Archive for the ‘Biopython’ Category
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 ...
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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 ...
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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.
Posted in Biopython, Code, Community, Development, OBF | 1 Comment »
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 ...
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Monday, April 27th, 2009
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 ...
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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 ...
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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 ...
Posted in Biopython, Community, Development, OBF Projects | No Comments »
Friday, March 27th, 2009
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 ...
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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 ...
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Sunday, March 22nd, 2009
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 ...
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