Bioperl 1.0 milestone

by Bruce Stewart

Related link: http://bio.perl.org



Bioperl is the leading open source project for the use of Perl in bioinformatics, providing extensions to Perl for handling biological data. After almost 7 years in the making, the Bioperl project has posted its 1.0 release.



Facilitated by the Open Bioinformatics Foundation, work on Bioperl is coordinated with related bio* efforts including biojava.org, biopython.org, DAS, bioruby.org, and biocorba.org.



O'Reilly & Associates recently cosponsored two bioinformatics "hackathons" -- the first one was in Tucson at our recent Bioinformatics conference -- which were a big help in moving these open source efforts along. Along with Electric Genetics, O'Reilly arranged these events so the programmers involved could get together face-to-face and do some serious coding.



Getting the best bioinformatics programmers from around the world together in a room full of computers proved to be a really good idea. Jason Stajich, a core developer for Bioperl, and the coordinator of the BioCORBA project, says "the real-time interactions that I was able to have with the other developers allowed us to quickly address problems and discuss solutions."



A partial list of feature additions to BioPerl that were achieved during the hackathons include OBDA data access, Bio::Graphics (a sequence drawing module), and
Bio::Biblio (a bibliographic query objects module). Sequence caching and sequence parsing speedup were also tackled, as well as interoperability
testing and debugging with the other toolkit projects.



While the geographic spread of the bio* programmers make these projects models of collaborative development, sometimes there's still no replacement for pizza, coffee, a whiteboard, and a late night of hacking. Stajich summed up the sentiments of many of the programmers,
"It's incredible how much we were able to get done when we could bounce problems and solutions off each other and not wait for timezone email lag."