From p.j.a.cock at googlemail.com  Fri Aug  7 16:43:02 2009
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 7 Aug 2009 21:43:02 +0100
Subject: [Biopython-announce] ANN: Python for Bioinformatics book
In-Reply-To: <b43bf2080908071115h7acee494qa302a2db93a255ba@mail.gmail.com>
References: <b43bf2080908071115h7acee494qa302a2db93a255ba@mail.gmail.com>
Message-ID: <320fb6e00908071343i46e7268qb6bbe1e79db36346@mail.gmail.com>

Hi all,

Congratulations to Sebastian on his new book's release!
See below...

Peter

---------- Forwarded message ----------
From: Sebastian Bassi <sbassi at gmail.com>
Date: Fri, Aug 7, 2009 at 7:15 PM
Subject: [Biopython] ANN: Python for Bioinformatics book
To: Biopython List <biopython at lists.open-bio.org>


Just want to announce the availability of the book "Python for
Bioinformatics". It has a Biopython chapter and I made it thanks to
lot of people of this list (and biopython-dev) who help me since I
began programming Python about 7 years ago.

Here is the official announce:

"Python for Bioinformatics"
ISBN 1584889292
Amazon: http://www.tinyurl.com/biopython
Publisher: http://www.crcpress.com/product/isbn/9781584889298

This book introduces programming concepts to life science researchers,
bioinformaticians, support staff, students, and everyone who is
interested in applying programming to solve biologically-related
problems. Python is the chosen programming language for this task
because it is both powerful and easy-to-use.

It begins with the basic aspects of the language (like data types and
control structures) up to essential skills on today's bioinformatics
tasks like building web applications, using relational database
management systems, XML and version control. There is a chapter
devoted to Biopython (www.biopython.org) since it can be used for most
of the tasks related to bioinformatics data processing.

There is a section with applications with source code, featuring
sequence manipulation, filtering vector contamination, calculating DNA
melting temperature, parsing a genbank file, inferring splicing sites,
and more.

There are questions at the end of every chapter and odd numbered
questiona are answered in an appendix making this text suitable for
classroom use.

This book can be used also as a reference material as it includes
Richard Gruet's Python Quick Reference, and the Python Style Guide.

DVD: The included DVD features a virtual machine with a special
edition of DNALinux, with all the programs and complementary files
required to run the scripts commented in the book. All scripts can be
tweaked to fit a particular configuration. By using a pre-configured
virtual machine the reader has access to the same development
environment than the author, so he can focus on learning Python. All
code is also available at the http://py3.us/## where ## is the code
number, for example: http://py3.us/57

I've been working on this book for more than two years testing the
examples under different setups and working to make the code
compatible for most versions of Python, Biopython and operating
systems. Where there is code that only works with a particular
dependency, this is clearly noted.

Finally, I want to highlight that non-bioinformaticians out there can
use this book as an introduction to bioinformatics by starting with
the included "Diving into the Gene Pool with BioPython" (by Zachary
Voase and published originally in Python Magazine).
_______________________________________________
Biopython mailing list ?- ?Biopython at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biopython


From chapmanb at 50mail.com  Mon Aug 17 08:11:56 2009
From: chapmanb at 50mail.com (Brad Chapman)
Date: Mon, 17 Aug 2009 08:11:56 -0400
Subject: [Biopython-announce] Biopython 1.51 released
Message-ID: <20090817121156.GC12768@sobchak.mgh.harvard.edu>

Biopythonistas;
We're pleased to announce the release of Biopython 1.51. This new stable
release enhances version 1.50 (released in April) by extending the
functionality of existing modules, adding a set of application
wrappers for popular alignment programs and fixing a number of minor
bugs. Sources and Windows Installer are available from the 
downloads page:

http://biopython.org/wiki/Download

In particular, the SeqIO module can now write Genbank files that
include features, and deal with FASTQ files created by Illumina
1.3+. Support for this format allows interconversion between FASTQ
files using Solexa, Sanger and Ilumina variants using conventions
agreed upon with the BioPerl and EMBOSS projects.

Biopython 1.51 is the first stable release to include the
Align.Applications module which allows users to define command line
wrappers for popular alignment programs including ClustalW, Muscle
and T-Coffee.

Bio.Fasta and the application tools ApplicationResult and
generic_run() have been marked as deprecated - Bio.Fasta has been
superseded by SeqIO's support for the Fasta format and we provide
ducumentation for using the subprocess module from the Python
Standard Library as a more flexible approach to calling 
applications.

As always, the Tutorial and Cookbook has been updated to document all
the changes:

http://biopython.org/wiki/Documentation

Thank you to everyone who tested our 1.51 beta or submitted bugs
since out last stable release and to all our contributors.

