Synopsis of the Hackathon
The Phyloinformatics Hackathon took place 11th to 15th December, 2006, at NESCent in Durham, North Carolina. On day 1, we heard user stories and chose six of the use cases as top-priority targets for development. At the end of the day we assembled into toolkit-specific groups to devise toolkit-specific plans focusing on one or more targets. For the rest of the week, we worked.
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. Details are outlined further in the formal proposal.
The hackathon took place Dec 11-15 in Durham, NC, at NESCent. In addition to providing the facilities, NESCent sponsored travel, accommodation, and expenses for meals etc. Due to the nature of the hackathon and the limited space, attendance was by invitation.
The process and results of the hackathon were published in a 2007 paper: Lapp, Hilmar, Sendu Bala, James P. Balhoff, Amy Bouck, Naohisa Goto, Mark Holder, Richard Holland, et al. 2007. “The 2006 NESCent Phyloinformatics Hackathon: A Field Report.” Evolutionary Bioinformatics Online 3: 287–296.
Documentation of and for hackathon activities
- Full list of use cases
- Detailed documentation of priority use cases and outcomes
- Toolkit-specific hackathon targets and to-dos.
- Jim Balhoff, User Story (PDF)
- Brian Sidlauskas, User Story (PDF)
- Alisha Holloway, User Story (PDF)
- Jason Stajich, User Story (PDF)
- Stefanie Hartmann, User Story (PDF)
- Amy Bouck, User Story (PDF)
- Rutger Vos, BioPhylo (PDF)
- Arlin Stoltzfus, Core EIG Use Cases (PDF)
- Jason Stajich and Albert Vilella gave a tutorial at the ISMB 2007 Conference titled "Implementing phylogenetic workflows for comparative genomics using BioPerl". The tutorial teaches, among other things, how to apply some of the BioPerl accomplishments made at the hackathon.
- Tutorial slides and hand-outs. Available under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 License.