molecular biology software

Lee F. Kolakowski lfk at eastman1.mit.edu
Mon Feb 18 17:28:37 EST 1991


On 18 Feb 91 17:03:10 GMT,
lamoran at gpu.utcs.utoronto.ca (L.A. Moran) said:
> Brian R. Smith writes,
>>      "Yes, there are platforms that do not (or cannot) support X.  I don't
>>       mean to sound snobbish, but I think they'll fall by the
>>       wayside.  (Even if you get a Mac or PC X server, you still
>>       can't run a program on the Mac/PC and display on another X
>>       server - it's only a one-way support.)  And, if they are
>>       replaced by Unix machines, many departments are going to HAVE
>>       to hire an experienced system administrator to care for and
>>       feed them.  Even if workstation manufacturers manage to put a
>>       workable system administration layer over Unix (as NeXT is
>>       trying to do), the underlying software still must be
>>       understood."

> This opinion seems to be shared by Chris Dow who is also a fan of X-windows
> and UNIX. 
And many other people..

> I use PC's and Mac's. They are quite sufficient for all of my
> molecular biology needs so I find it quite puzzling to read comments
> such as those expressed on this newsgroup. Most of us do not need to
> manipulate complex structures in three dimensions - this is the only
> reason that I can think of to purchase an expensive workstation and
> software that is so complex that I would need to hire an expert just
> to run it.

There are several reasons to use Unix. And a few more to use X-Windows.
Most of these reasons stem of the ability of machines with
these features to do multiple things at once, with reasonable throughput.

Alas not every lab needs a Unix workstation, but most would really
benefit if they did. First costs of hardware:

	Macs are not cheap but neither are workstations

	For about $10,000 you can get a workstation
	of modest means to do most of the things you want to
	do in molecular biology or biochemistry.

	This workstation will allow n individuals to access
	the "same" files at the same time.

	3 macs and a laser printer is a whole lot more
	than 1 workstation, 1 laser printer and a few dumb
	terminals.

Next multiple "jobs":
	In our lab we would like to have the ability to
	search GenBank, write a manuscript and 
	analyze data by more than one person simultaneously.

	With your mac or PC first you probably dial up to
	a campus wide facility to do the database search
	since multiple databases are not such a good idea.
	While you are doing that, it is difficult to do
	anything else.

	With X and Unix, you could open up a window,
	run telnet, and do your search, while you have your
	wordprocessor running in another window, and a graph of
	your latest experiment in a third.

> Perhaps Brian Smith or Chris Dow could explain what kind of
> applications they are referring to when they make such claims. Do
> they think that a MAJORITY of molecular biologists should purchase
> expensive workstations that run UNIX and X-windows? If so, why?

It is incorrect that if you have a workstation you must do
crystallography or analysis of structures. But, if you wanted to with
a Unix box and X, you could. Further, the notion that it is difficult
to run a unix system is only partially correct. There is a lot of
information about Unix available, if you need to know something you
can find it. Having looked at the internals of a Mac, I would hesitate
to say that the same is true.

Further, research is about breaking new ground. So sure you don't want
to spend enough time to get a CS degree in order to write a grant, but
Unix has progressed very far from that, and in the next few years, may
be light years from the notion that Unix is hard.

The second part about research is that you want to maximize your time
(that is true about almost every thing else too). Unix and X allow you
to be more productive. If you want to send mail to a colleague, send
it, don't login to another system to do it.

Well, I'll stop now, but this could go on and on.

Computers are research tools. If your research does not need to do
anything more than write papers and grants, a PC or Mac is all you
need. Any more than that, get a unix machine.


--

Frank Kolakowski

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| Lee F. Kolakowski                 M.I.T.                            |
| Dept of Chemistry                 Room 18-506                       |
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