Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-01-15

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

All times shown according to UTC.

Time Nick Message
01:59 towodo joined #opentreeoflife
11:59 towodo joined #opentreeoflife
12:22 mtholder joined #opentreeoflife
12:37 towodo joined #opentreeoflife
14:37 josephwb joined #opentreeoflife
15:30 kcranstn joined #opentreeoflife
15:31 kcranstn question: given a study id and a tree id, what is the link to that tree in the curator app?
15:32 kcranstn ah, I see it. Link doesn’t change until you actually open the tree window (as opposed to hovering over the name in the list)
15:32 kcranstn https://tree.opentreeoflife.org/curator/study/view/pg_2711/?tab=trees&tree=tree6295
15:46 towodo_ joined #opentreeoflife
15:46 kcranstn uh-oh. There are two towodos
16:14 mtholder joined #opentreeoflife
16:35 kcranstn hey mtholder - if I wanted to use peyotl to iterate over the nexsons, can you point me to an example script that does that?
16:38 kcranstn I see the phylesystem-api-wrapper.py script, which looks different from http://opentreeoflife.github.io/peyotl/phylesystem/
16:38 kcranstn happy to update docs
16:44 kcranstn *crickets*
16:44 jimallman kcranstn: good thought about the links in tree-list. i can add these URLs, even if the default behavior is to open a popup. (making an ‘enhancement’ ticket now…)
16:46 jimallman https://github.com/OpenTreeOfLife/opentree/issues/548
16:47 kcranstn cool, thanks
16:58 mtholder hi kcranstn. Sorry was muted.
16:58 mtholder the text on the github.io is correct.
16:58 mtholder I'll fix the link
16:59 mtholder do you want something that does not require a local copy?
17:00 kcranstn no, local copy fine
17:00 kcranstn I don’t see the tutorials dir mentioned on the .io site
17:02 mtholder emily jane just merged the tutorials branch to master. If you pull it, you should get the tutorials dir.
17:02 mtholder "just" = "sometime earlier today"
17:03 kcranstn I must have missed that by a very short amount of time
17:03 mtholder the github.io site has referred to it for a while. it has only been true of master for a few hours.
17:04 kcranstn cool, thanks
17:04 kcranstn josephwb thought you had an existing script to add the preferred tags from pg to the nexsons?
17:05 josephwb no, i said mtholder probably did.
17:05 mtholder I do have a (dusty) script for the import from pg. What do you wnat to do?
17:05 kcranstn josephwb thought that mtholder had an existing script to add the preferred tags from pg to the nexsons
17:06 kcranstn romina was asking about the choose me tags from pg, which do not appear to have been set as preferred trees in ot
17:07 mtholder I think the tags are in the NexSONs, but we never implemented a parsing of the free text -> updating of boolean fields like "preferred..."
17:07 josephwb mtholder: i believe you processed all of the synth source trees to set rooting information (maybe?)
17:07 kcranstn I am going through and grabbing all of the tags from the NexSONs to see what is in there
17:07 josephwb good luck with that!
17:07 josephwb freeform tags...
17:08 mtholder we did not do much clean up with the export from phylografter. Just added fields to make each doc legal in the eyes of the peyotl validator...
17:13 josephwb we don't need the tags to set the preferred tree; we know which trees should be tagged.
17:14 josephwb barf; that was not clear at all.
17:14 kcranstn I got it
17:34 josephwb kcranstn: i can grab inference type from the nexsons that store the information
17:34 kcranstn and focal clade?
17:36 josephwb should point out that for people looking up these things, they should input any missing information
17:38 josephwb yes, got that now
17:41 josephwb but datatype will be a pain
17:42 jimallman joined #opentreeoflife
17:45 jimallman kcranstn: thanks for chasing the “choose me” tag question!
17:52 mtholder kcranstn: https://github.com/OpenTreeOfLife/peyotl/pull/100 adds a new script to print out the tags for studies and trees (it also fixes a very old broken example).
17:53 mtholder with that branch checked out, one can run:
17:53 mtholder python scripts/phylesystem/ot_phylesystem_list_tags.py
17:53 mtholder to list all study and tree tags
17:54 mtholder the tree tags are "heat shock protein 80–1" "pPF-076" "MrBayes consensus tree" "rooted" "GPD3" "BEAST" "OPA1-3" "EF-1" "BI" "ingroup added" "MAT1-2" "mtLSU" "5.8S" "ACT" "morphology" "MP?" "mit rns gene" "Choose me" "IGS1" "Suppl." "NJ" "HIS" "RPB1" "RPB2" "delet" "Delete me" "IGS-1" "NAD" "cpDNA" "benA" "Test-TREE," "LSU" "genome" "mtSSU" "AT" "apn2/MAT1-2" "UPGMA" "choose me" "rooted;" "b-tub2" "Distance" "b
17:54 mtholder tubulin" "IGS" "gene family phylogeny" "delete me" "ITS2" "CAl" "topology differs from figure" "ATP6" "GAPDH" "MCM7" "nrITS" "plant taxa" "choose me;" "ingroup added;" "caM" "cladogram" "CAL" "B-tub" "nrDNA" "endoPG" "HIS3" "apn2" "FG1093" "unrooted" "HMG" "H3" "SSU" "ML" "cpDNA & nrDNA" "COX-1" "15 loci" "pPF-018" "acetaldehydedehydrogenase gene" "MP" "act" "b-tub" "G3P" "ITS" "delete"
17:57 mtholder oops.
