Re: GCG non-support
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Re: GCG non-support
by Steve Thompson-7
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Hello Peter - Thanks for joining the dialogue. I was hoping you would.
I will only quote and respond to your replies to avoid excessive length in this thread. On Thu, 2 Aug 2007, you replied (for the most part): > When Alan Bleasby and I started EMBOSS some 11 years ago, we > deliberately avoided writing a GUI in the hope that someone, somewhere > would come up with a killer GUI and we could just fit under it. > Although there have now been over 100 interfaces and packages developed > out there that include EMBOSS, none seems to have taken over. > > One of the interfaces was indeed SeqLab which one of our commercial > users reported customising to include EMBOSS some years ago. As far as I > am aware it was only ever used internally. Yes, I have heard reports of extensive SeqLab customizing, and in fact, Lynn Miller at GCG tried to spearhead a SeqLab extensions public library, but she was never able to get folk to contribute. Alas, the project shriveled away. It seems as if most of this work was done behind the closed doors of the corporate world where sharing is not the norm. > SeqLab was originally GDE, written by Steve Smith at Harvard and much > extended when he was at GCG Inc. Yes, I am well aware of this history, and wonder what Steve Smith would have to say about the current situation. He has been 'out of the loop' since the late '90's. My last correspondence with him was Jan. 2001. > If SeqLab does appear as public domain or open source, then I may be > able to help put EMBOSS under it. Many years ago (before EMBOSS) I > modified SeqLab as an interface to its predecessor the EGCG package. > The code was pretty clean and it was not hard to do. I was hoping this would be your response! Let's see if we, the worldwide molecular/cellular/evolutionary biology community, can make it happen. > Making SeqLab's source public domain (or open source) is a little tricky > as it depends on things like how GDE was licensed to GCG Inc and who > contributed in the past. . . . > . . . I have seen a revival of GDE, but presumably not with the full > functionality that was added to SeqLab. See > http://www.msu.edu/~lintone/macgde/. The MacGDE page says they believe > GDE cannot be distributed by commercial enterprises, but I don't see any > prohibition. The licence is the original GDE one. I suspect BioLateral > were just being cautious. Yes, Eric Linton, MacGDE's maintainer, was a student here at the Marine Biological Laboratory's Workshop on Molecular Evolution, where I am working this month, many, many years ago when he began thinking about this MacGDE project. Another of our past Mol Evol Workshop students, Tulio de Oliveira, has created a robust Linux port (See http://www.bioafrica.net/GDElinux/index.html). Both a wonderful pieces of work, but neither includes all of the SeqLab's functionality. > Ah, the old crowd are still around. I first encountered GCG in 1987 at > EMBL Heidelberg when they were still "UWGCG" and was one of the first > users of their fragment assembly. Those were the days! (yikes! ... they > were 20 years ago :-) Yep, I started with their stuff as a user in Bruce McFadden's biochemistry lab at Washington State University in 1988 (almost 20 years ago)! > I have not seen any announcement (though I was aware of the rumour). Yes, I didn't see it until a couple of weeks ago. It was dated July 1. Though I also had heard rumblings and realized it was likely happening. > Two questions: > > Does it say what will happen to the GCG products after retirement, or is > that still to be decided? > > Does the GCG licence still allow you to run GCG after it expires? (Or, > to be more specific, running it on your own machines, for external > access through SeqWeb, for logins from outside) It describes some vague "perpetual license" concept that leaves many questions unanswered. It does not offer source code. It does not offer any pricing information. And, perhaps most importantly, it offers no method of transferring the current license, which has been tied to a specific node that the package is installed on ever since Accelrys took over, to a new node, when that old node becomes obsolete or breaks. I'll post it on my Web system: http://bio.fsu.edu/~stevet/GCG.death.pdf. > [Re. EMBOSS] Three separate issues here: > > EMBOSS functionality can be compared to the GCG applications, and we do > hear from our users that most things in GCG are covered > (peptidestructure/plotstructure is an outstanding request, RNA folding > is covered by the ViennaRNA package as an "EMBASSY" addon to EMBOSS, > paup is covered similarly by PHYLIP. Yes, most GCG program app's are available elsewhere. Again, I argue it's SeqLab that really needs to be released. If they let the rest of the package out, great!, but SeqLab is what I really want. > LookUp I never liked ... it is SRS version 4, only partly integrated > (database links and other features missing). SRS version 5 was still > public but they never made the (huge) effort to integrate it. I always > had SRS