Here at U. Virginia, we offered a poorly documented (but
functional) set of programs on Unix for several years, as well as the
be much better documented more comprehensive Wisconsin package on the
VAX. The VAX charges for usage, Unix was free. For this reason
alone, unix was far more popular. All incoming graduate students got
a 1 hour course on how to use unix for sequence analysis.
I don't think that there is a bit of difference between the
two systems, or even betwen Unix, VMS, and DOS, for runing sequence
analysis programs. (The Mac has the potential to be much better, but
program development on the mac is much more demanding) We now have the
Baylor MBIR Eugene/SAM packages running on Unix, and people are much
happier than before. They also like Eugene/Sam better than GCG, both
because Eugene/SAM is free (GCG is not) and because it is menu-driven
(GCG requires having the (excellent) manual in hand).
Most biologists want functionality over userfriendliness. If
your program package is user-friendly, but cannot search libraries
quickly, meld sequencing runs, or align multiple sequences, who cares?
Today (and for the forseeable future), computers that run UNIX have a
price/performance ratio that is about 5X better than either VMS or
Macintosh systems. Until more true 32-bit programs become available
under Microsoft Windows 3.0 for 386/486 machines, IBM-PC clones,
though cheap, are limited. (By the time you add TCP/IP, NFS, and
other capabilities that are standard on a Sun or DecStation, Unix is
currently extraordinarily expensive on 386/486 machines.) For the
sequence analysis program developer, Unix offers the largest set of
potential users for sophisticated computationally intensive programs,
(and the best programming environment) and thus is the system where
the software is developed first. As a result, Unix continues to have
the functionality first.
People learn to use what they need. Anyone who can design and
perform a subcloning experiment - with all the steps required to
isolate fragments, match ends, ligate, and transform - can figure out
how to login, check a directory, edit a file, and run the sequence
analysis programs on unix or VMS. Anyone who is doing a sequencing
project MUST learn to the machine. So they do.
Bill Pearson