17:57 mtholder i had not pulled from GH.
17:57 mtholder updated list of tags is:
17:57 mtholder "heat shock protein 80–1" " pPF-076" " MrBayes consensus tree" " rooted" " GPD3" " BEAST" " OPA1-3" " EF-1" " BI" " ingroup added" " MAT1-2" " mtLSU" " 5.8S" " ACT" " morphology" " MP?" " mit rns gene" " Choose me" " IGS1" " Suppl." " NJ" " HIS" " RPB1" " RPB2" " delet" " Delete me" " IGS-1" " NAD" " cpDNA" " benA" " Test-TREE," " LSU" " genome" " mtSSU" " AT" " apn2/MAT1-2" " UPGMA" " choose me" " rooted;" "
17:57 mtholder b-tub2" " Distance" " b-tubulin" " IGS" " gene family phylogeny" " delete me" " ITS2" " CAl" " topology differs from figure" " ATP6" " GAPDH" " MCM7" " nrITS" " plant taxa" " choose me;" " ingroup added;" " caM" " cladogram" " CAL" " B-tub" " nrDNA" " endoPG" " HIS3" " apn2" " FG1093" " unrooted" " HMG" " H3" " SSU" " ML" " cpDNA & nrDNA" " COX-1" " 15 loci" " pPF-018" " acetaldehyde dehydrogenase gene" " MP" "
17:57 mtholder act" " b-tub" " G3P" " ITS" " delete"
17:57 kcranstn thanks, mtholder!
18:01 kcranstn is there a reason for both the examples and tutorials dirs?
18:03 mtholder the tutorials have more comments.
18:03 kcranstn :)
18:03 mtholder i just throw things in the examples dir on a whim.
18:04 kcranstn vs scripts?
18:04 mtholder scripts get installed.
18:04 kcranstn ah, ok
18:04 kcranstn thanks
18:04 mtholder (or should0
18:04 mtholder should)
18:04 mtholder in other words: no good reason for 3 dirs
18:12 towodo joined #opentreeoflife
18:14 kcranstn so, the peyotl docs say “Peyotl will treat any git directory in this parent that has a study subdirectory as if it was a shard of phyleystem"
18:14 kcranstn but I get an error if there is a git dir in the parent that does not contain a study dir
18:15 kcranstn i.e. I have a non-phylesystem git repo in the parent
18:15 mtholder doh. can you post the stacktrace?
18:15 kcranstn Traceback (most recent call last):
18:15 kcranstn File "ot_phylesystem_list_tags.py", line 13, in <module>
18:15 kcranstn phy = Phylesystem()
18:15 kcranstn File "/Users/karen/Documents/opentreeoflife/software/peyotl/peyotl/phylesystem/phylesystem_umbrella.py", line 542, in Phylesystem
18:15 kcranstn infrastructure_commit_author=infrastructure_commit_author)
18:15 kcranstn File "/Users/karen/Documents/opentreeoflife/software/peyotl/peyotl/phylesystem/phylesystem_umbrella.py", line 177, in __init__
18:15 kcranstn infrastructure_commit_author=infrastructure_commit_author)
18:15 kcranstn File "/Users/karen/Documents/opentreeoflife/software/peyotl/peyotl/phylesystem/phylesystem_shard.py", line 104, in __init__
18:15 kcranstn raise ValueError('"{p}" is not a directory'.format(p=study_dir))
18:15 kcranstn ValueError: "/Users/karen/Documents/opentreeoflife/data/avatol_nexsons/study" is not a directory
18:15 kcranstn my peyotl config is  parent = ~/Documents/opentreeoflife/data/
18:15 mtholder thanks. that'll help...
18:16 kcranstn and /Users/karen/Documents/opentreeoflife/data/phylesystem
18:16 kcranstn is location of phylesystem
18:16 kcranstn but that data dir has other git repos
18:16 jar286 joined #opentreeoflife
18:17 kcranstn want an issue?
18:17 mtholder is there a /Users/karen/Documents/opentreeoflife/data/phylesystem/study or /Users/karen/Documents/opentreeoflife/data/phylesystem/phylesystem-1/study
18:17 mtholder ?
