Phyloinformatics Hackathon

Date11-Dec-2006 ~ 15-Dec-2006
SummaryOverview & Background
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.
A hackathon is a hands-on software development meeting that allows programmers from different teams to intensively work on a common set of objectives and interact face-to-face.

The focus of this first NESCent phyloinformatics hackathon will be on leveraging the Bio* open source software tools to provide the "glue" and lower the barriers for using phylogenetic tools within automated workflows. Please check out the formal proposal.

The hackathon will take place Dec 11-15 in Durham, NC, at NESCent.

Due to the nature of the hackathon and limited space, attendance is by invitation. If you have not been contacted by the organizers but desire to attend, please contact Hilmar Lapp.
NESCent is sponsoring travel, accommodation, and expenses for meals etc. Details will be emailed to confirmed participants.

Call For Input
The organizers invite community input in order to focus efforts on the most urgent or pervasive problems. Input may take several forms:

  • changes to the current list of use cases
  • actual data files (e.g., alignments, trees, other data) for use in testing
  • citations to published papers that pose challenging problems or that provide useful methods
  • your "wish list" for a phyloinformatics computing platform

The favored mechanism for providing input is to post your comments directly to this wiki. In order to do so, you may simply register at the wiki site and start editing the document. If you have a data file to use for testing, you may upload it to the wiki (and add a link describing it). Alternatively, you may send comments (and files) to Hilmar Lapp (please indicate if you don't wish to share your comments or data files on the wiki). You may also contact any of the organizers with questions or comments.
Click here for more information.