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Peter Cock | 24 Apr 2013 21:19
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Biopython GSoC 2013 applications via NESCent

To all the Biopythoneers,

For the last few years Biopython has participated in the
Google Summer of Code (GSoC) program under the umbrella
of the Open Bioinformatics Foundation (OBF):
https://developers.google.com/open-source/soc/
https://github.com/OBF/GSoC

Unfortunately like quite a few previously accepted organisations,
this year the OBF not accepted. Google has kept the total about
the same year on year, so this is probably simply a slot rotation
to get some new organisations involved.

The good news (for those not following the Biopython-dev
mailing list) is we have an alternative option agreed with
the good people at NESCent, as we did back in 2009:

http://biopython.org/wiki/Google_Summer_of_Code
http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2013

I'd like to thank Eric for co-ordinating this, and encourage
any interested potential students to sign up to the Biopython
development list and NESCent's Google+ group as soon as
possible (if you haven't done so already):

http://lists.open-bio.org/mailman/listinfo/biopython-dev
https://plus.google.com/communities/105828320619238393015

Google are already accepting student applications, and the
deadline is Friday 3 May.  That doesn't leave very long for
(Continue reading)

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Peter Cock | 5 Feb 2013 23:05
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Biopython 1.61 released

Dear Biopythoneers,

Source distributions and Windows installers for Biopython 1.61 are now
available from the downloads page on the Biopython website and from
the Python Package Index (PyPI).

The updated Biopython Tutorial and Cookbook is online (PDF).

Platforms/Deployment:

We currently support Python 2.5, 2.6 and 2.7 and also test under
Python 3.1, 3.2 and 3.3 (including modules using NumPy), and Jython
2.5 and PyPy 1.9 (Jython and PyPy do not cover NumPy or our C
extensions). We are still encouraging early adopters to help test on
these platforms, and have included a ‘beta’ installer for Python 3.2
(and Python 3.3 to follow soon) under 32-bit Windows.

Please note we are phasing out support for Python 2.5. We will
continue support for at least one further release (Biopython 1.62).
This could be extended given feedback from our users. Focusing on
Python 2.6 and 2.7 only will make writing Python 3 compatible code
easier.

New Features:

GenomeDiagram has three new sigils (shapes to illustrate features).
OCTO shows an octagonal shape, like the existing BOX sigil but with
the corners cut off. JAGGY shows a box with jagged edges at the start
and end, intended for things like NNNNN regions in draft genomes.
Finally BIGARROW is like the existing ARROW sigil but is drawn
(Continue reading)

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Peter Cock | 1 Nov 2012 20:40
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Fwd: OBF server outage announcement / call for SysAdmin volunteers

FYI regarding the Biopython website and recent mailing list outage.

Peter

PS you also keep an eye on  <at> Biopython and  <at> OBF_news on Twitter,
which are a useful alternative when the mailing lists are down.

---------- Forwarded message ----------
From: *Peter Cock*
Date: Thursday, November 1, 2012
Subject: OBF server outage announcement / call for SysAdmin volunteers
To: open-bio-l <at> lists.open-bio.org, OBF Members <members <at> lists.open-bio.org>
Cc: Chris Dagdigian <chris <at> bioteam.net>, OBF Board <board <at> open-bio.org>

Dear all,

As many of you may have noticed, yesterday the Open Bioinformatics
Foundation (OBF) server hosting the mailing lists and most of the
Bio* websites went down.

The mailing lists and simple static webpages (e.g. download pages
for Bio* releases) seem to be back online, as is the OBF news blog:
http://news.open-bio.org/news/ - but the wiki pages are down
(which unfortunately means the Bio* homepages are unavailable).

Services on the failing server are being moved to virtual machines
on the Amazon Cloud, so it may take a few days until everything
has been set up properly and the wiki will be back.

If there is anybody from the Bio* projects who wants to join the OBF's
(Continue reading)

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Peter Cock | 22 Oct 2012 19:17
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Dropping Python 2.5 and Jython 2.5 support?

Dear Biopythoneers,

Would anyone object to us preparing to drop support for Python 2.5 and
Jython 2.5, perhaps after the next Biopython release?

To reassure those of you using Jython, we'd wait until Jython 2.7 is out
first. Jython 2.7 is already in alpha, and brings support for C Python 2.7
language features.

Thanks,

Peter
_______________________________________________
Biopython-announce mailing list  -  Biopython-announce <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biopython-announce
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Peter Cock | 25 Jun 2012 20:22
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Biopython 1.60

Dear Biopythoneers,

Biopython 1.60 is out:
http://news.open-bio.org/news/2012/06/biopython-1-60-released/

Thank you to everyone who has contributed.

