[Phylobase-devl] misc.

Brian O'Meara bcomeara at nescent.org
Wed Dec 17 22:31:38 CET 2008 

For teleconferencing tomorrow, NESCent recommends Adobe Connect  
(NESCent has a license, no downloads required). You can connect at  
<http://dukeuniversity.na3.acrobat.com/phylobase/>. It allows multi- 
user voice and video chat (video degrades with enough users), also  
screen sharing of windows, applications, or the entire computer, file  
transfer, etc. It seems pretty easy (this is my first time using it):  
you log on as a guest, enter your name, and then press a button on  
the bottom of the screen to start voice chat (it's the second full  
button from the left -- it says "Talk". Click on the thing that looks  
like a printer icon to have the mic always on, otherwise just press  
the Talk button when you have something to say). Headsets, or at  
least headphones, are recommended. If anything goes wrong, we can  
switch to a backup voice-only approach.  IRC is constantly up, too.

Note that we still haven't talked about Steve's comments below about  
priorities  and NeXML -- I didn't want that lost in this organizing  
thread.

Brian


On Dec 17, 2008, at 11:40 AM, Brian O'Meara wrote:

> IRC channel is now up on freenode. Our channel is phylobase. Since
> we're all in different timezones, I'm logging output to my computer
> and posting it online every 5 minutes so we can see what went on
> while we slept: you can see it at < http://snipurl.com/irclog>. Feel
> free to add more sophisticated logging -- I don't know about IRC bots
> and the like.
>
> Brian
>
> On Dec 16, 2008, at 11:32 PM, Steven Kembel wrote:
>
>> Hi all,
>>
>> Noon eastern on Thursday works for me for a virtual meeting. Skype/
>> Gizmo or whatever NESCent IT recommends is fine. How about an IRC
>> channel as well for Thursday/Friday?
>>
>> Off the top of my head my preference is to work first on the bug and
>> feature requests related to phylo4d objects and metadata, and then  
>> the
>> tree traversal and ordering methods. This will initially involve  
>> going
>> through the phylo4d constructors and methods and making sure
>> everything is working well, or getting rid of methods that are  
>> broken,
>> to allow submitting the package to CRAN.
>>
>> Hilmar mentioned implementing NeXML support in phylobase as a  
>> possible
>> target. I think the feature request for metadata/annotation slot
>> implementation for phylo4 and phylo4d objects should try to follow
>> existing metadata/annotation standards as implemented in things like
>> NeXML rather than coming up with another format, so I'd like to
>> discuss this on Thursday as well.
>>
>> Cheers,
>> Steve
>>
>> On Dec 16, 2008, at 2:29 PM, Brian O'Meara wrote:
>>
>>> Should we start on the back and forth regarding minihack planning  
>>> and
>>> agenda? Ben suggested noon Eastern for daily virtual meetings. Any
>>> preferences on how to set them up, or should I just ask NESCent IT
>>> for its current recommendation? How should we start adding things to
>>> the agenda? We have 11 feature requests <https://r-forge.r-
>>> project.org/tracker/?atid=491&group_id=111&func=browse> and 1 bug
>>> <https://r-forge.r-project.org/tracker/?
>>> atid=488&group_id=111&func=browse> on R-forge, but these haven't  
>>> been
>>> changed in months. We could add things there and modify their
>>> priority and assignment, do it more informally over email, throw
>>> things on a wiki, etc.
>>>
>>> Brian
>>>
>>> On Dec 8, 2008, at 3:15 PM, Ben Bolker wrote:
>>>
>>>>  Yes.
>>>>
>>>>  I was thinking of setting up another time for a preliminary
>>>> skype/conference/chat meeting, but that feels like overkill.
>>>> Perhaps we can set an agenda/tentative task assignments by
>>>> back-and-forth over e-mail.
>>>>
>>>>  cheers
>>>>    Ben
>>>>
>>>>
>>>> Brian O'Meara wrote:
>>>>> Hi, all. It appears that Dec. 18-19 are the only days when
>>>>> everyone who
>>>>> has filled out the poll can do the minihack (Thursday and Friday
>>>>> of next
>>>>> week). See the poll at <http://www.doodle.com/9pndm3xaszh7gpck>.
>>>>> Shall
>>>>> we thus schedule the minihack for both of those days?
>>>>>
>>>>> Brian
>>>>>
>>>>>
>>>>> On Dec 5, 2008, at 7:44 PM, Marguerite Butler wrote:
>>>>>
>>>>>> Hi Folks,
>>>>>>
>>>>>> Sorry for the silence. Still teaching my two classes, so I'm
>>>>>> pretty
>>>>>> tied up.
>>>>>>
>>>>>> Basically next week (week of Dec. 15) and week of Jan 13 are the
>>>>>> only
>>>>>> possibilities for me.  (I'll be spending some much needed time
>>>>>> with my
>>>>>> daughter over Xmas and then I have to get ready for the SICB
>>>>>> meetings
>>>>>> in the first week of Jan. (I'm back to work Jan 12, but things
>>>>>> will be
>>>>>> pretty nuts that day, so Jan 13 is the first day for me).
