[Computational-biology] Re: GCG non-support (Steve Thompson)

[Amit Dattatreya Parhar]

Hello Nick and Steve ,
                                     I am working with Bioinformatics
products and services company called Ocimumbio solutions based in India. We
have a product called Genchek which is a direct compitetor of GCG and other
commercial Sequence analysis software.

With due respect to the legacy of GCG, its creators and its user fans, I
would like to make point here. The fact that GCG was allowed to be taken
over by Accelrys was a mistake. GCG should been made an open source tool
like EMBOSS . Probably this way it would have grown in better fashion. So I
support Steve's idea that let it not die!

The other thing is if people are still interested in GCG like features and
functionalities (or even better ), then there are other very affordable and
good packages like Genchek. To my knowledge we are on par with any
commercial sequence analysis tools. We provide 24X5 tech support (Live chat,
emails and Telephones) with first year free upgrades and after that very
affordable tech support. We also give full warranty for a year.

my second point is only to draw your attention to this fact that there are
other good and affordable tools available which provide you the ease of use
and a nice range tools with affordable price and technical support.

regards,
Amit Parhar,

Product Specialist,
Ocimum BioSolutions.






----- Original Message ----- 
From: <comp-bio-request from oat.bio.indiana.edu>
To: <comp-bio from magpie.bio.indiana.edu>
Sent: Thursday, August 02, 2007 10:31 PM
Subject: Comp-bio Digest, Vol 27, Issue 1


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>    1. Re: GCG non-support (Steve Thompson)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Wed, 1 Aug 2007 16:22:05 -0400 (EDT)
> From: Steve Thompson <stevet from bio.fsu.edu>
> Subject: [Computational-biology] Re: GCG non-support
> To: "Staffa, Nick (NIH/NIEHS)" <staffa from niehs.nih.gov>
> Cc: mol-evol from magpie.bio.indiana.edu, bio-soft from magpie.bio.indiana.edu,
> info-gcg from magpie.bio.indiana.edu, comp-bio from magpie.bio.indiana.edu
> Message-ID: <20070801153224.D496 from epsilon.bio.fsu.edu>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
> 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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