18:17 towodo left #opentreeoflife
18:17 mtholder I've got plenty of issues ;-)
18:18 * jar286 towodo is now jar286
18:18 * jar286 I doubt there is another jar286
18:18 kcranstn mtholder - nope
18:19 kcranstn only /Users/karen/Documents/opentreeoflife/data/phylesystem/shards/phylesystem-1/study
18:19 mtholder right I forgot the shards.
18:20 mtholder I can reproduce your bug. so no need for an issue. thanks.
18:30 mtholder I think that you want your parent variable to be set to /Users/karen/Documents/opentreeoflife/data/phylesystem
18:30 mtholder but I also pushed a fix to make the code more robust...
18:31 kcranstn ValueError: No git repos in ['/Users/karen/Documents/opentreeoflife/data/phylesystem']
18:31 kcranstn seems to be looking for .git in a subdir but not in the parent
18:31 mtholder sorry /Users/karen/Documents/opentreeoflife/data/phylesystem/shards
18:31 mtholder as the parent.
18:32 kcranstn win!
18:32 mtholder it is confusing to call it "phylesystem/parent" in the settings but really mean the shards dir...
18:33 mtholder I'll note that in the docs.
18:58 pmidford2 joined #opentreeoflife
19:02 kcranstn PR reiew?
19:02 kcranstn review
19:02 kcranstn towodo really rolled off the fingers, jar286 not so much
19:03 mtholder what is the link for PRs across all repos?
19:03 jar286 PR review
19:03 jimallman yeah, i’ve gotten used to it too
19:03 jar286 https://github.com/pulls?user=OpenTreeOfLife
19:04 mtholder thanks
19:04 jar286 start with opentree repo, earliest PR first…
19:04 jar286 https://github.com/OpenTreeOfLife/opentree/pull/495
19:04 kcranstn having serious déja vu
19:05 jimallman yes. i thought this one was retired (superceded by otu-stats-area)…
19:05 jar286 last comment was at last PR review
19:05 jar286 no new review
19:05 jar286 so I think we can move on
19:05 jar286 unless we want to look at it again now
19:05 pmidford2 I've made progress with the rsync stuff
19:06 jimallman agreed, if anything we should look at the otu-stats-area branch (or devtree)
19:06 jar286 https://devtree.opentreeoflife.org/about/statistics - 404
19:06 jimallman yes, i’ve been revising this in line with recent discussion. starting page is https://devtree.opentreeoflife.org/about/release-history
19:07 jar286 editing first comment
19:07 jimallman almost got another round of (needed) changes up in time for this mtg, but not quite
19:08 jimallman new stuff here is the markers for synthesis and taxonomy releases. all tabular stats will be on linked “release pages” along with downloads, notes, etc.
19:08 jar286 but why is it called release-history? isn’t it continuallly updated?
19:08 jar286 i.e. it’s information about the current state of the phylesystem, in addition to info about treemachine releases.
19:08 jimallman yes, but it always represents the complete history to date (alternate names welcome)
19:09 jar286 progress ?
19:09 jar286 info ?
19:09 jar286 status ?
19:09 jimallman see the About menu to see how this phrasing looks in navigation
19:09 mtholder boo to info - too vauge.
19:09 kcranstn progress is good
19:09 mtholder otu-status or progress seem ok to me
19:10 jar286 I fear any one or two word file name will be too vague
19:10 jimallman “coverage” is too specific, probably not right
19:10 jar286 +1 mtholder
19:10 jar286 ok with progress, jimallman?
19:11 jar286 or rather ‘progress’
19:11 jimallman mtholder: i’m trying to encompass OTUs + synthesis releases + taxonomy releases, and how they’re related
19:11 jimallman but yes, i’ll try “Open Tree progress” (?)
19:11 mtholder sounds good.
19:11 jar286 I was just looking at the URL. page title can be longer. but let’s not dwell on it
19:12 jar286 moving on then…
19:12 jimallman i take your point /about/progress is nice
19:12 mtholder we're only going to get a (S) circle when there are new synths, right?
19:12 mtholder (not everyday)
19:12 jar286 right
19:12 kcranstn yes
19:12 jar286 unless we start doing synth every day, which would be nice
19:12 jimallman yes, i’m sure the current markers are bogus. we really need a separate huddle on stats and their meaning.
19:12 mtholder looks good.
19:12 jimallman and where to find other supporting information.
19:12 mtholder gotcha
19:12 jar286 https://github.com/OpenTreeOfLife/opentree/pull/528
19:12 kcranstn if we get to synth every day, we can revisit this them
19:13 pmidford2 agree, this 'looks' good
19:13 jimallman this has been expanded based on last pr review (scroll down)
19:13 kcranstn +1
19:13 jimallman this = tree legend
19:13 jar286 looks good
19:14 pmidford2 +1
19:14 jimallman Mac tip: use the built-in ’Grab’ app in OS X to get screen caps with cursors!
