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.
• After a final  1.6 branch point release, we may ‘freeze’ BioPerl in a maintenance mode, primarily so that we can reorganize core into several more easily installed subdistributions on a branch.  New modules will essentially be additional separate repos that will depend on BioPerl core.  This reorganization has been discussed for a few years now, and as we edge closer to starting this (probably this spring) we’ll announce more details.
• Some initial thoughts on how to handle circular genomes more efficiently.  We essentially do this already, but it isn’t full-proof.
• Need some significant time dedicated towards GFF3-based coding (reimplement FeatureIO but allow some flexibility).  Rob Buels had started the initial run at splitting out FeatureIO, so next step is a true reimplementation.
• We don’t plan on including Moose support for the immediate future, feeling that it would be better to reimplement some of the classes from scratch using Moose and similar as a BioPerl 2.0, or possibly await the impending Rakudo Perl 6 alpha and start afresh using that instead of Moose.

Anything we missed?  Anything you would like to address?  Please add comments and we’ll discuss them on list.

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. All of the three FASTQ format variants are supported. The code is written by Naohisa Goto, with the help of discussions in the open-bio-l mailing list. The prototype of Bio::Fastq class was first developed during the BioHackathon 2009 held in Okinawa.

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.  You may send your suggestions to the bosc@open-bio.org e-mail address  or add suggestions to the BOSC 2010 talk/discussion wiki page at: /wiki/Talk:BOSC_2010. Please respond to any or all of the questions below:

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:10.1093/nar/gkp1137

This will hopefully serve as a reference describing the original standard Sanger FASTQ, and the two variants from Solexa/Illumina, and how to inter-convert between them.

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.

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.

Agenda

1. Old business
   • 2008 BoD meeting minutes
2. New business
   1. BOSC
      • BOSC 2009 (Kam)
        • Money spent/made attendee number, any other feedback
      • BOSC 2010 - held with ISMB2010 in Boston, MA, USA
   2. Treasurer’s 2009 report (ChrisD)
      • 2009 Financial report
   3. BoD membership and succession.
      • Nomination of Nomi Harris for election to the BoD
      • Need plan to elect new BoD members and rotate officers.
   4. OBF Hardware & Sysadmin report (JasonS and ChrisD)
      • Domain names currently registered, upcoming expirations, newly purchased names
      • Proposal to purchase new hardware - 2009 hardware purchase proposal
      • Proposal to purchase box for upstream SPAM filtering
      • System Administration status & coverage report (who, what, issues, future)
      • Consider possibility of moving code mirroring to public (code.google.com; etc) mailling lists to googlegroups?
   5. Hackathons 2010 (Tokyo hackathon in Feb 2010) will involve some OBF projects/developers
   6. Additional topics proposed by community

Minutes from the meeting

Venue: held by conference call, scheduled for 4pm EST (21:00 UTC).

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 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.