>>>>>>
>>>>>> Mike Alfaro and I are going to be teaching two sessions at  
>>>>>> SICB, a
>>>>>> first day for complete beginners in R and a second evening
>>>>>> session o
>>>>>> comparative analysis in R, so if there is anything you'd like to
>>>>>> show
>>>>>> off, please let me know. Hopefully I can get stuff ready in
>>>>>> time to
>>>>>> get feedback from the developers:).
>>>>>>
>>>>>> Feel free to go ahead without me on the Hackathon, though, if my
>>>>>> schedule is a problem.
>>>>>>
>>>>>> Marguerite
>>>>>>
>>>>>> On Dec 5, 2008, at 12:26 PM, Peter Cowan wrote:
>>>>>>
>>>>>>> The list was cc'd, and Steve has already filled out a slot in  
>>>>>>> the
>>>>>>> 'doodle'.
>>>>>>>
>>>>>>> peter
>>>>>>>
>>>>>>> On Dec 5, 2008, at 2:23 PM, Ben Bolker wrote:
>>>>>>>
>>>>>>>> For what it's worth, Thibaut sent his apologies --
>>>>>>>> he's going to start a new postdoc very soon.
>>>>>>>> (I don't remember if he cc'd this list.)
>>>>>>>> Marguerite, Steve?
>>>>>>>>
>>>>>>>> Ben
>>>>>>>>
>>>>>>>> Peter Cowan wrote:
>>>>>>>>> I've added my schedule to http://www.doodle.com/
>>>>>>>>> 9pndm3xaszh7gpck
>>>>>>>>>
>>>>>>>>> On Dec 4, 2008, at 7:31 AM, Brian O'Meara wrote:
>>>>>>>>>> On Dec 3, 2008, at 2:47 PM, Steven Kembel wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi all,
>>>>>>>>>>>
>>>>>>>>>>>> * chat on the list about a deadline and milestones needed
>>>>>>>>>>>> for a CRAN release?  (My votes: merged plotting code, all
>>>>>>>>>>>> known
>>>>>>>>>>>> bugs fixed [I don't actually think that would be hard],
>>>>>>>>>>>> node-
>>>>>>>>>>>> labeling
>>>>>>>>>>>> scheme updated).
>>>>>>>>>>>> * have one or more additional conference calls?
>>>>>>>>>>> Discussing this on the list or in a conference call would be
>>>>>>>>>>> great. I
>>>>>>>>>>> think we are in pretty good shape for most of these things.
>>>>>>>>>>> -plotting code should be a straightforward merge of the
>>>>>>>>>>> summer of
>>>>>>>>>>> code
>>>>>>>>>>> branch into trunk
>>>>>>>>>
>>>>>>>>> Agreed this shouldn't take long and might even happen before
>>>>>>>>> the
>>>>>>>>> virtual hackathon if I can find a few hours to button up loose
>>>>>>>>> ends.
>>>>>>>>>
>>>>>>>>>>> I will go through the list of bugs/feature requests on R-
>>>>>>>>>>> Forge and try to clean out the requests that have been dealt
>>>>>>>>>>> with. If
>>>>>>>>>>> others have fixed bugs/feature requests go ahead and change
>>>>>>>>>>> their
>>>>>>>>>>> status to resolved.
>>>>>>>>>>> -The node-labeling scheme has been updated already unless
>>>>>>>>>>> there
>>>>>>>>>>> were
>>>>>>>>>>> further changes needed.
>>>>>>>>>>>
>>>>>>>>>>>> * an ambitious plan: have a "virtual hackathon" sometime
>>>>>>>>>>>> between now and mid-January, where we all agree to the best
>>>>>>>>>>>> of our abilities to spend the same day or two investing
>>>>>>>>>>>> a significant amount of hacking time ... we could have
>>>>>>>>>>>> one or two 'plenary sessions' a day and do Skype/chat
>>>>>>>>>>>> in between ... what do you think?
>>>>>>>>>>> This sounds like a great idea, I'd be interested, will have
>>>>>>>>>>> some
>>>>>>>>>>> time
>>>>>>>>>>> over the 'holidays' to work on this. What are people's
>>>>>>>>>>> schedules
>>>>>>>>>>> like
>>>>>>>>>>> - would a brief call sometime in the next few weeks work?
>>>>>>>>>> I'm generally unconstrained, as we're not traveling for the
>>>>>>>>>> holidays.
>>>>>>>>>> We can set up a poll to schedule a conference call once we
>>>>>>>>>> have a
>>>>>>>>>> general idea of when people can talk. I've started a poll
>>>>>>>>>> about a
>>>>>>>>>> mini-hackathon itself at http://www.doodle.com/
>>>>>>>>>> 9pndm3xaszh7gpck .
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> 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
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> -- 
>>>>>>>> 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
>>>>>>>
>>>>>>
>>>>>> ____________________________________________
>>>>>> Marguerite A. Butler
>>>>>> Department of Zoology
>>>>>> University of Hawaii
>>>>>> 2538 McCarthy Mall, Snyder 405
>>>>>> Honolulu, HI  96822
>>>>>>
>>>>>> Dept: 808-956-8617
>>>>>> Lab:  808-956-5867
>>>>>> FAX:   808-956-9812
>>>>>> http://www.hawaii.edu/zoology/faculty/butler.html
>>>>>> http://www2.hawaii.edu/~mbutler
>>>>>> http://www.hawaii.edu/zoology/
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>>
>>>>
>>>> -- 
>>>> 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
>>
>> _______________________________________________
>> 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


________________________________
Brian O'Meara
NESCent
Durham, NC
http://www.brianomeara.info
________________________________

More information about the Phylobase-devl mailing list