available locally (it came from EMBL Heidelberg) so I always > turned GCG's LookUp off. As I have worked with SRS rather a lot, > including a couple of years at LION Bioscience writing parts of it, I'll > shut up about it :-) I again agree - LookUp has always been problematic. SRS 5 is way better, especially if it could be integrated into SeqLab's list file mechanism. > SeqLab is a big issue - we do not know of an EMBOSS interface that quite > compares (and I rather miss GDE) You hit the nail on the head here! I've checked everything out there. Nothing compares or offers nearly the extent of functionality. > [Re. GCG and EGCG's early history] Indeed, I was very much part of that > community. And we all benefitted and appreciated it greatly. > When EMBOSS started I had to kill EGCG. GCG claimed rights to the code > and refused to allow its reuse, so I claimed rights to the code and > refused to allow them to continue distribution. All the useful > applications had to be rewritten from scratch for EMBOSS. Only prettybox > survived - Rick Westerman contributed it to GCG. Yes, we all understood this regrettable but necessary maneuver. This was right about when Oxford Molecular took over GCG, wasn't it? And coincident when they made the decision to no longer distribute source? > There was a release 9.0 of EGCG (despite the GCG source code licence > problems) but it only ever went for beta test at one institute, and that > institute is now closed down. Yes! When I was at Washington State University's VADMS Center with Susan Johns, she contributed to EGCG and I think I remember testing v.9.0. But, you're correct, VADMS is no longer an entity (admin' never fully funded nor appreciated it - seems we were ahead of our times). > I wonder what the future holds ... As do I, Peter, as do I . . . . > Peter Rice European Bioinformatics Institute Cheers - Steve Steven M. Thompson A C T G stevet@... \-/ 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 _______________________________________________ Mol-evol mailing list Mol-evol@... http://www.bio.net/biomail/listinfo/mol-evol |
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Re: GCG non-support
by pmr-2
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Steve Thompson wrote:
> Hello Peter - Thanks for joining the dialogue. I was hoping you would. > > Yes, I have heard reports of extensive SeqLab customizing, and in fact, > Lynn Miller at GCG tried to spearhead a SeqLab extensions public > library, but she was never able to get folk to contribute. Alas, the > project shriveled away. It seems as if most of this work was done > behind the closed doors of the corporate world where sharing is not the > norm. In this case, sharing may be possible. I can ask anyway. > Yes, Eric Linton, MacGDE's maintainer, was a student here at the Marine > Biological Laboratory's Workshop on Molecular Evolution, where I am > working this month, many, many years ago when he began thinking about > this MacGDE project. Another of our past Mol Evol Workshop students, > Tulio de Oliveira, has created a robust Linux port (See > http://www.bioafrica.net/GDElinux/index.html). Both a wonderful pieces > of work, but neither includes all of the SeqLab's functionality. Can you make a quick list of the additional functionality you would like to see? I seem to recall "rich sequence format" was one of GCG's major extensions. > It describes some vague "perpetual license" concept that leaves many > questions unanswered. It does not offer source code. It does not offer > any pricing information. And, perhaps most importantly, it offers no > method of transferring the current license, which has been tied to a > specific node that the package is installed on ever since Accelrys took > over, to a new node, when that old node becomes obsolete or breaks. > I'll post it on my Web system: http://bio.fsu.edu/~stevet/GCG.death.pdf. Interesting. I see it mentions Pipeline Pilot. EMBOSS is an ISV partner and committed to interfacing EMBOSS applications as Pipeline Pilot components. I hope there is some source code release. We had the source code at Sanger not just for EGCG - but also because the sequencers needed more than the 350kb limit on sequence length. But I see no quick way to decide on possible source code licensing. Too many authors, too many companies/institutes. I am not surprised that nothing is promised at this stage. Hang on to your licences though ... one (legally speaking) relatively easy possibility would be a cheap source license for existing licensees. > I again agree - LookUp has always been problematic. SRS 5 is way > better, especially if it could be integrated into SeqLab's list file > mechanism. That would be difficult ... and I am not too confident of the status of SRS5 code anyway. But there are some alternatives around. >> When EMBOSS started I had to kill EGCG. GCG claimed rights to the code >> and refused to allow its reuse, so I claimed rights to the code and >> refused to allow them to continue distribution. All the useful >> applications had to be rewritten from scratch for EMBOSS. Only >> prettybox survived - Rick Westerman contributed it to GCG. > > Yes, we all