We are happy to announce the long-awaited release of BioPerl v1.7.0. The release is now available on CPAN and Github.
During this release series, we will move some extraneous code to separate repositories and CPAN releases, primarily to reduce the number of dependencies required for BioPerl installation (in many cases for modules that are never used) and also reduce maintenance overhead.
This may only impact you if your code incorrectly list the immediate downstream dependencies that you utilize. For example, we have now moved Bio::Coordinate code to a separate repo and will release it as a separate distribution on CPAN. If your tools require Bio::Coordinate::Result and list this module as a dependency, you should be fine: a separate Bio::Coordinate release should pull in the latest BioPerl, until then it would pull in the last BioPerl release with that module. However, if you list Bio::Root::Root or Bio::Perl as a dependency to pull in Bio::Coordinate::Result, your installation will not work correctly (as Bio::Root::Root is not the proper code dependency). We can work with distributions affected to help with this transition and will be more consistently evaluating reverse dependencies on CPAN for upcoming releases as we split out code. Please post issues on Github if you see problems with your code and the latest release.
[Read More]Last year’s Google Summer of Code 2014 was very productive for the OBF with six students working on Bio* and related bioinformatics projects. We applied to be part of GSoC 2015, but unfortunately this year were not accepted.
Google’s program is enormously popular, and over-subscribed, meaning Google has had to rotate organisation membership. The OBF is grateful to have been accepted in 2010, 2011, 2012 and 2014. This year any participation will be down to individual projects to find a willing umbrella group from the organisations accepted for GSoC 2015. For example, a Biopython project was included under NESCent for GSoC 2013.
[Read More]Update: The deadline for responding has been extended to January 25. 
The 2014 Google Summer of Code (GSoC) is coming up soon. The published timeline puts the mentoring organization applications from Feb 3 to 14.
OBF participated on behalf of our member projects in 2010, 2011, and 2012. Those participations were both important and successful. Through them, our projects gained new contributors, new features, and new community members. The mentors involved from our projects learned as much from the experience as the students, and formed bonds. The mentoring organization payment allowed OBF to sponsor community events and infrastructure.
[Read More]The latest BioPerl release (v1.6.923) is now available on CPAN. This is a point release to address a few bugs, as well as push out the recent code updates that Francisco Ossandón has made to improve Windows support and improve Bio::Location (among other bits and pieces).
Contributing to the release:
Enjoy!
chris
UPDATE:
As a bit of time has passed since we originally intended to make a new release, I forgot that (in that time period) Carnë Draug had released a split-out version of Bio::Biblio to CPAN this past March.
Unfortunately that release (v1.7) appears to have version collisions with this one (v.1.6.910); therefore I’m packaging a new point release ( v1.6.920) that removes Bio::Biblio to prevent this. That has now been uploaded to CPAN and should be available shortly.
[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]The latest BioPerl-DB, BioPerl-Run, and BioPerl-Network code has been released to CPAN:
Please report any bugs to our Redmine server.
Enjoy!
chris
BioPerl 1.6.9 is now available in CPAN. In this release:
Just to note, this is the first release after we reworked the Build.PL system, so we will probably hit a few speed bumps along the way. This is in effort to simplify the process for further work this summer on modularizing BioPerl, but it also makes new releases much easier to make. In particular, this has only been tested on Ubuntu Linux and Mac OS X (no Windows testing has occurred yet). Please post if there are any problems.
[Read More]Great news: Google announced today that the Open Bioinformatics Foundation (OBF) has been accepted as a mentoring organization for this summer’s Google Summer of Code!
GSoC is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). Students are paid a $5000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see GSoC 2011 FAQ.
[Read More]
