Archive for the ‘Development’ Category

Biopython 1.51 beta released

Tuesday, June 23rd, 2009

A beta release for Biopython 1.51 is now available for download and testing. In the two months since Biopython 1.50 was released, we have introduced support for writing features in GenBank files using Bio.SeqIO, extended SeqIO's support for the FASTQ format to include files created by Illumina 1.3+, and added a ...

Clever tricks with NCBI Entrez EInfo (& Biopython)

Sunday, June 21st, 2009

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 ...

Dropping Python 2.3 Support

Wednesday, May 6th, 2009

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

Wednesday, April 29th, 2009

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 ...

Biopython release 1.50

Monday, April 20th, 2009

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 ...

Biopython 1.50 beta released

Friday, April 3rd, 2009

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 ...

Biopython and next generation sequencing

Thursday, March 26th, 2009

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 ...

Biopython and version control systems

Tuesday, March 17th, 2009

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 ...

Google Summer of Code: Project ideas page

Tuesday, March 10th, 2009

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. has been setup: http://open-bio.org/wiki/Google_Summer_Code_2009

Release 1.6 of BioPerl-run, BioPerl-db, BioPerl-network

Thursday, February 26th, 2009

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: 1) Bio::Tools::Run::Primer3 now accepts primer3 or primer3_core as executable ...