Obf

One of the small changes coming in Biopython 1.54 (which you can try out already using the Biopython 1.54 beta) is to Bio.SeqIO and Bio.AlignIO. Previously the input and output functions had required file handles, but they will now also accept filenames. This is a case of practicality beats purity (to quote the Zen of Python), and is particularly handy when doing very short scripts or working at the Python prompt. [Read More]

A beta release for Biopython 1.54 is now available for download and testing. Since Biopython 1.53 was released at the end of last year, several new features and more documentation have been added, plus the usual bug fixes. For full details see the NEWS file. All the new features have been tested by the dev team but it’s possible there are cases that we haven’t been able to foresee and test, especially for the updated multiple sequence alignment object (which is what you’ll now get when parsing alignments with Bio. [Read More]

**Abstract submissions for the 11th Annual Bioinformatics Open Source Conference (BOSC 2010) are now open.**At-a-glance BOSC is an ISMB 2010 Special Interest Group (SIG) Date: July 9-10, 2010 Location: Boston, Massachusetts, USA BOSC 2010 web site: /wiki/BOSC_2010 Abstract submission via Open Conference System site: http://events.open-bio.org/BOSC2010/openconf.php E-mail: bosc@open-bio.org Bosc-announce list: http://lists.open-bio.org/mailman/listinfo/bosc-announce Important Dates April 15: Abstract deadline May 5: Notification of accepted abstracts May 28: Early Registration Discount Cut-off date July 8-9: Codefest 2010 July 9-10: BOSC 2010 August 15: Manuscript deadline for BOSC 2010 Proceedings published in BMC Bioinformatics [Read More]

BioPerl developers and users attended the BioPerl satellite meeting on January 13th, just prior to the GMOD Meeting. Several items were covered on the agenda: In order to start addressing whole genome data with more lightweight objects, we are planning on setting up a lightweight Bio::SeqI object that has a flexible DB backend (i.e. Bio::DB::SeqFeature::Store or similar). We are also contemplating adding lazy parsing for some parsers, possibly using the Bio::PullParserI methods (or similar) that Sendu Bala created. [Read More]

We are pleased to announce the release of BioRuby 1.4.0. This new release contains many new features, in addition to bug fixes and improvements. PhyloXML support: Support for reading and writing PhyloXML file format is added, developed by Diana Jaunzeikare, mentored by Christian M Zmasek and co-mentors, supported by Google Summer of Code 2009 in collaboration with the National Evolutionary Synthesis Center (NESCent). FASTQ file format support: Support for reading and writing FASTQ file format is added. [Read More]

BOSC 2010 is currently in the planning stages. It will be held for 2 days in conjunction with the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010) in Boston, Massachusetts, USA. The dates of BOSC 2010 are July 9-10; the main ISMB Conference runs July 11-13, 2010. The BOSC 2010 web site can be accessed here: /wiki/BOSC_2010. The BOSC organizing committee is soliciting input on the planning of BOSC 2010 so that we can make it a successful and productive conference for the O|B|F community. [Read More]

I’m delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the conventions agreed by the OBF projects: The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants Peter J. A. Cock ( Biopython), Christopher J. Fields ( BioPerl), Naohisa Goto ( BioRuby), Michael L. Heuer ( BioJava) and Peter M. Rice ( EMBOSS). Nucleic Acids Research, doi:10. [Read More]

The official 2009 Board of Directors meeting is taking place today, Monday Dec 14, at 4pm EST (21:00 UTC) via teleconference. If you are an O|B|F member, you will have received the announcement and dial-in information earlier. O|B|F Board of Director meetings are public - anyone interested in O|B|F business can participate, which is one reason we are holding the meeting over teleconference. The dial-in number is +1-518-825-1400, participant code 279610. [Read More]