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
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!
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Biopython projects chosen for Google Summer of Code
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).
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Biopython release 1.50
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.
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Biopython 1.50 beta released
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.
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Biopython on twitter
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
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.
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Biopython paper published
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:
P.J.A. Cock, T. Antao, J.T. Chang, B.A. Chapman, C.J. Cox, A. Dalke, I. Friedberg, T. Hamelryck, F. Kauff, B. Wilczynski and M.J.L. de Hoon (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, doi:10.1093/bioinformatics/btp163
Biopython and version control systems
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. At the start of 2008, BioPerl and BioJava moved over to Subversion (SVN), followed by BioSQL.
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Biopython release 1.49
We are pleased to announce the release of Biopython 1.49. There have been some significant changes since Biopython 1.48 was released a few months ago, which is why we initially released a beta for wider testing. Thank you to all those who tried this and reported the minor problems uncovered.
As previously announced, the big news is that Biopython now uses NumPy rather than its precursor Numeric (the original Numerical Python library).
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