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 nearly $9 million. My programming skills include Java (Spring, Hibernate), Perl, C, web standards (XML/XSLT/XSD/HTML/CSS), ontologies (OWL, protege), databases (MySQL, PostgreSQL, dbxml, DB2), 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. I presently volunteer some of my time as the developer of the web service API.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, Jason Caravas and Mark Jensen.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.
