[Phylobase-devl] Phyloinformatics Summer of Code 2008

[Steve Kembel]

I may have left this too long, but was anyone else interested in  
applying to mentor a student to work on a phylobase-related project?  
It sounds like this would be something that we could do collaboratively.

Peter said...
> Areas that come to mind for me would be:
> * Optimizing basic operations, analyses on multitree objects are
> likely to be memory intensive and slow.
> * Non-ape or ade4 based plotting.  Perhaps implemented in the grid
> system.
> * Transitioning ape and ade4 code to code that operates directly on
> phylo4 objects


I'd add finishing the implementation of a data standard for phylo4d  
objects - either completing the basics of implementing trees +  
(meta)data, or linking some specific existing metadata standard to  
trees (do we have a phyloXML yet?).

I think Peter's last suggestion would be particularly useful -  
implementation and optimization of some of the basic tree operations  
natively in phylobase. To prune a tree we currently are extracting the  
phylo4 tree back into the ape format and pruning it using the ape  
drop.tip function and then turning it back into phylo4... I haven't  
tried manipulating any huge trees yet but this cannot be very  
efficient. I'd be happy to mentor someone working on this. If this  
alone wasn't sufficient for a 12-week project, perhaps other  
objectives (plotting? multiTrees? phylo4d?) could be added and several  
of us could be the primary mentors?

Anyone else interested in participating? My assumption is that we  
could do some collaborative mentoring via phylobase-devl. Hilmar, when  
would we need a proposal ready, and how much detail would be required?

Cheers,
Steve