Nabble - Perl - Bioperl-Announce-L

[ANNOUNCEMENT] BioPerl Meeting at the GMOD Conference

2009-12-10T11:09:54Z

Begin forwarded message:

> From: Chris Fields <cjfields@...>
> Date: December 8, 2009 8:30:26 PM PST
> To: BioPerl List <bioperl-l@...>
> Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl Meeting at the GMOD
> Conference
>
> All,
>
> For those interested, we will be holding a general BioPerl meeting,
> tentatively scheduled for January 13, 2010, just prior to the GMOD
> Community Meeting from Jan 14-15 in San Diego. This will be just
> following the Plant and Animal Genome (PAG) conference Jan 9-13.
> The exact day and time is somewhat flexible depending on attendees'
> schedules.
>
> For those interested, sign up here:
>
> http://www.bioperl.org/wiki/GMOD_2010_Meeting
>
> For those interested in attending the GMOD meeting or PAG:
>
> http://gmod.org/wiki/January_2010_GMOD_Meeting
>
> I can envision the following items popping up:
>
> * Refactoring of Alignment and GFF3/FeatureIO
> * Addressing BioPerl's monolithic nature
> * Moose and Perl 6
> * Documentation
>
> Any others?
>
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
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jason.stajich@...
jason@...

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Re: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0

2009-01-26T07:25:19Z

Great job Chris et al. Congratulations!! :)

Chris Fields wrote:

> All,
>
> I am proud to announce, on behalf of the BioPerl core developers, that
> BioPerl 1.6.0 is now available. This is the first BioPerl core release
> in the 1.6 series and is considered a 'stable' (non-developer) release.
> The distribution has been uploaded to CPAN and is available under author
> name CJFIELDS; it should be hitting the various CPAN nodes over the next
> 24 hours. A direct CPAN link is here:
>
> http://search.cpan.org/~cjfields/BioPerl-1.6.0/
>
> The release can also be directly downloaded here:
>
> http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2
> http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz
> http://bioperl.org/DIST/BioPerl-1.6.0.zip
>
> Signature file:
> http://bioperl.org/DIST/SIGNATURES.md5
>
> Please feel free to report issues with testing, installation, etc. on
> the mail list, on this page:
>
> http://www.bioperl.org/wiki/Release_1.6_Testing
>
> or via Bugzilla:
>
> http://bugzilla.open-bio.org/
>
> We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and other
> BioPerl distributions separately in the next few days. These will
> likely go through a short alpha release cycle depending on any problems
> that arise. A PPM release for all distributions (including BioPerl
> core) will also be announced in the near future.
>
> Thanks to everyone for chipping in on getting this release out the
> door! It's been a looooong wait...
>
> Enjoy!
>
> chris
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

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Re: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0

2009-01-25T21:06:03Z

Good job! It's very exciting to have a new BioPerl release out there
Florent

Chris Fields wrote:

> All,
>
> I am proud to announce, on behalf of the BioPerl core developers, that
> BioPerl 1.6.0 is now available. This is the first BioPerl core
> release in the 1.6 series and is considered a 'stable' (non-developer)
> release. The distribution has been uploaded to CPAN and is available
> under author name CJFIELDS; it should be hitting the various CPAN
> nodes over the next 24 hours. A direct CPAN link is here:
>
> http://search.cpan.org/~cjfields/BioPerl-1.6.0/
>
> The release can also be directly downloaded here:
>
> http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2
> http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz
> http://bioperl.org/DIST/BioPerl-1.6.0.zip
>
> Signature file:
> http://bioperl.org/DIST/SIGNATURES.md5
>
> Please feel free to report issues with testing, installation, etc. on
> the mail list, on this page:
>
> http://www.bioperl.org/wiki/Release_1.6_Testing
>
> or via Bugzilla:
>
> http://bugzilla.open-bio.org/
>
> We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and
> other BioPerl distributions separately in the next few days. These
> will likely go through a short alpha release cycle depending on any
> problems that arise. A PPM release for all distributions (including
> BioPerl core) will also be announced in the near future.
>
> Thanks to everyone for chipping in on getting this release out the
> door! It's been a looooong wait...
>
> Enjoy!
>
> chris
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

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[ANNOUNCEMENT] BioPerl 1.6.0

2009-01-25T16:22:16Z

All,

I am proud to announce, on behalf of the BioPerl core developers, that
BioPerl 1.6.0 is now available. This is the first BioPerl core
release in the 1.6 series and is considered a 'stable' (non-developer)
release. The distribution has been uploaded to CPAN and is available
under author name CJFIELDS; it should be hitting the various CPAN
nodes over the next 24 hours. A direct CPAN link is here:

http://search.cpan.org/~cjfields/BioPerl-1.6.0/

The release can also be directly downloaded here:

http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2
http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz
http://bioperl.org/DIST/BioPerl-1.6.0.zip

Signature file:
http://bioperl.org/DIST/SIGNATURES.md5

Please feel free to report issues with testing, installation, etc. on
the mail list, on this page:

http://www.bioperl.org/wiki/Release_1.6_Testing

or via Bugzilla:

http://bugzilla.open-bio.org/

We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and
other BioPerl distributions separately in the next few days. These
will likely go through a short alpha release cycle depending on any
problems that arise. A PPM release for all distributions (including
BioPerl core) will also be announced in the near future.

Thanks to everyone for chipping in on getting this release out the
door! It's been a looooong wait...

Enjoy!

chris

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BioPerl 1.6 RC2 is now available

2009-01-07T10:57:14Z

All,

I would like to announce the second release candidate for BioPerl 1.6
is available for testing.