understood this regrettable but necessary maneuver. This > was right about when Oxford Molecular took over GCG, wasn't it? And > coincident when they made the decision to no longer distribute source? Well, there was at least a year when I tried to make all the code changes needed for 9.0 and worked closely enough with GCG for the EGCG users to upgrade to version 9.0 (many were using the external users licence and had no real choice). The problems were with the code itself. It took a lot of effort to convert to 9.0, which made it worth the effort to write new libraries and even rewrite applications for EMBOSS - 3 years for 2 developers to reimplement EGCG. Source code licensing was a problem too ... I had a special licence that allowed me to distribute code to other sites who had source code ... but they would still be unable to send code to me. Ideally I would have given EGCG to GCG in exchange for the right to reuse my own code, but that never happened. A pity, as it cost us no extra effort in the end to reimplement and a lot of GCG users lost out. Oxford Molecular were as helpful as they could be at the time, but all the decisions were left to GCG. In those days open source was something that scared companies, so I was not surprised by the result. Sad though, as it immediately made EMBOSS into a competitor rather than a partner. It has taken us 10 years (and some luck) to become an Accelrys partner. >> There was a release 9.0 of EGCG (despite the GCG source code licence >> problems) but it only ever went for beta test at one institute, and >> that institute is now closed down. > > Yes! When I was at Washington State University's VADMS Center with > Susan Johns, she contributed to EGCG and I think I remember testing > v.9.0. But, you're correct, VADMS is no longer an entity (admin' never > fully funded nor appreciated it - seems we were ahead of our times). Hah! Not the one I meant (VADMS had an alpha binary release). The beta test was at HGMP/RFCGR in Hinxton - where the EMBOSS development team was and it was their closure that threw EMBOSS into crisis mode. Susan's TOPO was one of our first EMBASSY package add-ons, along with Will Gilbert's MSE editor. An early version of MSE was used by GCG for several of their editing applications, so at least that and GDE 2.3 are currently available with source code. EMBOSS's MSE is under GPL. I will try to figure out what GDE's licence really means. Peter Rice European Bioinformatics Institute _______________________________________________ Mol-evol mailing list Mol-evol@... http://www.bio.net/biomail/listinfo/mol-evol |
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Re: GCG non-support
by Steve Thompson-7
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On Fri, 3 Aug 2007, Peter Rice wrote (in part):
> [Re. SeqLab custom extensions availablity] In this case, sharing may be > possible. I can ask anyway. Yes, that would be great, especially if we get Accelrys to release SeqLab's code. I was quite pessimistic a couple of weeks ago, but have some [small] hope now. But I do realize not to 'hold my breath.' > Can you make a quick list of the additional functionality you would like > to see [in GDE]? I seem to recall "rich sequence format" was one of > GCG's major extensions. Yes, some have already been mentioned in this thread; I think these two are the most important: 1) The ability to directly load sequence data from output sequence lists from other programs such as BLAST, FastA, and a reference searching program (in GCG that is the SRS derivative LookUp) with the option of trimming that data to the length id'ed by a similarity search. As Nick mentioned this ability to handle "ad-hoc" databases can be very powerful. 2) The ability to display FEATURE information from database entries in colored and graphical representations. This is especially helpful for homology inference of active sites and secondary structure. > [Re. Accelrys' "perpetual license" plan] Interesting. I see it mentions > Pipeline Pilot. EMBOSS is an ISV partner and committed to interfacing > EMBOSS applications as Pipeline Pilot components. Pipeline Pilot is exciting and incredibly powerful from all I can tell, but also incredibly expensive - well beyond the budget of most university departments and/or research institutes, especially these days. > I hope there is some source code release. We had the source code at Sanger > not just for EGCG - but also because the sequencers needed more than the > 350kb limit on sequence length. > > But I see no quick way to decide on possible source code licensing. Too > many authors, too many companies/institutes. I am not surprised that > nothing is promised at this stage. > > Hang on to your licences though ... one (legally speaking) relatively easy > possibility would be a cheap source license for existing licensees. Oh yes, I don't plan on letting anything that we already own get lost. > [Re. getting SRS5 code under SeqLab or GDE] That would be difficult ... > and I am not too confident of the status of SRS5 code anyway. But there > are some alternatives around. Too bad, but I'm glad there are alternatives. Perhaps some variation of NCBI's stand