Nabble - Bio.net - Info-gcg

Announcement: GenPept 174.0 available

2009-10-22T08:12:42Z

This is to announce the availability of release 174.0 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: 20-Oct-2009

If you have questions or comments concerning this data, or you experience any
difficulty in downloading the data via ftp, please contact:

Gary Smythers smytherg@... 301-846-5778

================================================================
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.

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Announcement: GenPept 173.0 available

2009-08-28T08:00:42Z

This is to announce the availability of release 173.0 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: 27-Aug-2009

If you have questions or comments concerning this data, or you experience any
difficulty in downloading the data via ftp, please contact:

Gary Smythers smytherg@... 301-846-5778

================================================================
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.

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Announcement: GenPept 172.0 available

2009-06-16T07:25:56Z

This is to announce the availability of release 172.0 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: 15-Jun-2009

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@... 301-846-5778
or
Bob Stephens bobs@...

================================================================
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.

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Announcement: GenPept 171.0 available

2009-04-16T07:13:27Z

This is to announce the availability of release 170.1 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: 15-Apr-2009

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@... 301-846-5778
or
Bob Stephens bobs@...

================================================================
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.

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Announcement: GenPept 170.0 available

2009-02-20T12:49:51Z

This is to announce the availability of release 170.0 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: 20-Feb-2009

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@... 301-846-5778
or
Bob Stephens bobs@...

================================================================
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.

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Announcement: GenPept 169.0 available

2008-12-17T07:34:10Z

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@... 301-846-5778
or
Bob Stephens bobs@...

================================================================
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.

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

RE: Other: Re - GCG non-support

2008-12-11T07:28:30Z

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

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@...
> \-/
> 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@...
> http://www.bio.net/biomail/listinfo/info-gcg

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Other: Re - GCG non-support

2008-11-03T12:56:23Z

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@...
\-/ 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@...
http://www.bio.net/biomail/listinfo/info-gcg

Announcement: GenPept 168.0 available

2008-11-02T12:20:02Z

This is to announce the availability of release 168.0 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: 31-Oct-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@... 301-846-5778
or
Bob Stephens bobs@...

================================================================
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.

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Announcement: GenPept 167.0 available

2008-08-27T12:18:49Z

This is to announce the availability of release 167.0 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: 27-Aug-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@... 301-846-5778
or
Bob Stephens bobs@...

================================================================
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.

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Announcement: GenPept 166.0 available

2008-06-17T08:04:00Z

This is to announce the availability of release 166.0 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-Jun-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@... 301-846-5778
or
Bob Stephens bobs@...

================================================================
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.
-----------------------------
Gary W. Smythers [Contractor]
Programmer Analyst IV
Advanced Biomedical Computing Center
SAIC NCI-Frederick
National Cancer Institute at Frederick
Post Office Box B
Frederick, MD 21702-1201 USA
Phone: 301-846-5778
FAX: 301-846-5762
gws@...
-----------------------------

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Other: another followup (apology)

2008-04-27T17:08:49Z

Hi all -

I would like to offer my apology to Accelrys and its employees for
suggesting that the company would not follow through on their commitment
to supply non-node-locked, non-expiring license keys to all current GCG
custyomers with "perpetual" licenses. As I mentioned in my last posting
Accelrys is now involved in that process and I have received my new key.
It was never my intent to discredit Accelrys, nor its employess. I merely
had not been informed that the process was underway. I am sorry that I
miswrote and hope that any hard feelings can be overcome. Thank you.

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

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Other: followup to Accelrys petition followup

2008-04-25T06:16:28Z

Hello all -

A brief note to let you know what's happened since my posting this last
Wednesday:

Rob Brown of Accelrys did contact me, finally. He says, and I quote:

"The petition and the subsequent BioInform article produced a significant
response and generated inquiries from a number of third party companies
who now wish to discuss various possibilities relating to GCG with us.
We are now in the process of following up on all of those which is taking
some time."

So, it looks like some good has come out of the process, although this
doesn't look like the open source type of arrangement that many of us
hoped for. Regardless, it may mean that the package will not be dying.

And, Accelrys sent me my new non-node-locked, non-expiring license key!

