From p.j.a.cock at googlemail.com  Fri Apr  2 13:41:02 2010
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 2 Apr 2010 18:41:02 +0100
Subject: [Biopython-announce] Biopython 1.54 beta released
In-Reply-To: <g2j320fb6e01004021040veb833ab0v40233622690271a7@mail.gmail.com>
References: <t2o320fb6e01004021034p44915b44w421d6e9a152b13e4@mail.gmail.com>
	<g2j320fb6e01004021040veb833ab0v40233622690271a7@mail.gmail.com>
Message-ID: <i2r320fb6e01004021041y1a654f76w9563c46422cfbd4f@mail.gmail.com>

Dear all,

A beta release for Biopython 1.54 is now available for download
and testing, as announced here:

http://news.open-bio.org/news/2010/04/biopython-1-54-beta-released/

Noted that I haven't done a fully detailed release announcement,
we'll leave that for the official release.

Source distributions and Windows installers are available from
the downloads page on the Biopython website.
http://biopython.org/wiki/Download

We are interested in getting feedback on the beta release as
a whole, but especially on the new features - including the
updated multiple sequence alignment object (which is what
you?ll now get when parsing alignments with Bio.AlignIO), the
new Bio.Phylo module, and the Bio.SeqIO support for Standard
Flowgram Format (SFF) files.

(At least) 10 people contributed to this release (so far), which
includes 4 new people:

Anne Pajon (first contribution)
Brad Chapman
Christian Zmasek
Eric Talevich
Jose Blanca (first contribution)
Kevin Jacobs (first contribution)
Leighton Pritchard
Michiel de Hoon
Peter Cock
Thomas Holder (first contribution)

On behalf of the Biopython team, thank you for any feedback,
bug reports, and contributions.

Peter

P.S.

You may wish to subscribe to our news feed. ?For RSS links etc, see:
http://biopython.org/wiki/News

Biopython news is also on twitter:
http://twitter.com/biopython


From p.j.a.cock at googlemail.com  Mon Apr 26 18:30:54 2010
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 26 Apr 2010 23:30:54 +0100
Subject: [Biopython-announce] Google Summer of Code - accepted students
In-Reply-To: <4BD60D63.1040400@cornell.edu>
References: <4BD60D63.1040400@cornell.edu>
Message-ID: <m2l320fb6e01004261530zd9f1a723ge8958362426bb7be@mail.gmail.com>

---------- Forwarded message ----------
From: Robert Buels <rmb32 at cornell.edu>
Date: Mon, Apr 26, 2010 at 11:02 PM
Subject: Google Summer of Code - accepted students
To: rmb32 at cornell.edu


Hi all,

I'm pleased to announce the acceptance of OBF's 2010 Google Summer of
Code students, listed in alphabetical order with their project titles
and primary mentors:

Mark Chapman (PM Andreas Prlic) - Improvements to BioJava including
Implementation of Multiple Sequence Alignment Algorithms

Jianjiong Gao (PM Peter Rose) - BioJava Packages for Identification,
Classification, and Visualization of Posttranslational Modification of
Proteins

Kazuhiro Hayashi (PM Naohisa Goto) - Ruby 1.9.2 support of BioRuby

Sara Rayburn (PM Christian Zmasek) - Implementing Speciation &
Duplication Inference Algorithm for Binary and Non-binary Species Tree

Joao Pedro Garcia Lopes Maia Rodrigues (PM Eric Talevich) - Extending
Bio.PDB: broadening the usefulness of BioPython's Structural Biology
module

Jun Yin (PM Chris Fields) - BioPerl Alignment Subsystem Refactoring

Congratulations to our accepted students!

All told, we had 52 applications submitted for the 6 slots (5
originally assigned, plus 1 extra) allotted to us by Google.
Proposals were extremely competitive: 6 out of 52 translates to an
11.5% acceptance rate. ?We received a lot of really excellent
proposals, the decisions were not easy.

Thanks very much to all the students who applied, we very much
appreciate your hard work.

Here's to a great 2010 Summer of Code, I'm sure these students will do
some wonderful work.

