Staden for Mac/PC

Robert J. Forster ac562 at FreeNet.Carleton.CA
Thu Oct 3 12:06:12 EST 1996

In answer to James Bonfield's question about what
program/platform is chosen by the enduser, I would like to make
some general/personal observations.

I started out as a dedicated PC user after having a few run ins
with IBM and DEC mainframes in the late 70's.  I acquired a
Macintosh along the way to run some molecular biology programs
that a colleague was using.  I then inherited an HP-UX unix
system and also ended up porting Linux to a Pentium.  Oh yes, I
also have a dedicated OS/2 machine and couple of computers
running Windows for HPLC's and specs.

What programs do I run?

Mac - Sequencher, Hybsimulator, NIH Image, BioImage (Intelligent
Quantifier), SeqPup, Assemblylign, BioMax 1D, Clustal, Phylip,
Oligo, Photoshop, Illustrator, EndNote, Word, Netscape etc.

Linux - Treetool, DCSE (Tk based) and GDE (only a bit of GDE

HP-UX - Phylip, Netscape

OS/2 - Li-Cor sequencer

Do I want to run all these machines?  NO! Why do I do it?  Well
because the particular program (or subset of a program) that I
need to run generally is machine specific.  I ended up spending
almost a week getting TreeTool up and running with Linux but it
was worth it (I was unable to get it going on the HP). 
Sequencher has rendered most of my assembly programs redundant.
This program has saved me days, if not weeks when it comes to
final assembly and editing of sequences.  The days of sorting
through autorads, flipping them over and reading backwards, and
where was that sequence on the other autorad? are thank goodness
gone forever!  I generally use Clustal and SeqPup (Hooray for Don
Gilbert!) for multiple alignment of sequences.

What factors influence my choice of a program?
 1.  How much is it going to cost me?
 2.  Will it do the job that I need it to do with as little pain as
 3.  Does it run on a Mac?

These are balanced before I make a decision.  If the program runs
under Windows I would avoid it like the plague.  I realize that
some people actually like windows as an operating system but
after having made the switch to the Mac I'm much the same as
someone who has given up on smoking and goes around telling other
people to do the same thing.  I've never had access to a SUN
workstation, and if I did my life may have been a bit easier as
far as getting GDE and Treetool to work.  I therefore can't
comment on the Staden package. However based on my experience
with other Unix machines I would say they are great if the
program you are running on it is the only reason you are using
it, or if you have a good deal of unix experience.  If you try to
modify the computer to run other programs it can be a pain in the
butt.  With Macintosh machines becoming quite fast (I have a
7500/100, and I can hardly wait for a 604e daughterboard), easily
upgradable, damned easy to configure and expand, and easy to work
with, they will remain my platform of choice.  It's a pity my
organization doesn't think so!  They have decided not to support
Macs anymore, deciding that Windows should be the standard. 
However I will bravely soldier on with my mac.

I realize that machine preference seems to be a highly personal
matter. When it comes right down to it the decision really hangs
on whether the program does what you need or want it to do.  I
still use a program which regularily hangs my machine (and I paid
$2,000 for the program) because I NEED to use it (and no its not
Sequencher or SeqPup).


Bob Forster 
Centre for Food and Animal Research
Agriculture and Agri-Food Canada 
Ottawa, On forster at em.agr.ca
R.J. Forster					ac562 at FreeNet.Carleton.ca
tel (613) 759-1725 

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