[Phylobase-devl] a graphics challenge ...

[Steven Kembel]

Hi all,

this reply is late but maybe just in time since NESCent was just  
accepted into the GSoC. Since it sounds like a parser for phylogenetic  
XML is going into NCL it might be useful to prepare phylobase to  
accept metadata gracefully, although this alone might not be a  
summer's worth of work, perhaps the project could be to fully  
integrate NCL into phylobase as well as modify the phylo4 object to  
work with arbitrary metadata? Brian or others, is it possible to use  
the tree-parsing parts of NCL to allow reading of newick strings into  
phylobase directly? This would be useful. I also like the idea of  
writing some of the performance-sensitive methods in C, I have  
embarassingly not looked at the code in a while but i think some of  
the C code that we were using from ape (i.e. for pruning) may not work  
with the changes we made to tree structure? Tree rearrangement could  
fall into this category as well.

Peter, all the ideas you suggested sound useful, did you have a  
favorite from that list?

Steve

On Mar 10, 2009, at 9:30 PM, Peter Cowan wrote:

> As a former student myself, I'd be willing to help mentor this time
> around.
>
> What types of projects would move phylobase forward?  A parser for one
> of the xml phylogeny formats?  Metadata support?  Multi-phylo4?
> Tighter integration with NCL? Rewrites of performance sensitive
> methods in C? A testing framework for the package?
>
> Other ideas?
>
> Peter
>
>
>
> On Mar 9, 2009, at 7:35 PM, Hilmar Lapp wrote:
>
>> I'd like to echo Brian's comment. You (phylobase) can have students
>> working over the summer for you; all you need to do is put up a
>> project idea and designate mentor(s).
>>
>> I know that mentoring is also work, but the results can greatly push
>> along a project.
>>
>> Let me know if there's anything I can help with coordinating this.
>>
>> 	-hilmar
>>
>> On Mar 9, 2009, at 12:05 PM, Brian O'Meara wrote:
>>
>>> Good link, Ben. Google Summer of Code is starting up again, and  
>>> there
>>> are no R projects yet on the NESCent page (<https://www.nescent.org/
>>> wg_phyloinformatics/Phyloinformatics_Summer_of_Code_2009>).  
>>> Perhaps a
>>> way to charge the paddles?
>>>
>>> Brian
>>>
>>> On Mar 9, 2009, at 2:07 AM, Ben Bolker wrote:
>>>
>>>>
>>>> http://www.stat.columbia.edu/~cook/movabletype/archives/2009/03/
>>>> more_on_display.html
>>>>
>>>> Someday soon I hope to get out the defibrillator and see if we
>>>> can get phylobase going again ...
>>>>
>>>> cheers
>>>>  Ben
>>>>
>>>> -- 
>>>> Ben Bolker
>>>> Associate professor, Biology Dep't, Univ. of Florida
>>>> bolker at ufl.edu / www.zoology.ufl.edu/bolker
>>>> GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc
>>>>
>>>> _______________________________________________
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>>>
>>>
>>> ________________________________
>>> Brian O'Meara
>>> NESCent
>>> Durham, NC
>>> http://www.brianomeara.info
>>> ________________________________
>>>
>>>
>>>
>>> _______________________________________________
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>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
>> ===========================================================
>>
>>
>>
>>
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