[Computational-biology] RE: [Info-gcg] Other: Re - GCG non-support

Staffa, Nick (NIH/NIEHS) [C] via comp-bio%40net.bio.net (by staffa from niehs.nih.gov)
Thu Dec 11 10:28:30 EST 2008


I've heard that the legal cost is a measly $70,000.
Can we find 70 people to put up $1000?
Or 140 to put up $500?
Or........

Accelrys is being very wimpy about this;
They should give the thing away and let the chips fall where they may.

 
Nickolas G. Staffa, Jr. Ph.D.
Telephone: 919-316-4569  (NIEHS: 6-4569) 
Scientific Computing Support Group
NIEHS E-WITS Contract 
National Institute of Environmental Health Sciences 
National Institutes of Health 
Research Triangle Park, North Carolina
 

> -----Original Message-----
> From: Steve Thompson [mailto:stevet from bio.fsu.edu]
> Sent: Monday, November 03, 2008 3:56 PM
> To: Peter Rice
> Cc: mol-evol from magpie.bio.indiana.edu; evoldir from evol.biology.McMaster.CA;
> bio-soft from magpie.bio.indiana.edu; info-gcg from magpie.bio.indiana.edu;
comp-
> bio from magpie.bio.indiana.edu
> Subject: [Info-gcg] Other: Re - GCG non-support
> 
> Hi Peter -
> 
> I'm picking back up on an old thread from summer 2007 re. the Acclerys
GCG
> 'retirement.'  Since that time several developments, only a few
positive
> in my opinion, have clarified the situation.
> 
> One - my online petition at www.petitiononline.com was very successful
> (http://bio.fsu.edu/~stevet/Accelrys_petition.pdf) in gathering
> signatures, almost 200 in a month, and in fostering international
> exposure, as the BioInform article from April 2008 attests
> (http://bio.fsu.edu/~stevet/BioInformGCG.pdf).  But Accelrys remains
> committed to not releasing any GCG code, due to exhorbiant and without
> profit legal expense.  So be it and understood - we tried.
> 
> Two - Accelryrs did distirbute the 'perpetual' licenses to all valid
> license holders that were entitled to it, as I announced in this forum
> April 2008, and they worked great, even across multiple nodes in a
> cluster.  Thany you Accelrys.  However . . .
> 
> Three - We (FSU) upgraded our Linux cluster that supports GCG and many
> other bioinformatics tools to CentOS version 5.  Unfortunately, almost
> half of the GCG package now fails due to unresolvable library
conflicts
> (as I warned would happen - unfortunately sooner than I had hoped).
Our
> systems operations folk initially thought they could fix this but the
> solution has remained ellusive.  The affected programs are all the
oldest
> 'legacy' programs in the package, although some longtime GCG pragrams
like
> Pearson's FastA package remain viable.
> 
> Four - SeqLab continues to operate just fine, but without access to
many
> of the analytic tools of the package, its usefullness is quite
impacted,
> though I still think it's one of the best multiple sequence alignment
> editors around.  This is where you come back in Peter.  It may seem
odd to
> ask, but the need is actually larger now that so much of the package
no
> longer works in an Enterprise (or CentOS) Linux version 5 environment.
> I'm sure that I am not alone in this situation.  So here goes - I've
asked
> it many time before, and I've begun to do the work myself starting
with
> PlotCon, but has anybody built SeqLab extension configuration files to
> launch EMBOSS programs?
> 
>                               Cheers - Steve
>                                                  Steven M. Thompson
>                                  A C T G         stevet from bio.fsu.edu
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