After 10 years of development, the BioRuby paper is finally published in the Bioinformatics journal.  The article is open access, so please take a look.

BioRuby: Bioinformatics software for the Ruby programming language
Naohisa Goto, Pjotr Prins, Mitsuteru Nakao, Raoul Bonnal, Jan Aerts and Toshiaki Katayama
Bioinformatics 2010; doi: 10.1093/bioinformatics/btq475

The Biopython team is proud to announce Biopython 1.54, a new stable release of the Biopython library. Biopython 1.54 comes five months after our last release and brings new features, tweaks to some established functions and the usual collection of bug fixes.

This is the first stable release to feature the new Bio.Phylo module which can be used to read, write and take data from phylogenetic trees in Newick, Nexus and PhyloXML formats. The module is the result of Eric Talevich’s Google Summer of Code project which was supported by The National Evolutionary Synthesis Center (NESCent).

Biopython now supports the reading, writing and indexing of Standard Flowgram Format (SFF) files produced in 454 sequencing. Jose Blanca (the brains behind the widely used sff_extract tool) provided code to handle SFF files and Peter Cock has integrated that code with Bio.SeqIO. Adding SFF support to SeqIO makes it possible to convert these files to the FASTQ, FASTA and QUAL formats (as trimmed or untrimmed reads).

As well as adding features the new release tweaks and extends some of the core modules:

• Both Bio.SeqIO and Bio.AlignIO will accept filenames as well as handles, as detailed here.
• The multiple sequence alignment object that underlies Bio.AlignIO has been improved.
• Bio.SeqIO can read and write EMBL nucleotide files.
• The dictionary-like objects returned by Bio.SeqIO.index() have a new method “get_raw” that gets unparsed data from a file as a string, as detailed here.
• Bio.Entrez includes some more DTD files, in particular eLink_090910.dtd, used by our NCBI Entrez Utilities XML parser.

Binaries and source files for Biopython 1.54 are available from the downloads page. The documentation has been updated to include the changes made since our last release.

A big thanks to every one who tested our beta release or submitted bugs since Biopython 1.53. And an especially big thanks to everyone who contributed to this release, including five first time contributors:

• Anne Pajon (first contribution)
• Brad Chapman
• Christian Zmasek
• Diana Jaunzeikare (first contribution)
• Eric Talevich
• Jose Blanca (first contribution)
• Kevin Jacobs (first contribution)
• Leighton Pritchard
• Michiel de Hoon
• Peter Cock
• Thomas Holder (first contribution)

BioPerl has migrated to git and GitHub!  We have also set up a mirror set of several key repositories at the great public git hosting site repo.or.cz.

If you are a current BioPerl developer (had a previous account for direct access to our prior Subversion repository), please sign up for a GitHub account and let us know your user ID.  Also, add the extra email (where ‘DEVNAME’ is your original Subversion account ID).  This should map any previous commits from the older Subversion and CVS repository to your new GitHub account.

The following are ways everyone can download the latest code.

Using git

Note you can replace ‘bioperl-live.git’ with any of the repository names (bioperl-db, bioperl-run, etc).  For BioPerl developers (GitHub collaborators) you have a choice of SSH or HTTP:

  git clone git@github.com:bioperl/bioperl-live.git

  git clone https://bioperl@github.com/bioperl/bioperl-live.git

The open read-only link (for everyone):

  git clone git://github.com/bioperl/bioperl-live.git

or using the mirror site:

  git clone git://repo.or.cz/bioperl-live.git

Using SVN (read-only)

We will also support read-only access to GitHub with Subversion.  We may allow write support at some later point.  To use svn:

  svn checkout http://svn.github.com/bioperl/bioperl-live.git

Direct downloads

Tagged releases can be found here:

http://github.com/bioperl/bioperl-live/downloads

The latest source code here:

http://github.com/bioperl/bioperl-live/archives/master

Forking BioPerl and Pull Requests

We intend on using git and GitHub to their fullest.  With that in mind, we encourage users to fork BioPerl code, make changes, commit them to your forked repository, and submit pull requests.

Documentation

We’re also in the process of updating our local developer documents for help with those who haven’t used git before.  In particular, we have a Using Git page, and have added RSS feeds for our repository commits.

Enjoy!

chris

Update: SVN version fixed, thanks to DaveMessina++ for pointing it out.