A quick note on versioning: due to issues with alpha numbered versions
on CPAN possibly overwriting a stable release, this release candidate
has a VERSION of 1.005009_002 (or 1.005009002). This will be switched
to 1.006000 (no alpha) once the release is final.

RC2 has been uploaded to CPAN is available under authorname CJFIELDS.
From the CPAN shell:

cpan[1]> install CJFIELDS/BioPerl-1.5.9_2.tar.gz

RC2 can be directly downloaded here:

http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.bz2
http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.gz
http://bioperl.org/DIST/BioPerl-1.5.9_2.zip

Signature file:
http://bioperl.org/DIST/SIGNATURES.md5

A preliminary ActiveState PPM is also available and is located in the
BioPerl Release Candidate repository; the directions for installation
are here:

http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows

Please feel free to report issues with testing, installation, etc. on
the mail list and on this page:

http://www.bioperl.org/wiki/Release_1.6_Testing

Again, just to note we will be releasing bioperl-run, bioperl-db,
bioperl-network, and others separately once the final 1.6 release is
complete.

Since the last release:

Fixed:

1) Some cruft from testing the last release is no longer present.
2) Several warnings and test failures (via CPAN Testers) now fixed.

Known Issues:

1) A very recent change in ENSembl data causes one of the Map.t tests
to fail; this has already been fixed and will be present in the next
(final?) release.
2) Some odd warnings for Bio::Assembly tests are still present, but
they are harmless. Nevertheless they will be addressed prior to the
next release.
3) Warnings for Bio::Annotation tests can be fixed by an upgrade to
the latest Data::Stag (this is NOT a required upgrade).
4) PPM issues; note this is not high on our priority list ATM but I
will try to address it for the next release).

Enjoy!

chris
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BOSC 2008 Announcement and Call For Submissions

2008-05-05T07:08:18Z

BOSC 2008 Call for Abstracts Reminder

The 9th annual Bioinformatics Open Source Conference (BOSC 2008) will take place in Toronto, Ontario, Canada, as one of several Special Interest Group (SIG) meetings occurring in conjunction with the 16th annual Intelligent Systems for Molecular Biology Conference (ISMB 2008).

This is the final reminder to submit your proposals for talks to the BOSC submission system before May 11.

Submission Process:
All abstracts must be submitted through our Open Conference Systems site (http://events.open-bio.org/BOSC2008/openconf.php).
The form will ask for a small Abstract Text to be pasted into it, and a full paper. The small Abstract text should be a summary, while the longer abstract (should provide more details, including the open-source license requirement details)
Full-length abstracts are limited to one page with one inch (2.5 cm) margins on the top, sides, and bottom. The full-length abstract should include the title, authors, and affiliations. We prefer your abstract to be in PDF format, although plain t

Important Dates:
May 11: Abstract submission deadline.
June 2: Notification of accepted talks.
June 4: Early registration discount cut-off.
July 18-19: BOSC 2008!

We hope to see you at BOSC 2008!

Kam Dahlquist and Darin London
BOSC 2008 Co-organizers

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BOSC 2008 Announcement and Call For Submissions

2008-04-29T09:49:33Z

BOSC 2008 Call for Abstracts Reminder

The 9th annual Bioinformatics Open Source Conference (BOSC 2008) will take place in Toronto, Ontario, Canada, as one of several Special Interest Group (SIG) meetings occurring in conjunction with the 16th annual Intelligent Systems for Molecular Biology Conference (ISMB 2008).

This is a reminder to submit your proposals for talks to the BOSC submission system before May 11.

Submission Process:
All abstracts must be submitted through our Open Conference Systems site (http://events.open-bio.org/BOSC2008/openconf.php).
The form will ask for a small Abstract Text to be pasted into it, and a full paper. The small Abstract text should be a summary, while the longer abstract (should provide more details, including the open-source license requirement details)
Full-length abstracts are limited to one page with one inch (2.5 cm) margins on the top, sides, and bottom. The full-length abstract should include the title, authors, and affiliations. We prefer your abstract to be in PDF format, although plain t

Important Dates:
May 11: Abstract submission deadline.
June 2: Notification of accepted talks.
June 4: Early registration discount cut-off.
July 18-19: BOSC 2008!

We hope to see you at BOSC 2008!

Kam Dahlquist and Darin London
BOSC 2008 Co-organizers

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BOSC 2008 Announcement and Call For Submissions

2008-03-18T11:16:58Z

BOSC 2008 Call for Abstracts

The 9th annual Bioinformatics Open Source Conference (BOSC 2008) will take place in Toronto, Ontario, Canada, as one of several Special Interest Group (SIG) meetings occurring in conjunction with the 16th annual Intelligent Systems for Molecular Biology Conference (ISMB 2008).

The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. Many Open Source bioinformatics packages are widely used by the research community across many application areas and form a cornerstone in enabling research in the genomic and post-genomic era. Open source bioinformatics software has facilitated rapid innovation and dissemination of new computational methods as well as informatics infrastructure. Since the work of the Open Source Bioinformatics Community represents some of the most cutting edge of Bioinformatics in general, the overall theme for the conference this year is "Tackling Hard Problems with Emerging Technologies". Topics under this umbrella include cyberinfrastructure, grid computing and workflow management and discovery, and visualization. We will also have a s!
eries of update talks about the main Open Source Bioinformatics Software suites.

One of the hallmarks of BOSC is the coming together of the open source developer community in one location. A face-to-face meeting of this community creates synergy where participants can work together to create use cases, prototype working code, or run bootcamps for developers from other projects as short, informal, and hands-on tutorials in new software packages and emerging technologies. In short, BOSC is not just a conference for presentations of completed work, but is a dynamic meeting where collaborative work gets done.