alone Entrez, but it is designed for ASN.1 data . . . . . > [Re. my old days at WSU's VADMS Center] Hah! Not the one I meant (VADMS > had an alpha binary release). The beta test was at HGMP/RFCGR in Hinxton > - where the EMBOSS development team was and it was their closure that > threw EMBOSS into crisis mode. Yes, that was another terrible shame of funding drying up. > An early version of MSE was used by GCG for several of their editing > applications, so at least that and GDE 2.3 are currently available with > source code. EMBOSS's MSE is under GPL. I will try to figure out what GDE's > licence really means. A clarification of GDE's license would help a lot. Thanks! Cheers - Steve Steven M. Thompson A C T G stevet@... \-/ 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 _______________________________________________ Mol-evol mailing list Mol-evol@... http://www.bio.net/biomail/listinfo/mol-evol |
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Re: GCG non-support
by pmr-2
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Steve Thompson wrote:
>> Can you make a quick list of the additional functionality you would >> like to see [in GDE]? I seem to recall "rich sequence format" was one >> of GCG's major extensions. > > Yes, some have already been mentioned in this thread; I think these two > are the most important: > > 1) The ability to directly load sequence data from output sequence lists > from other programs such as BLAST, FastA, and a reference searching > program (in GCG that is the SRS derivative LookUp) with the option of > trimming that data to the length id'ed by a similarity search. As Nick > mentioned this ability to handle "ad-hoc" databases can be very powerful. That input should be simple (something like EMBL:X13776) and the code is relatively easy to do > 2) The ability to display FEATURE information from database entries in > colored and graphical representations. This is especially helpful for > homology inference of active sites and secondary structure. That was the part that used "rich sequence format" to store rearranged features and markup. I expect it can be reproduced using GFF as the feature standard (EMBOSS uses GFF internally, it is a good fit with even the EMBL/Genbank/DDBJ feature table and extendable for colouring etc - Artemis does something similar) > Too bad, but I'm glad there are alternatives. Perhaps some variation of > NCBI's stand alone Entrez, but it is designed for ASN.1 data . . . . . Or MRS from CMBI in Nijmegen. Or something using web services. There are many possibilities. Peter _______________________________________________ Mol-evol mailing list Mol-evol@... http://www.bio.net/biomail/listinfo/mol-evol |
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Re: [Info-gcg] Re: GCG non-support
by Steve Thompson-7
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Hi all -
Sorry about dropping out of the conversation for the past couple of days - I've been too busy with students at the MBL Mol Evol Course. Anyway, thanks to all that have participated, including GCG's Michael Perry, who clarified the "perpetual license" issue a bit. However, in spite of now knowing that a node-independent license will be a part of it, which was a huge biggy for me, there are still problems. As has been pointed out - database formats change; however, what I think is most dangerous, OSs upgrade. Eventually stuff will break. It's not a perfect solution, but it is better than none. Michael did argue re. the difficulty of releasing the entire package due to all the original author license complications. As Peter mentioned, OK, perhaps that it too complicated for GCG to do it for free. But, please, let SeqLab go. There are plenty of people out there, including Peter (who, I believe has already offered in this thread) and other folk in the EMBOSS team who would gladly take it upon themselves to incorporate outside, already open source programs, into SeqLab's menus. Peter has already dug into the SeqLab (GDE) license terms. Let's make it happen. Cheers - Steve Steven M. Thompson A C T G stevet@... \-/ 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 _______________________________________________ Mol-evol mailing list Mol-evol@... http://www.bio.net/biomail/listinfo/mol-evol |
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RE: [Info-gcg] Other: Re - GCG non-support
by Staffa, Nick (NIH/NIEHS)
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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@...] > Sent: Monday, November 03, 2008 3:56 PM > To: Peter Rice > Cc: mol-evol@...; evoldir@...; > bio-soft@...; info-gcg@...; comp- > bio@... > 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 > (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@... > \-/ > http://bio.fsu.edu/~stevet/cv.html > /\ > /--| FSU SCS / BioInfo 4U > /---/ > |--/ Florida State University > 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@... > http://www.bio.net/biomail/listinfo/info-gcg _______________________________________________ Mol-evol mailing list Mol-evol@... http://www.bio.net/biomail/listinfo/mol-evol |
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