The Open Bioinformatics Foundation (OBF) is a non-profit, volunteer-run group that promotes open source software development and Open Science within the biological research community. Membership in the OBF is free and open to anyone who wants to help promote open source or open science in a biological field.
OBF runs the annual Bioinformatics Open Source Conference (BOSC).
BOSC 2025 took place July 21-22, 2025, in Liverpool, UK (as part of ISMB/ECCB 2025). BOSC 2026 will be part of ISMB 2026 in Washington, DC.
The OBF Event Fellowship program aims to increase diverse participation at events promoting open source bioinformatics software development and open science in the biological research community.
It’s my great pleasure to announce the availability of the BioPerl-run packages (stable & developer releases) for the FreeBSD operating system.
For instructions on how to install BioPerl ports in FreeBSD, please take a look into the Getting Bioperl section of the BioPerl Wiki.
I’ve added a page about RSS feeds in BioPerl. These include links to CVS commits as a RSS feed. This a bit of a hack using cvs2rss and cvs2cl and I have hardcoded it to show the last 30 commits only.
In addition RSS news is now embedded on the main BioPerl and Tracking CVS commits webpages to make for better interlinking between the news and wiki site ( you might even be reading this there).
[Read More]The newest summary of the BioPerl mailing lists has been posted to the wiki:
Post gripes, harrassments, and faint praises at the regular places.
The first of a biweekly summary of BioPerl mailing list summaries has been posted to the wiki:
These will likely be archived on the wiki but may be moved to a more suitable location in the future (maybe to this blog?).
I plan on starting a weekly, possibly biweekly, summary of mailing list traffic. These will be somewhat in the same vein as the Perl5 or Perl6 summaries and will be posted on the blog here and sent to the bioperl-l mail list. Barring another natural disaster here, these should start up next week (covering mail list traffic starting from April 1). The summaries will cover traffic mainly from bioperl-l (the main mail list) but will include biosql-l, since it’s fairly low traffic, and bugs/module updates from bioperl-guts-l.
[Read More]GMANE has been tracking BioPerl traffic for a few years now.
You can see the page here There are several interfaces there including threaded and BLOG-like.
Those interested in tracking the mailing list in RSS readers should grab this link.
There is also a search option for the archives. Try to search GMANE for BLAST
The CVS repository is migrating from ‘pub’ to a new host called ‘dev’ and requires us to re-issue accounts. This will be a good opportunity to verify email addresses and remove unused accounts.
You should have received an email from Chris D requesting specific information and you will get a new password in the response. If not you will need to send a note to the helpdesk at support_AT_open-bio.org. The changover will happen around March 25th.
[Read More]We are moving developer repository to a new server which will require you to get a new developer account. To fix your local repository you should be able to run this on your local repository:
$ find bioperl -name 'Root' | xargs perl -i.backup -p -e 's/pub.open/dev.open/'
or just check out a clean version.
Note that before (and sometime ON) the 25th of March anything that is committed to the dev machine CVS repository will likely get wiped out so it is best to either hold off commits on the 25th or keep copies of stuff around.
[Read More]Installation instructions for Bioperl have been added to the main Bioperl website. They have been updated with links and tags for the wiki. Currently, both pages are accessible through links from Getting Bioperl and Installing Bioperl; these links will be subject to change. Please correct lins/tags/information as necessary.