Software

I am an active contributor of open source bioinformatics software. In the past, I have developed educational software (web-based, for BioMedia, the Zoological Museum of Amsterdam, Simon Fraser University; and CD-ROM based for the AMSTEL institute). The projects listed below – for which I am the primary author – are current and ongoing. Their combined worth is estimated by an independent open source code analysis group at $600,000. My programming skills include Perl, Java, C, web standards (XML/XSLT/XSD/HTML/CSS), ontologies (OWL, protege), databases (MySQL, PostgreSQL, dbxml), collaborative development best practices (svn, test-driven development) and design patterns.

TreeBASE

TreeBASE is a relational database of phylogenetic information hosted by the San Diego Supercomputing Center. In the Fall of 2008 I joined the development project to redesign TreeBASE from the ground up.

Bio::Phylo

Bio::Phylo is a collection of modules for phylogenetic analysis and biodiversity assessments. Primary author: Rutger Vos, with contributions from Aki Mimoto, Klaas Hartmann and Jason Caravas.

NEXML

NEXML is an emerging data exchange standard for phylogenetics and bioinformatics.

CIPRES

The CyberInfrastructure for Phylogenetic Research is an NSF-sponsored 5 year project to develop an architecture for data exchange and distributed analysis. I am the designer of the perl5 branch of the infrastructure.

COPE

An implementation of OMG-compliant CORBA ORB and related architecture, COPE was originally conceived by Bart Schuller, I am the current maintainer.

Exception::Class::TCF

A port of Java/C++ style exception handling.