I’m pleased to announce the acceptance of OBF’s 2010 Google Summer of Code students, listed in alphabetical order with their project titles and primary mentors:

Mark Chapman (PM Andreas Prlic) – Improvements to BioJava including Implementation of Multiple Sequence Alignment Algorithms

Jianjiong Gao (PM Peter Rose) – BioJava Packages for Identification, Classification, and Visualization of Posttranslational Modification of Proteins

Kazuhiro Hayashi (PM Naohisa Goto) – Ruby 1.9.2 support of BioRuby

Sara Rayburn (PM Christian Zmasek) – Implementing Speciation & Duplication Inference Algorithm for Binary and Non-binary Species Tree

Joao Pedro Garcia Lopes Maia Rodrigues (PM Eric Talevich) – Extending Bio.PDB: broadening the usefulness of BioPython’s Structural Biology module

Jun Yin (PM Chris Fields) – BioPerl Alignment Subsystem Refactoring

Congratulations to our accepted students!

All told, we had 52 applications submitted for the 6 slots (5 originally assigned, plus 1 extra) allotted to us by Google.  Proposals were extremely competitive: 6 out of 52 translates to an 11.5% acceptance rate.  We received a lot of really excellent proposals, the decisions were not easy.

Thanks very much to all the students who applied, we very much appreciate your hard work.

Here’s to a great 2010 Summer of Code, I’m sure these students will do wonderful work.

Rob Buels
O|B|F GSoC 2010 Administrator

In another quirk to the FASTQ story, recent Illumina FASTQ files don’t actually use the full range of PHRED scores – and a score of 2 has a special meaning, The Read Segment Quality Control Indicator (RSQCI, encoded as ‘B’).

Hats off to Dr Torsten Seemann for raising awareness of this issue in his post on the seqanswers.com forum, referring to a presentation by Tobias Mann of Illumina which says:

The Read Segment Quality Control Indicator:

• At the ends of some reads, quality scores are unreliable. Illumina has an algorithm for identifying these unreliable runs of quality scores, and we use a special indicator to flag these portions of reads
• A quality score of 2, encoded as a “B”, is used as a special indicator. A quality score of 2 does not imply a specific error rate, but rather implies that the marked region of the read should not be used for downstream analysis.
• Some reads will end with a run of B (or Q2) basecalls, but there will never  be an isolated Q2 basecall.

So, armed with this knowledge, you might want to apply a simple trimming criteria to any Illumina FASTQ files – remove anything after and including a PHRED quality score of 2 (encoded as ASCII ‘B’).

We could do this with the rich object orientated SeqRecord based API in Biopython, but when dealing with massive FASTQ files this overhead matters. Instead we’ll stick with plain Python strings:

from Bio.SeqIO.QualityIO import FastqGeneralIterator
handle = open("B_trimmed.fastq", "w")
min_length = 10
for title, seq, qual in FastqGeneralIterator(open("untrimmed.fastq")) :
    #Find the location of the first "B" (PHRED quality 2)
    trim = qual.find("B")
    if trim == -1:
        #No need to trim
        handle.write("@%s\n%s\n+\n%s\n" % (title, seq, qual))
    elif trim >= min_length:
        #Take everything up to the first B
        handle.write("@%s\n%s\n+\n%s\n" % (title, seq[:trim], qual[:trim]))
handle.close()

The above will work fine on any recent Illumina FASTQ files using the RSQCI scheme, but on older Illumina FASTQ files the “B” character is just a low quality score – and can occur even in the middle of a read. Here trimming at the first “B” might be unwise. Instead, we can trim any trailing “B” characters – which will do the same thing on RSQCI based FASTQ files where the “B” should only appear at the end:

from Bio.SeqIO.QualityIO import FastqGeneralIterator
handle = open("B_trimmed.fastq", "w")
min_length = 10
for title, seq, qual in FastqGeneralIterator(open("untrimmed.fastq")) :
    qual = qual.rstrip("B") #Remove any trailing B characters
    length = len(qual)
    if length >= min_length:
        seq = seq[:length] #trim to match
        handle.write("@%s\n%s\n+\n%s\n" % (title, seq, qual))
handle.close()

You could easily modify this example to read from stdin and write to stdout (see this cookbook example), or take filenames as command line arguments to turn this into a general purpose “FASTQ B-trimming script”.

Just a friendly reminder that abstracts for BOSC 2010 are due next Thursday, April 15.  See the BOSC web site at http://www.open-bio.org/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.

On behalf of the BOSC 2010 organizing committee, I hope to see you there!

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.

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