19:14 jar286 ok, merging
19:15 jar286 while I’m thinking about it, how about I file an issue about chaning question mark to the international information (i) icon
19:15 jar286 changing
19:16 kcranstn yes, please
19:16 jimallman sure, if “?” will cause confusion
19:16 jar286 it was a good suggestion at the nescent presentation
19:16 jar286 https://github.com/OpenTreeOfLife/opentree/issues/549
19:16 jimallman please indicate any styling or other parts of the convetion, or a link if it’s handy
19:17 kcranstn in the nescent meeting, people pointed out that ? = help and (i) = info
19:17 kcranstn generally
19:17 jimallman gotcha. so italic, lower-case (would have been my guess)
19:17 jimallman colors OK?
19:17 jimallman or is white-on-blue part of the convention?
19:17 jar286 looking
19:17 jar286 I think it’s ISO
19:18 jar286 http://www.iso.org/iso/graphical-symbols_booklet.pdf
19:18 jar286 but you can probably find an SVG of the correct graphic
19:18 jimallman thanks, will pursue this on my own time
19:19 jar286 https://github.com/OpenTreeOfLife/opentree/pull/536
19:19 jar286 hmm, same as 495
19:19 kcranstn is this deployed?
19:19 jar286 I forget why we have both issues open by expect we left a turd
19:20 mtholder i left no turd
19:20 jimallman i regret nothing
19:20 jar286 nor did I … was it because of the comments in the issue?
19:20 pmidford2 that's what I thought
19:20 jimallman i believe this PR supercedes the other, but i wasn’t sure at the time.
19:21 jimallman (comments are linked from here anyway)
19:21 jimallman we wanted to push both to devtree for review, but in practice this one (otu-stats-area) completely clobbered the older issue
19:21 jar286 I will make a(nother) link from this one to 495, set 495 as duplicate, and close 495
19:22 kcranstn is this on devtree?
19:22 jimallman yes, and i’ll have more to share by tomorrow.
19:22 jimallman show, i mean
19:22 kcranstn ok, so not reviewing now
19:23 jar286 moving on… https://github.com/OpenTreeOfLife/opentree/pull/538
19:23 jar286 not sure what a ‘highlight’ is…
19:23 jimallman just what it says on the tin (main commit msg)… fixed very annoying “disappearing highlight” bug
19:23 jar286 but this sounds great
19:23 jimallman red highlights in argus, when rolling over nodes and edges
19:24 jimallman earlier, if you roll the mouse over the “?” (very common event) the highlight would disappear before you could click it
19:24 mtholder cool. looks good.
19:24 jimallman SUPER ANNOYING
19:24 jar286 merging…
19:25 jar286 https://github.com/OpenTreeOfLife/opentree/pull/539
19:26 kcranstn looks good
19:26 kcranstn was there an associated issue?
19:26 jar286 the isLeaf property still really bugs me since it’s redundant (caches computable information). is there a validation check that it’s right?
19:26 jimallman romina found this bug, mtholder and i chased it down. teamwork!
19:27 kcranstn ah, yes, I see the link
19:27 jar286 mtholder ^
19:27 mtholder yes. there is a check, which is why romina's edits were rejected.
19:27 mtholder she was rerooting on a leaf.
19:27 jar286 excellent.  merging…
19:28 mtholder (there were also bugs in how peyotl reported the errors. jimallman spotted those, but they've been fixed now).
19:29 jar286 I’m puzzled that there were no peyotl PRs… but I assume that’s because the repo is so excellent it doesn’t need any
19:29 mtholder there were some. Emily merged them.
19:29 jar286 I think we’re done then
19:30 jar286 any review that is
19:31 jimallman sounds good. i’ll follow up (in discussion of #536, or maybe the opentree-dev group?) with questions about stats, release data, etc.
19:31 mtholder very minor, jimallman: when you browse a study and you aren't logged in. and then you log in, you are quicked back to the metadata tab. not a big deal, but it would be nice to remember the tab that the user was on.
19:32 mtholder kicked back not "quicked back"
19:32 jimallman agreed. adding an ‘enhancement’ issue for this...
19:32 kcranstn +1 for that
19:32 jimallman https://github.com/OpenTreeOfLife/opentree/issues/550
19:34 jimallman i’ve been trying to whittle down the open bugs/issues in opentree, but the number is slowly growing :(
19:34 jar286 by the way, if you want to see another group that does weekly PR reviews by IRC, look here http://irclogs.duraspace.org/index.php?date=2015-01-14
19:34 jimallman wow, a big group too
19:35 jimallman (lotsa folks on the chat, i mean)
19:35 kcranstn I see muttering and head scratching
19:35 kcranstn and deep appreciation of good documentation ;)
19:36 jimallman and busted unicode
20:06 kcranstn josephwb - what the status of the focal clades in the spreadsheet? people are starting to add them manually, which is not do good (no guarantee these will map to OTT)
20:06 kcranstn no *so* good
20:31 josephwb i will process them and let you know
20:37 josephwb mtholder: phycas has a paper! noce work!