Brad

From p.j.a.cock at googlemail.com  Fri Aug  7 20:43:02 2009
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 7 Aug 2009 21:43:02 +0100
Subject: [Biopython-announce] ANN: Python for Bioinformatics book
In-Reply-To: <b43bf2080908071115h7acee494qa302a2db93a255ba@mail.gmail.com>
References: <b43bf2080908071115h7acee494qa302a2db93a255ba@mail.gmail.com>
Message-ID: <320fb6e00908071343i46e7268qb6bbe1e79db36346@mail.gmail.com>

Hi all,

Congratulations to Sebastian on his new book's release!
See below...

Peter

---------- Forwarded message ----------
From: Sebastian Bassi <sbassi at gmail.com>
Date: Fri, Aug 7, 2009 at 7:15 PM
Subject: [Biopython] ANN: Python for Bioinformatics book
To: Biopython List <biopython at lists.open-bio.org>


Just want to announce the availability of the book "Python for
Bioinformatics". It has a Biopython chapter and I made it thanks to
lot of people of this list (and biopython-dev) who help me since I
began programming Python about 7 years ago.

Here is the official announce:

"Python for Bioinformatics"
ISBN 1584889292
Amazon: http://www.tinyurl.com/biopython
Publisher: http://www.crcpress.com/product/isbn/9781584889298

This book introduces programming concepts to life science researchers,
bioinformaticians, support staff, students, and everyone who is
interested in applying programming to solve biologically-related
problems. Python is the chosen programming language for this task
because it is both powerful and easy-to-use.

It begins with the basic aspects of the language (like data types and
control structures) up to essential skills on today's bioinformatics
tasks like building web applications, using relational database
management systems, XML and version control. There is a chapter
devoted to Biopython (www.biopython.org) since it can be used for most
of the tasks related to bioinformatics data processing.

There is a section with applications with source code, featuring
sequence manipulation, filtering vector contamination, calculating DNA
melting temperature, parsing a genbank file, inferring splicing sites,
and more.

There are questions at the end of every chapter and odd numbered
questiona are answered in an appendix making this text suitable for
classroom use.

This book can be used also as a reference material as it includes
Richard Gruet's Python Quick Reference, and the Python Style Guide.

DVD: The included DVD features a virtual machine with a special
edition of DNALinux, with all the programs and complementary files
required to run the scripts commented in the book. All scripts can be
tweaked to fit a particular configuration. By using a pre-configured
virtual machine the reader has access to the same development
environment than the author, so he can focus on learning Python. All
code is also available at the http://py3.us/## where ## is the code
number, for example: http://py3.us/57

I've been working on this book for more than two years testing the
examples under different setups and working to make the code
compatible for most versions of Python, Biopython and operating
systems. Where there is code that only works with a particular
dependency, this is clearly noted.

Finally, I want to highlight that non-bioinformaticians out there can
use this book as an introduction to bioinformatics by starting with
the included "Diving into the Gene Pool with BioPython" (by Zachary
Voase and published originally in Python Magazine).
_______________________________________________
Biopython mailing list ?- ?Biopython at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biopython



From chapmanb at 50mail.com  Mon Aug 17 12:11:56 2009
From: chapmanb at 50mail.com (Brad Chapman)
Date: Mon, 17 Aug 2009 08:11:56 -0400
Subject: [Biopython-announce] Biopython 1.51 released
Message-ID: <20090817121156.GC12768@sobchak.mgh.harvard.edu>

Biopythonistas;
We're pleased to announce the release of Biopython 1.51. This new stable
release enhances version 1.50 (released in April) by extending the
functionality of existing modules, adding a set of application
wrappers for popular alignment programs and fixing a number of minor
bugs. Sources and Windows Installer are available from the 
downloads page:

http://biopython.org/wiki/Download

In particular, the SeqIO module can now write Genbank files that
include features, and deal with FASTQ files created by Illumina
1.3+. Support for this format allows interconversion between FASTQ
files using Solexa, Sanger and Ilumina variants using conventions
agreed upon with the BioPerl and EMBOSS projects.

Biopython 1.51 is the first stable release to include the
Align.Applications module which allows users to define command line
wrappers for popular alignment programs including ClustalW, Muscle
and T-Coffee.

Bio.Fasta and the application tools ApplicationResult and
generic_run() have been marked as deprecated - Bio.Fasta has been
superseded by SeqIO's support for the Fasta format and we provide
ducumentation for using the subprocess module from the Python
Standard Library as a more flexible approach to calling 
applications.

As always, the Tutorial and Cookbook has been updated to document all
the changes:

http://biopython.org/wiki/Documentation

Thank you to everyone who tested our 1.51 beta or submitted bugs
since out last stable release and to all our contributors.

Brad