Minutes:2012 Nov ConfCall
Posted on November 13, 2012
| admin
Agenda Old business Sep 2012 BoD meeting minutes New business Election of new Board members. Nominated candidate is Chris Fields. Review and possibly revamping of the procedure for joining and maintaining the OBF membership Asset transfer to SPI Minutes Venue: held by conference call Nov 13, 2012, 11.30am EST (16:30 UTC)
Attending:
Directors: Jason Stajich, Nomi Harris, Peter Cock, Hilmar Lapp Guests: Scott Markel, Chris Fields Minutes:
Hilmar called meeting to order at 11:34am EST.
[Read More]OBF Board meeting 13 Nov
Posted on November 6, 2012
| peterc
The Open Bioinformatics Foundation (OBF) will be holding a public Board of Directors meeting on Tuesday, 13 Nov, 2012, at 11.30am EST (8.30am PST, 17:30 CET, 16:30 UTC/GMT).
The meeting will be held online or over conference call. We will post details about how to dial in or connect closer to the date ( here).
On the agenda Richard Holland and Chris Fields are running for election to the Board, and some other items primarily up for discussion, including how to keep our membership roll up-to-date and increasing with the least barriers.
[Read More]Server transition process to AWS servers
Posted on November 5, 2012
| stajich
Our aging server which has run for 5+ years the OBF sites has finally reached end of its lifespan. We are currently migrating sites to AWS volumes and sites for a temporary period while we decide about how to continue to support these services in the future. There will be some downtime while the all-volunteer OBF admin team makes time to fix this.
Nearly all projects use public source code repositories such as github or sourceforge so no problems with access to the code should be limiting.
[Read More]OBF is now an SPI-associated project
Posted on October 12, 2012
| hilmar
I am very pleased to announce that the Open Bioinformatics Foundation (O|B|F) is now a Software in the Public Interest (SPI) associated project, rather than its own not-for-profit incorporation.
An electronic vote of O|B|F members on whether or not to provisionally approve the invitation from SPI closed yesterday at 19:00 UTC. We had a participation of 39 out of 105 eligible, or 37%, which is far above the quorum of 10%.
[Read More]Minutes:2012 Sep ConfCall
Posted on September 11, 2012
| admin
Agenda Old business 2011 December BoD meeting minutes New business Approval of changes to O|B|F Bylaws Minutes Venue: held by WebEx conference with audio bridge through phone (donated by BioTeam), scheduled for Sep 11, 2012, 11.30am EDT (15:30 UTC)
Attending:
Directors: Hilmar Lapp, Nomi Harris, Chris Dagdigian, Jason Stajich, Peter Cock Guests: Scott Markel Minutes:
Hilmar called meeting to order at 11:38am EDT.
Old business: Hilmar moves to approve Dec 11 meeting minutes.
[Read More]BioRuby 1.4.3 released
Posted on August 21, 2012
| NaohisaGoto
We are pleased to announce the release of BioRuby 1.4.3. This new release fixes bugs existed in 1.4.2 and improves portability on JRuby and Rubinius.
Here is a brief summary of changes.
Bio::KEGG::KGML bug fixes and new class Bio::KEGG::KGML::Graphics for storing a graphics element. Many failures and errors running on JRuby and Rubinius are resolved. Strange behavior related with “circular require” is fixed. Fixed: Genomenet remote BLAST does not work. Fixed: Bio::NucleicAcid.
[Read More]Travis-CI for Testing
Posted on July 30, 2012
| peterc
Earlier this year BioRuby and then Biopython and BioPerl started using Travis-CI.org, a hosted continuous integration service for the open source community, to run their unit tests automatically whenever their GitHub repositories are updated:
BioRuby Biopython BioPerl The BioRuby team are also using Travis-CI for automated testing of their new ‘plugin’ ecosystem, BioRuby Gems, or BioGems.
Travis-CI gives us continuous testing, but for the moment only covers one operating system (currently 32 bit Ubuntu Linux using Virtual Machines).
[Read More]Biopython 1.60 released
Posted on June 25, 2012
| peterc
Source distributions and Windows installers for Biopython 1.60 are now available from the downloads page on the Biopython website and from the Python Package Index (PyPI).
Platforms/Deployment We currently support Python 2.5, 2.6 and 2.7 and also test under Jython 2.5 and PyPy 1.9 (which does not cover NumPy or our C extensions). Please note that Python 2.4 or earlier is not supported.
Most functionality is also working under Python 3.
[Read More]BioJava 3.0.4 released
Posted on May 23, 2012
| andreas
BioJava 3.0.4 has been released and is available from
http://www.biojava.org/wiki/BioJava:Download as well as from the
BioJava maven repository at http://www.biojava.org/download/maven/ .
- This is mainly a bug fix release addressing issues with the protein
structure and disorder modules
- One new feature: SCOP data can now be accessed from either the
original SCOP site in the UK (v. 1.75) or from Berkeley (v. 1.75A) .
Students selected for GSoC
Posted on April 24, 2012
| peterc
Hello all,
I’m very pleased and excited to announce that the Open Bioinformatics Foundation has selected 5 very capable students to work on OBF projects this summer as part of the Google Summer of Code (GSoC) program.
The accepted students, their projects, and their mentors (in alphabetical order):
Wibowo Arindrarto:
SearchIO Implementation in Biopython
mentored by Peter Cock Lenna Peterson:
Diff My DNA: Development of a Genomic Variant Toolkit for Biopython
[Read More]