This year, BOSC is accepting abstract submissions on the conference theme "Tackling Hard Problems with Emerging Technologies". The conference theme reflects that there are new technologies emerging on both the scientific front (new sequencing technologies, etc.) and the IT front (workflows, mashup/web 2.0, improvements in all of the major programming languages, etc.), which may allow the open source community to solve problems that were previously intractable. Abstracts may be submitted for the following topics.

1. Cyberinfrastructure - We are interested in presentations on topics dealing with the development of infrastructure on the web to facilitate software and data re-use (mashups, or traditional), interoperability and inter-process communication, system/service discovery, and data movement and modeling in distributed systems. This may include peer-to-peer systems of data transfer, Web Services, various flavors of data representation (SOAP, JSON, XML, others), and technologies commonly referred to under the Web 2.0 paradigm (e.g. folksonomies/tagging, user-based content generation, content feeds, and Social Networking).

2. Grid Computing and Workflow Management and Discovery - We particularly invite talks that report progress in making workflow systems easier to use and on how to do distributed-collaborative research , e.g. workflows that encompass the coordination of systems running in different parts of the world.

3. Visualization - Visualization is a maturing area of open source software development. We particularly invite talks that demonstrate innovative visualization systems in the context of workflows.

4. Open Source Software - Speakers will present talks on the use, development, or philosophy of open source software in bioinformatics.

5. Bio* Open Source Project Updates - We invite abstracts from the representatives of the open source projects sponsored by or affiliated to the O|B|F (see Projects).

Please consult the official BOSC 2008 website at http://www.open-bio.org/wiki/Upcoming_BOSC_conference for all updates and extra information.

Submission Process:
All abstracts must be submitted through our Open Conference Systems site (http://events.open-bio.org/BOSC2008/openconf.php).
The form will ask for a small Abstract Text to be pasted into it, and a full paper. The small Abstract text should be a summary, while the longer abstract (should provide more details, including the open-source license requirement details)
Full-length abstracts are limited to one page with one inch (2.5 cm) margins on the top, sides, and bottom. The full-length abstract should include the title, authors, and affiliations. We prefer your abstract to be in PDF format, although plain t

Important Dates:
May 11: Abstract submission deadline.
June 2: Notification of accepted talks.
June 4: Early registration discount cut-off.
July 18-19: BOSC 2008!

We hope to see you at BOSC 2008!

Kam Dahlquist and Darin London
BOSC 2008 Co-organizers

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BOSC 2007 Abstract Submission Deadline Extended

2007-05-14T08:44:56Z

Due to technical difficulties in sending out the 2nd call for papers, the BOSC organizers are extending the deadline for abstract submissions to Monday May 21st. The announcement day will remain the same so that it remains before the Early Discount Date.

http://open-bio.org/wiki/BOSC_2007

The BOSC organizing Committee

Please pass this email on to anyone that would be interested.

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BOSC 2007 Second Call For Papers

2007-05-10T10:17:38Z

The BOSC Organizing Committee are proud to announce BOSC 2007, occurring
in Vienna, Austria on July 19th, 20th. The conference this year
promises to be exciting, as the BOSC developers attempt to define and
solve currently intractable problems in Bioinformatics. Please refer to
the following website for complete information, and requests for
submissions. Thank you, and we hope to see you in Vienna.

http://open-bio.org/wiki/BOSC_2007

The BOSC organizing Committee

Please pass this email on to anyone that would be interested.

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Re: [Bioperl-l] BioPerl leadership additions

2007-03-03T11:15:43Z

Hear hear!

Lincoln

On 2/27/07, Steve Chervitz <sac@...> wrote:

>
> Welcome to the club, Chris & Sendu. Always good to have an infusion of new
> blood and capable, motivated hands.
>
> Steve
>
> On 2/26/07, Jason Stajich <jason@...> wrote:
> >
> > Dear BioPerl Users and Developers,
> >
> > I want to announce a addition in the leadership of BioPerl.
> > Christopher Fields and and Sendu Bala are now members of the BioPerl
> > Core developer group to recognize their ongoing leadership in the
> > project. Chris and Sendu were instrumental in the 1.5.2 Developer
> > release and have made a significant commitment and contribution to
> > the quality of the code and the documentation of the project. We
> > have invited them to be part of the core to recognize their work and
> > to feel comfortable to ask them to do more. ;-)
> >
> > The Core group was established to insure that someone was responsible
> > for making code releases, vetting new developers for CVS write
> > accounts, and generally dealing with things that might otherwise slip
> > through the cracks. We are very excited to have more people
> > contributing to and maintaining the toolkit. We look forward to
> > their help along with all the other developers, as we work towards a
> > 1.6 release release this year.
> >
> > As always, while their is a need for some individuals to lead the
> > project, we encourage contributions from all levels of expertise to
> > improve the code, documentation, and tutorials of the project.
> >
> > We plan to discuss the progress of the toolkit at this year's
> > Bioinformatics Open Source Conference held in Vienna, Austria in
> > conjunction with the SIG meetings at ISMB. We are trying to use
> > BOSC 2007 as a chance for the developers of Open Bioinformatics
> > Foundation sponsored and related projects to coordinate future
> > development and release cycles.
> >
> > Jason Stajich on behalf of the Core developers
> >
> > _______________________________________________
> > Bioperl-announce-l mailing list
> > Bioperl-announce-l@...
> > http://lists.open-bio.org/mailman/listinfo/bioperl-announce-l
> >
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

--
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
FOR URGENT MESSAGES & SCHEDULING,
PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT michelse@...
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Re: [Bioperl-l] BioPerl leadership additions

2007-03-01T13:10:52Z

Hear hear!

Lincoln

On 2/27/07, Steve Chervitz <sac@...> wrote:

Re: [Bioperl-l] BioPerl leadership additions

2007-03-01T08:30:59Z

Welcome to the club, Chris & Sendu. Always good to have an infusion of new
blood and capable, motivated hands.

