Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-01-29

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Time Nick Message
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00:24 blackrim towodo: you catching the taxonomic comments on the email list?
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00:32 blackrim1 new taxonomy (16) is going up now
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00:54 kcranstn are these comments on the list new? (i.e. problems that weren't in the last version but are now?)
01:01 kcranstn blackrim: do you have your lists of 'good' trees yet?
01:04 jimallman kcranstn: do you know if NESCent will be open tomorrow? (i've asked Hilmar if we can meet via Skype or Hangout.)
01:04 kcranstn we don't know yet, but we generally follow the durham public school closures
01:06 kcranstn dps closed until at least 2 pm wed
01:07 kcranstn snowpocalypse! 4 inches!
01:07 blackrim kcranstn: these comments are mostly new, but i suspect there are simple solutions to them. now that things are cleaned up a bit, it is easier for them to send comments
01:08 kcranstn lets continue to encourage people to put things in the patch files
01:08 kcranstn since someone needs to do that, else the problems won't be fixed in the next release
01:08 blackrim kcranstn: as for good list of trees, not really other than fungi. laura says that there won't be many more because of OTU mapping problems and rooting things, plants are on their way (they emailed today about it), animals I will talk to joseph about it tomorrow
01:09 blackrim kcranstn: i think before the patch bit we will need to see if there is a common problem (jonathan noted some incertae sedis issues) that will solve many. if not, we will go to patch
01:09 kcranstn so, it sounds like we are close to saying that we have our OTT and tree versions for release
01:10 kcranstn we haven't talked much about feedback mechanisms, but we should do that while the paper is in review / press
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01:10 blackrim i sure do hope so. i think we will haev a few more taxonomy versions but hopefully we are talking a couple weeks at the most
01:10 kcranstn I think we need to cut off the editing adn write this &^$%* paper
01:11 blackrim josephwb: do you think the good animal trees are all going into synth or are there some good ones that aren't going into synth that we can do other analyses on?
01:11 blackrim kcranstn: i share the sentiment. with the OTT though, we do have to get the errors that have species in the wrong kingdom/domain fixed. those are still there :-p but seems like we are getting there
01:12 blackrim hopefully the curator bit will be there by then
01:14 kcranstn I wonder if one solution is to have a way in the synthetic tree browser for 1. users to flag things as problematic; 2 be able to see those flags. That way, even if there are problems (which there will be), we can clearly say "yes, we know this is a problem..."
01:16 blackrim that would be nice
01:17 kcranstn but, that also means that we need to get the synthetic tree up on the main dev.opentreeoflife.org site
01:18 blackrim i imagine there is probably a reasonable way to do that but we need some sort of way of storing that info. yeah, that should be simple enough. right now the synth is just taxonomy so that they can see that
01:18 blackrim (and because some of the taxonomy issues like wrong domains for some species cause synth to be pretty jarbled as you might imagine -- when chromista is in fungi as Romina pointed out)
01:19 kcranstn I get depressed when I think too much about how much phylogeny relies on taxonomy
01:22 blackrim yeah, it is inevitable i think. there is no other way to compare things and obviously for our project, no other way to include 9/10 of life :-p if not more
01:22 blackrim still depressing. especially since our field has not really adequately tackled it seriously (or tried to talk to each other)
01:23 kcranstn partially because we've just been able to build bigger and bigger trees in single analyses rather than having to do synthesis
01:26 blackrim fo sho
01:26 kcranstn we can rant in the paper
01:26 kcranstn :)
01:26 blackrim yeah, and in talks
01:27 kcranstn phyloseminar!
01:28 blackrim yerp
01:29 towodo that incertae sedis problem was just 17 empty taxa.  fixed in draft 17. I'm not aware of any other problems with systematic fixes right now, besides maybe new taxonomic sources
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01:32 towodo the 'unclassified X' cases from bryan are the same problem as the 'incertae sedis'… I introduced what I thought was an innocuous change in the logic and it turned out not to be
01:33 kcranstn ah, good to hear
01:36 blackrim towodo: so are those in draft 17 now? i am moving over 16 now. should i do 17?
01:38 towodo well it's the same story again… they didn't seem important enough to make a new draft, I don't think it's a big effect. draft 17 could have Bryan and Romina's change suggestions too (for example)
01:39 blackrim ok, we can do that. i will let 16 sit overnight
01:48 towodo how can i get people to tell me what to do to the tree, instead of just complain about it?
01:49 towodo each time someone says "x is a problem" I have to either push back to get them to say, or I have to do the work myself
01:55 blackrim i have no idea. what would be the best way for you to get feedback? i am guess the problem is that they are not really prepared to do anything like grep, etc.
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16:16 kcranstn blackrim: can you send me your abstract for the australia meeting? I'll make sure mine doesn't overlap too much ;)
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18:44 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#276 (master - f48b988 : Jim Allman): The build passed.
18:44 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/5b16035f1062...f48b988d9183
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