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

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Other: Accelrys petition followup

2008-04-23T10:41:04Z

Hi all - re. http://www.petitiononline.com/gcg/

A huge THANKS to all of you that signed my petition! Within the first
week online I got almost 150 signatures, and John Devereux himself most
recently signed it. I sent Rob Brown of Accelrys an 'official' copy of
the petition and the signatures at the end of last month. However, but
not surprisingly, I have yet to receive one word back from Accelrys. I
realize that we can't force them to do anything, but I at least thought
that they would have the courtesy to respond to it somehow. The petition
did result in a news story though. GenomeWeb News' bioinformatics
newsletter, BioInform, published the story on April 4th. See my copy at:

http://bio.fsu.edu/~stevet/BioInformGCG.pdf

Some may feel that the BioInform story suggests the petition was merely a
means of influencing commercial negotiations with Accelrys regarding code
release, and have nothing to do with public domain availability, but this
was never my objective. It is and remains a plea not to kill the package,
and in particular SeqLab, by whatever means possible, but preferably
within some type of open source arrangement. Furthermore, Accelrys argues
in the article that many more people have signed the petition than
subscribe to the package, and that this somehow invalidates the petition.
This is completely irrelevant as the GCG license has always been to an
institution, allowing as many people in that institution access as wanted,
not to individual investigators. Here at FSU I have supported over 100
GCG users with one GCG license over the years. June should be interesting
for us all. We'll have to see if Accelrys honors their commitment to
those of us with "perpetual" licenses to provide non-node-locked, non-
expiring versions of the license after June 30, 2008. Time will tell.

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

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Announcement: GenPept 164.0 available

2008-02-22T13:27:36Z

This is to announce the availability of release 164.0 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: 20-Feb-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@... 301-846-5778
or
Bob Stephens bobs@...

================================================================
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.
-----------------------------
Gary W. Smythers [Contractor]
Programmer Analyst IV
Advanced Biomedical Computing Center
SAIC NCI-Frederick
National Cancer Institute at Frederick
Post Office Box B
Frederick, MD 21702-1201 USA
Phone: 301-846-5778
FAX: 301-846-5762
gws@...
-----------------------------

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

GCG substitute

2008-01-11T09:38:45Z

Working under the assumption that someday GCG will cease to work on any
computer/system we own, I am trying to compile a guide such that
for any GCG program, you can have a list of all the other resources that
would accomplish the same thing WWW, Emboss, Desktop, or whatever.
I'm thinking "this is a lot of work; maybe someone else has done something
similar and is willing to share it." I know about the tables of GCG to
EMBOSS programs; that is just a starting point.
Do you know of other work done to bring together all sequence analysis
resources?

Thanks

Nick Staffa
Telephone: 919-316-4569 (NIEHS: 6-4569)
Scientific Computing Support Group
NIEHS Information Technology Support Services Contract
(Science Task Monitor: Roy W. Reter (reter@...)
National Institute of Environmental Health Sciences
National Institutes of Health
Research Triangle Park, North Carolina

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Announcement: GenPept 163.0 available

2007-12-26T10:17:33Z

This is to announce the availability of release 163.0 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

Directory: pub/genpept/divisions
Files: 1 file for each GenBank file

Directory: pub/genpept/updates (daily, cumulative)
Files: gpseq_updates.dat.gz

Rel. Date: 26-Dec-2007

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@... 301-846-5778
or
Bob Stephens bobs@...

================================================================
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.
-----------------------------
Gary W. Smythers [Contractor]
Programmer Analyst IV
Advanced Biomedical Computing Center
SAIC NCI-Frederick
PO Box B, Bldg 430
Frederick, MD 21702-1201 USA
gws@...
(301) 846-5778
FAX:(301) 846-5762
-----------------------------

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Announcement: GenPept 161.0 available

2007-08-23T14:09:52Z

This is to announce the availability of release 161.0 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

Directory: pub/genpept/divisions
Files: 1 file for each GenBank file

Directory: pub/genpept/updates (daily, cumulative)
Files: gpseq_updates.dat.gz

Rel. Date: 23-Aug-2007

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@... 301-846-5778
or
Bob Stephens bobs@...

================================================================
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.
-----------------------------
Gary W. Smythers [Contractor]
Programmer Analyst IV
Advanced Biomedical Computing Center
SAIC NCI-Frederick
PO Box B, Bldg 430
Frederick, MD 21702-1201 USA
gws@...
(301) 846-5778
FAX:(301) 846-5762
-----------------------------

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Announcement: GenPept 161.0 available

2007-08-23T14:07:22Z

This is to announce the availability of release 160.0 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

Directory: pub/genpept/divisions
Files: 1 file for each GenBank file

Directory: pub/genpept/updates (daily, cumulative)
Files: gpseq_updates.dat.gz

Rel. Date: 26-Jun-2007

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@... 301-846-5778
or
Bob Stephens bobs@... 301-846-5787

================================================================
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.
-----------------------------
Gary W. Smythers [Contractor]
Programmer Analyst IV
Advanced Biomedical Computing Center
SAIC NCI-Frederick
PO Box B, Bldg 430
Frederick, MD 21702-1201 USA
gws@...
(301) 846-5778
FAX:(301) 846-5762
-----------------------------

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Re: Re: GCG non-support

2007-08-07T15:16:50Z

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

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Re: Re: GCG non-support

2007-08-07T02:45:41Z

Staffa, Nick (NIH/NIEHS) [C] wrote:
> I don't think it solves anything, just letting us keep using what we
> already purchased and at an extra price. The question is: how much?
>
> I'm sure that someone would adopt the package if allowed, else it will
> die a slow agonizing death.
> I was hoping someone could get thru to the accelrys folk even tho they
> have everybody there spouting the same party line.

Well .... I think they have done pretty well to announce the perpetual
licence.

Consider the effort involved in making a general release:

All the code has to be traced to its original authors. They, and/or
their employers, will hold the copyright to the code.

Determine how each "significant" section of code is licensed to GCG (as
University of Wisconsin, GCG, Oxford Molecular, Accelrys).

Gain agreement as necessary from each stakeholder. (or: remove that
stakeholder's code completely and make sure that the remainder still
functions without it.

Agree a licence for the remaining code, acceptable to all the remaining
stakeholders.

Make provision for paid support for anyone using the remaining code
(there will be enough users in need of support - and if any code is
removed some help will be required).

... and all with no hope of any financial reward.

The beauty of the perpetual licence is that existing users can carry on
with the way they work now.

Perhaps what you really need are two things:

Some continued support ... I would guess any group or company interesed
in taking over support cold make Accelrys an offer

Seqlab code ... which I still believe has a chance but it will take time
to work it ot. It is just a much simpler problem than the GCG
applications and libraries.

regards,

Peter Rice
European Bioinformatics Institute

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Re: Re: GCG non-support

2007-08-07T01:38:30Z

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

> I don't think it solves anything, just letting us keep using what we
> already purchased and at an extra price. The question is: how much?

From enquiries that we have made, it looks like the price for the
perpetual license will be the same as for a 1-year licence.

One of my main concerns about GCG not being maintained is that any
changes to the formats of EMBL and UniProt sequence files might break
GCG. There have been patches released in the past to cope with new
annotation fields in sequence files. How will this be coped with in the
future?

Raymond Dalgleish
Department of Genetics
University of Leicester
_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

RE: Re: GCG non-support

2007-08-06T12:15:15Z

> Hurrah! That looks an excellent solution.

I don't think it solves anything, just letting us keep using what we
already purchased and at an extra price. The question is: how much?

I'm sure that someone would adopt the package if allowed, else it will
die a slow agonizing death.
I was hoping someone could get thru to the accelrys folk even tho they
have everybody there spouting the same party line.

-----Original Message-----
From: Peter Rice [mailto:pmr@...]
Sent: Monday, August 06, 2007 9:28 AM
To: info-gcg@...
Subject: [Info-gcg] Re: GCG non-support

wmichaelperry@... wrote:
> We truly would like to have made GCG available as GPL or open source
> software. This possibility was investigated but several obstacles
were
> encountered that prevented a positive resolution. As there are no
plans to
> invest further legal and R&D effort into GCG (necessary to identify
and
> remove licensed, 3rd party software), it's unlikely that the GCG code
base
> will be made publically available. Instead GCG customers with a
perpetual
> license who have an active maintenance agreement on June 30, 2008 will
be
> eligible to receive a non-node- locked license that will allow GCG to
be used
> indefinitely on any currently supported platform. This offer requires
you to
> have a perpetual GCG license. If you have an annual license, special
reduced
> pricing is in effect that gives you the opportunity at your renewal
time to
> convert to a perpetual license.

Hurrah! That looks an excellent solution.

