardware efficiently, highly
scalable and configurable
 Extremely flexible command line interface
 Large number of freely available programs
and utilities
 Multiple users sharing common environment
The downside of Unix
 Command line interface difficult to learn
 GUI always incomplete
 Security not always optimal
 System management requires special skills
 Numerous small differences between
different flavors
The strange side of Unix
 the hidden distance!

PC or Macintosh Terminal Server

Networking basics (1)
 Networks allow computers to share and
exchange information
 Local area networks (within organization):
printer sharing, access to files on network
servers, distributed GUIs
 Wide area network (e.g. Internet): access
to information, transfer of files
Networking basics (2)

 Computers must be connected to a data

transmission medium and talk a common
language
 Transmission medium: local cable
(Ethernet), optical fibre, satellite link,
telephone line
 Protocol: AppleTalk (Apple), NetBEUI
(Microsoft), TCP/IP (Internet)
 NB: this is grossly simplified!
 Networking basics (3)
 To go on the Internet you need an ISP

at work

at home
Networking basics (4)
 Each computer connected to the network
must be identifiable
 Hard-coded serial number (all protocols)
 Unique name (most protocols)
 Hierarchical attribution of unique number
(TCP/IP)
 IP address: 192.42.197.67
 Associated name: macisrec-B310.unil.ch
IP domains and addresses
 High-level domains:
 com, edu, gov, org, net: by organization type
 ch, de, fr, se…: by country
 Organization domains:
 unil.ch, nih.gov: physical places
 embnet.org, aol.com: virtual groups
 IP addresses:
 Address domains attributed according to size
of organization (130.223: UNIL; 192.42.197:
ISREC)
Clients and servers
 A client is a computer that requests
services through the network
 A server is a computer that provides
services
 Usually, clients are personal computers or
workstations, servers are larger, shared
machines
Network services - local
 Services that require high bandwidth
 File and printer sharing: resources on
server appear as local
 AppleShare, SMB (Microsoft), Novell
 NFS, lp, lpr (Unix)
 Remote graphical display
 X-Windows (Unix), Windows NT
Network services - wide
 Services that can be slower; TCP/IP based
 Remote terminal: telnet
 File transfers: FTP
 Electronic mail; mailing lists
 Newsgroups
 Informations services: Gopher, WAIS
 World Wide Web
World-Wide Web (1)
 Extension of Gopher services
 Server presents information in a format
that is interpreted by a graphical client
 Central features:
 Common language: HTML
 Extensive use of “hyperlinks”
 Multiple media supported (MIME types)
 Server-side execution of programs triggered
by the client (“CGI scripts”)
World-Wide Web (2)
 Client programs (browsers):
 Netscape, Mosaic, Internet Explorer
 Servers: mostly Unix, but also MacOS,
Windows NT, OS/2
 Multiple protocols, specified in URL:
 http://www.ch.embnet.org
 ftp://ftp.ch.embnet.org
 telnet://gcg.ch.embnet.org
 Emerging extension: Java
World-Wide Web and Java
 Java: programs (“applets”) that are
transferred from the server and run on
the client
 Java programs can run on any type of
machine, but depend on an interpreter
 Advantage: the Web server can provide
programs, not just information
 Disadvantage: transfer often slow,
execution even slower, lack of standards
Some UNIX commands
 General: man, pwd, cd, ls, mkdir, rmdir,
passwd, exit
 Files manipulation: cat, more, cp, mv, rm,
grep, find, diff, head, tail, chmod
 Editing: vi, pico, emacs
 Compression: tar, (un)compress, gzip
 Various: redirection (<>>) and piping (|)