[Bio-software] Re: GCG non-support

Steve Thompson via bio-soft%40net.bio.net (by stevet from bio.fsu.edu)
Thu Aug 2 13:33:36 EST 2007


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 from bio.fsu.edu
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