http://blog.gmane.org/gmane.comp.python.bio.announce hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://comments.gmane.org/gmane.comp.python.bio.announce/70 <pre>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://list</pre> Peter Cock 2013-04-24T19:19:48 http://comments.gmane.org/gmane.comp.python.bio.announce/66 <pre>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 feature</pre> Peter Cock 2013-02-05T22:05:25 http://comments.gmane.org/gmane.comp.python.bio.announce/61 <pre>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&lt; at &gt;lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biopython-announce </pre> Peter Cock 2012-10-22T17:17:34 http://comments.gmane.org/gmane.comp.python.bio.announce/60 <pre>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 &lt; at &gt;Biopython - see also &lt; at &gt;obf_news https://twitter.com/#!/biopython _______________________________________________ Biopython-announce mailing list - Biopython-announce&lt; at &gt;lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biopython-announce </pre> Peter Cock 2012-06-25T18:22:12 http://comments.gmane.org/gmane.comp.python.bio.announce/58 <pre>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 &lt; at &gt;Biopython _______________________________________________ Biopython-announce mailing list - Biopython-announce&lt; at &gt;lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biopython-announce </pre> Peter Cock 2012-02-24T16:56:11 http://comments.gmane.org/gmane.comp.python.bio.announce/57 <pre>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 &lt; at &gt;Biopython _______________________________________________ Biopython-announce mailing list - Biopython-announce&lt; at &gt;lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biopython-announce </pre> Peter 2011-08-18T19:32:57 http://comments.gmane.org/gmane.comp.python.bio.announce/56 <pre>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</pre> Brad Chapman 2011-04-02T12:21:19 http://comments.gmane.org/gmane.comp.python.bio.announce/54 <pre>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) Source distributions and Windows installers are available from the downloads page on the Biopython website: http://www.biopython.org/wiki/Download As usual, feedback is most welcom</pre> Peter 2010-11-26T23:12:14 http://comments.gmane.org/gmane.comp.python.bio.announce/53 <pre>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&lt; at &gt;lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biopython-announce </pre> Peter 2010-11-18T15:47:08 http://comments.gmane.org/gmane.comp.python.bio.announce/52 <pre>Dear Biopythoneers, After the beta earlier this month (thank you to everyone who helped test this), we’ve just released Biopython 1.55 . For full details see: http://news.open-bio.org/news/2010/08/biopython-1-55-released/ Note we are phasing out support for Python 2.4. We will continue to support it for at least one further release (i.e. Biopython 1.56). This could be delayed given feedback from our users (e.g. if this proves to be a problem in combination with other libraries or a popular Linux distribution). (At least) 12 people have contributed to this release, including 6 new people – thank you all: * Andres Colubri (first contribution) * Carlos Rios Vera (first contribution) * Claude Paroz (first contribution) * Cymon Cox * Eric Talevich * Frank Kauff * Joao Rodrigues (first contribution) * Konstantin Okonechnikov (first contribution) * Michiel de Hoon * Nathan Edwards (first contribution) * Peter Cock * Tiago Antao Source distributions and Windo</pre> Peter Cock 2010-08-31T23:00:37 http://comments.gmane.org/gmane.comp.python.bio.announce/49 <pre>Hi all, We appear to have a temporary problem with our biopython.org domain, which I trust the OBF admin team will address shortly. As a fallback you can use http://biopython.open-bio.org/wiki/Main_Page and http://biopython.open-bio.org/DIST/ for the downloads. Source code is hosted separately on github, http://github.com/biopython/biopython/ Apologies, Peter _______________________________________________ Biopython-announce mailing list - Biopython-announce&lt; at &gt;lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biopython-announce </pre> Peter 2010-08-26T10:57:27 http://comments.gmane.org/gmane.comp.python.bio.announce/48 <pre>Dear Biopythoneers, We’ve just released a beta of Biopython 1.55 for user testing, as announced on the news server (which has RSS and atom feeds) and on twitter: http://news.open-bio.org/news/2010/08/biopython-1-55-beta-released/ http://twitter.com/biopython Since Biopython 1.54 was released three months ago, we’ve made a good start on work for Python 3 support (via the 2to3 script), but as a side effect of this we’ve had to update quite a lot of the older parts of the library. Although the unit tests are all fine, there is a small but real chance that we’ve accidentally broken things – which is why we’re doing this beta release. In terms of new features, the most noticeable highlight is that the command line tool application wrapper classes are now executable, which should make it much easier to call external tools. This is described in the updated documentation. http://biopython.org/DIST/docs/tutorial/Tutorial.html http://biopython.org/DIST/docs/tutorial/Tutorial.pdf Note we are phasing out</pre> Peter 2010-08-19T15:43:56 http://comments.gmane.org/gmane.comp.python.bio.announce/47 <pre>Dear Biopythoneers, Earlier today we released Biopython 1.54 (a little later than originally planned) which addresses a few bugs found in the beta release, has some changes to the new Bio.Phylo module, adds a whole chapter to the tutorial. Thank you to everyone who contributed code, reported bugs, etc. For more details please see this announcement (kindly drafted by David Winter): http://news.open-bio.org/news/2010/05/biopython-release-154/ Regards, Peter _______________________________________________ Biopython-announce mailing list - Biopython-announce&lt; at &gt;lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biopython-announce </pre> Peter 2010-05-20T21:59:43 http://comments.gmane.org/gmane.comp.python.bio.announce/43 <pre>Dear Biopythoneers, The Open Bioinformatics Foundation (the Bio* umbrella organisation) is preparing an application for the 2010 Google Summer of Code (GSoC). http://code.google.com/soc/ If you are interested in becoming a mentor for a Biopython related project, you can join us in the application. If you are a student and are interested in a project (or would like to propose one), please take a look at these pages: http://www.open-bio.org/wiki/Google_Summer_of_Code http://biopython.org/wiki/Google_Summer_of_Code Regards, Brad &amp; Peter _______________________________________________ Biopython-announce mailing list - Biopython-announce&lt; at &gt;lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biopython-announce </pre> Peter Cock 2010-03-10T14:30:57 http://comments.gmane.org/gmane.comp.python.bio.announce/41 <pre>Dear Biopythoneers, We are pleased to announce the availability of Biopython 1.53, a new stable release of the Biopython library, three months after the release of Biopython 1.52. This is our first release since migrating from CVS to git for source code control. There have been some additions to our core objects – the Seq (and related UnknownSeq) objects gained upper and lower methods (like the string methods of the same name but alphabet aware) plus a new ungap method. The SeqFeature object now has an extract method to get the region of sequence it describes (useful for getting CDS nucleotide sequences from GenBank files). Also SeqRecord objects now support addition, giving a new SeqRecord with the combined sequence, all the SeqFeatures, and any common annotation. SQLite support (built into Python 2.5+) was added to our BioSQL interface. This is still a little experimental as we are using a draft BioSQL SQLite schema, but this should be merged into the next BioSQL release. Biopython now includes wrapp</pre> Peter 2009-12-15T17:01:38 http://comments.gmane.org/gmane.comp.python.bio.announce/40 <pre>Dear all, Those of you who signed up to our newsfeed will know this already, but we are pleased to announce the release of Biopython 1.52: http://news.open-bio.org/news/2009/09/biopython-release-152/ Thank you to all our developers, including David Winter for drafting the release announcement, and everyone else who as contributed with feedback, bug reports etc. Could I also take this opportunity to remind you all we have an application note out in the OUP journal Bioinformatics: http://news.open-bio.org/news/2009/03/biopython-paper-published/ http://dx.doi.org/10.1093/bioinformatics/btp163 In any scientific publication using Biopython, we kindly request you cite this, or another appropriate publication from this list: http://biopython.org/wiki/Documentation#Papers Thank you, Peter _______________________________________________ Biopython-announce mailing list - Biopython-announce&lt; at &gt;lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biopython-announce </pre> Peter Cock 2009-09-22T16:38:21 http://comments.gmane.org/gmane.comp.python.bio.announce/39 <pre>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 deprecate</pre> Brad Chapman 2009-08-17T12:11:56 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.comp.python.bio.announce