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Re: GCG non-support

2007-08-06T07:28:16Z

wmichaelperry@... wrote:

> We truly would like to have made GCG available as GPL or open source
> software. This possibility was investigated but several obstacles were
> encountered that prevented a positive resolution. As there are no plans to
> invest further legal and R&D effort into GCG (necessary to identify and
> remove licensed, 3rd party software), it's unlikely that the GCG code base
> will be made publically available. Instead GCG customers with a perpetual
> license who have an active maintenance agreement on June 30, 2008 will be
> eligible to receive a non-node- locked license that will allow GCG to be used
> indefinitely on any currently supported platform. This offer requires you to
> have a perpetual GCG license. If you have an annual license, special reduced
> pricing is in effect that gives you the opportunity at your renewal time to
> convert to a perpetual license.

Hurrah! That looks an excellent solution.

I posted a separate message about SeqLab.

> For those who are interested in using commercially supported product,
> Accelrys has partnered with BioTeam's iNquiry to offer custom bioinformatics
> solutions with similar or enhanced functionality to that of Accelrys GCG,
> SeqWeb and the Data Update Service. Most notably, BioTeam's iNquiry can give
> you a high performance, extensible framework for incorporating EMBOSS (which
> is similar to GCG) and other bioinformatics tools.

I met one of the BioTeam developers at ISMB in Vienna. There appear to be ways
we can make EMBOSS easier to maintain in iNquiry ... an obvious one is helping
to maintain the XML definitions of each application when we build a new release.

We are open to suggestions for new EMBOSS applications. A major task for us this
summer will be compiling a list of new applications and new feature requests. We
are aware that there are GCG applications that have no equivalent in EMBOSS, and
others that use different algorithms.

We are also looking for volunteers to help write some of the new applications
and add new features :-)

regards,

Peter Rice
European Bioinformatics Institute
_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Re: GCG non-support

2007-08-06T07:13:31Z

Don Gilbert wrote:
> Steve Smith is still hanging around Wisconson, at Nimblegen
> http://www.nimblegen.com/corporate/management/ssmith.html If anyone could
> answer the question of copyrights to SeqLab, outside Accelrys lawyers, he
> probably could.

I found why the Mac version is concerned about "commercial products."

There is a more complete version of the license at
http://www.bioafrica.net/GDElinux/gde2.2.txt
(see below for a quote). As I understand it this is from the GDE 2.2 manual.

The code conditions appear compatible with open source licenses, including GPL
(assuming the "modifications ... should be forwarded to the author" is satisfied
by Stevn Smith having access to the modified code).

The "commercial product" condition is a problem ... but obviously it has been
licensed to GCG Inc (and now to Accelrys) with some special permission.

That suggests that the best way to make GDE/SeqLab available as open source is
for Accelrys
and Steve Smith to have a little chat.

regards,

Peter Rice

The GDE 2.2 manual ends with:

> Copyright Notice
>
> The Genetic Data Environment (GDE) software and documentation are not in the
> public domain. Portions of this code are owned and copyrighted by the The
> Board of Trustees of the University of Illinois and by Steven Smith. External
> functions used by GDE are the proporty of, their respective authors. This
> release of the GDE program and documentation may not be sold, or incorporated
> into a commercial product, in whole or in part without the expressed written
> consent of the University of Illinois and of its author, Steven Smith.
>
> All interested parties may redistribute the GDE as long as all copies are
> accompanied by this documentation, and all copyright notices remain intact.
> Parties interested in redistribution must do so on a non-profit basis,
> charging only for cost of media. Modifications to the GDE core editor should
> be forwarded to the author Steven Smith. External programs used by the GDE
> are copyright by, and are the property of their respective authors unless
> otherwise stated.
>
>
> While all attempts have been made to insure the integrity of these programs:
>
> Disclaimer
>
> THE UNIVERSITY OF ILLINOIS, HARVARD UNIVERSITY AND THE AUTHOR, STEVEN SMITH
> GIVE NO WARRANTIES, EXPRESSED OR IMPLIED FOR THE SOFTWARE AND DOCUMENTATION
> PROVIDED, INCLUDING, BUT NOT LIMITED TO WARRANTY OF MERCHANTABILITY AND
> WARRANTY OF FITNESS FOR A PARTICULAR PURPOSE. User understands the software
> is a research tool for which no warranties as to capabilities or accuracy are
> made, and user accepts the software "as is." User assumes the entire risk
> as to the results and performance of the software and documentation. The
> above parties cannot be held liable for any direct, indirect, consequential
> or incidental damages with respect to any claim by user or any third party on
> account of, or arising from the use of software and associated materials.
> This disclaimer covers both the GDE core editor and all external programs
> used by the GDE.

