[Phylobase-devl] a graphics challenge ...

[Peter Cowan]

Steve et. al,

I agree that it we shouldn't miss the opportunity to get a student on  
the project.  I like Steve's ideas.  My personal favorite is a testing  
framework, but I think that it's not really a good project for a  
student.  I think a better project would be, the metadata support.  I  
would see this project involving, writing and implementing a metadata  
spec, and also updating the NCL integration (hopefully updating to the  
latest version) to take advantage of metadata.  The improved NCL  
integration would lead nicely into finishing the multiphylo stuff (not  
sure what needs to be done here).

If we structure the project like that, we have 3 distinct landmarks  
that a student can work on.  Thus if we only get one or two done,  
we've been successful.

Cheer

Peter



On Mar 18, 2009, at 11:49 AM, Steven Kembel wrote:

> 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
>>>>>
>>>>> _______________________________________________
>>>>> Phylobase-devl mailing list
>>>>> Phylobase-devl at lists.r-forge.r-project.org
>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/
>>>>> phylobase-devl
>>>>
>>>>
>>>> ________________________________
>>>> Brian O'Meara
>>>> NESCent
>>>> Durham, NC
>>>> http://www.brianomeara.info
>>>> ________________________________
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Phylobase-devl mailing list
>>>> Phylobase-devl at lists.r-forge.r-project.org
>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-devl
>>>
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
>>> ===========================================================
>>>
>>>
>>>
>>>
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