Archive for the ‘BioPerl’ Category
Monday, January 18th, 2010
BioPerl developers and users attended the BioPerl satellite meeting on January 13th, just prior to the GMOD Meeting. Several items were covered on the agenda:
In order to start addressing whole genome data with more lightweight objects, we are planning on setting up a lightweight Bio::SeqI object that has a flexible DB ...
Posted in BioPerl, Code, Community, Development, OBF, OBF Projects | No Comments »
Thursday, December 17th, 2009
I'm delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the conventions agreed by the OBF projects:
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
Peter J. A. Cock (Biopython), Christopher J. Fields (BioPerl), Naohisa Goto ...
Posted in BioJava, BioPerl, BioRuby, Biopython, Blogroll, Community, Development, Documentation, General, OBF, OBF Projects | No Comments »
Sunday, November 22nd, 2009
Two of the core BioPerl developers, Jason Stajich and Chris Fields, were interviewed by FLOSS Weekly. The interview is now available as an MP3 on the FLOSS Weekly website; several streaming versions (including podcast) are also available.
Posted in BOSC/ISMB, BioPerl, Code, Community, Development, General, OBF, OBF Projects | No Comments »
Saturday, October 10th, 2009
BioPerl 1.6.1 is now available for ActivePerl as a PPM, instructions for downloading can be found on the BioPerl wiki. This has been tested only for ActivePerl 5.10 and above, so any feedback with older versions of BioPerl would be greatly appreciated.
Posted in BioPerl, Development, Documentation, OBF, OBF Projects | No Comments »
Thursday, October 1st, 2009
Running a bit late on this, so just a quick note that the first alphas for BioPerl-Run, BioPerl-DB, and BioPerl-Network have been uploaded to CPAN:
BioPerl-Run
BioPerl-DB
BioPerl-Network
They can also be downloaded from the BioPerl website:
http://bioperl.org/DIST/RC/
This is the first run where we've switched to a regular Module::Build installation, so expect some initial bumps! ...
Posted in BioPerl, Code, Development, OBF, OBF Projects | No Comments »
Tuesday, September 29th, 2009
We are pleased to announce the immediate availability of BioPerl 1.6.1, the latest release of BioPerl's core code. You can grab it here:
Via CPAN:
http://search.cpan.org/~cjfields/BioPerl-1.6.1/
Via the BioPerl website:
http://bioperl.org/DIST/BioPerl-1.6.1.tar.bz2
http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz
http://bioperl.org/DIST/BioPerl-1.6.1.zip
The PPM for Windows should also finally be available this week, ActivePerl problems permitting (we will post more information when it ...
Posted in BioPerl, Community, Development, Documentation, General, OBF, OBF Projects | 1 Comment »
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 ...
Posted in BioPerl, Code, Development, Documentation | No Comments »
Sunday, January 25th, 2009
Release Pumpkin Chris Fields has announced the release of BioPerl 1.6 - the first stable release in a several years containing many significant improvements and bug fixes.
I am proud to announce, on behalf of the BioPerl core developers, that BioPerl 1.6.0 is now available. This is the first BioPerl core ...
Posted in BioPerl, Code, Development | No Comments »
Friday, January 23rd, 2009
RC4 is up, we are days away from final release...
Posted in BioPerl, Code, Development | No Comments »
Friday, December 26th, 2008
BioPerl has branched for 1.6 and the RC1 is up for testing as Chris announced.
Posted in BioPerl, Development | No Comments »