The document discusses the UNIX operating system. It defines UNIX as an interactive, reliable, multi-user operating system that optimizes hardware resources. Most bioinformatics software is written for UNIX. The document outlines the history and development of UNIX, its core components like the kernel and shell, common commands, and differences between UNIX variants like Linux, BSD, and SVR4.

1. UNIX Operating System
Unit 1
410.634, Johns Hopkins University
©John M. Greene, Ph.D., 1999-2011
All Rights Reserved

2. What is an operating system?
• Hardware
• OS
• Applications
• OS is the interface between the applications
and the hardware - takes care of hardware
initialization and shutdown, manages
processes, and allocates resources

3. What is UNIX, and Why Is It
Used in Bioinformatics?
• UNIX is an interactive, reliable, multi-user
operating system which optimizes available
hardware power.
• UNIX experienced renewed interest due, in part,
to the availability of computer systems designed to
run it which offer better performance at a lower
price than their proprietary counterparts.
• Most real bioinformatics software (BLAST,
FASTA; relational databases) is written for UNIX.

4. The Mouse Is For Wimps
 The quickest way to do something on a computer is
with the keyboard, not the mouse.
 Many times for UNIX, there is no mouse!

5. UNIX
• OS, plus a set of standard libraries and
standard applications
• Kernel - hardware and process management
– UNIX sees each device as a file
– implements security
– allocates resources, including use of the CPU
• Shell - program that talks to the kernel and
passes on requests

6. UNIX Philosophy
• Open source (not proprietary) - more or less
• Simple, orthogonal commands - each tool
does one thing really well
• Commands connected through pipes
• Common interface style - mainly command-
line, but there is the X Window System - a
large program from MIT allowing
computers to create graphical windows,
used on many different Unix platforms
• No file types required

7. UNIX drawbacks
• Inconsistencies and overlapping functions - too
many cooks over 25 years
• Much higher learning curve than Mac/Windows
• Few popular programs currently available -
Netscape,WordPerfect, and Star Office (from Sun
Microsystems; can read Microsoft formats)
• Until Linux and open source, relatively expensive

8. UNIX History
• Unix history goes back to 1969. Ken Thompson and
Dennis Ritchie sketched out a new operating system that
would meet Bell Labs' needs.
• For the first 10 years, Unix development was essentially
confined to Bell Labs. The C language was originally
designed for the Unix operating system, and hence there
is a strong synergy between C and Unix. In fact, the
UNIX OS was re-written into C.
• The name "Unix" was intended as a pun on Multics, an
effort to develop a multiplex user system that could do
time-sharing (UNIX was written "Unics" at first --
UNiplexed Information and Computing System).

9. UNIX Families
• System 5 Release 4 ; SVR4 (AT&T Bell Labs
origins)
• BSD (UC Berkeley origins)
• Linux (LIH-nucks)
• UNIX is available for mainframes, workstations,
Windows PCs, and even Macs! (Mac OS X has a
Berkeley-derived UNIX kernel - Darwin)

10. UNIX Family Tree
Linux
Berkeley (BSD)
SVR4
Bell Labs
1969
~1979
~1990?

11. UNIX Vendor Versions
• IRIX - SGI (SVR4)
• SunOS, Solaris – Sun (SVR4)
• HP-UX - Hewlett-Packard
• AIX - IBM
• Red Hat, Caldera, SuSE (Linux)
• FreeBSD – bio.pgp.jhu.edu (Berkeley)
• MacOS X – Darwin (Berkeley)

12. Login
• Username
• Password
• Receive shell prompt
• UNIX IS CASE SENSITIVE!!!!
• Root (superuser) - can do anything; usually
the system administrator

13. UNIX Shells
• Shell interprets commands and talks to kernel
• Bourne (sh) - lacks job control
• C shell (csh) - job control but difficult for shell
scripts
• Korn (ksh) - C/Bourne hybrid
• Bourne-Again (bash)
• tcsh - extended C shell
• zsh

14. Control characters
• Hold down Ctrl key and press letter simultaneously
• Ctrl-C Interrupt (terminates current job)
• Ctrl-H Backspace
• Ctrl-Z Quit; suspend job
• Ctrl-S Pause output (but not on JHUNIX)
• Ctrl-Q Resume output (“)
• Ctrl-D logout/exit; end of input
• Ctrl-U kill; erases entire line
• Can use stty erase Ctrl-H to set backspace key, if
different on a given terminal

15. Getting out
• exit
• Logout (on some systems)
• CTRL-D

16. UNIX command syntax
command option(s) filename(s)
– commands are entered in lowercase
– options modify how the command works; often
they are preceded by a - (dash) and separated
by spaces. They are also called flags
– options come before filenames
– options and filenames are called arguments

17. Simple commands
• date
• who - lists users logged on
• whoami – lists logged-in user
• uname -a - name of computer, OS
• passwd - changing your password
• ls – list all files in the current directory
• ls –a – list all files, including hidden files
• ls –l - list all files in long format

18. Weird vocabulary
• ! Bang
• * Splat, star
• " Double quote
• ' Single quote, tick
• ` Backtick
• . Dot, point
• # Sharp

19. UNIX error messages
Segmentation fault(core dumped)
- memory error; creates a large file named
core - please delete it!
Broken pipe - one part terminates before
the rest