Rob Buels
OBF GSoC 2010 Administrator


From p.j.a.cock at googlemail.com  Fri Apr  2 17:41:02 2010
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 2 Apr 2010 18:41:02 +0100
Subject: [Biopython-announce] Biopython 1.54 beta released
In-Reply-To: <g2j320fb6e01004021040veb833ab0v40233622690271a7@mail.gmail.com>
References: <t2o320fb6e01004021034p44915b44w421d6e9a152b13e4@mail.gmail.com>
	<g2j320fb6e01004021040veb833ab0v40233622690271a7@mail.gmail.com>
Message-ID: <i2r320fb6e01004021041y1a654f76w9563c46422cfbd4f@mail.gmail.com>

Dear all,

A beta release for Biopython 1.54 is now available for download
and testing, as announced here:

http://news.open-bio.org/news/2010/04/biopython-1-54-beta-released/

Noted that I haven't done a fully detailed release announcement,
we'll leave that for the official release.

Source distributions and Windows installers are available from
the downloads page on the Biopython website.
http://biopython.org/wiki/Download

We are interested in getting feedback on the beta release as
a whole, but especially on the new features - including the
updated multiple sequence alignment object (which is what
you?ll now get when parsing alignments with Bio.AlignIO), the
new Bio.Phylo module, and the Bio.SeqIO support for Standard
Flowgram Format (SFF) files.

(At least) 10 people contributed to this release (so far), which
includes 4 new people:

Anne Pajon (first contribution)
Brad Chapman
Christian Zmasek
Eric Talevich
Jose Blanca (first contribution)
Kevin Jacobs (first contribution)
Leighton Pritchard
Michiel de Hoon
Peter Cock
Thomas Holder (first contribution)

On behalf of the Biopython team, thank you for any feedback,
bug reports, and contributions.

Peter

P.S.

You may wish to subscribe to our news feed. ?For RSS links etc, see:
http://biopython.org/wiki/News

Biopython news is also on twitter:
http://twitter.com/biopython



From p.j.a.cock at googlemail.com  Mon Apr 26 22:30:54 2010
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 26 Apr 2010 23:30:54 +0100
Subject: [Biopython-announce] Google Summer of Code - accepted students
In-Reply-To: <4BD60D63.1040400@cornell.edu>
References: <4BD60D63.1040400@cornell.edu>
Message-ID: <m2l320fb6e01004261530zd9f1a723ge8958362426bb7be@mail.gmail.com>

---------- Forwarded message ----------
From: Robert Buels <rmb32 at cornell.edu>
Date: Mon, Apr 26, 2010 at 11:02 PM
Subject: Google Summer of Code - accepted students
To: rmb32 at cornell.edu


Hi all,

I'm pleased to announce the acceptance of OBF's 2010 Google Summer of
Code students, listed in alphabetical order with their project titles
and primary mentors:

Mark Chapman (PM Andreas Prlic) - Improvements to BioJava including
Implementation of Multiple Sequence Alignment Algorithms

Jianjiong Gao (PM Peter Rose) - BioJava Packages for Identification,
Classification, and Visualization of Posttranslational Modification of
Proteins

Kazuhiro Hayashi (PM Naohisa Goto) - Ruby 1.9.2 support of BioRuby

Sara Rayburn (PM Christian Zmasek) - Implementing Speciation &
Duplication Inference Algorithm for Binary and Non-binary Species Tree

Joao Pedro Garcia Lopes Maia Rodrigues (PM Eric Talevich) - Extending
Bio.PDB: broadening the usefulness of BioPython's Structural Biology
module

Jun Yin (PM Chris Fields) - BioPerl Alignment Subsystem Refactoring

Congratulations to our accepted students!

All told, we had 52 applications submitted for the 6 slots (5
originally assigned, plus 1 extra) allotted to us by Google.
Proposals were extremely competitive: 6 out of 52 translates to an
11.5% acceptance rate. ?We received a lot of really excellent
proposals, the decisions were not easy.

Thanks very much to all the students who applied, we very much
appreciate your hard work.

Here's to a great 2010 Summer of Code, I'm sure these students will do
some wonderful work.

Rob Buels
OBF GSoC 2010 Administrator