Open Bioinformatics Foundation

BOSC Schedule Posted

Posted on June 2, 2009 | kdahlquist

The BOSC 2009 schedule of speakers with links to abstracts has been posted at /wiki/BOSC_2009_Schedule.

BOSC Update: Ruttenberg, Hanmer confirmed as Keynotes, Early Registration Deadline Friday

Posted on May 14, 2009 | kdahlquist

Alan Ruttenberg of Science Commons and Robert Hanmer of the Hillside Group have been confirmed as Keynote Speakers for BOSC 2009. For more information, see the BOSC 2009 web site at /wiki/BOSC_2009. Abstract acceptances went out today–stay tuned for the schedule, which will be posted once the speakers have confirmed their invitations. The early registration deadline for BOSC is Friday, May 15; don’t forget to take advantage of the discounted fee for early registrants at http://www. [Read More]

Dropping Python 2.3 Support

Posted on May 6, 2009 | johnm

As announced here, any last minute requests to postpone dropping support for Python 2.3 from the next release of Biopython must be posted to the main Biopython mailing list no later than Friday, May 8.

Introducing (and expanding) the Biopython Cookbook

Posted on April 30, 2009 | davidw

Hi all, You may have noticed we’re trying out using the wiki for Biopython cookbook entries. It’s a new idea so at the moment there are only a few ‘recipes’ on offer. If you have some tricks you find yourself using time and again to solve a problem why not share them? Similarly, if you find yourself coming up against a problem you can’t seem to solve easily with Biopython’s tools send a message to one of the mailing lists proposing it as a cookbook example and someone just might solve it for you! [Read More]

Biopython projects chosen for Google Summer of Code

Posted on April 27, 2009 | davidw

Congratulations to Nick Matzke and Eric Talevich who have had Biopython projects accepted for this year’s Google Summer of Code. Both projects were accepted as part of The National Evolutionary Synthesis Center’s (NESCent) involvement as a mentoring organisation with the program. Nick will spend his summer working on modules that access locality data from biodiversity databases and incorporate this information in biogeographical and phylogenetic analyses ( Nick’s abstract) while Eric will be building a parser for the emerging PhyloXML format for storing and sharing phylogenetic trees ( Eric’s abstract). [Read More]

Biopython release 1.50

Posted on April 20, 2009 | peterc

We are pleased to announce Biopython release 1.50, featuring some significant additions since Biopython 1.49 was released late last year. GenomeDiagram by Leighton Pritchard has been integrated into Biopython as the Bio.Graphics.GenomeDiagram module. A new module Bio.Motif has been added, which is intended to replace the existing Bio.AlignAce and Bio.MEME modules. Also have a look at Bio.SwissProt and Bio.ExPASy and their revised parsers. As noted in a previous news posting, Bio. [Read More]

Reminder: Abstracts for BOSC 2009 Due April 13

Posted on April 10, 2009 | kdahlquist

This is a reminder from the BOSC 2009 Organizing committee that abstracts for BOSC are due on Monday, April 13.

Biopython 1.50 beta released

Posted on April 3, 2009 | peterc

We are pleased to announce a beta release of Biopython 1.50 for public testing. There have been some significant changes since Biopython 1.49 was released late last year. GenomeDiagram by Leighton Pritchard has been integrated into Biopython as the Bio.Graphics.GenomeDiagram module. A new module Bio.Motif has been added, which is intended to replace the existing Bio.AlignAce and Bio.MEME modules. Also have a look at Bio.ExPASy and the revised Prosite and Enzyme parsers. [Read More]

Biopython on twitter

Posted on March 27, 2009 | peterc

Just to let you all know, Biopython is now on twitter. And in case you missed the OBF announcement last month, so is the O|B|F News feed (and BioPerl). You are welcome to follow us (all) on twitter.

I’d also like to remind people there are news feeds for the Biopython news posts (as RDF, RSS, RSS2, or Atom format). We’re planning to have these automatically echoed onto twitter in future… (update) …and that seems to be working now :)

Biopython and next generation sequencing

Posted on March 26, 2009 | peterc

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. Solexa/Illumina sequencers produce a FASTQ variant where the quality scores are encoded differently, and this is also supported. [Read More]