O|B|F News

Biopython 1.54 beta released

April 2, 2010 – 1:19 pm
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.AlignIO), the new Bio.Phylo module, and the Bio.SeqIO support for Standard Flowgram Format (SFF) files. Source distributions and Windows installers are available from the downloads page on the Biopython website (biopython.org). We are interested in getting feedback on the beta release as a whole, but especially on the new features and the Biopython Tutorial and Cookbook (PDF). (At least) 10 people contributed to this release (so ...

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O|B|F in Google Summer of Code

March 21, 2010 – 2:26 pm
The Open Bioinformatics Foundation has been accepted as a mentoring organization for this summer's Google Summer of Code.  Our list of project ideas and mentors is linked from the O|B|F GSoC page. Student applications must be submitted to Google by April 9, 2010, see the official GSoC 2010 FAQ. That is less than three weeks away!

Posted in BioDAS, BioJava, BioLib, BioMOBY, BioPerl, BioRuby, Biopython, Blipkit, Community, Google Summer of Code, OBDA / BioSQL, OBF, OBF Projects | No Comments »

BOSC 2010 Call for Abstracts

March 2, 2010 – 9:19 pm
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 ...

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OpenBio solution challenge: Project updates at BOSC 2010

January 28, 2010 – 4:45 pm
The BOSC 2010 organizing committee is hard at work getting prepared for this July's meeting in Boston: http://www.open-bio.org/wiki/BOSC_2010 One of the items we've traditionally had at the conference is a project update from each of the OpenBio affiliated groups. This year, we're thinking about organizing these talks around a central theme: the OpenBio solution challenge. We start with a biological question of general interest, and each of the project talks would 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). For this to be successful, it of course requires interest and enthusiasm from y'all fine folks involved with the projects. Specifically: Is there interest from your group ...

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BioPerl at GMOD Meeting 2010

January 18, 2010 – 11:58 pm
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 ...

Posted in BioPerl, Code, Community, Development, OBF, OBF Projects | No Comments »

BioRuby 1.4.0 released

December 29, 2009 – 6:22 am
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 & ...

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BOSC 2010 Request for Input

December 18, 2009 – 9:39 pm
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 ...

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Sanger FASTQ format and the Solexa/Illumina variants

December 17, 2009 – 12:28 pm
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.

Posted in BioJava, BioPerl, BioRuby, Biopython, Blogroll, Community, Development, Documentation, General, OBF, OBF Projects | No Comments »

Biopython 1.53 released

December 15, 2009 – 12:57 pm
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. SQLite support (built into Python 2.5+) was added to our BioSQL interface (Brad Chapman). This is still a little experimental as we are using a draft BioSQL SQLite ...

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2009 O|B|F Board of Directors meeting

December 14, 2009 – 3:24 pm
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).

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