20:38 mtholder mainly paul's work.
20:38 mtholder i did a lot on it a long time ago.
20:38 josephwb received 13 August, accepted 24 December? did someone else handle the paper for Syst. Biol.?
20:39 josephwb is the "received" for the revision?
20:39 josephwb or is it the fastest SB paper ever?
20:40 mtholder august was the original submission.
20:40 josephwb wow.
20:40 mtholder reviews back on sept 18
20:40 mtholder can't remember when we (read "Paul") got the revisions back in.
20:41 mtholder sys bio really is trying to be faster than it used to be...
20:41 josephwb i've heard that for years.
20:41 mtholder it's been true for years :-)
21:19 josephwb focal clades:
21:19 josephwb pg_43Hoya
21:19 josephwb pg_405Botryosphaeria
21:19 josephwb pg_1478Polypodiaceae
21:19 josephwb pg_1312Polypodiidae
21:19 josephwb pg_404Nalanthamala psidii
21:19 josephwb pg_99
21:19 josephwb pg_2738Oscillatoriales
21:19 josephwb pg_1927Cetacea
21:19 josephwb pg_1887Accipitridae
21:19 josephwb ot_124Otididae
21:19 josephwb pg_2404Passeriformes
21:19 josephwb pg_2669Lamioideae
21:19 josephwb pg_430Anamika
21:19 josephwb pg_2657Percomorpha
21:19 josephwb pg_1443Peperomia
21:19 josephwb pg_139Nierembergia
21:19 josephwb pg_474Laetiporus
21:19 josephwb pg_387Ajellomycetaceae
21:19 josephwb pg_475Marasmius
21:19 josephwb pg_358Ceratocystis pirilliformis
21:19 josephwb pg_482Penicillium
21:19 josephwb pg_2659Otophysi
21:19 josephwb pg_2713Arthrospira
21:19 josephwb pg_2691Procyonidae
21:19 josephwb pg_2670Atyidae
21:19 josephwb pg_1966Maluridae
21:19 josephwb pg_2032Acanthaceae
21:19 josephwb pg_2816Primates
21:19 josephwb pg_403Monacrosporium drechsleri
21:19 josephwb pg_2707Icteridae
21:19 josephwb pg_2539
21:19 josephwb ot_150Megalaimidae
21:20 josephwb pg_408Colletotrichum
21:20 josephwb pg_934Echinops
21:20 josephwb pg_2645Menispermaceae
21:20 josephwb pg_2731Archaea (domain in cellular organisms)
21:20 josephwb ot_138Ciconiidae
21:20 josephwb pg_367Armillaria
21:20 josephwb pg_251Formicidae
21:20 josephwb pg_2912Calliandra
21:20 josephwb pg_136Cestrum
21:20 josephwb pg_270Indigofereae
21:20 josephwb pg_2695Ursidae
21:20 josephwb pg_372Boletus
21:20 josephwb pg_366Hypochnicium punctulatum
21:20 josephwb pg_1336Brachyura
21:20 josephwb pg_1483Zamiaceae
21:20 josephwb pg_2614Nicrophorinae
21:20 josephwb pg_2624Veronica
21:20 josephwb pg_343Corethromyces bicolor
21:20 josephwb pg_1868Marsilea
21:20 josephwb pg_1567Equisetum
21:20 josephwb pg_704Molluginaceae
21:20 josephwb pg_415
21:20 josephwb pg_2610Malpighiales
21:20 josephwb pg_420Aves
21:20 josephwb pg_1776Lepidoptera
21:20 josephwb pg_2001Astragalus
21:20 josephwb pg_2629Insecta
21:20 josephwb pg_1382Rhodophyceae
21:20 josephwb pg_313Stramenopiles
21:20 josephwb ot_123Aegotheles
21:20 josephwb ot_153Pteroglossus
21:20 josephwb pg_2753Enterobacteriaceae
21:20 josephwb pg_2830Brassaiopsis
21:20 josephwb ot_173Poecile
21:20 josephwb pg_1129Solanum
21:20 josephwb pg_2638Santalales
21:20 josephwb pg_52Cucumis
21:20 josephwb pg_2655Cichlidae
21:20 josephwb ot_102Pheucticus
21:20 josephwb pg_2864Platalea
21:21 josephwb pg_2684Hyaenidae
21:21 josephwb pg_2870Micrastur
21:21 josephwb ot_122Phoenicopteridae
21:21 josephwb pg_414Trichoderma
21:21 josephwb pg_263
21:21 josephwb pg_437Diptera
21:21 josephwb pg_2676Scyllaridae
