[Phylobase-devl] Google summer of code and NESCent

Peter Cowan pdc at berkeley.edu
Wed Mar 10 02:29:19 CET 2010

NESCent has participated in the last several Google Summer of Code (GSOC) programs.  Hilmar does a great job organizing both the mentors and the students, and smoothing out the process.  Working with NESCent was a positive experience for me as a GSOC student and hopefully phylobase got something worthwhile out of it as well.  

The application period for mentoring organizations has begun, so if we are interested we should submit ideas soon/now.  In addition to ideas we would need volunteers to mentor students also (~5hr a week).  GSOC is a good deal because we get a student to devote significant time to the project and perhaps be recruited for long term contribution.  It's also a good opportunity to attract someone with a skill set different from our own. 

Last year Steve and I wrote and offered to mentor the following project idea.  In the end we didn't get strong enough applicants to beat out the other project proposals.  What other areas are good candidates for summer of code students?



=== Adding metadata support to phylogenetic data representations in R ===

; Rationale : One result of the recent NESCent Hackathon on Comparative Methods in R has been the development of the phylobase package, which seeks to provide a set of S4 classes and methods for representing and manipulating phylogenetic trees and associated data in R. Phylobase contains structures for representing phylogenetic trees and associated data, but methods for representation of metadata and multiple trees, and interfaces with other data formats (i.e. nexus, nexml) remain incomplete.

; Approach : The methods for tree/data manipulation and import in phylobase are currently a mixture of S3 and S4 methods and C/C++ extensions. The goal for this project will be to implement metadata support for trees and associated data using object-oriented S4 classes and methods. It would also be necessary to extend/rewrite the interface with the Nexus Class Library which phylobase uses for reading trees in the Nexus format.  A final part of this project could be writing and implementing a multi-tree data format for phylobase.  Nexus files, and the Nexus Class Library both support multi-tree files, however phylobase has only a rudimentary implementation.

; Challenges : The general challenge for this project will be to identify and implement data structures for metadata that accommodate current metadata needs yet are flexible enough for future use.  Additional challenges involve interfacing R and the C++ Nexus Class Library, and will likely require programming skills not only in R, but also in C/C++ and make.

; Involved toolkits or projects : R, phylobase, Nexus Class Library, make.

; Degree of difficulty and needed skills : Easy to medium. Need knowledge of R and S4 classes, C++, and make

; Mentors : Peter Cowan, Steve Kembel

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