Obf-Projects

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]

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. [Read More]

This post is about paired end data (FASTA or FASTQ) and manipulating it with Biopython’s Bio.SeqIO module (see also FASTQ conversions & speeding up FASTQ). [Read More]

Running a bit late on this, so just a quick note that the first alphas for BioPerl-Run, BioPerl-DB, and BioPerl-Network have been uploaded to CPAN: BioPerl-Run BioPerl-DB BioPerl-Network They can also be downloaded from the BioPerl website: http://bioperl.org/DIST/RC/ This is the first run where we’ve switched to a regular Module::Build installation, so expect some initial bumps! There are a few initial problems that I plan on addressing soon, the main one being none of the modules are assigned version numbers (this may be a consequence of not pulling the version from a specific module). [Read More]

We are pleased to announce the immediate availability of BioPerl 1.6.1, the latest release of BioPerl’s core code. You can grab it here: Via CPAN: http://search.cpan.org/~cjfields/BioPerl-1.6.1/ Via the BioPerl website: http://bioperl.org/DIST/BioPerl-1.6.1.tar.bz2 http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz http://bioperl.org/DIST/BioPerl-1.6.1.zip The PPM for Windows should also finally be available this week, ActivePerl problems permitting (we will post more information when it becomes available). Tons of bug fixes and changes have been incorporated into this release. For a more complete change list please see the ‘Changes’ file included with the distribution. [Read More]