Venue: held by conference call Nov 13, 2012, 11.30am EST (16:30 UTC)
Attending:
Minutes:
Hilmar called meeting to order at 11:34am EST.
[Read More]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. We will post a more detailed agenda in advance of the meeting ( here).
[Read More]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. Mailing lists are still using the old server but will be moved to the AWS site in the next few days and we are working to have little downtime for the lists. Mediawiki sites are moving in stages and so far Bioperl, Biopython, and the OBF wikis have been migrated. This news site has also been migrated to AWS and this is the 1st post from it (will it work!?)
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%. The tally is 38 for provisionally accepting and 1 against. The tally can be seen (and audited) here: https://vote.heliosvoting.org/helios/e/OBFjoiningSPI
[Read More]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:
Minutes:
Hilmar called meeting to order at 11:38am EDT.
i. Approval of changes to O|B|F Bylaws.
[Read More]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.
In addition, many changes have been made, including incompatible changes. For more information, see RELEASE_NOTES.rdoc and ChangeLog.
[Read More]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:
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). This automated testing is therefore complementary to our existing OBF BuildBot server which aims to run nightly tests on volunteer developer machines setup to cover a broad range of operating systems and configurations.
[Read More]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).
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 3.1 and 3.2 (including modules using NumPy). We are now encouraging early adopters to help beta testing on these platforms, and have included a ‘beta’ installer for Python 3.2 under 32-bit Windows.
[Read More]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) .
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):
As in every year, we received many great applications and ideas. However, funding and mentor resources are limited, and we were not able to accept as many as we would have liked. Our deepest thanks to all the students who applied: we sincerely appreciate the time and effort you put into your applications, and hope you will still consider being a part of the OBF’s open source projects, even without Google funding. I speak for myself and all of the mentors who read and scored applications when I say that we were truly honored by the number and quality of the applications we received.
[Read More]