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Re: GCG non-support

2007-08-04T12:12:15Z

Hi Nick, Steve, and Peter,

We truly would like to have made GCG available as GPL or open source
software. This possibility was investigated but several obstacles
were encountered that prevented a positive resolution. As there are no
plans to invest further legal and R&D effort into GCG (necessary to
identify and remove licensed, 3rd party software), it's unlikely that
the GCG code base will be made publically available. Instead GCG
customers with a perpetual license who have an active maintenance
agreement on June 30, 2008 will be eligible to receive a non-node-
locked license that will allow GCG to be used indefinitely on any
currently supported platform. This offer requires you to have a
perpetual GCG license. If you have an annual license, special reduced
pricing is in effect that gives you the opportunity at your renewal
time to convert to a perpetual license.

A perpetual license gives you the flexibility of using GCG (and
SeqLab) for as long as you want and will be particularly useful if you
have built infrastructure around GCG or if you have used, or plan to
use, GCG algorithms to support intellectual property claims. The
software will be provided "as is" but you will have hotline scientific
application support through the retirement date of June 30, 2008 and
you can continue to receive value from the existing GCG bioinformatics
algorithms beyond our retirement date and into the future.

For those who are interested in using commercially supported product,
Accelrys has partnered with BioTeam's iNquiry to offer custom
bioinformatics solutions with similar or enhanced functionality to
that of Accelrys GCG, SeqWeb and the Data Update Service. Most
notably, BioTeam's iNquiry can give you a high performance, extensible
framework for incorporating EMBOSS (which is similar to GCG) and other
bioinformatics tools.

iNquiry provides:

- Fully configured operating system for the cluster master node and
compute nodes. This includes all OS settings and network services.
- Fully configured cluster scheduling and distributed resource
management software (Grid Engine or Platform LSF).
- An XML-based extensible framework for application integration and
customization
- Consistent interface to many integrated open source scientific
applications.
- Web-based portal to cluster resources, applications and management
functionality.

See the following web page for more information about BioTeam and
iNquiry:

http://www.bioteam.net/

Feel free to contact me directly or your account manager if you have
any questions about your GCG license or our GCG retirement plans.

Regards

Mike

Michael Perry, Ph.D.
Manager, Scientific and Technical Support
Email: perry@...
Direct: 858-799-5686

Accelrys Scientific and Technical Support
Tollfree: 800-756-4674
Email: support@...
Web: https://customer.accelrys.com

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Re: GCG non-support

2007-08-03T15:55:10Z

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

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Re: GCG non-support

2007-08-03T12:55:28Z

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

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Re: GCG non-support

2007-08-03T03:18:27Z

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

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Re: GCG non-support

2007-08-02T12:33:36Z

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

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Re: GCG non-support

2007-08-02T11:12:31Z

Steve Smith is still hanging around Wisconson, at Nimblegen
http://www.nimblegen.com/corporate/management/ssmith.html
If anyone could answer the question of copyrights to SeqLab, outside
Accelrys lawyers, he probably could.

- Don
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd@...--http://marmot.bio.indiana.edu/

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Re: GCG non-support

2007-08-02T04:15:04Z

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.

Steve Thompson wrote:
> 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.

> 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.

> On Wed, 1 Aug 2007, Staffa, Nick (NIH/NIEHS) wrote:
>
>> 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 :-)

>> 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)

>> 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)

>> 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

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

Re: GCG non-support

2007-08-02T04:15:04Z

Re: GCG non-support

2007-08-01T14:22:05Z

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 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

On Wed, 1 Aug 2007, Staffa, Nick (NIH/NIEHS) wrote:

> 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: 919-316-4569 (NIEHS: 6-4569)
> Scientific Computing Support Group
> NIEHS Information Technology Support Services Contract
> (Science Task Monitor: John D. Grovenstein (grovens1@...)
> National Institute of Environmental Health Sciences
> National Institutes of Health
> Research Triangle Park, North Carolina

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

GCG non-support

2007-08-01T12:08:26Z

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: 919-316-4569 (NIEHS: 6-4569)
Scientific Computing Support Group
NIEHS Information Technology Support Services Contract
(Science Task Monitor: John D. Grovenstein (grovens1@...)
National Institute of Environmental Health Sciences
National Institutes of Health
Research Triangle Park, North Carolina

_______________________________________________
Info-gcg mailing list
Info-gcg@...
http://www.bio.net/biomail/listinfo/info-gcg

GCGSunsetNotice.pdf (28K) Download Attachment