[Phylobase-devl] a graphics challenge ...

[Brian O'Meara]

Just a couple of clarifications on NCL: it's been proposed to put  
nexml in NCL as a GSOC project, but there's no guarantee that students  
for that project will be chosen in the end. That said, just checking  
over the latest NCL code there are some comments about nexml, so I  
imagine it will get in there eventually (especially given the apparent  
enthusiasm of NESCent and NESCent-affiliated working groups and  
scientists for nexml). Also, NCL is good at reading in even complex  
nexus files, but its tree handling code is pretty basic, mainly just  
exporting newick or Nexus trees with or without translation. For tree  
manipulation (traversal, etc.) in C++ I use Rod Page's TreeLib, which  
integrates well with NCL. As to Peter's question about newick strings,  
the way NCL gives trees to phylobase is by passing a newick string and  
then phylobase parses it using modified (and appropriately credited, I  
think) ape code, so we could just modify that slightly more to have it  
get newick strings directly. Having a student work on easier updating  
of NCL for phylobase would be helpful, too. At least with my coding  
skills, I've had trouble incorporating changes in the NCL branch into  
phylobase.

Thanks to Peter and Steve (and Hilmar) for pushing this forward.

Brian


On Mar 18, 2009, at 3:09 PM, Peter Cowan wrote:

> 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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