Those of you doing next generation sequencing may be pleased to know that the next release of Biopython is expected to include support for reading and writing FASTQ and QUAL files within our Bio.SeqIO interface. These formats are used for traditional Sanger capillary sequencing, and Roche 454 sequencing (Roche provide tools to convert from their binary SFF files) with PHRED quality scores.
An Application Note describing Biopython has recently been accepted for publication in the Oxford Journal Bioinformatics . An advance copy of the Open Access article is available online:
Initially for evaluation purposes only, Giovanni and Bartek have setup a mirror of Biopython on GitHub, which is automatically updated from the OBF hosted Biopython CVS repository. See our git migration wiki page for details. If this is favorably received, then moving Biopython from CVS to git seems likely at some point this year. Originally, all the OBF hosted projects used CVS for their source code repositories.
A wiki page for collecting ideas, possible projects, prerequisites, possible solution approaches, mentors, other people or channels to contact for more information or to bounce ideas off of, etc.
All, I am proud to announce that the 1.6 release for BioPerl-run, BioPerl- db, and BioPerl-network are now available by direct download and via CPAN. These are designated as 1.006000, with a requirement for BioPerl 1.6 and higher (1.006000). FIXED: Bio::Tools::Run::Primer3 now accepts primer3 or primer3_core as executable names Bio::Tools::Run::Vista tests now pass if Vista.jar is installed.
Please forward as appropriate and forgive multiple postings.
Google is committed to run the Summer of Code program again this year. It will be for the 5th time. In broad strokes, the program funds what you might call remote summer internships for students to contribute to an open-source software project.
O|B|F News feed is now available in Twitter! You are welcome to follow us. Cheers, The O|B|F Admins.
Release Pumpkin Chris Fields has announced the release of BioPerl 1.6 - the first stable release in a several years containing many significant improvements and bug fixes.
RC4 is up, we are days away from final release…
Belated, and probably most of you knew already, but just in case you didn’t, the 2009 Bioinformatics Open Source Conference (BOSC) was accepted on Dec 16 as a Special Interest Group (SIG) meeting by the respective ISMB 2009 review committee. Special thanks and congratulations to Kam Dahlquist, who agreed again this year to chair the conference, and who pulled the proposal together.