http://permalink.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://permalink.gmane.org/gmane.comp.python.bio.announce/71 <pre>Dear all, After the disappointing news that the Open Bioinformatics Foundation (OBF) was not accepted as a Google Summer of Code (GSoC) organisation this year, Biopython was fortunate to once again offer some projects with the NESCent team: http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2013 As always the student proposals have been very competitive, and we've not been able to take on everyone. This year NESCent was fortunately to be able to accept seven students through GSoC and one through the GNOME Outreach Program for Women. Two of these GSoC projects are Biopython related: Codon Alignment and Analysis in Biopython Student: Zheng Ruan Mentors: Eric Talevich, Peter Cock http://www.google-melange.com/gsoc/project/google/gsoc2013/rzzmh12345/32001 Phylogenetics in Biopython: Filling in the gaps Student: Yanbo Ye http://www.google-melange.com/gsoc/project/google/gsoc2013/yeyanbo/45001 Mentors: Mark Holder, Jeet Sukumaran, Eric Talevich Thank you NESCe</pre> Peter Cock 2013-05-30T16:18:41 http://permalink.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://permalink.gmane.org/gmane.comp.python.bio.announce/69 <pre> Peter; Thanks for sending this out. I'm helping with the organization of the SciPy bioinformatics session thanks to Peter's recommendation and wrote up a little bit about the types of abstracts that would fit will with the overall theme of SciPy: http://j.mp/Z4xxXB This is a great chance to connect with another open source scientific community so definitely send in an abstract if this is of interest; the deadline is coming up next month: March 20th. Austin also has awesome music and barbecue in addition to science and hacking so lots of reasons to attend, Brad _______________________________________________ Biopython-announce mailing list - Biopython-announce&lt; at &gt;lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biopython-announce </pre> Brad Chapman 2013-03-01T02:36:34 http://permalink.gmane.org/gmane.comp.python.bio.announce/68 <pre>The new bioinformatics mini-symposium this year makes SciPy 2013 especially interesting. Peter ---------- Forwarded message ---------- From: *Jonathan Rocher* Date: Wednesday, February 27, 2013 Subject: [Numpy-discussion] [ANN] SciPy2013: Call for abstracts To: SciPy Users List &lt;scipy-user&lt; at &gt;scipy.org&gt;, numfocus&lt; at &gt;googlegroups.com, Discussion of Numerical Python &lt;numpy-discussion&lt; at &gt;scipy.org&gt; [Apologies for cross-posts] Dear all, The annual SciPy Conference (Scientific Computing with Python)&lt;http://conference.scipy.org/scipy2013/about.php&gt; allows participants from academic, commercial, and governmental organizations to showcase their latest projects, learn from skilled users and developers, and collaborate on code development. *The deadline for abstract submissions is March 20th, 2013. * Submissions are welcome that address general Scientific Computing with Python, one of the two special themes for this years conference (machine learning &amp; reproducible science), or the domain-specific mini-symposia&lt;http://c</pre> Peter Cock 2013-02-27T22:32:35 http://permalink.gmane.org/gmane.comp.python.bio.announce/67 <pre> For those of you wanting to try Biopython on Python 3.3 on Windows, there is now an installer for Biopython 1.61 built against NumPy 1.7.0rc2. NumPy 1.7 is their first release to support Python 3.3, and the official release is expected to be near-identical to this second release candidate, see: http://mail.scipy.org/pipermail/numpy-discussion/2013-February/065384.html 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 Cock 2013-02-07T11:33:25 http://permalink.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://permalink.gmane.org/gmane.comp.python.bio.announce/65 <pre> Hello all, Having recently back-ported some Python 3 code with a C extension to Python 2.6 and 2.7, I can now more clearly appreciate the benefits dropping Python 2.5 support has for writing code for both Python 2 and 3 - and am keen to be able to exploit this for Biopython. Given no major objections to the email I sent round in October last year (thank you for your input Nathan), we will press ahead with phasing out support for Python 2.5, provisionally supporting it in the forthcoming Biopython 1.61 and at least one more release (which would mean Biopython 1.62 due Summer 2013). https://github.com/biopython/biopython/commit/3f17f75b320fb6624d332809ef07314bab97477c My only significant concern is for Jython users, since this will also mean dropping support for Jython 2.5 (which implements the Python 2.5 language). The replacement Jython 2.7 is still only at the alpha release stage. Regards, Peter _______________________________________________ Biopython-announce mailing list - Biopython-announce&lt; at &gt;lis</pre> Peter Cock 2013-01-07T18:55:25 http://permalink.gmane.org/gmane.comp.python.bio.announce/64 <pre> Hosting of biopython.org (and the bioperl.org and open-bio.org websites) was transferred to an Amazon cloud machine over the weekend, which fixed the wiki but temporarily disabled the static pages (like the Tutorial and downloads). Those should all be working again now. At some later date (to be announced) the server running the OBF mailing lists will be transferred, which would make the mailing lists unavailable for a short period. 