GCG non-support

[Steve Thompson]

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 ***@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

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: [phone] (NIEHS: 6-4569)
Scientific Computing Support Group
NIEHS Information Technology Support Services Contract
National Institute of Environmental Health Sciences
National Institutes of Health
Research Triangle Park, North Carolina

[Peter Rice]

I just saw a messsage in this thread in the bionet.software and
bionet.software.gcg newsgroups (they will match the bio-soft and info-gcg
mailing lists I noted in the header).

I fear I may be missing other messages.

Post by Steve Thompson
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.

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.

Post by Steve Thompson
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.

SeqLab was originally GDE, written by Steve Smith at Harvard and much extended
when he was at GCG Inc.

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.

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.

The licence in the 2.2 distribution (last release before GCG adopted it) is a
little unusual by today's standards. The GDE.readme file says:

The programs are not in the public domain, but are and will continue to be
available for free. Distribution includes full source code, and binaries
along with a users manual.

That was from 1992. Is it perhaps an early open source licence? I read "not in
the public domain" to say "author retains copyright" but I see no restrictions on
modification or reuse. There is also no obligation for later modifications to be
under the same licence.

Release 2.2 is still available from
http://iubio.bio.indiana.edu/soft/molbio/unix/GDE/

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.

Post by Steve Thompson

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.

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 :-)

Post by Steve Thompson

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 have not seen any announcement (though I was aware of the rumour).

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)

Post by Steve Thompson

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.

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.

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 :-)

SeqLab is a big issue - we do not know of an EMBOSS interface that quite
compares (and I rather miss GDE)

Post by Steve Thompson

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.

Indeed, I was very much part of that community :-)

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.

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.

I wonder what the future holds ...

Peter Rice
European Bioinformatics Institute

[Steve Thompson]

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

Post by Peter Rice
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.

Post by Peter Rice
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.

Post by Peter Rice
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.

Post by Peter Rice
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.

Post by Peter Rice
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)!

Post by Peter Rice
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.

Post by Peter Rice
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.

Post by Peter Rice
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.

Post by Peter Rice
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.

Post by Peter Rice
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.

Post by Peter Rice
[Re. GCG and EGCG's early history] Indeed, I was very much part of that
community.

And we all benefitted and appreciated it greatly.

Post by Peter Rice
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?

Post by Peter Rice
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).

Post by Peter Rice
I wonder what the future holds ...

As do I, Peter, as do I . . . .

Post by Peter Rice
Peter Rice European Bioinformatics Institute

Cheers - Steve
Steven M. Thompson
A C T G ***@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

[Peter Rice]

Post by Steve Thompson
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.

Post by Steve Thompson
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.

Post by Steve Thompson
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.

Post by Steve Thompson
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.

Post by Steve Thompson

Post by Peter Rice
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.

Post by Steve Thompson

Post by Peter Rice
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

[Steve Thompson]

[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 ***@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

[Peter Rice]

Post by Steve Thompson

Post by Peter Rice
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
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

Post by Steve Thompson
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)

Post by Steve Thompson
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

[Steve Thompson]

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 ***@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

[Steve Thompson]

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 ***@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

[Staffa, Nick (NIH/NIEHS) [C]]

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: [phone] (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-----
Sent: Monday, November 03, 2008 3:56 PM
To: Peter Rice

comp-

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
\-/
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
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