Constructing complicated NCBI Entrez searches can be tricky, but it turns out one of the Entrez Programming Utilities called Entrez EInfo can help. For example, suppose you want to search for mitochondrial genomes from a given taxa - either just in the Entrez web interface, for use in a script with EFetch. I knew from past experience about using name[ORGN] in Entrez to search for an organism name - but how would you specify just mitochondria?

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

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.

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.

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?

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.

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.

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

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.

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.

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.