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.

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Poster session at GCCBOSC2018

OBF Treasurer Heather Wiencko introducing OBF at BOSC 2024

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.

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Ruth Nanjala, an OBF Travel Award winner, by her poster

Bioperl 1.5.0 released

Bioperl 1.5.0 Developer’s release is available for download.

We’ll update the website to reflect this new release.

The odd-numbered releases are called developer releases and are not deposited on CPAN. Please note that the API in 1.5.0 may change before the 1.6.0 release. which will be consider a stable API. We may do another developer release before 1.6.0 goes out.

Lots of people have contributed to this release, I apologize for not naming them all. I’ll try to cover some: thanks to Aaron Mackey for getting this release started, Brian Osborne for extensive documentation improvements, Nathan Haigh for volunteering to make a PPM of the release and Barry Moore and Nathan answering many of the windows related questions, Allen Day & Scott Cain & Steffen Grossmann for the work on FeatureIO, GFF3, and SeqFeature::Annotated, Chris Mungall for the work with Unflattener to merge GenBank annotations into GFF3 objects.

Please see the AUTHORS file for a complete list of contributors.

Jason Stajich on behalf of the Bioperl developers.

http://portal.open-bio.org/pipermail/bioperl-l/2005-January/018031.html

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Bioperl 2005 Summary

I just wanted to use the end of the year as a chance to reflect on what we’ve accomplished in 2004 and think about what 2005 holds for Bioperl. List Message [Read More]

Bioperl preparing 1.5 release

Bioperl developers are preparing a 1.5 release, you can grab the pre-release for testing at http://bioperl.org/DIST. We would greatly appreciate you downloading and testing this code before it is released by running ‘make test’.

See Aaron’s post announcing the RC1 candidate.

Biopython 1.30 Release

I’m happy to announce a new release of Biopython 1.30, available today from http://biopython.org. This release contains a number of new modules and substantial changes to older modules. As a result of the changes, we’ve bumped up to a brand new major number. Please do download, test with your code, and report any bugs or problems to the normal lists (biopython at biopython.org or biopython-dev at biopython.org). For the full details about changes, please see: http://portal. [Read More]

Bioperl Bootcamp June 21-25

The Mailing list post Continuing on the BioJava Bootcamp of 2003, The Quebec Bioinformatics Network (BioneQ) is organizing its first BioPerl Bootcamp, to be held at the Universite de Montreal from June 21-25 2004. The invited speakers are leaders in the use of Perl in bioinformatics and development of BioPerl: Aaron Mackey (U. of Pennsylvania) Jason Stajich (Duke University) Lincoln Stein (Cold Spring Harbor Labs) Seminars and exercise sessions will be in a Linux computer lab for a total hands-on experience. [Read More]

Bioperl 1.4 for Windows

Bioperl version 1.4 for Windows is available. Thanks once again to Nigam Shah for creating and testing the PPM and PPD files.

BioKnoppix

BioKnoppix is a new live CD linux, based on KNOPPIX, with EMBOSS 2.8.0, jemboss, artemis, clustalx, Cn3D, ImageJ, BioPython, Rasmol, Bioperl, Bioconductor. It being made available by The University of Puerto Rico High Performance Computing facility (HPCf) and the Puerto Rico Biomedical Research Infrastructure Network (BRIN-PR). Great stuff!

Biopython 1.24 Release

I’m happy to announce the 1.24 release of Biopython. As normal Biopython is available from http://biopython.org. The major changes in this release, in addition to the usual bug fixes, are: New parsers for Phred and Ace format files – thanks to Frank Kauff New Code for dealing with NMR data – thanks to Bob Bussell New SeqUtils modules for codon usage, isoelectric points and other protein properties – thanks to Yair Benita New code for dealing with Wise contributed by Michael EZ-Retrieve sequence retrieval now supported thanks to Jeff Bio. [Read More]

Bioperl Release 1.4

The stable Bioperl release 1.4 is available for immediate use at: http://bioperl.org/DIST.

We are releasing simultaneously three modules:

  • bioperl-core - core bioperl modules ( gz b2z)

  • bioperl-ext - C compiled extensions ( gz b2z)

  • bioperl-run - wrappers for external programs ( gz b2z)

They will also appear shortly at the IUBIO mirror (later today) and in CPAN.

Remember, all the external modules needed by bioperl-core can be installed from CPAN under name Bundle-BioPerl.

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