Archive for the ‘OBF’ Category

BOSC 2010 Call for Abstracts

Tuesday, March 2nd, 2010

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

BioPerl at GMOD Meeting 2010

Monday, January 18th, 2010

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 ...

BioRuby 1.4.0 released

Tuesday, December 29th, 2009

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 ...

BOSC 2010 Request for Input

Friday, December 18th, 2009

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, ...

Sanger FASTQ format and the Solexa/Illumina variants

Thursday, December 17th, 2009

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 ...

2009 O|B|F Board of Directors meeting

Monday, December 14th, 2009

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 ...

BioPerl interview in latest FLOSS Weekly

Sunday, November 22nd, 2009

Two of the core BioPerl developers, Jason Stajich and Chris Fields, were interviewed by FLOSS Weekly.  The interview is now available as an MP3 on the FLOSS Weekly website; several streaming versions (including podcast) are also available.

BioPerl core 1.6.1 PPM available

Saturday, October 10th, 2009

BioPerl 1.6.1 is now available for ActivePerl as a PPM, instructions for downloading can be found on the BioPerl wiki. This has been tested only for ActivePerl 5.10 and above, so any feedback with older versions of BioPerl would be greatly appreciated.

First 1.6.1 alphas of BioPerl-Run, BioPerl-DB, BioPerl-Network

Thursday, October 1st, 2009

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! ...

BioPerl 1.6.1 released

Tuesday, September 29th, 2009

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 ...