Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-07-08

| Channels | #opentreeoflife index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
04:00 jimallman joined #opentreeoflife
06:45 jimallman joined #opentreeoflife
10:50 jimallman joined #opentreeoflife
12:15 jimallman joined #opentreeoflife
12:20 kcranstn joined #opentreeoflife
13:33 jimallman joined #opentreeoflife
13:49 josephwb joined #opentreeoflife
14:14 kcranstn joined #opentreeoflife
14:15 kcranstn joined #opentreeoflife
14:50 josephwb hey jimallman
14:50 josephwb which version of OTT is the curator using?
15:08 jimallman hm… i think it’s ott2.9? checking the About pages now...
15:13 jimallman nope, more likely 2.8:  http://files.opentreeoflife.org/ott/
15:14 jimallman josephwb: ^
15:16 jar286 joined #opentreeoflife
15:20 josephwb ok, thanks
15:20 josephwb we'd have to install 2.9 in taxomachine, yes?
15:21 kcranstn yes
15:21 kcranstn jar286 - is ott 2.9 ready?
15:21 josephwb is tht close?
15:21 jar286 2.9 is awaiting some information from Romina so we can get the Hibbett 2007 revised taxonomy in
15:22 josephwb ok, just curious
15:22 jar286 I just did a lot of work on taxonomy synthesis, need to do just a bit more regression testing  (lots of improvements in method)
15:24 jimallman joined #opentreeoflife
15:25 jar286 josephwb, would you like to take a look?  I’ll push out another draft to the files site
15:32 josephwb sure
15:32 josephwb jar286 ^
15:33 jar286 ok, give me a half hour or so, I’ll do another run, and commit + push to a branch  (more than a half hour if my deprecation QC check shows some disaster)
15:37 josephwb no rush at all
16:09 jimallman joined #opentreeoflife
16:23 jar286 wow this one is popular: 555363pg_986,pg_798,pg_1644,pg_782,pg_988,pg_936,pg_1642,pg_1740,pg_1736,pg_1682,ot_89,pg_772,pg_1031,pg_438,pg_785,pg_241,pg_752,pg_967,pg_966,pg_667,pg_2225,pg_2224,pg_666,pg_457,pg_1699,pg_2260,pg_970,pg_238Blumeria graminisif:309596,ncbi:34373,gbif:2578272,irmng:10393588
16:24 kcranstn that grass mildew is everywhere
16:40 kcranstn hey josephwb - question about Table 1 from the manuscript
16:50 josephwb yes?
16:50 josephwb kcranstn ^
16:50 kcranstn reviewer is asking about why we switched from edge support to node support in revision
16:51 kcranstn and why support seems lower in the node table than edge table
16:51 josephwb treemachine edge support was incorrect. node support (from otcetera) was accurate
16:52 kcranstn so the original submission was just wrong?
16:52 kcranstn and does it matter if we call this node support vs edge support?
16:52 josephwb yeah. it was mark and ruchi that found the discrepancies
16:53 josephwb just a sec; getting tea
16:53 kcranstn ok
16:53 kcranstn (I just grabbed tea)
16:57 josephwb i think they are subtley(?) different things, right?
16:58 kcranstn depends how we are calculating this
16:58 josephwb right
16:59 josephwb originally it was (trying) to associate source tree edges with synthetic tree edges
16:59 kcranstn and now?
17:00 josephwb source tree edges that traverse a particualr node
17:00 josephwb for example
17:01 josephwb if a source tree unites clades A & B, the edge metric would count 2 things (the edges leading to the MRCA), while the node metric just counts the node
17:01 josephwb i think
17:02 josephwb to be honest, we are not 100% sure how otcetera does things
17:02 kcranstn jar286 and josephwb - you joining the hangout
17:02 jar286 oh yeah
17:02 josephwb logging in
17:02 josephwb been hanging
17:02 pmidford2 joined #opentreeoflife
18:10 jimallman kcranstn: sorry, i was on the call but your audio (and mine?) was still breaking up
18:10 kcranstn I think your internet is slow  - no one else seemed to be having a problem
18:10 kcranstn when are you back?
18:11 jimallman gotcha. i’m planning to head home on Friday.
18:11 kcranstn ok, let’s talk Monday
18:11 jimallman ok. i’ll keep working on collection tickets in GitHub
18:12 jimallman and i’ll be here off-and-on, so feel free to chat
18:12 kcranstn ok
18:15 kcranstn let’s brainstorm on an interim solution to the lack of collections UI
18:16 kcranstn josephwb - where are the current lists of trees?
