Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-03-19

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Time Nick Message
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02:48 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
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15:17 josephwb using internal node label processing (post. probs) in curator for first time. feels clunky
15:18 kcranstn suggestions for improvement?
15:18 josephwb select post. prob as metric, wasn't obvious that i had to "capture" them
15:19 josephwb only figured it out b/c warning did not go away
15:19 kcranstn can you make an issue for that? screen caps help
15:19 josephwb when i click "capture" weird warning comes up too
15:19 josephwb "Warning: This can shift ambiguous node labels to their adjacent edges..."
15:20 josephwb don't know what that means, or whether my tree is good after the procedure
15:31 jimallman from fuzzy memory: these labels are originally attached to nodes, but sometimes we make a choice that associates them with edges. changes to tree structure (even re-rooting) changes the relationship betw. nodes and edges, so can affect how these labels are ultimately applied in the Nexson.
15:32 josephwb hmm.
15:32 josephwb maybe say: associated with nodes, so make sure rooting is correct first
15:32 jimallman maybe we can hint at best practices, depending on how we interpret the internal node labels. some interpretations might best be applied ASAP (on the original tree as rooted), others might better wait.
15:32 josephwb maybe NOT ALLOW it until rooting is formally confirmed
15:32 jimallman til after rooting, etc
15:33 jimallman re: NOT ALLOW, that’s an option if this is always the right choice.
15:33 jimallman but i’m not sure about that.
15:35 josephwb NOT ALLOW in a nice way: please confirm rooting first
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18:09 jar286 it’s that time…
18:09 jimallman indeed   https://github.com/pulls?user=OpenTreeOfLife
18:09 jimallman no progress on ‘OTU stats (area chart version)’
18:11 jar286 no progress on MIAPA review
18:11 jar286 re https://github.com/OpenTreeOfLife/reference-taxonomy/pull/127 …
18:11 jar286 I implemented the tests and ran them, and they passed
18:11 jar286 I should commit the test script
18:11 kcranstn correct, karen has been distracted with synthesis and nescent stuff
18:13 jar286 I *did* commit the test script…
18:13 jar286 if kcranstn is satisfied with that we can merge 127
18:14 kcranstn yup
18:14 jar286 ok, here goes…
18:15 jar286 done. so how about https://github.com/OpenTreeOfLife/opentree/pull/622
18:15 jimallman #622 is tiny, cosmetic, but low-risk (see https://github.com/OpenTreeOfLife/opentree/issues/619 for symptom description)
18:16 kcranstn looks fine to me
18:16 jar286 ok, looks good
18:16 jar286 I’ll merge
18:16 jimallman it doesn’t justify rebuilding production, imo, unless we have other reasons
18:16 kcranstn where are the results of the monophyly tests?
18:17 jar286 right, I agree
18:17 jar286 the results?… the script prints nothing if a test passes.  so there was no output
18:17 kcranstn ah, ok
18:17 jar286 you can run them yourself if you like (I’d need to find the URL for 2.9)
18:18 kcranstn no, I trust you :)
18:18 jar286 it’s a bit weird since there are a lot of homonyms.
18:19 kcranstn argument for another field in the monophyly test?
18:19 jar286 for the inclusion tests you can’t just look up the two taxa independently, you have to look for one inside the other
18:19 jar286 probably, yes
18:19 kcranstn I think we decided that the inclusion tests needed to be rewritten
18:19 jar286 they’re certainly useful for OTT testing
18:19 jar286 e.g. Bacteria is a homonym (there’s a genus)
18:20 jar286 the tests ought to be 3-way tests:  A is outside (or inside) the mrca(B,C) clade
18:21 jar286 I’ve been thinking about internal node labeling a bit… goes back to my idea of obtaining identifier stability in a phylocode-like way
18:22 kcranstn this seems like a good conversation for when you are here in April
18:22 jar286 sure
18:23 jimallman so labels could be defined, and float along with a set of “phylo-coordinates” to any internal node??
18:24 jar286 yes
18:24 jar286 we could have outgroups as well as ingroups, to protect against completely ridiculous assignments
18:24 jimallman thanks, i was just pondering how that could go wrong as the tree changes
18:25 jimallman sanity checks seem advisable
18:25 kcranstn hilmar and nico just got a grant for phyloreferences
18:25 jar286 interesting.
18:25 kcranstn also part of the annotation database
18:37 jimallman if we’re done with PR review, i’m going to grab lunch…
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