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 Cock 2012-11-05T23:07:09 http://permalink.gmane.org/gmane.comp.python.bio.announce/63 <pre> I should have added that while the wiki is down (which does unfortunately include the Biopython home page), the Biopython downloads remain available via http://biopython.org/DIST/ and other 'static' content like the Tutorial and API pages are up: http://biopython.org/DIST/docs/tutorial/Tutorial.html http://biopython.org/DIST/docs/tutorial/Tutorial.pdf http://biopython.org/DIST/docs/api/ Our source code repository is on GitHub, also fine: https://github.com/biopython/biopython Issue tracking is on our RedMine server, also fine: https://redmine.open-bio.org/projects/biopython Nightly unit tests are on our Buildbot server, also fine: http://testing.open-bio.org/biopython/tgrid Continuous integration testing is on TravisCI, also fine: http://travis-ci.org/biopython/biopython 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 Cock 2012-11-01T19:50:50 http://permalink.gmane.org/gmane.comp.python.bio.announce/62 <pre>FYI regarding the Biopython website and recent mailing list outage. Peter PS you also keep an eye on &lt; at &gt;Biopython and &lt; at &gt;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&lt; at &gt;lists.open-bio.org, OBF Members &lt;members&lt; at &gt;lists.open-bio.org&gt; Cc: Chris Dagdigian &lt;chris&lt; at &gt;bioteam.net&gt;, OBF Board &lt;board&lt; at &gt;open-bio.org&gt; 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 A</pre> Peter Cock 2012-11-01T19:40:32 http://permalink.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://permalink.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://permalink.gmane.org/gmane.comp.python.bio.announce/59 <pre>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&lt; at &gt;illinois.edu Cc: p.j.a.cock&lt; at &gt;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. other tracks are welcome! Pj. _______________________________________________ Biopython-announce mailing list - Biopython-announce&lt; at &gt;lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biopython-announc</pre> Peter Cock 2012-06-10T10:24:20 http://permalink.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://permalink.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://permalink.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://permalink.gmane.org/gmane.comp.python.bio.announce/55 <pre>Dear Biopythoneers, BOSC will be in Vienna, Austria this year. Peter ---------- Forwarded message ---------- From: Nomi Harris &lt;nlharris&lt; at &gt;lbl.gov&gt; Date: Thu, Mar 3, 2011 at 7:37 PM Subject: [Bosc] Bioinformatics Open Source Conference (BOSC 2011)--Call for Abstracts To: bosc-announce&lt; at &gt;lists.open-bio.org, members&lt; at &gt;open-bio.org, GMOD Announcements List &lt;gmod-announce&lt; at &gt;lists.sourceforge.net&gt;, GMOD Developers List &lt;gmod-devel&lt; at &gt;lists.sourceforge.net&gt; Cc: Nomi Harris &lt;nlharris&lt; at &gt;lbl.gov&gt; We invite you to submit an abstract to BOSC 2011!  Please forward this message as appropriate, and forgive multiple postings. Call for Abstracts for the 12th Annual Bioinformatics Open Source Conference (BOSC 2011) An ISMB 2011 Special Interest Group (SIG) Dates: July 15-16, 2011 Location: Vienna, Austria Web site: http://www.open-bio.org/wiki/BOSC_2011 Email: bosc&lt; at &gt;open-bio.org BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce Important Dates: April 18, 2011: Deadline for submitting abstra</pre> Peter Cock 2011-03-03T20:32:11 http://permalink.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://permalink.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://permalink.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://permalink.gmane.org/gmane.comp.python.bio.announce/51 <pre> Thanks for the speedy response Chris - www.biopython.org is back up now. If anyone is still having trouble, please allow another day or so for DNS servers to update. 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/ 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 2010-08-27T08:57:04 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.comp.python.bio.announce