EventID: 1
Shortname: phylohack
URL: http://informatics.nescent.org/wiki/Phylohackathon_1
Original proposal: http://informatics.nescent.org/wiki/Proposal
While powerful analysis tools exist for comparison of evolutionary models, inference of phylogenetic trees, and testing of hypotheses in a comparative framework, these tools can sometimes be difficult to incorporate into automated workflows due to incompatible interfaces and data exchange formats.
A number of software development projects have striven to address this issue, for example by creating a modular architecture that the phyloinformatic community can contribute to (e.g. Mesquite, R, Bio* toolkits) or by advocating object and data models that the community can adopt (e.g. BioSQL, BioCORBA, CIPRES).
The widely-used Bio* toolkits (BioPerl, BioJava, BioPython, BioRuby, …) have successfully provided a “glue” that allows interoperability of diverse applications, automation over large scales, and integration of data from diverse sources, primarily in genomics. Other, modular architectures along comparable lines (pise, CIPRES, phycas, mesquite) are in various stages of development and adoption. This wiki, and the “hackathon” it documents, seeks to integrate the knowledge of phylogenetic programmers from these different projects.
The objective of this first NESCent phyloinformatics hackathon was (and is on a continuing basis) on leveraging the Bio* open source software tools to provide the “glue” and lower the barriers for using phylogenetic tools within automated workflows.
This event called them use cases rather than pitches. The link is here: http://informatics.nescent.org/wiki/UseCases. There was also a list of targets.
The documentation page of the hackathon wiki contains a list of projects.