Peter

P.S. We're on Twitter as  <at> Biopython - see also  <at> obf_news
https://twitter.com/#!/biopython
_______________________________________________
Biopython-announce mailing list  -  Biopython-announce <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biopython-announce
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Peter Cock | 10 Jun 2012 12:24
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EU-codefest

Dear Biopythoneers,

Some of you might like to attend an Open-Bio Hackathon in Italy this
summer - 19 and 20 July 2012, in Lodi.

This is about a week after BOSC and the pre-BOSC CodeFest in California
http://www.open-bio.org/wiki/BOSC_2012

Peter

---------- Forwarded message ----------
From: *Pjotr Prins*
Date: Saturday, June 9, 2012
Subject: EU-codefest
To: cjfields <at> illinois.edu
Cc: p.j.a.cock <at> googlemail.com

Hi Chris and Peter,

Would you mind sending a reminder of the EU-codefest to your lists?

Registration form is up:

 http://www.open-bio.org/wiki/EU_Codefest_2012

Three main topics will be worked on during the CodeFest:

   NGS and high performance parsers for OpenBio projects.
   RDF and semantic web for bioinformatics.
   Bioinformatics pipelines definition, execution and distribution.
(Continue reading)

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Peter Cock | 24 Feb 2012 17:56
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Biopython 1.59 released

Dear Biopythoneers,

Biopython 1.59 is out:
http://news.open-bio.org/news/2012/02/biopython-1-59-released/

Thank you to everyone who has contributed.

Peter

P.S. We're on Twitter as  <at> Biopython
_______________________________________________
Biopython-announce mailing list  -  Biopython-announce <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biopython-announce
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Peter | 18 Aug 2011 21:32
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Biopython 1.58 released

Dear All,

Biopython 1.58 is out:
http://news.open-bio.org/news/2011/08/biopython-1-58-released/

Thank you to everyone who has contributed.

Peter

P.S. We're on Twitter as  <at> Biopython

_______________________________________________
Biopython-announce mailing list  -  Biopython-announce <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biopython-announce
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Brad Chapman | 2 Apr 2011 14:21
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Biopython 1.57 released

The Biopython community is pleased to announce the release of
Biopython 1.57. Source distributions are available from the 
downloads page on the Biopython website and from the Python 
Package Index (Windows installers coming soon):

http://biopython.org/wiki/Download
http://pypi.python.org/pypi/biopython

Bio.SeqIO now includes an index_db() function which extends the existing
indexing functionality to allow indexing many files, and more importantly
this keeps the index on disk in a simple SQLite3 database rather than in
memory in a Python dictionary.

Bio.Blast.Applications now includes a wrapper for the BLAST+ blast_formatter
tool from NCBI BLAST 2.2.24+ or later. This release of BLAST+ added the
ability to run the BLAST tools and save the output as ASN.1 format, and then
convert this to any other supported BLAST ouput format (plain text, tabular,
XML, or HTML) with the blast_formatter tool. The wrappers were also updated
to include new arguments added in BLAST 2.2.25+ such as -db_hard_mask.

The SeqRecord object now has a reverse_complement method (similar to that of
the Seq object). This is most useful to reversing per-letter-annotation (such
as quality scores from FASTQ) or features (such as annotation from GenBank).

Bio.SeqIO.write's QUAL output has been sped up, and Bio.SeqIO.convert now
uses an optimised routine for FASTQ to QUAL making this much faster.

Biopython can now be installed with pip. Thanks to David Koppstein and 
James Casbon for reporting the problem.
(Continue reading)

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Peter | 27 Nov 2010 00:12
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Biopython 1.56

Dear Biopythoneers,

On behalf of the developers, I'm pleased to announce we
released Biopython 1.56 earlier today. For more details
please see:

http://news.open-bio.org/news/2010/11/biopython-1-56-released/

Please note this will probably be the last release to
support Python 2.4, see:

http://news.open-bio.org/news/2010/11/dropping-python24-support/

(At least) 13 people have contributed to this release,
including 6 new people – thank you all:

    * Andrea Pierleoni (first contribution)
    * Bart de Koning (first contribution)
    * Bartek Wilczynski
    * Bartosz Telenczuk (first contribution)
    * Cymon Cox
    * Eric Talevich
    * Frank Kauff
    * Michiel de Hoon
    * Peter Cock
    * Phillip Garland (first contribution)
    * Siong Kong (first contribution)
    * Tiago Antao
    * Uri Laserson (first contribution)
(Continue reading)

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Peter | 18 Nov 2010 16:47
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Dropping Python 2.4 Support?

Dear Biopythoneers,

Are any of you still using Biopython on Python 2.4?
http://news.open-bio.org/news/2010/11/dropping-python24-support/

Please get in touch if dropping support for Python 2.4 would be a
problem. Otherwise we plan for Biopython 1.56 (expected by the
end of this month) to be our last release to work with Python 2.4.

Thanks,

Peter
_______________________________________________
Biopython-announce mailing list  -  Biopython-announce <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biopython-announce
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Gmane