- BOSC 2010 Call for Abstracts
- Abstract submissions for the 11th Annual Bioinformatics Open Source Conference (BOSC 2010) are now open. At-a-glance BOSC is an ISMB 2010 Special Interest Group (SIG) Date: July 9-10, 2010 Location: Boston, Massachusetts, USA BOSC 2010 web site: http://www.open-bio.org/wiki/BOSC_2010 Abstract submission via Open Conference System site:
- OpenBio solution challenge: Project updates at BOSC 2010
- The BOSC 2010 organizing committee is hard at work getting prepared for this July’s meeting in Boston: http://www.open-bio.org/wiki/BOSC_2010 One of the items we’ve traditionally had at the conference is a project update from each of the OpenBio affiliated groups. This year, we’re thinking about organizing these talks around a central theme: the OpenBio solution challenge. We start with a biological question [...]
- BioPerl at GMOD Meeting 2010
- BioPerl developers and users attended the BioPerl satellite meeting on January 13th, just
- BioRuby 1.4.0 released
- We are pleased to announce the release of BioRuby 1.4.0. This new release contains many new features, in addition to bug fixes and improvements. PhyloXML support: Support for reading and writing PhyloXML file format is added, developed by Diana Jaunzeikare, mentored by Christian M Zmasek and co-mentors, supported by Google Summer of Code 2009 in collaboration with [...]
- BOSC 2010 Request for Input
- The BOSC organizing committee is soliciting input on the planning of BOSC 2010 so that we can make it a successful and productive conference for the O|B|F community. You may send your suggestions to the bosc@open-bio.org e-mail address or add suggestions to the BOSC 2010 talk/discussion wiki page at: http://www.open-bio.org/wiki/Talk:BOSC_2010. Please respond to the questions in this post by January 8, 2010.
- Sanger FASTQ format and the Solexa/Illumina variants
- 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 (BioRuby), Michael L. Heuer (BioJava) [...]
- Biopython 1.53 released
- We are pleased to announce the availability of Biopython 1.53, a new stable release of the Biopython library, three months after the release of Biopython 1.52. This is our first release since migrating from CVS to git for source code control. There have been some additions to our core objects – the Seq (and related UnknownSeq) [...]
- 2009 O|B|F Board of Directors meeting
- The official 2009 Board of Directors meeting is taking place today, Monday Dec 14, at 4pm EST (21:00 UTC) via teleconference. If you are an O|B|F member, you will have received the announcement and dial-in information earlier. O|B|F Board of Director meetings are public – anyone interested in O|B|F business can participate, which is one reason [...]
- Interleaving paired FASTQ files with Biopython
- This post is about paired end data (FASTA or FASTQ) and manipulating it with Biopython’s Bio.SeqIO module (see also FASTQ conversions & speeding up FASTQ). There are two main ways of presenting paired end data in FASTA or FASTQ files: Paired files, with matching entries for the forward and reverse reads (probably the norm with Illumina data) Single [...]
- BioPerl interview in latest FLOSS Weekly
- Two of the core BioPerl developers, Jason Stajich and Chris Fields, were interviewed by FLOSS Weekly.
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- BioPerl at GMOD Meeting 2010
- BioPerl developers and users attended the BioPerl satellite meeting on January 13th, just
- Sanger FASTQ format and the Solexa/Illumina variants
- 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 (BioRuby), Michael L. Heuer (BioJava) [...]
- BioPerl interview in latest FLOSS Weekly
- Two of the core BioPerl developers, Jason Stajich and Chris Fields, were interviewed by FLOSS Weekly.
- BioPerl core 1.6.1 PPM available
- 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.
- First 1.6.1 alphas of BioPerl-Run, BioPerl-DB, BioPerl-Network
- 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! There are a few [...]
- BioPerl 1.6.1 released
- 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 becomes available). Tons of bug fixes [...]
- Release 1.6 of BioPerl-run, BioPerl-db, BioPerl-network
- 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 names 2) Bio::Tools::Run::Vista tests now pass if Vista.jar is installed. 3) bug fix in [...]
- BioPerl 1.6 released
- 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.
- BioPerl 1.6 RC4
- RC4 is up, we are days away from final release…
- BioPerl branched for 1.6, RC1 is up
- BioPerl has branched for 1.6 and the RC1 is up for testing as Chris announced.
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