21:21 josephwb pg_1414Orchidaceae
21:21 josephwb ot_160Cacatuidae
21:21 josephwb pg_2087Austrogoniodes
21:21 josephwb pg_1575Asteraceae
21:21 josephwb pg_2909Exochaenium
21:21 josephwb pg_1518
21:21 josephwb pg_2046Trebouxiophyceae
21:21 josephwb pg_2715Archaea
21:21 josephwb pg_368Macrolepiota
21:21 josephwb pg_20Galium
21:21 josephwb pg_330Santalum
21:21 josephwb pg_1022Pontederiaceae
21:21 josephwb pg_2708Cnidaria
21:21 josephwb pg_1453Isoetes
21:21 josephwb pg_1975Tragopogon
21:21 josephwb pg_1764Pelecanidae
21:21 josephwb pg_2892Cyanobacteria
21:21 josephwb pg_2628Heteronychia
21:21 josephwb pg_386Brunfelsia
21:21 josephwb pg_1434Puya
21:21 josephwb pg_2128Plantago
21:21 josephwb pg_596
21:21 josephwb pg_2876Tinamidae
21:21 josephwb pg_73Passifloraceae
21:21 josephwb ot_165Forpus
21:21 josephwb pg_1318Polypodiaceae
21:21 josephwb ot_158Colaptes
21:21 josephwb pg_754Ribes howellii
21:21 josephwb pg_142Asclepias
21:21 josephwb ot_167Pyrrhura
21:21 josephwb pg_2076Garrya
21:21 josephwb pg_2845Sittidae
21:21 josephwb pg_2000Coffea
21:22 josephwb pg_1401Dactylorhiza
21:22 josephwb pg_450Clavariaceae
21:22 josephwb pg_1797Tenrecidae
21:22 josephwb pg_62Lymania
21:22 josephwb pg_1962Adoxaceae
21:22 josephwb pg_2554Oscillatoriales
21:22 josephwb pg_1866Thesium
21:22 josephwb pg_1858Chamaesyce
21:22 josephwb pg_288Croton
21:22 josephwb pg_1338Pterygota
21:22 josephwb pg_376Botryosphaeria
21:22 josephwb ot_144Alcidae
21:22 josephwb pg_1252Anomura
21:22 josephwb pg_2454Thamnophilus
21:22 josephwb ot_142Diomedeidae
21:22 josephwb pg_338Cudonia
21:22 josephwb pg_2052Lundia
21:22 josephwb ot_166Psittacidae
21:22 josephwb pg_2875Oriolus
21:22 josephwb ot_106
21:22 josephwb pg_1940Drosophilidae
21:22 josephwb ot_172Passeriformes
21:22 josephwb ot_125Psophiidae
21:22 josephwb ot_170Regulus
21:22 josephwb pg_2712rosids
21:22 josephwb ot_182Nematoda
21:22 josephwb pg_441Morinia
21:22 josephwb pg_2857Gyps
21:22 josephwb ot_148Meropidae
21:22 josephwb pg_1942Salviniaceae
21:22 josephwb pg_369Rhizopogon vinicolor
21:22 josephwb pg_485Metarhizium
21:22 josephwb ot_156
21:22 josephwb pg_2696Demospongiae
21:22 josephwb pg_721Commelinaceae
21:22 josephwb pg_2682Procarididae
21:22 josephwb pg_1997Percidae
21:22 josephwb pg_2683Dendrobranchiata
21:22 josephwb pg_566Lowiaceae
21:22 josephwb pg_283Celastrales
21:23 josephwb pg_1118Nepetoideae
21:23 josephwb pg_56Tsuga
21:23 josephwb pg_30Illicium
21:23 josephwb pg_480
21:23 josephwb pg_37Rhus
21:23 josephwb pg_2556Myxogastria
21:23 josephwb pg_2484Amoebozoa
21:23 josephwb pg_2739Cyanobacteria
21:23 josephwb ot_118Megapodiidae
21:23 josephwb pg_1788Siphonophora
21:23 josephwb pg_380Lasiosphaeria
21:23 josephwb pg_471Alternaria
21:23 josephwb pg_2542Bacteria
21:23 josephwb pg_2444Columbiformes
21:23 josephwb pg_373Penicillium brocae
21:23 josephwb pg_787Ephedra
21:23 josephwb pg_2061Campydora
21:23 josephwb pg_1264Isoetaceae
21:23 josephwb pg_2551Labroidei
21:23 josephwb pg_2831Escallonia
21:23 josephwb pg_1948Galatheoidea
21:23 josephwb pg_2654Leiognathidae
21:23 josephwb pg_393
21:23 josephwb pg_1474Phaeophyceae
21:23 josephwb pg_2709Demospongiae
21:23 josephwb ot_147Trogonidae
21:23 josephwb pg_2085Araceae
21:23 josephwb pg_1916Brassicaceae
21:23 josephwb pg_2678Echinodermata
21:23 josephwb pg_2898Osmolindsaea
21:23 josephwb pg_421Mollusca
