From staffa from niehs.nih.gov Thu Dec 11 10:28:30 2008 From: staffa from niehs.nih.gov (Staffa, Nick (NIH/NIEHS) [C]) Date: Thu Dec 11 12:09:33 2008 Subject: [Info-gcg] Other: Re - GCG non-support In-Reply-To: <20081103121427.E74728@epsilon.bio.fsu.edu> References: <46B1AEA8.2040308@ebi.ac.uk><20070802081845.D3246@epsilon.bio.fsu.edu><46B2F2E3.4020305@ebi.ac.uk><20070803131050.H7747@epsilon.bio.fsu.edu><1186251135.996351.149470@g12g2000prg.googlegroups.com><46B721F0.8050407@ebi.ac.uk><7930EE6CD7CA354D93B444D0433C061103A8C70D@NIHCESMLBX6.nih.gov><46B83135.7050107@ebi.ac.uk> <20081103121427.E74728@epsilon.bio.fsu.edu> Message-ID: <7930EE6CD7CA354D93B444D0433C061106848CD6@NIHCESMLBX6.nih.gov> 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@bio.fsu.edu] > Sent: Monday, November 03, 2008 3:56 PM > To: Peter Rice > Cc: mol-evol@magpie.bio.indiana.edu; evoldir@evol.biology.McMaster.CA; > bio-soft@magpie.bio.indiana.edu; info-gcg@magpie.bio.indiana.edu; comp- > bio@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@bio.fsu.edu > \-/ > http://bio.fsu.edu/~stevet/cv.html > /\ > /--| FSU SCS / BioInfo 4U > /---/ > |--/ Florida State University School > of > \-/ Computational Science > /\ > /--\ 1st floor DIRAC 150G > |---\ Tallahassee, Florida > \---\ 32306-4120 > \--| 850-644-4490 > \-/ > /\ 2538 Winnwood Circle > /--\ Valdosta, Georgia > /---| 31601-7953 > |--/ 229-249-9751 > > _______________________________________________ > Info-gcg mailing list > Info-gcg@net.bio.net > http://www.bio.net/biomail/listinfo/info-gcg From gws from ncifcrf.gov Wed Dec 17 10:34:10 2008 From: gws from ncifcrf.gov (Gary Smythers) Date: Wed Dec 17 11:00:12 2008 Subject: [Info-gcg] Announcement: GenPept 169.0 available Message-ID: <20081217153410.634EAA4001@bio1.ncifcrf.gov> This is to announce the availability of release 169.0 of the GenPept(R) (GenBank Gene Products) Database. GenPept is provided in a format similar to that formerly distributed by GenBank(R) under the administration of Intelligenetics Inc. This GenPept release IS _NOT_ AN OFFICIAL RELEASE FROM THE NCBI-GENBANK, but an attempt to provide a data file format compatible with existing software products. This data format is suitable as an input data file for the GCG program genbanktogcg -genpept. Compatibility with other software has not been tested. Site: ftp.ncifcrf.gov Directory: pub/genpept Files: gprel.txt.gz, gpdat.seq.gz, gpdat.fasta.gz Directory: pub/genpept/divisions Files: 1 file for each GenBank file Directory: pub/genpept/updates (daily, cumulative) Files: gpseq_updates.dat.gz Rel. Date: 16-Dec-2008 If you have questions or comments concerning this data, or you experience any difficulty in downloading the data via ftp, please contact: Gary Smythers gws@ncifcrf.gov 301-846-5778 or Bob Stephens bobs@ncifcrf.gov ================================================================ GenPept (R) and GenBank (R) are registered trademarks of the U.S. Department of Health and Human Services for the GenBank Gene Products and the GenBank Genetic Sequence Data Banks.