finally walked toward the light of BioPerl in October 2008. He is the author of
in the 1.6 release, and
- Bio::Tools::Run::Maq & Bio::Assembly::IO::maq (howto)
- Bio::Tools::Run::BWA, Bio::Tools::Run::Samtools, & Bio::Assembly::IO::sam (howto)
- Bio::Tools::Run::StandAloneBlastPlus and related modules (howto)
- Bio::DB::SoapEUtilities and related modules (howto)
in the bioperl-run trunk, as well as
for viewing BioPerl pod and inserting BioPerl templates in many convenient ways in the Emacs editor.
Under the kindly eye of Chris Fields, he has contributed to some significant renovations of
- Bio::LocatableSeq (see Bugs #2476, #2682, #2689) (looking at 1.7 integration);
Bio::Treenamespace (#2456) (1.6.1);
Bio::Restrictionnamespace (#2855) (1.6.1);
and quite a few other little doodads. He was honored with a commit bit in January 2009, wiki sysop privs in March 2009, and invited to become a core developer in July 2009. He also is helping to wrangle the BioPerl Scrapbook, to which you ought to contribute. He cast his own kindly eye upon Chase Miller, a 2009 Google Summer of Code student via NESCent, mentoring him through the development of BioPerl modules for the reading and writing of NeXML.
But enough of the third-person-emanuative. My major professional interest is the epidemiological sequence analysis of pathogens, with particular emphasis on HIV and Staphylococcus aureus. I work regularly with some excellent human beings in Canada, Europe, India, and the US. Currently, I am doing business as Fortinbras Research, where BioPerl can be seen in action.
I received my PhD in Molecular Evolution at the University of Chicago in 2000, and am currently an associate editor for the Journal of Molecular Evolution. I was once an assistant professor, and I was once a housekeeper at a Salvation Army summer camp. And so on.
ISMB 2010 poster: BioPerl at 15: New Features, New Directions.