21:23 josephwb pg_1102Collinsia
21:23 josephwb pg_2039Hymenophyllum
21:23 josephwb pg_1843Euphorbia
21:23 josephwb pg_2667Kiwaidae
21:23 josephwb pg_2872Caprimulgidae
21:23 josephwb pg_2323Bombyliidae
21:23 josephwb pg_2140Annonaceae
21:23 josephwb ot_116Aves
21:23 josephwb pg_1581Asteraceae
21:24 josephwb pg_2641Rubiaceae
21:24 josephwb pg_1979Arinia
21:24 josephwb pg_152Coreopsis
21:24 josephwb pg_2675Cambarus
21:24 josephwb pg_2822Eukaryota
21:24 josephwb pg_59Aristolochiaceae
21:24 josephwb pg_225
21:24 josephwb ot_152Ramphastos
21:24 josephwb pg_1130Nicotiana
21:24 josephwb pg_2098Stenocercus
21:24 josephwb pg_2850Columbidae
21:24 josephwb pg_2415Testudines
21:24 josephwb pg_606
21:24 josephwb pg_2600Paridae
21:24 josephwb pg_2127Papilionoideae
21:24 josephwb pg_444Cryphonectriaceae
21:24 josephwb pg_1101Rubiaceae
21:24 josephwb pg_58Crotalarieae
21:24 josephwb pg_2661Ericales
21:24 josephwb ot_129Musophagidae
21:24 josephwb pg_2585Tetraodontiformes
21:24 josephwb pg_361Fusarium
21:24 josephwb pg_2664Ditrysia
21:24 josephwb pg_2092Albinaria
21:24 josephwb pg_385Begonia
21:24 josephwb pg_2828Caprifoliaceae
21:24 josephwb pg_80Rhododendron
21:24 josephwb pg_1087Fabaceae
21:24 josephwb pg_1944Campanulaceae
21:24 josephwb pg_625Hoheria
21:24 josephwb pg_1407
21:24 josephwb pg_2357Evaniscus
21:24 josephwb pg_1901Lentibulariaceae
21:24 josephwb pg_1821Helichrysum
21:24 josephwb pg_2838Pleocyemata
21:24 josephwb ot_121Cuculiformes
21:24 josephwb pg_479Flammulina
21:24 josephwb pg_2405Phyllodocidae
21:24 josephwb pg_2564Polystichum
21:24 josephwb pg_2742Dinophyceae
21:25 josephwb pg_2685Mustelidae
21:25 josephwb pg_2825Xenarthra
21:25 josephwb pg_335Magnaporthe
21:25 josephwb pg_2757Proteobacteria
21:25 josephwb pg_293Mimosa
21:25 josephwb pg_1137Erythronium
21:25 josephwb pg_1988Mantodea
21:25 josephwb pg_400Botryosphaeria
21:25 josephwb pg_597Fabaceae
21:25 josephwb pg_180Araceae
21:25 josephwb ot_104Gaviiformes
21:25 josephwb pg_2544Hexactinellida
21:25 josephwb pg_599Costaceae
21:25 josephwb pg_1573Mutisieae
21:25 josephwb pg_50Anagallis
21:25 josephwb ot_164Brotogeris
21:25 josephwb pg_53Euryops
21:25 josephwb pg_2842Thecostraca
21:25 josephwb pg_443Hypocrea
21:25 josephwb pg_411Botryosphaeria
21:25 josephwb pg_2798Sphenisciformes
21:25 josephwb pg_1870Cyprinidae
21:25 josephwb pg_713Lamiales
21:25 josephwb pg_397Alternaria
21:25 josephwb pg_244Gymnosperma
21:25 josephwb ot_119Cracidae
21:25 josephwb pg_481Neurospora
21:25 josephwb pg_1278Marchantiophyta
21:25 josephwb pg_2045
21:25 kcranstn joined #opentreeoflife
21:25 josephwb pg_2891Cyanobacteria
21:25 josephwb pg_915Dipsacales
21:25 josephwb pg_2648Marchantiales
21:25 josephwb pg_463Neotyphodium
21:25 josephwb pg_598Poaceae
21:25 josephwb pg_374Penicillium
21:25 josephwb pg_548Fabaceae
21:25 josephwb ot_159Picidae
21:25 josephwb pg_131Trifolium
21:25 josephwb pg_407Penicillium
21:25 josephwb pg_2565Ericoideae
21:26 josephwb pg_2687Phocidae
21:26 josephwb pg_2599Alaudidae
21:26 josephwb pg_1428Mammalia
21:26 josephwb pg_2811Vespidae
21:26 josephwb pg_921Oryzeae
21:26 josephwb pg_348Rhizopogon
21:26 josephwb pg_339Leptosphaeria
21:26 josephwb ot_185Lepidoptera
21:26 josephwb pg_2844Talpa
21:26 josephwb pg_483Neofusicoccum
21:26 josephwb pg_2711Henophidia
21:26 josephwb pg_1867Cycadaceae