Steve

On 2/26/07, Jason Stajich <jason@...> wrote:

>
> Dear BioPerl Users and Developers,
>
> I want to announce a addition in the leadership of BioPerl.
> Christopher Fields and and Sendu Bala are now members of the BioPerl
> Core developer group to recognize their ongoing leadership in the
> project. Chris and Sendu were instrumental in the 1.5.2 Developer
> release and have made a significant commitment and contribution to
> the quality of the code and the documentation of the project. We
> have invited them to be part of the core to recognize their work and
> to feel comfortable to ask them to do more. ;-)
>
> The Core group was established to insure that someone was responsible
> for making code releases, vetting new developers for CVS write
> accounts, and generally dealing with things that might otherwise slip
> through the cracks. We are very excited to have more people
> contributing to and maintaining the toolkit. We look forward to
> their help along with all the other developers, as we work towards a
> 1.6 release release this year.
>
> As always, while their is a need for some individuals to lead the
> project, we encourage contributions from all levels of expertise to
> improve the code, documentation, and tutorials of the project.
>
> We plan to discuss the progress of the toolkit at this year's
> Bioinformatics Open Source Conference held in Vienna, Austria in
> conjunction with the SIG meetings at ISMB. We are trying to use
> BOSC 2007 as a chance for the developers of Open Bioinformatics
> Foundation sponsored and related projects to coordinate future
> development and release cycles.
>
> Jason Stajich on behalf of the Core developers
>
> _______________________________________________
> Bioperl-announce-l mailing list
> Bioperl-announce-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-announce-l
>

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Re: [Bioperl-l] BioPerl leadership additions

2007-03-01T08:30:59Z

Congrats Chris & Sendu! Very well-deserved. Keep up the great work.

Cheers!
Mauricio.

Jason Stajich wrote:

> Dear BioPerl Users and Developers,
>
> I want to announce a addition in the leadership of BioPerl.
> Christopher Fields and and Sendu Bala are now members of the BioPerl
> Core developer group to recognize their ongoing leadership in the
> project. Chris and Sendu were instrumental in the 1.5.2 Developer
> release and have made a significant commitment and contribution to
> the quality of the code and the documentation of the project. We
> have invited them to be part of the core to recognize their work and
> to feel comfortable to ask them to do more. ;-)
>
> The Core group was established to insure that someone was responsible
> for making code releases, vetting new developers for CVS write
> accounts, and generally dealing with things that might otherwise slip
> through the cracks. We are very excited to have more people
> contributing to and maintaining the toolkit. We look forward to
> their help along with all the other developers, as we work towards a
> 1.6 release release this year.
>
> As always, while their is a need for some individuals to lead the
> project, we encourage contributions from all levels of expertise to
> improve the code, documentation, and tutorials of the project.
>
> We plan to discuss the progress of the toolkit at this year's
> Bioinformatics Open Source Conference held in Vienna, Austria in
> conjunction with the SIG meetings at ISMB. We are trying to use
> BOSC 2007 as a chance for the developers of Open Bioinformatics
> Foundation sponsored and related projects to coordinate future
> development and release cycles.
>
> Jason Stajich on behalf of the Core developers
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

--
MAURICIO HERRERA CUADRA
arareko@...
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM

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Re: BioPerl leadership additions

2007-02-27T09:59:22Z

Welcome to the club, Chris & Sendu. Always good to have an infusion of new
blood and capable, motivated hands.

Steve

On 2/26/07, Jason Stajich <jason@...> wrote:

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Re: [Bioperl-l] BioPerl leadership additions

2007-02-26T13:44:49Z

Congrats Chris & Sendu! Very well-deserved. Keep up the great work.

Cheers!
Mauricio.

Jason Stajich wrote:

BioPerl leadership additions

2007-02-26T11:13:00Z

Dear BioPerl Users and Developers,

I want to announce a addition in the leadership of BioPerl.
Christopher Fields and and Sendu Bala are now members of the BioPerl
Core developer group to recognize their ongoing leadership in the
project. Chris and Sendu were instrumental in the 1.5.2 Developer
release and have made a significant commitment and contribution to
the quality of the code and the documentation of the project. We
have invited them to be part of the core to recognize their work and
to feel comfortable to ask them to do more. ;-)

The Core group was established to insure that someone was responsible
for making code releases, vetting new developers for CVS write
accounts, and generally dealing with things that might otherwise slip
through the cracks. We are very excited to have more people
contributing to and maintaining the toolkit. We look forward to
their help along with all the other developers, as we work towards a
1.6 release release this year.

As always, while their is a need for some individuals to lead the
project, we encourage contributions from all levels of expertise to
improve the code, documentation, and tutorials of the project.

We plan to discuss the progress of the toolkit at this year's
Bioinformatics Open Source Conference held in Vienna, Austria in
conjunction with the SIG meetings at ISMB. We are trying to use
BOSC 2007 as a chance for the developers of Open Bioinformatics
Foundation sponsored and related projects to coordinate future
development and release cycles.

Jason Stajich on behalf of the Core developers

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Re: [Bioperl-l] Bioperl 1.5.2 Release

2006-12-07T15:15:53Z

This has been a great effort. Congrats and thanks to everyone involved!

Mauricio.

