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Introduction to the RCR Alpha and UNIX

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One definition of bioinformatics is "the use of computers to analyze biological problems." However, as biological data sets have grown larger and biologicial problems have become more complex, the requirments for computing power have also grown. At the present time, virtually all powerful computers use the UNIX operating system, so an introductory bioinformatics course must teach UNIX.

The RCR (Research Computing Resource) here at the NYU Medical Center has a very powerful DEC Alpha 4100 (a.k.a. The Big Blue Box) as our primary computing workhorse for GCG.

***This machine has 4 parallel 500 Mhz processors, over 50 GB of hard disk space and lots of other cutting edge computer hardware.

***The RCR now uses the UNIX operating system - this is a recent change and we are still getting the bugs out. You will need to know the basics of UNIX in order to manage an RCR account and use GCG.

*** UNIX is a command line interface, typical of many large powerful computers. In fact UNIX is the underlying structure for most of the Internet and most large scale bioinformatics operations.

***A knowledge of UNIX is likely to be helpful in your future interactions with bioinformatics problems.

UNIX has some distinct advantages:

  • It is very popular, so it is easy to find information and get help
    • lots of books at the local bookstore
    • lots of websites
    • lots of USENET discussions and e-mail lists
    • most Comp. Sci. students know UNIX
  • UNIX can run on virtually any computer (Sun, Compaq, Macintosh,etc)

  • UNIX is free or nearly free
    • Linux/open source software movement
    • RedHat, FreeBSD, MKLinux, LinuxPPC, etc.


  • Most bioinformatics software is created for UNIX

  • UNIX is very stable - computers running UNIX almost never crash

  • UNIX is very efficient
    • it gets maximum number crunching power out of your processors
    • it can smoothly manage extremely huge amounts of data
    • it can give a new life to otherwise obsolete Macs and PCs


UNIX also has some serious drawbacks

  • UNIX computers are controlled by a command line interface
    • NOT user-friendly
    • difficult to learn, even more difficult to truly master


  • hackers love UNIX
    • there are lots of security holes
    • most computers on the internet run UNIX, so hackers can apply the same tricks to many different computers


  • there are many different versions of UNIX with subtle (or not so subtle) differences
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Using Computers for Molecular Biology
Stuart M. Brown, Ph.D, RCR, NYU Medical Center
Comments to: browns02@mcrcr.med.nyu.edu