Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-02-17

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All times shown according to UTC.

Time Nick Message
01:28 kcranstn joined #opentreeoflife
02:49 ilbot3 joined #opentreeoflife
02:49 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
12:26 jar286 joined #opentreeoflife
13:00 kcranstn joined #opentreeoflife
13:10 kcranstn how should we orchestrate the web testing today?
13:46 kcranstn joined #opentreeoflife
14:13 jar286 kcranstn, sorry just now saw your message
14:15 kcranstn no problem
14:16 jar286 I have no sophisticated ideas
14:16 jar286 I can watch what’s going on on the two servers using ‘top’ …
14:17 jar286 but as for what people should do all I can think of is to navigate to and around their favorite taxa
14:20 kcranstn searches?
14:20 jar286 yes that too
14:21 jar286 maybe some curation stuff… read-only perhaps
14:22 kcranstn open a study, open a tree?
14:22 jar286 something like that
14:23 kcranstn the specific API calls don’t really matter, just that we generate many of them, right?
14:24 jar286 if the question is general load testing, yes.
14:46 josephwb joined #opentreeoflife
15:21 jimallman fyi, i’ve broken the devapi server for the moment, will have it back up in a sec
15:25 jimallman all better now
15:44 kcranstn joined #opentreeoflife
15:58 kcranstn joined #opentreeoflife
16:25 kcranstn this look reasonable for testing instructions: https://docs.google.com/document/d/1bw_ePrR1j7dhou-V4Q6HYJbmzFE-Z6aPGBtK7L5tGeU/edit#
16:34 kcranstn a different suggestion for studies and trees?
16:56 kcranstn this is going to be embarassing if our small group of opentree folks hurts performance
17:39 pmidford2 joined #opentreeoflife
20:05 kcranstn joined #opentreeoflife
20:40 kcranstn joined #opentreeoflife
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21:55 josephwb you there jar286?
21:55 josephwb and/or kcranstn
21:55 kcranstn here
21:56 josephwb do you know of a metric for the binary-ness of a tree?
21:57 kcranstn something other than ratio of branches to nodes?
21:57 josephwb yeah
21:57 josephwb (num internal nodes) / N-2
21:58 josephwb seems to work for a rooted tree
21:58 josephwb where N is num tips
21:58 josephwb but is there some go-to metric?
21:59 kcranstn not that I know of off the top of my head
22:00 kcranstn why not simply use that ratio?
22:00 josephwb depends on if i count the root node or not
22:00 kcranstn are only some of the trees rooted?
22:00 josephwb no, all are rooted
22:01 kcranstn then it shouldn’t matter
22:02 josephwb ((A,B,C,D),(E,F,G,H));
22:03 josephwb if i don't count root, it has:
22:03 josephwb 2 / 8-2 = 1/3
22:04 josephwb if i count root:
22:04 josephwb 3 / 8-1 = 3/7
22:05 kcranstn but if you are comparing trees, and they are all rooted it doesn’t matter if you count the root
22:05 josephwb oh, they have different leaf sets
22:05 josephwb num leaves
22:05 kcranstn so fraction of potential nodes?
22:05 kcranstn which you can define as including the root (or not)
22:08 josephwb (((A,B),E),(G,H));
22:08 josephwb has ratio of 1 whether i include root or not:
22:08 josephwb 4 / 5-1 = 1
22:09 josephwb 3 / 5-2 = 1
22:09 josephwb but the tree above is either 3/7 or 1/3
22:09 josephwb oh, yer gone
22:10 josephwb [to self] can binary-ness ranking change if root is included/excluded?
22:22 kcranstn joined #opentreeoflife

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