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This is another blog post to highlight one of the neat tricks you’ll be able to do with Biopython 1.54 (which you can help test with the Biopython 1.54 beta release).

It is often useful to be able to extract a few records from a larger sequence file - for example, some sequences of interest from a full UniProt or GenBank dump. One obvious way to try to do this is to parse the file into an object representation (i.e. SeqRecord objects using Bio.SeqIO.parse(...)), filter to pick out the entries you want, and then write them back to disk (using Bio.SeqIO.write(...)). However, for complex file formats like GenBank this can be lossy ( Bio.SeqIO does not support a 100% identical round trip), and Biopython don’t currently support writing out the SwissProt plain text format used by UniProt. So, that approach won’t work.

Just a friendly reminder that abstracts for BOSC 2010 are due next Thursday, April 15.  See the BOSC web site at /wiki/BOSC_2010 for details.  Submissions will only be accepted electronically at http://events.open-bio.org/BOSC2010/openconf.php.

Graduate students, don’t forget we are offering $250 student travel awards this year. Be sure to check the box indicating that you are a graduate student to be considered for the award.

We are also pleased to announce that Guy Coates, Group leader of the Informatics Systems Group at the Wellcome Trust Sanger Institute, and Ross Gardler, Vice President of the Apache Software Foundation, will be giving keynote presentations at BOSC. http://www.sanger.ac.uk/

One of the small changes coming in Biopython 1.54 (which you can try out already using the Biopython 1.54 beta) is to Bio.SeqIO and Bio.AlignIO. Previously the input and output functions had required file handles, but they will now also accept filenames.

This is a case of practicality beats purity (to quote the Zen of Python), and is particularly handy when doing very short scripts or working at the Python prompt.

For example, filtering a FASTA file to take only entries with a minimum length of 100 can be done like this (with handles):

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.

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!

**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: /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 BOSC 2010 organizing committee is hard at work getting prepared for this July’s meeting in Boston:

/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.

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: