Sequencher program for ABI373 data

Jason E Stewart jasons at
Sat Mar 13 20:34:21 EST 1993

In article <13MAR199307012366 at>,
broe at (Bruce Roe) wrote:
> 	I disagree quite strongly with Jason's comments.  The TED/XBAP package
> from Staden, et al. contains EXCELLENT documentation, both on line and
> in Mac Microsoft Word format.  It contains binary files on the distribution
> tape so all that is needed is for someone to correctly install the programs,
> add the path and declare a couple of commands.  The install procedure does
> not take a UNIX guru, just someone who knows how to read and type.  As for
> the learning curve to use the programs, here there is no real requirement
> for much UNIX knowledge since they are X-windows based and it's all point
> and click, and if someone takes the time to read the manual, then the learning
> curve is dramatically shortenend.
> 	I agree that dealing with UNIX is a big fat pain in the you-know
> what, but if you are doing sequencing on the ABI's and have the money to
> buy a Sparcstation, have someone to whom you can turn for some UNIX advice,
> and JUST use the Sparcstation for the Staden et al programs, then this very
> inexpensive, efficient and useful set of programs is invaluable.  They are
> well worth the small amount of time spent learning a little UNIX to get them
> operational.  However, there are so very many useful tools for molecular
> biology that now are available for UNIX-based computers, that once you have
> the Staden et al. programs up and running, you'll be off getting others.

I think Bruce makes some important points here worth noting, but also
oversimplifies a bit. I am waiting on my Staden update from one of the
original versions of the X-programs where the help was minimal, but as
Bruce indicates, is now much better. But.... Help files ain't everything. 

I know what a pain (and more importantly, a real time sink) it is
maintaining a DNA analysis software package for a bunch of
don't-know-UNIX-from-squat users. Bruce's comments apply more to the
adventurous individual who is planning on setting things up so that he
himself can use the package, but if about 50 other users are concerned you
have a hell of a lot of trips to the Tylenol cabinet ahead of you. That is
why we (read that: "I")made the the decision to make both alternatives
available, but to dish out help and advice for only the Mac programs. Since
we pointed out that the Staden package is more powerful but harder to
learn, only the few dedicated ones who are really interested must take the
initiative themselves to figure things out. But still a Sparc just ain't a
Mac IIcx that you turn on when you want it and off when your done. It needs
a full time sysadmin with UNIX experience, who will deal with accounts and
crashes and the like. 

So where I agree in principal with all the things that Bruce has said, I
still think that biologists have a ways to go before X-based stuff will be
in general use - biologist operated and maintained.
> 	<stuff deleted>
> > 
> >Trying to get ABI to make changes is about as teaching a pig to sing so I
> >have stopped trying.
> > 
> 	Please don't give up on trying to get ABI to make changes in their
> software and hardware.  The more of us that continue to "make suggestion"
> to them the more they eventually may listen.  I have the strong tendency
> to agree completely with your statement, but it is clear to me that because
> they have little competition, the push for improvements MUST come from users.

I am outraged that I am forced to pay money to third party developers for
software that I feel ABI should be supplying free to the customers that
have paid hefty amounts to use their technology. But after more than two
years of ABI hassle, I prefer paying the money to third party designers
because ABI has no respect for their customers needs/desires (that is after
we've paid for the machines) and the third party companies do. 

So, besides having shelled out some god-awful sum for a 373 sequencer we
now produce everything down to the buffers in our reactions ourselves. I
will not give another cent to ABI, until they overhaul their public
attitude division. 

Jason Stewart                                 Father at large
Department of Medical Genetics            jasons at
Biomedical Center, Box 589                Tel 46 18 17 49 10
751 23 Uppsala                            Fax 46 18 52 48 69

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