Sendu Bala wrote:

> I am proud to announce the final release of Bioperl 1.5.2.
>
> http://www.bioperl.org/wiki/Release_1.5.2
>
> bioperl (core):
> cpan>install S/SE/SENDU/bioperl-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-1.5.2_100.tar.bz2
> http://bioperl.org/DIST/bioperl-1.5.2_100.zip
>
> bioperl-run:
> cpan>install S/SE/SENDU/bioperl-run-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-run-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-run-1.5.2_100.tar.bz2
> http://bioperl.org/DIST/bioperl-run-1.5.2_100.zip
>
> bioperl-db:
> cpan>install S/SE/SENDU/bioperl-db-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-db-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-db-1.5.2_100.tar.bz2
> http://bioperl.org/DIST/bioperl-db-1.5.2_100.zip
>
> bioperl-network:
> cpan>install S/SE/SENDU/bioperl-network-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-network-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-network-1.5.2_100.tar.bz2
> http://bioperl.org/DIST/bioperl-network-1.5.2_100.zip
>
> http://bioperl.org/DIST/SIGNATURES.md5
>
> (all are also available via CVS, and for Windows users, using the Perl
> Package Manager - see the wiki for details)
>
> The other bioperl packages (bioperl-ext, bioperl-gui, bioperl-pedigree
> and bioperl-pipeline) did not see a unified release for 1.5.2.
>
>
>
> This release represents a developer release which has been thoroughly
> tested. We consider it the most stable (in terms of bugs) version of
> Bioperl and believe it to be suitable for most people. It is marked
> 'developer' or even 'unstable' because its API may change on short
> notice. It will also not be maintained or supported beyond the next
> bioperl release.
>
> 1.5.2 introduces the following new (core) features:
>
> * Taxonomy (Bio::Species) overhaul
> * Bio::Map improvements
> * Bio::SearchIO speedup
> * Build.PL installation
>
> For details, and a complete change log, see the wiki.
>
> API documentation is available here: http://doc.bioperl.org/
>
>
> Acknowledgements:
> Enumerable thanks are due for the tireless efforts of Christopher Fields
> (bug fixing, testing, documentation, discussion), Nathan Haigh
> (Windows&pre-requisite issues, testing) and Mauricio Herrera Cuadra
> (testing, documentation, support). Feedback and ideas provided by Hilmar
> Lapp, Jason Stajich, Torsten Seemann and others on the mailing list and
> elsewhere proved invaluable. None of this would have been possible
> without the behind-the-scenes work of the open-bio support team. I'd
> also like to acknowledge Andreas J. Koenig for his help with CPAN matters.
>
> Finally, thank you to everyone who tried out the release candidates, and
> especially those that took the time to file bug reports or report problems.
>
>
> Remember, Bioperl can only go from strength to strength with /your/
> help. If you'd like to experience the fame and fortune that naturally
> follow becoming a Bioperl developer (?!), become one!
> http://www.bioperl.org/wiki/Becoming_a_developer
>
> On behalf of the Bioperl team,
> Sendu Bala.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

Re: [Bioperl-l] Bioperl 1.5.2 Release

2006-12-07T15:00:43Z

Great job Sendu!

A bit of icing on the cake: all the WinXP PPMs (core, db, network, run)
installed w/o a hitch following normal instructions using PPM4 (GUI and
command line shell) using clean ActiveState installations. Looks like all
the correct prereqs were installed with shell (only XML::SAX::ExpatXS was
left out in the GUI installation for reasons outlined before).

I'll run more tests tomorrow to see if tests pass with the installed bioperl
(this should catch any prereq issues with PPM installation we missed).

chris

> I am proud to announce the final release of Bioperl 1.5.2.
>
> http://www.bioperl.org/wiki/Release_1.5.2
>
> bioperl (core):
> cpan>install S/SE/SENDU/bioperl-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-1.5.2_100.tar.bz2
> http://bioperl.org/DIST/bioperl-1.5.2_100.zip
>
> bioperl-run:
> cpan>install S/SE/SENDU/bioperl-run-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-run-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-run-1.5.2_100.tar.bz2
> http://bioperl.org/DIST/bioperl-run-1.5.2_100.zip
>
> bioperl-db:
> cpan>install S/SE/SENDU/bioperl-db-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-db-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-db-1.5.2_100.tar.bz2
> http://bioperl.org/DIST/bioperl-db-1.5.2_100.zip
>
> bioperl-network:
> cpan>install S/SE/SENDU/bioperl-network-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-network-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-network-1.5.2_100.tar.bz2
> http://bioperl.org/DIST/bioperl-network-1.5.2_100.zip
>
> http://bioperl.org/DIST/SIGNATURES.md5
>
> (all are also available via CVS, and for Windows users, using
> the Perl Package Manager - see the wiki for details)
>
> The other bioperl packages (bioperl-ext, bioperl-gui,
> bioperl-pedigree and bioperl-pipeline) did not see a unified
> release for 1.5.2.
>
>
>
> This release represents a developer release which has been thoroughly
> tested. We consider it the most stable (in terms of bugs) version of
> Bioperl and believe it to be suitable for most people. It is marked
> 'developer' or even 'unstable' because its API may change on short
> notice. It will also not be maintained or supported beyond the next
> bioperl release.
>
> 1.5.2 introduces the following new (core) features:
>
> * Taxonomy (Bio::Species) overhaul
> * Bio::Map improvements
> * Bio::SearchIO speedup
> * Build.PL installation
>
> For details, and a complete change log, see the wiki.
>
> API documentation is available here: http://doc.bioperl.org/
>
>
> Acknowledgements:
> Enumerable thanks are due for the tireless efforts of
> Christopher Fields
> (bug fixing, testing, documentation, discussion), Nathan Haigh
> (Windows&pre-requisite issues, testing) and Mauricio Herrera Cuadra
> (testing, documentation, support). Feedback and ideas
> provided by Hilmar
> Lapp, Jason Stajich, Torsten Seemann and others on the
> mailing list and
> elsewhere proved invaluable. None of this would have been possible
> without the behind-the-scenes work of the open-bio support team. I'd
> also like to acknowledge Andreas J. Koenig for his help with
> CPAN matters.
>
> Finally, thank you to everyone who tried out the release
> candidates, and
> especially those that took the time to file bug reports or
> report problems.
>
>
> Remember, Bioperl can only go from strength to strength with /your/
> help. If you'd like to experience the fame and fortune that naturally
> follow becoming a Bioperl developer (?!), become one!
> http://www.bioperl.org/wiki/Becoming_a_developer
>
> On behalf of the Bioperl team,
> Sendu Bala.

