molecular biology software

Paul Bieganski biegansk at cs.umn.edu
Mon Feb 18 19:55:34 EST 1991


In article <9102182122.AA02187 at genbank.bio.net> BROE at AARDVARK.UCS.UOKNOR.EDU (Bruce Roe) writes:
>...
>>	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.
>>
>
>Sorry Frank, but I disagree.  Your e-mail was received in the VersaTermPro 
>window on my MacIIcx with 2 page monitor, while I was working on a manuscript
>in a MicroSoft Word window and printing a figure just created with MacDraw
>in another window.  Oh yes, I also was running a GenBank search in Batch
>on our VAX.  I'm running MultiFinder with Mac OS version 6.05 and although
>it is not "true" multiprocessing, it works just fine.

Try this: establish a connection to a database/search engine running on
a Cray, _paste_ a sequence-object into a sequence editor running on a
Sparc, paste part of that sequence into an primer design tool running
on a Sun 3/50.  All on the same screen, NO text paste/copy involved
(i.e. you have a networked, hardware independent inter-client
communication protocol). I don't want to get into a holly war - I would
just like to point out that there is MUCH more to X/Unix then 'windows'
(!) - i.e.  the general concept of networked compute-servers, which
allow for easy integration of software running on different machines in
different locations - without having to hardwire all possible
interactions into each and every piece of software.

>
>My question is "Why do I have to learn an operating system?"  I have no
>idea of how the Mac OS works, but do know that it is easy to use, has a
>very short learning curve and uses routines from the Mac Toolbox.  I've
>even programmed in C and FORTRAN on the Mac, used toolbox calls and written
>real live Mac applications.  Ifyou tell me that it's the same as X-windows
>or similar than that's fine, I can learn that.  But your 2 arguments above
>are way off........
> 
>It seems to me there are 2 good reasons for getting into a Unix environment.
>1. You're forced to because that's the only system on which your favorate
>   programs will run on.
>2. You want more mips for your $, because for under $20 K you can get a
>   SparkStation with 16 meg RAM and blow the socks off your Mac, VAX or
>   whatever.  (DOS is so outdated it's not worth discussing)
>
>Another reason is multi users, but why bother when the VAX is there.
>Yet another reason is that you were a CS major, learned C and love Unix.
>Fine, but who is going to learn the Unix OS in my lab?  Guess it will be
>Me.  
>
>	"Is it time to do Molecular Biology yet Daddy"
>	"No son, it's time to learn Unix"

        "How do we do molecular biology, Daddy ?" :-)
       (Re: excellent article by Gilbert in Nature).

Again - no flames, PLEASE ! All I'm trying to point out is that this
discussion is not (should not ?) be about what's better - Macs/PCs or
X/UNIX, but about facilities any modern molecular biology lab should
have (more and more of them being computational in nature).

Happy searches !
-Paul

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| Paul Bieganski | biegansk at cs.umn.edu |                                     |
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| Paul Bieganski | biegansk at cs.umn.edu |                                     |
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