Obf-Projects

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]

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. [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]

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. [Read More]

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. [Read More]

**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 [Read More]

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. [Read More]