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Call for Abstracts for the 12th Annual Bioinformatics Open Source Conference ( BOSC 2011), an ISMB 2011 Special Interest Group (SIG). Dates: July 15-16, 2011 Location: Vienna, Austria Web site: /wiki/BOSC_2011 Email: bosc@open-bio.org BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce Important Dates: April 18, 2011: Deadline for submitting abstracts to BOSC 2011 May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors July 13-14, 2011: Codefest 2011 programming session July 15-16, 2011: BOSC 2011 July 17-19, 2011: ISMB 2011 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. [Read More]

This is a reminder that the forthcoming Biopython 1.56 release is planned to be our last release to support Python 2.4. Looking back, we supported Python 2.3 for about six years - it was released July 2003, and Biopython 1.50 released in April 2009 was the last to support it. Similarly, Python 2.4 was released six years ago (November 2004). Dropping Python 2.4 support will allow use to assume standard library modules like the ElementTree XML parser and SQLite 3 support will be available. [Read More]

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. [Read More]

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). [Read More]

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 [Read More]

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: [Read More]

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. [Read More]