Why Do Bioinformatics People Use Unix?

Combination of practical and historical reasons.

Historical

• Unix is an academic OS
• The core tools -- BLAST, FASTA, CLUSTALW, PHRAP, MAPMAKER -- are written for Unix.
• The Web in general, and CGI scripts in particular, are built on Unix.
• Most heavy-duty database management systems started out on Unix.

Practical

• Unix has a simple I/O model.
• Unix has good programming tools.
• Unix has a "building block" approach to programming.
• Unix has many text manipulation programs.
• Unix networking is easy.
• Unix developers are lazy.
  • Don't need to write graphical user interfaces.
  • Can "borrow" source code from other people.

Key features

Multitasking

Can run multiple programs "simultaneously."

Multiuser

Multiple users can log in at the same time.

Network-ready

Built with the network in mind. Supports remote users as easily as local ones.

Unix Variants

• Commercial
  1. Solaris (Sun Sparc hardware)
  2. HP-UX (Intel hardware)
  3. Tru64 Unix (Alpha hardware)
  4. IRIX (MIPS hardware)
  5. SCO UNIX (Intel hardware)
• Open Source (Free)
  1. FreeBSD (Intel architecture)
  2. Linux (Intel, Alpha, Sun Sparc, PowerPC, ARM, Amiga)

Linux is a special case because it has many "distributions," which differ in installation script, default desktop manager, and installed packages. Some distributions cost money (usually nominal). Others cost only the price of the installation media or free for download. Some Linux packages:

• RedHat -- everything but the kitchen sink ($$)
• Caldera -- highly polished interface ($$)
• Slackware -- for the do-it-yourselfer
• SuSE -- the BMW of Linux
• Debian -- not for the faint of heart

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