18:43 kcranstn jar286 - is this more what you were thinking? https://opentreeoflife.mybalsamiq.com/projects/taxonomybrowser/OTT_browse_v2
18:46 josephwb kcranstn isn't it a table in the paper?
18:46 kcranstn do you have them split by clade?
18:47 josephwb yeah, let me find them
18:47 kcranstn thanks
18:47 jar286 hmm. for browse I prefer higher vertical density.  so the info for Bison should be whatever fits on one line.  usually first taxonomy link is enough for my purposes.  so the single line could be ‘Bison NCBI:1234 2 descendants’,  with single little icon or letters for each flag
18:49 kcranstn what’s the priority for which taxonomy to list?
18:51 kcranstn (actually, that’s not important for the mockup)
18:51 kcranstn reload and let me know about latest versin
18:51 kcranstn version
18:58 kcranstn is the number of children really necessary? you can simply look at the list below the taxon
18:58 jar286 not at the tips
18:59 kcranstn ?
18:59 kcranstn you want number of descendents?
18:59 jar286 if there’s no list below the taxon, that’s exactly when you *do* want to know the size, because you can’t just look at the list
18:59 kcranstn instead of children?
18:59 jar286 descendants
18:59 kcranstn when would there not be a list?
19:00 jar286 some of the taxa on the browse page won’t have lists below them.
19:00 kcranstn for the third level taxa in browse...
19:00 jar286 right, the tipmost level of the browse display
19:01 josephwb lists sent
19:03 josephwb kcranstn, i think i know what is going on with the table
19:03 kcranstn I am all ears
19:03 kcranstn (thanks for the lists)
19:03 josephwb treemachine checks if each synthetic edge has source tree support
19:04 josephwb otcetera looks at nodes, but NOT terminal nodes, so that is where the lack of correspondence comes from (probably)
19:05 josephwb e.g. take a completely unsampled clade of size N. otcetera will give that a score of 1 for taxonomy (the MRCA node). treemachine will give it a score of N (because N edges come from taxonomy)
19:05 josephwb that is my best guess at the moment
19:06 kcranstn can you put this in an email to me and mark? I want to make sure we are right before I put it in the response to reviewers
19:06 josephwb i.e. in rooted trees, "edge support" is equivalent to "node support" of the descenant node
19:06 josephwb ok
19:06 kcranstn thanks
19:07 kcranstn jar286 - another version to review
19:09 jar286 yes, now it needs a frowning face for incertae sedis, and a skull for extinct
19:10 jar286 the species need NCBI links too
19:10 josephwb just to correct that last statement: i.e. in rooted trees, "edge support" is equivalent to "node support" of the descendant node, except terminal edges, because terminal nodes are not reconstructed.
19:10 josephwb sending email now
19:23 kcranstn I made incertae sedis a bucket ;)
19:24 kcranstn actually, I hate these little icons
19:25 jar286 right. I was thinking letters (clickable or mouseoverable for explanation).  but there are so many that making them take space would lead to too much clutter
19:25 jar286 color coding maybe
19:27 kcranstn I think that there should be 1-2 critical flags that show up on these pages and put the rest on the taxon page
19:27 kcranstn reload
19:36 jar286 I don’t see it at https://opentreeoflife.mybalsamiq.com/projects/taxonomybrowser/grid
19:37 jar286 oh sorry
19:37 kcranstn https://opentreeoflife.mybalsamiq.com/projects/taxonomybrowser/OTT_browse_v2
19:38 jar286 right, saw it, looks reasonable
19:38 kcranstn cool
19:38 kcranstn we have a plan
19:38 jar286 welll… then there’s the hard part, the back end
19:39 jar286 (hard is relative)
19:39 kcranstn couldn’t a first pass just work off flat (json) files?
19:40 kcranstn rather than SQL database
19:40 jar286 you mean, add http services to smasher, for example?
19:40 jar286 or a python program
19:41 jar286 oh, we need to do homonym disambiguation somehow
19:41 jar286 ncbi has a page for that
19:41 jar286 but it could be combined with the taxon page (“other taxa with this name”)
19:42 kcranstn yup
20:13 pmidford2 joined #opentreeoflife
20:35 jimallman joined #opentreeoflife
21:47 jimallman joined #opentreeoflife

| Channels | #opentreeoflife index | Today | | Search | Google Search | Plain-Text | summary