If you’ll be at BOSC or ISMB - please see this page and sign your name if you would like to try and meet up. We’ll do a developer’s dinner as well as have a BoF.
About the OBF
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 will be July 21-22, 2025, in Liverpool, UK (as part of ISMB/ECCB 2025). BOSC 2024 took place July 15-16, 2024, as part of ISMB 2024 in Montréal, Canada.
OBF Event Awards
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.
Hey what’s happening?
So Mailing list summaries have stopped because we need someone else to help post these summaries. Not a light job unfortunately. If you are interested, please post to the mailing list or contact Jason, Sendu, or Chris for more details. This is one way you can help BioPerl without contributing code if you aren’t comfortable with that type of commitment.
Two things that have been discussed on the mailing list lately are:
[Read More]
HOWTO automate tree drawing
I updated the Trees HowTo with some code demonstrating how to automatically generate postscript trees from newick or nexus tree files. This uses the Bio::Tree::Draw::Cladogram module that will draw Phylograms or Cladograms. With a few unix tools ( eps2png and epstopdf [part of TeX]) you can generate png and pdf files automatically making this an easy addition to phylogenetic pipelines that generate webpages as well as stand alone applications.
mediawiki updated
Updated mediawiki to 1.10
Did a bulk creation of a number of modules wiki pages for modules that had been previously created but not added to the wiki. Added them with default module templates.
Biopython release 1.43
We are pleased to announce the release of Biopython 1.43.
This release includes a brand-new set of parsers in Bio.SeqIO by Peter Cock for reading biological sequence files in various formats, an updated Blast XML parser in Bio.Blast.NCBIXML, a new UniGene flat-file parser by Sean Davis, and numerous improvements and bug fixes in Bio.PDB, Bio.SwissProt, Bio.Nexus, BioSQL, and others. Believe it or not, even the documentation was updated.
Source distributions and Windows installers are available from the Biopython website at http://biopython.
[Read More]
Bioperl 1.5.2 Release
I’m proud to announce the final release of Bioperl 1.5.2. Full details are available at http://www.bioperl.org/wiki/Release_1.5.2
Bioperl 1.5.2 Release
I’m proud to announce the final release of Bioperl 1.5.2. Full details are available at http://www.bioperl.org/wiki/Release_1.5.2
RC5 for 1.5.2
Sendu has posted 1.5.2 RC5. There may be a few more kinks to work out, so try this release and report if there are problems with the tests.
RC 1.5.3
Sendu has announced that Release Candidate 3 is available for download and testing. This may be the last RC before the 1.5.2 release so give it a whirl and speak up with any problems or concerns.
Mediawiki updated
Bioperl wiki is now running Mediawiki 1.8.2. nothing too different under the hood at this point, the mediawiki people probably have more to say in the release-notes.