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 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

The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form.

We have some exciting things planned this year, including:

• Codefest 2010 programming session for the two days preceeding BOSC:  See http://www.open-bio.org/wiki/Codefest_2010 for details.
• OpenBio Solution Challenge:  See session description below and http://www.open-bio.org/wiki/SolutionChallenge for details.
• Student Travel Fellowships:  Through generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce the competition for three Student Travel Awards for BOSC 2010. Each winner will be awarded $250 to defray the costs of travel to BOSC 2010.  See http://www.open-bio.org/wiki/BOSC_2010#Student_Travel_Awards for details.
• First-ever BOSC Proceedings will be published in the Open Access journal, BMC Bioinformatics.  Manuscripts will be due after BOSC on August 15.  See http://www.open-bio.org/wiki/BOSC_2010#First-ever_Published_BOSC_Proceedings for details.
• Sessions on approaches to analyzing high-throughput ‘omics data, cloud-based approaches to improving software and data accessibility, the semantic web in open source bioinformatics, see below:

We invite abstracts for talks at the following sessions:

OpenBio SolutionChallenge — Bioinformatics library providers: please join us in a friendly competition to solve a shared biological problem, demonstrating the utility of your toolkit alongside other developers. Instead of the traditional Bio* updates that we’ve had at previous conferences, this year, we’re planning to organize these talks around a central theme: the OpenBio Solution Challenge. We start with a biological question of general interest, and the project talks will focus around how you would solve that problem using your toolkit and programming language. This is meant to provide a challenge for OpenBio contributors, a nice tutorial style overview of various projects and approaches for other programmers, and a fun opportunity to compete and learn from other projects. Conference attendees will vote on their favorite solution, with the winner receiving fame and fortune (warning: fortune not guaranteed). Specific challenges are being discussed on the SolutionChallenge page and through the various Bio* mailing lists. Alternately, each project could highlight a challenge that they particularly do well, focusing tutorial-style on how to solve a particular problem.

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.

DNA chromatogram support: Support for reading DNA chromatogram files are added. SCF and ABIF file formats are supported. The code is developed by Anthony Underwood.

MEME (motif-based sequence analysis tools) support: Support for running MAST (Motif Alignment & Search Tool, part of the MEME Suite, motif-based sequence analysis tools) and parsing its results are added,  developed by Adam Kraut.

Improvement of KEGG parser classes: Some new methods are added to parse new fields added to some KEGG file formats. Unit tests for KEGG parsers are also added and improved. These are contributed by Kozo Nishida.

Many sample scripts are added: Many sample scripts showing demonstrations of usages of classes are added. They were originally primitive test codes written in the “if __FILE__ == $0″ convention.

Unit tests can test installed BioRuby: Mechanism to load library and to find test data in the unit tests are changed, and target library path and test data path can be changed with environment variables.

Incompatible change: Bio::NCBI::REST needs email address: NCBI announced that all Entrez Utilities (E-utilities)  requests must contain email and tool parameters, and requests without them will return error after June 2010. In BioRuby, to set default email address and tool name, following methods are added.

• Bio::NCBI.default_email=(email)
• Bio::NCBI.default_tool=(tool_name)

Note that no default email address is preset in BioRuby. Library users must set their own email address or implement to get user’s email address in some way (from input form, configuration file, etc).

In addition, many changes have been made, including incompatible changes. For more information, see RELEASE_NOTES.rdoc and ChangeLog.

The archive is available at: http://bioruby.org/archive/bioruby-1.4.0.tar.gz

Gem file is also available at:  http://bioruby.org/archive/gems/bio-1.4.0.gem

We also put RubyGems pacakge at RubyForge and Gemcutter. You can easily install by using RubyGems.
First, check the version number by using search command:
% gem search –remote bio
and find “bio (1.4.0)” in the list. Then,
% sudo gem install bio

Hope you enjoy.

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:  http://www.open-bio.org/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: http://www.open-bio.org/wiki/Talk:BOSC_2010. Please respond to any or all of the questions below:

1.  For the last several years BOSC has consisted mainly of one or two keynote presentations, other talks chosen from among the submitted abstracts organized into sessions by topic, updates from the Bio* projects, Lightning Talks, and informal Birds of a Feather sessions.  Would you rather see BOSC continue in this fashion, or would you support changing the format to one or all of the following:

