molecular biology software

frist at ccu.umanitoba.ca frist at ccu.umanitoba.ca
Tue Feb 19 18:52:34 EST 1991

Some comments on the recent recent thread concerning the plusses and
minuses of X/Unix vs. MacOS.

1) UNIX IS NOT HARD TO LEARN! The thing that annoys me most is the
underlying assumption that you have to be a computer whiz to use Unix. This
is not because Unix is any harder to learn than any other operating system,
(it's easier than most) but that Macintosh propogated the (IMHO)
counterproductive idea that you shouldn't have to read any documentation to
use a computer. This is like saying you shouldn't have to know anything
about electricity to run a gel, or shouldn't have to know anything about
DNA polymerases to do PCR. 

I contend that learning to use Unix is less difficult than
learning to drive a car.  The reason that many people have trouble with
computer operating systems is that they don't take the time to read a book,
or take a short course (eg. most computer service centers on university
campuses will offer short courses requiring one or two afternoons.)

To become a competent Unix user, all you need to learn is:
 a)  A  core of about 15 commands. 
 b)  How to use the online help  in situations where the core won't
 c)  How to use a text editor. The new X-platforms usually give you a nice
screen editor that any Mac-user could easily figure out. Otherwise, it is
necessary to plod along with the vi or emacs editor. 
 d) How to use the mailer.  Again, on the X-platforms, that is now as
simple as any of the Macintosh mailers.
 e) How to organize your files in directories.

speak for itself.	

which I can't forgive Steve Jobs is that he deliberately emasculated MacOS. Let
me explain what I mean.  Stipulated, it's nice to create an operating system 
that anybody can use. However, it was NOT
necessary to remove all of the features necessary to do things like
programming, easily creating and editing datafiles, reference to files by
name, or direct movement from directory to another. Let me take these
things in order:

a) PROGRAMMING. Because of the need for rapidly making changes in programs,
specifying compiler options, linking, Make-ing etc., you can't just buy a
compiler for a Macintosh. Instead, you have to buy (and learn how to use)
something like the MPW Workbench, which creates what is essentially an
internal operating system in which you do all of the programming steps. In
cases in which your program is too big (ie. most of the time) you can't
even test it within the environment, but you have to go out to the main
environment (if you have enough memory).  Ironically, these programmers'
environments are usually patterned after Unix!  

b) What if you have a sequence in one format, and the next program you want
to use requires a different format? (Say, a 1 or 2  at the end of the 
sequence to indicate topololgy.) Under Unix, you enter the vi (or other)
editor, jump to the end, add a character, and quit. In Macintosh, you have
to traverse the directory tree to your copy of MacWrite (or whatever),
click on the cute icon, find your file by clicking through the filelist, import 
your ASCII file, make your change, export your file, and click back through
the directory tree to where your datafile is. The point is YOU CAN'T MAKE

c) Oh, there's another problem. Now, to use your program, you can't just
execute it by typing its name, but you have to click through the directory
tree, find the program, and click on it. Now, you have to open a directory
window, find the datafile, click on it...  In Unix, I simply go to the
subdirectory containing particular sequence or other files, type the name
of the program, and go.  If I need a second sequence or other datafile
while the program is running, and can't remember the name, I just open another
window, go browse through
the directory until I find the one I want (no harder than browsing through
a directory bar on the Mac) and now that I have the filename in front of me,
I can type it ( or maybe even paste it) in response to the prompt.  I don't
need to know where the programs are, so I can concentrate on the data.

d) REFERENCE TO FILES BY NAME. If you dig real deep, you can discover that
Macintosh OS does, in fact support tree-structured directory names (eg.
/usr/home/bill/seq) but these are NOT accessible through the normal
operating system. Programming languages usually (grudgingly)let you access
these names, but it is not encouraged.  Furthermore, names must be fully
qualified. Relative pathnames (eg ../../rest_enz) are not part of MacOS.
Neither are environment variables, (easy ways to specify distant
directories) or a host of other conveniences that make Unix powerful. 

And while we`re at it...
In Unix, you can view a file with more (or less), or head, tail, or cat.
This gives you a quick way to see what's in it. To print a file, use lpr.
To do any of these things in Mac, you have to enter a word processor (eg
MacWrite) import the file, and print it or examine it from there.

f) How about shell scripts (.bat files in DOS). There is no such thing on
the Mac.

Again, I pose the question: Why did Macintosh have to eliminate all of the
features that make an operating system truely useful? They had to have had
these things in-house, or they couldn't have written the thing in the first
place.  They DELIBERATELY make it as hard as possible to use anything other
than what has been specifically provided.

4) THE OVERHEAD ASSOCIATED WITH UNIX workstations. There are two kinds: system
administration, and costs. At present, if you have your own Unix
workstation, you have to do a certain amount of system administration. NeXT
has probably done the best job of giving you a turnkey system that requires
a minimal amount of work in getting the system going and keeping it going.
Hopefully, the other manufacturers will follow suit in automating the
administration overhead. 

The second issue is cost. Yes, a SUN Sparcstation is more expensive than a
MacSE, but that's not a fair comparison. Although I never seriously
contemplated buying a Mac, I did find that to approximate the power of the
Sparcstation that I ended up buying, an equivalently-configured MacII  would
have cost MORE.

I am not advocating that everyone should have a Sparcstation. Rather, the
best approach is for each department or large working group to have a
workstation, and for each individual to buy an X-terminal (~$2000) or a
client workstation (such as a SUN-SLC). Now, we are talking about the
individual having hardware for processing, and sharing programs and
diskspace (both of which save $$). In addition to saving money, this
concept also means that only one or a few people in the department has to know
enough to perform systems administration functions. 

WORD PROCESSING IN UNIX. There are perfectly good products for all of the
really popular tasks available for Unix systems. In some cases, the same
programs are available as on PC's or Mac's (eg. WordPerfect)

There are very good reasons why computer operating systems are written the
way they are. Nobody ever wrote an operating system with the intention of
making it hard for people to learn. They wrote them to be versatile and
powerful.  A chain saw is powerful too, but you need to learn a few things
before you can use it.

I wish to reiterate that there doesn't have to be a tradeoff between
having a system that is straightforward to use, and yet versatile enough to
let you use it creatively. I think that in the near future, the X-platforms
will do a very good job of redefining the way people use computers for
their work. But there will have to be some learning on the part of those
wishing to take advantage of it. 

I have now satisfyingly vented my spleen. Thank you for your indulgence. 

Brian Fristensky                | What can literature do against the pitiless 
Department of Plant Science     | onslaught of naked violence? Let us not for-
University of Manitoba          | get that violence does not and cannot flourish
Winnipeg, MB R3T 2N2  CANADA    | by itself; it is inevitably intertwined with
frist at ccu.umanitoba.ca          | LYING... Lies can stand up against much in
Office phone:   204-474-6085    | world, but not against art.
FAX:            204-275-5128    |     Alexander Solzhenitsyn, NOBEL LECTURE 

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