[Bioperl-l] Bioperl 1.5.2 Release

2006-12-07T14:45:32Z

I am proud to announce the final release of Bioperl 1.5.2.

http://www.bioperl.org/wiki/Release_1.5.2

bioperl (core):
cpan>install S/SE/SENDU/bioperl-1.5.2_100.tar.gz
http://bioperl.org/DIST/bioperl-1.5.2_100.tar.gz
http://bioperl.org/DIST/bioperl-1.5.2_100.tar.bz2
http://bioperl.org/DIST/bioperl-1.5.2_100.zip

bioperl-run:
cpan>install S/SE/SENDU/bioperl-run-1.5.2_100.tar.gz
http://bioperl.org/DIST/bioperl-run-1.5.2_100.tar.gz
http://bioperl.org/DIST/bioperl-run-1.5.2_100.tar.bz2
http://bioperl.org/DIST/bioperl-run-1.5.2_100.zip

bioperl-db:
cpan>install S/SE/SENDU/bioperl-db-1.5.2_100.tar.gz
http://bioperl.org/DIST/bioperl-db-1.5.2_100.tar.gz
http://bioperl.org/DIST/bioperl-db-1.5.2_100.tar.bz2
http://bioperl.org/DIST/bioperl-db-1.5.2_100.zip

bioperl-network:
cpan>install S/SE/SENDU/bioperl-network-1.5.2_100.tar.gz
http://bioperl.org/DIST/bioperl-network-1.5.2_100.tar.gz
http://bioperl.org/DIST/bioperl-network-1.5.2_100.tar.bz2
http://bioperl.org/DIST/bioperl-network-1.5.2_100.zip

http://bioperl.org/DIST/SIGNATURES.md5

(all are also available via CVS, and for Windows users, using the Perl
Package Manager - see the wiki for details)

The other bioperl packages (bioperl-ext, bioperl-gui, bioperl-pedigree
and bioperl-pipeline) did not see a unified release for 1.5.2.

This release represents a developer release which has been thoroughly
tested. We consider it the most stable (in terms of bugs) version of
Bioperl and believe it to be suitable for most people. It is marked
'developer' or even 'unstable' because its API may change on short
notice. It will also not be maintained or supported beyond the next
bioperl release.

1.5.2 introduces the following new (core) features:

* Taxonomy (Bio::Species) overhaul
* Bio::Map improvements
* Bio::SearchIO speedup
* Build.PL installation

For details, and a complete change log, see the wiki.

API documentation is available here: http://doc.bioperl.org/

Acknowledgements:
Enumerable thanks are due for the tireless efforts of Christopher Fields
(bug fixing, testing, documentation, discussion), Nathan Haigh
(Windows&pre-requisite issues, testing) and Mauricio Herrera Cuadra
(testing, documentation, support). Feedback and ideas provided by Hilmar
Lapp, Jason Stajich, Torsten Seemann and others on the mailing list and
elsewhere proved invaluable. None of this would have been possible
without the behind-the-scenes work of the open-bio support team. I'd
also like to acknowledge Andreas J. Koenig for his help with CPAN matters.

Finally, thank you to everyone who tried out the release candidates, and
especially those that took the time to file bug reports or report problems.

Remember, Bioperl can only go from strength to strength with /your/
help. If you'd like to experience the fame and fortune that naturally
follow becoming a Bioperl developer (?!), become one!
http://www.bioperl.org/wiki/Becoming_a_developer

On behalf of the Bioperl team,
Sendu Bala.
_______________________________________________
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Bioperl-announce-l@...
http://lists.open-bio.org/mailman/listinfo/bioperl-announce-l

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Re: [Bioperl-l] Bioperl 1.5.2 Release

2006-12-06T19:53:21Z

This has been a great effort. Congrats and thanks to everyone involved!

Mauricio.

Sendu Bala wrote:

