[Bio-software] Re: GCG non-support

Steve Thompson via bio-soft%40net.bio.net (by stevet from bio.fsu.edu)
Wed Aug 1 15:22:05 EST 2007


Hello Nick -

>From one 'old-timer' to another (my GCG support track record is 1990-1998 
at Washington State University, 1992-2007 for the Workshop on Molecular 
Evolution at the Woods Hole Marine Biological Laboratory, and 1999-2007 
for Florida State University).  Thanks for posting!  I've been meaning to; 
this got me 'kickstarted' -

I too am dismayed at Accelrys' terrible plan to 'retire' GCG.  Yes, they 
argue all of the individual components are available in the public domain, 
and sure EMBOSS even puts most of them under one umbrella.  However, and 
I've been looking for years, I completely agree with your letter (included 
below in its entirety) there is no GUI/sequence editor out there that 
comes anywhere near approaching SeqLab's functionality.

You mentioned the manner in which it integrates the entire package under 
one environment, and the power of its ability to handle list outputs from 
other programs, which are both fantastic - I am also a huge fan of its 
feature annotation coloring schemes, and of its ability to mask unrealible 
columns from alignments.  I realize I'm preaching to the choir here . . .

Regardless, I have personally urged my rep' there to encourage the 
'powers-to-be' of allowing the package to move on elsewhere, even if it's 
just SeqLab's source, and preferably to the public-domain.  If Accelrys 
has decided they are not making enough money on it, then let it continue 
elsewhere, so that its 25 year legacy of making sequence analysis 
approachable to scientists worldwide can continue!  Furthermore, I am 
willing to organize, and wish to begin, some type of a petition process 
that will allow scientists over the world to add their voice to this 
opinion.  Since this is such recent news I have not yet began this 
process, but am anxious to get started, and happy to entertain others' 
thoughts on the matter.  Let's not let it silently fade away.

                             Sincerely - Steve
                                                 Steven M. Thompson
                                 A C T G         stevet from bio.fsu.edu
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On Wed, 1 Aug 2007, Staffa, Nick (NIH/NIEHS) wrote:

> I am the employee of a sub-contractor serving in IT support at the 
> National Institute of Environmental Health Sciences in Research Triangle 
> Park, NC. I have supported GCG and sequence analysis at this Institute 
> since before GCG even had fragment assembly. Although job related, the 
> opinions expressed here are solely MY OWN OPINIONS. These opinions do 
> not represent the opinions or policy of my employer(PSGS) nor anyone 
> employed by my employer(PSGS), nor its primary contractor, nor do they 
> represent the opinions of the US government, the NIH, NIEHS or any of 
> their employees or agents.
>
> Accelrys's plan to "retire GCG products" comes as rather a shock. They 
> were right in the middle of bringing it into the genomic age. It is 
> especially alarming since many IT types seem to want to get rid of 
> un-supported software. NIH in Bethesda MD has removed GCG and urges 
> people to use EMBOSS.
>
> I don't think EMBOSS - an eclectic collection of miscellaneous programs 
> - approaches the usefulness of the SeqLab environment. One very useful 
> and important feature of SeqLab is its ability to easily make lists and 
> ad-hoc databases (with LookUp and other programs) and to do fasta or 
> other searches in them.
>
> GCG started out at the University of Wisconsin as a collection of 
> existing programs that were given a unified (for want of a better word) 
> user interface by the then UWGCG.  There was a hint that the founders 
> were thinking of a consortium of some sort - a cooperation among users, 
> scientists and developers. The sources were available up through version 
> 8.
>
> The attitude of the founders as true supporters of science was quite 
> refreshing and much to be praised. Over the years they kept the product 
> much affordable, yet managed to provide service and survive, even after 
> they were forced to leave the University and become a self-supporting 
> company.  Their one competition in the beginning was a product called 
> Intelligenetics that cost twenty times as much. Apparently 
> Intelligenetics was out to make money, but were eventually forced out of 
> the game.
>
> It would be a crying shame if this product were to die just because its 
> new owners won't feed it. Accelrys must be made to give it all away to 
> company or group who is interested in its further support and 
> development. They cannot be allowed to be so selfish and childish to 
> withhold this from the world.
>
> The opinions expresses above are my own personal opinions and do not 
> represent the opinions or policy of my employer(PSGS) nor anyone 
> employed by my employer(PSGS), nor its primary contractor, nor do they 
> represent the opinions of the US government, the NIH, NIEHS or any of 
> their employees or agents
>
>
> Nick Staffa
> Telephone: 919-316-4569  (NIEHS: 6-4569)
> Scientific Computing Support Group
> NIEHS Information Technology Support Services Contract
> (Science Task Monitor: John D. Grovenstein (grovens1 from niehs.nih.gov)
> National Institute of Environmental Health Sciences
> National Institutes of Health
> Research Triangle Park, North Carolina



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