• Tutorials where there were in depth demonstrations and code tutorials. This could be lead off by the OBF projects instead of the traditional update talks, but could feature any open source projects interested. These would be hands on sessions with real code examples, with a focus on teaching people how to leverage various code bases to make real life work easier.  Would you be willing to organize/lead such a session for your project?
• Discussion following the hands on tutorials, these would be interactive sessions focused around dealing with unsolved issues. The “speaker” would be responsible for setting up a set of discussion topics around an issue of interest, and then facilitating ideas and opinions from the attendees. The goals would be to talk through problems and gather a consensus about options for solving them.  Would you be willing to organize/lead such a session for your project?
• Mini-hackathon either before, during, or after the 2-day BOSC.  The subject of the hackathon would need to be organized by the individual project leaders/teams.  Some suggestions would be adding/extending support for next-gen sequencing; organizing bugs/tasks so that new beginners can start contributing to the project easily and working on some of those bugs/tasks; organizing some type of contest like the Genome Annotation Assessment Project (GASP) where solutions from different projects compete on arriving at some type of goal.  Would you be willing to organize/lead this type of session?
• Organizing/creating a LiveCD or Debian download of Bio* projects with documentation to support outreach to the larger bioinformatics community.  Would you be willing to organize/lead this type of session?
• What session topics would you like to see represented for traditional talks?
• Who would you like to hear as a keynote speaker?

2.  The BOSC 2010 organizing committee is in discussion with an open access journal to publish a formal Proceedings for BOSC.  If you are planning on submitting an abstract for BOSC 2010, are you interested in submitting a more formal paper to the BOSC proceedings, given that as the author you would need to pay the page charges that could run between US$500-1000?  We are likely to move ahead with plans to have a proceedings, but it would be helpful to know how many submissions to expect.

3.  Call for volunteers.  Organizing tutorial/hackathons and such will only be possible if individuals step forward to lead these sessions.  Please let us know if you would be willing to serve in any capacity.  We also need volunteers to review abstracts for the more “traditional” sessions, please let us know if you are willing to do this as well.

Timeline: We are planning on putting out the Call for Abstracts in mid-January.  To be on track, we would like to receive your input by Friday, January 8.  If you are willing to step forward to organize a tutorial/discussion/hackathon, you would need to commit by that time, although there would still be some more time to put the actual program together in the new year.

Thanks and Happy Holidays!

Kam Dahlquist
Chair, BOSC 2010 on behalf of the BOSC 2010 Organizing committee:
Brad Chapman, Michael Heur, Darin London, Anton Nekrutenko, Steffen Moeller, Jim Procter
And the O|B|F Board:
Chris Dagdigian, Nomi Harris, Hilmar Lapp, Jason Stajich

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.

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.

All you need to participate is a telephone (this is a US toll number, and if you are located international or outside of the area code, pertinent charges from your phone carrier will apply). Or use SkypeOut, which costs a few cents per minute from many locations (check SkypeOut rates).

The agenda for the meeting is on the OBF wiki (and minutes will be posted there later).

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.

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). The other, more serious one, is that the Build.PL script checks for DBI but isn’t checking for any compatible DBD::* adaptors for BioPerl-DB (so it fails tests if DBI is installed). We have code in core to check for DBI drivers, so I may adapt that for BioPerl-DB.

Enjoy!

chris

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.

A few highlights:

• FASTQ parsing and interconversion of the three FASTQ variants (Sanger, Illumina, Solexa) now works (a concerted OBF effort!)
• Significant refactoring of Bio::Restriction methods
• Complete refactoring of Bio::Search-related tiling code, including HOWTO documentation
• GBrowse-related fixes:
• - berkeleydb database now autoindexes wig files and locks correctly
• - add Pg, SQLite, and faster BerkeleyDB implementations
• Infernal 1.0 output is now parsed
• New SearchIO-based parser for gmap -f9 output
• BLAST XML parsing essentially complete
• Installation via CPANPLUS should now work
• For those using Strawberry Perl on Windows, the latest build is expected to pass all tests.
• ‘raw’ sequence format now parsed by line or optionally as a single sequence
• SCF parsing/writing now round-trips
• Demo code for using RPS-BLAST and Bio::Tools::Run::RemoteBlast
• Bio::Tools::SeqPattern now has a backtranslate() method
• Bio::Tree::Statistics now has methods to calculate Fitch-based score, internal trait values, statratio(), sum of leaf distances
• Scripts
• - update to bp_seqfeature_load for SQLite
• - hivq.pl – commmand-line interface to Bio::DB::HIV
• - fastam9_to_table – fix for MPI output
• - gccalc – total stats
• - einfo – simple script to find up-to-date NCBI databases, list field and link values for a specific database

We will shortly release updates for BioPerl-db, BioPerl-run, and BioPerl-network. Enjoy!

chris