Re: [Bioperl-l] Bioperl 1.5.2 Release

2006-12-06T18:30:44Z

> I am proud to announce the final release of Bioperl 1.5.2.
>
> http://www.bioperl.org/wiki/Release_1.5.2
>
> bioperl (core):
> cpan>install S/SE/SENDU/bioperl-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-1.5.2_100.tar.bz2
> http://bioperl.org/DIST/bioperl-1.5.2_100.zip
>
> bioperl-run:
> cpan>install S/SE/SENDU/bioperl-run-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-run-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-run-1.5.2_100.tar.bz2
> http://bioperl.org/DIST/bioperl-run-1.5.2_100.zip
>
> bioperl-db:
> cpan>install S/SE/SENDU/bioperl-db-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-db-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-db-1.5.2_100.tar.bz2
> http://bioperl.org/DIST/bioperl-db-1.5.2_100.zip
>
> bioperl-network:
> cpan>install S/SE/SENDU/bioperl-network-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-network-1.5.2_100.tar.gz
> http://bioperl.org/DIST/bioperl-network-1.5.2_100.tar.bz2
> http://bioperl.org/DIST/bioperl-network-1.5.2_100.zip
>
> http://bioperl.org/DIST/SIGNATURES.md5
>
> (all are also available via CVS, and for Windows users, using
> the Perl Package Manager - see the wiki for details)
>
> The other bioperl packages (bioperl-ext, bioperl-gui,
> bioperl-pedigree and bioperl-pipeline) did not see a unified
> release for 1.5.2.
>
>
>
> This release represents a developer release which has been thoroughly
> tested. We consider it the most stable (in terms of bugs) version of
> Bioperl and believe it to be suitable for most people. It is marked
> 'developer' or even 'unstable' because its API may change on short
> notice. It will also not be maintained or supported beyond the next
> bioperl release.
>
> 1.5.2 introduces the following new (core) features:
>
> * Taxonomy (Bio::Species) overhaul
> * Bio::Map improvements
> * Bio::SearchIO speedup
> * Build.PL installation
>
> For details, and a complete change log, see the wiki.
>
> API documentation is available here: http://doc.bioperl.org/
>
>
> Acknowledgements:
> Enumerable thanks are due for the tireless efforts of
> Christopher Fields
> (bug fixing, testing, documentation, discussion), Nathan Haigh
> (Windows&pre-requisite issues, testing) and Mauricio Herrera Cuadra
> (testing, documentation, support). Feedback and ideas
> provided by Hilmar
> Lapp, Jason Stajich, Torsten Seemann and others on the
> mailing list and
> elsewhere proved invaluable. None of this would have been possible
> without the behind-the-scenes work of the open-bio support team. I'd
> also like to acknowledge Andreas J. Koenig for his help with
> CPAN matters.
>
> Finally, thank you to everyone who tried out the release
> candidates, and
> especially those that took the time to file bug reports or
> report problems.
>
>
> Remember, Bioperl can only go from strength to strength with /your/
> help. If you'd like to experience the fame and fortune that naturally
> follow becoming a Bioperl developer (?!), become one!
> http://www.bioperl.org/wiki/Becoming_a_developer
>
> On behalf of the Bioperl team,
> Sendu Bala.

_______________________________________________
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Bioperl-announce-l@...
http://lists.open-bio.org/mailman/listinfo/bioperl-announce-l

Bioperl 1.5.2 Release

2006-12-06T14:39:49Z

Call For Birds of a Feather Suggestions

2006-07-03T06:41:33Z

The BOSC organizing comittee is currently seeking suggestions for Birds
of a Feather meeting ideas. Birds of a Feather meetings are one of the
more popular activities at BOSC, occurring at the end of each days
session. These are free-form meetings organized by the attendees
themselves to discuss one or a few topics of interest in greater detail.
BOF’s have been formed to allow developers and users of individual OBF
software to meet each other face-to-face to discuss the project, or to
discuss completely new ideas, and even start new software development
projects. These meetings offer a unique opportunity for individuals to
explore more about the activities of the various Open Source Projects,
and, in some cases, even take an active role influencing the future of
Open Source Software development. If you would like to create a BOF,
just sign up for a wiki account, login, and edit the <a
href="http://www.open-bio.org/wiki/BOSC_2006/Birds-of-a-Feather">BOSC
2006 Birds of a Feather page</a>.
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[Bioperl-l] BOSC 2006 2nd Call for Papers

2006-05-22T10:00:55Z

2nd CALL FOR SPEAKERS

This is the second and last official call for speakers to submit their
abstracts to speak at BOSC 2006
in Fortaleza, Brasil. In order to be considered as a potential speaker,
an abstract must be recieved by
Monday, June 5th, 2006. We look forward to a great conference this
year. Please consult
The Official BOSC 2006 Website at:

http://www.open-bio.org/wiki/BOSC_2006

for more details and information.

In addition, a BOSC weblog has been setup to make it easier to
desiminate all BOSC
related announcements:

http://wiki.open-bio.org/boscblog/

And if you have an ICAL compatible Calendar, there is an EventDB
calendar set up with all
BOSC related deadlines.

http://eventful.com/groups/G0-001-000014747-0

More information about ISMB can be found at the Official ISMB 2006 Website:

http://ismb2006.cbi.cnptia.embrapa.br/

Thank You, and we look forward to seeing you all,

The BOSC Organizing Committee.

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BOSC 2006 2nd Call for Papers

2006-05-22T09:29:45Z

Announcing BOSC 2006

2006-03-28T06:42:45Z

MEETING ANNOUNCEMENT & CALL FOR SPEAKERS

The 7th annual Bioinformatics Open Source Conference (BOSC 2006) is
organized by the
not-for-profit Open Bioinformatics Foundation. The meeting will take place
Aug 4,5th in Fortaleza, Brasil, and is one of several Special Interest
Group (SIG) meetings occurring in conjunction with the 14th
International Conference
on Intelligent Systems for Molecular Biology. Please consult The Official
BOSC 2006 Website at

http://www.open-bio.org/wiki/BOSC_2006

for details and information.

In addition, a BOSC weblog has been setup to make it easier to
desiminate all BOSC
related announcements:

http://wiki.open-bio.org/boscblog/

And if you have an ICAL compatible Calendar, there is an EventDB calendar
set up with all BOSC related deadlines.

http://eventful.com/groups/G0-001-000014747-0

More information about ISMB can be found at the Official
ISMB 2006 Website:

http://ismb2006.cbi.cnptia.embrapa.br/

Thank You, and we look forward to seeing you all,
The BOSC Organizing Committee.
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Bio-ext module

2006-03-09T08:28:17Z

hello there, just getting used to Bioperl now, i wanted to use dpalign in one of my scripts, and was asked to install the bio-ext package. so i got it downloaded, used ppm, read the read-me file, done everything, just doesnt work ! ! if someone could please give me a step by step instruction on how to get this thing on i would be grateful ! im using windows, ive got bioperl already properly installed and working, its just this module which is not working ! please help ! thnks anir

positions at Berkeley

2006-02-16T20:46:40Z

Hello all,

We (Berkeley, Chris Mungall, Suzi Lewis, GO, NCBO, and all) are looking
for help. I apologize for the bullhorn approach, but I wanted to get
the word out there. There are both post-doc and staff positions open,
and all of our work revolves around biology, ontologies, and their
intersection. We'd really appreciate it, if you would contact us if you
are interested, or pass the word along if you know someone else who
might be interested.

