Friday, December 15, 2006

Phyloinformatics Hackathon

Two dozen leading bioinformatics and phylogenetics software developers are meeting at the National Evolutionary Synthesis Center in a unique hands-on exercise that will produce new open-source software for phylogenetic analysis.
From the press release:

Phylogenetics is the study of the evolutionary relationships between organisms and their genes. The field is fundamental to many areas of basic biological research, and has applications from tracking the progress of disease epidemics to figuring out how best to conserve endangered populations. Techniques from phylogenetics even have been used to study the relationships among human languages and among medieval manuscripts.

Researchers rely on a bewildering array of phylogenetic methods for various specialized tasks. Solving complex problems often relies putting these individual methods together in complex ways. "The flowchart can get very complicated very fast", says Amy Zanne, a postdoctoral researcher at NESCent whose research combines morphological, physiological and ecological data with phylogenetic methods. "Glue software is needed to make these tools speak the same language".

Leading programmers from as far away as Japan and New Zealand have come to NESCent to build the missing pieces of glue software. Participants include developers of specific phylogenetic software packages, on the one hand, and experts in designing glue software toolkits such as BioPerl and BioJava.

The software produced will be freely available under an open-source license, and it is being documented as it is being produced. The first Phyloinformatics Hackathon is taking at place at NESCent in Durham, NC from December 11-15, 2006.