The official positions are listed here, but please feel free to contact
us directly to learn more.

Have fun, Suzi

http://jobs.lbl.gov/LBNLCareers/details.asp?jid=18728&p=3
http://jobs.lbl.gov/LBNLCareers/details.asp?jid=18726&p=3

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new website launched

2006-01-24T19:31:38Z

I am pleased to announce the release of a new website for BioPerl.
The site is based on the mediawiki software that was developed for
the wikipedia project. We intend the site to be a place for
community input on documentation and design for the BioPerl project.
There is also a fair amount of documentation started surrounding
bioinformatics tools and techniques applicable to using BioPerl and
some of the authors who created these resources.

The website continues to be at the URL http://www.bioperl.org. The
DNS updates may take up to 24 hours to reach everyone.

The initial content of the site is result of the work of myself,
Mauricio Herrera Cuadra, Brian Osborne, and Torsten Seemann. We
encourage you to contribute to the site's content by signing up for
an account.

There are several guides for style of the site and how to link to
Modules for example which can contain additional information from the
POD
http://bioperl.org/wiki/Module:Bio::SeqIO

You'll notice that many of the paths have changed but the DIST and
SRC continues to be available at http://bioperl.org/DIST and http://
bioperl.org/SRC. The HOWTOs are now available from http://
bioperl.org/wiki/HOWTOs

The FAQ is available at http://bioperl.org/wiki/FAQ and I encourage
you to add your questions to it so they can be properly archived and
addressed.

We also have initiated a News site for Bioperl for posting
announcements regarding development and software. I would like to
see if there are volunteers to post weekly or monthly summaries of
mailing list traffic and development.
http://www.bioperl.org/news/

Jason Stajich on behalf of Mauricio Herrera Cuadra, Brian Osborne,
Torsten Seemann.

--
Jason Stajich
Duke University
http://www.duke.edu/~jes12

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new mailing list server

2006-01-24T13:44:34Z

Chris Dagdigian has switched our mailing lists over to a new server
to upgrade us to newer hardware. In the switch the default mailing
list the server name is 'lists.open-bio.org' instead of 'portal.open-
bio.org'. That should be the only change you should notice at the
bottom of your mails. All mail should get delivered to any of those
addresses (although @bioperl.org is preferred).

We hope this changeover will help improve the performance and
scalability of our mail and webservices.

We also will aim to move the developer read-write CVS server to a new
machine in the coming weeks. We hope this will only be a minor
inconvenience but will allow us to move to a more recent operating
system and larger disk space.

If you have questions or concerns they can be directed to support AT
open-bio.org
-jason
--
Jason Stajich
Duke University
http://www.duke.edu/~jes12

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[Bioperl-l] parse Blast Output and Composition Based Statistics parameter

2006-01-12T15:57:16Z

Hello,
I want to know, if there is a possibility to get from a Blast Outputfile
the whole Sequence of a protein not only the best local alignment...
for example:

>ref|XP_480077.1| hypothetical protein [Oryza sativa (japonica
cultivar-group)]
dbj|BAD33542.1| hypothetical protein [Oryza sativa (japonica
cultivar-group)]
Length=95

Score = 24.1 bits (47), Expect = 493
Identities = 6/7 (85%), Positives = 7/7 (100%), Gaps = 0/7 (0%)

Query 2 KKRRRWW 8
K+RRRWW
Sbjct 87 KRRRRWW 93

and now, if I parse the file, I want to get the whole Sequence of this
hypothetical protein....is that possible with hsp for example, or any
other way....

my second question is:
I do my blast search with bioperl and the remoteblast module.....each
parameter is working very well, except the composition based statistics
parameter....
it looks like that:

my $factory =
$Bio::Tools::Run::RemoteBlast::HEADER{'COMPOSITION_BASED_STATISTICS'} =
'yes';

it should work like that, but it doesn't....

Thanks for your help in advance......

regards
Hubert
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[Bioperl-l] remoteblast

2006-01-12T15:48:30Z

Hi,
I have encountered an error, while my remoteblast file was running...
I have used that file since two weeks, and all of a sudden, I got the
following message error:

-------------------- WARNING ---------------------
MSG: req was POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
User-Agent: bioperl-Bio_Tools_Run_RemoteBlast/1.5
Content-Length: 210
Content-Type: application/x-www-form-urlencoded

GAPCOSTS=9+1&DATABASE=nr&QUERY=%3E+%0AKWRRWKRR&COMPOSITION_BASED_STATISTICS=off&EXPECT=20000&WORD_SIZE=2&SERVICE=plain&FORMAT_OBJECT=Alignment&CMD=Put&MATRIX_NAME=PAM30&FILTER=L&DESCRIPTIONS=1000&PROGRAM=blastp

<HTML>
<HEAD><TITLE>An Error Occurred</TITLE></HEAD>
<BODY>
<H1>An Error Occurred</H1>
302 Found
</BODY>
</HTML>

---------------------------------------------------

I hope somebody can help....thanks in advance

regards
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remoteblast cannot set the Gap Cost Parameter

2005-12-05T13:46:04Z

Hi,
I'm trying to search the database via bioperl and the remoteblast
module, everything is working fine, except
I don't know how to set the Gap Opening and the Gap Extend Parameter.

Thanks for help in Advance

regards
Hubert
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