21:26 josephwb pg_72Malpighiaceae
21:26 josephwb pg_2576Euteleostei
21:26 josephwb pg_424Caprifoliaceae
21:26 josephwb ot_151Capito
21:26 josephwb pg_603Cymbidieae
21:26 josephwb pg_388Hirsutella
21:26 josephwb pg_719Menyanthaceae
21:26 josephwb pg_2805Psittaciformes
21:26 josephwb pg_2634Galanthus
21:26 josephwb pg_61Bromeliaceae
21:26 josephwb ot_161Amazona
21:26 josephwb pg_582Danthonioideae
21:26 josephwb pg_41Feddea
21:26 josephwb pg_2604Apoidea
21:26 josephwb pg_2896Selaginellaceae
21:26 josephwb pg_77Anaxagorea
21:26 josephwb pg_2859Muroidea
21:26 josephwb pg_88Erodium
21:26 josephwb ot_183Nematoda
21:26 josephwb pg_2871Falconidae
21:26 josephwb pg_2674Fallicambarus
21:26 josephwb pg_1563Hymenoptera
21:26 josephwb ot_112Apodidae
21:26 josephwb pg_2860Anatidae
21:26 josephwb pg_423Amphibia
21:26 josephwb pg_197Phaseolus
21:26 josephwb pg_449Sparassis
21:26 josephwb pg_2642Caryophyllales
21:27 josephwb pg_2626Amaranthaceae
21:27 josephwb ot_136Jacanidae
21:27 josephwb pg_573Aponogeton
21:27 josephwb pg_2460Squamata
21:27 josephwb pg_1109Castilleja
21:27 josephwb pg_389Kohninia
21:27 josephwb pg_2673Parastacidae
21:27 josephwb pg_605Strophostyles
21:27 josephwb pg_294Detarieae
21:27 josephwb pg_2808Lysmata
21:27 josephwb pg_14Bignoniaceae
21:27 josephwb pg_21Solanaceae
21:27 josephwb pg_261Caesalpinieae
21:27 josephwb pg_81Pinus
21:27 josephwb ot_174Rhipidura
21:27 josephwb pg_2644Ranunculales
21:27 josephwb pg_1391Dioscorea
21:27 josephwb pg_2653Percomorpha
21:27 josephwb pg_2737Nostocales
21:27 josephwb pg_2048Allium
21:27 josephwb pg_332
21:27 josephwb pg_1522Columnea
21:27 josephwb pg_2820Streptophyta
21:27 josephwb pg_2827Ilex
21:27 josephwb pg_2881Anolis
21:27 josephwb ot_181Selachii
21:27 josephwb pg_259Cercis
21:27 josephwb pg_470Lecania
21:27 josephwb pg_595Senna
21:27 josephwb pg_2878Lepechinia
21:27 josephwb pg_1996Lomariopsis
21:27 josephwb pg_2869Bucerotidae
21:27 josephwb pg_1384Gracilariaceae
21:27 josephwb pg_353Aspergillus
21:27 josephwb pg_2042
21:27 josephwb pg_2243Munididae
21:27 josephwb pg_2047Cuscuta
21:27 josephwb ot_177Hirundo
21:27 josephwb pg_200Encelia
21:27 josephwb pg_82Campanula
21:28 josephwb pg_2633Narcissus
21:28 josephwb pg_1366Annelida
21:28 josephwb pg_370
21:28 josephwb pg_2843Talpidae
21:28 josephwb pg_38Heliotropium
21:28 josephwb pg_2861Elephantidae
21:28 josephwb pg_1572Metalasia
21:28 josephwb pg_898Schefflera
21:28 josephwb pg_562Poales
21:28 josephwb pg_1583
21:28 josephwb pg_1539Carex
21:28 josephwb pg_581Crocus
21:28 josephwb pg_2690Fabaceae
21:28 josephwb pg_2359Artiodactyla
21:28 josephwb ot_110
21:28 josephwb pg_1981Felidae
21:28 josephwb pg_1872Gruiformes
21:28 josephwb pg_382Cryphonectria
21:28 josephwb pg_2853Trochilidae
21:28 josephwb pg_588Asparagales
21:28 josephwb pg_2422Ascaridoidea
21:28 josephwb pg_2677Anomura
21:28 josephwb pg_1524Rhipsalideae
21:28 josephwb pg_2577Galliformes
21:28 josephwb pg_2851Kinosternidae
21:28 josephwb pg_2055Bowdichia
21:28 josephwb ot_157Celeus
21:28 josephwb pg_1446Hymenophyllaceae
21:28 josephwb pg_93Symplocos
21:28 josephwb pg_1634Chiroptera
21:28 josephwb pg_126Solanum
21:28 josephwb pg_477Agaricus
21:28 josephwb pg_2156Ophryotrocha
21:28 josephwb pg_2834Metatheria
21:28 josephwb ot_140Phalacrocoracidae
21:28 josephwb pg_2849Amphora commutata
21:28 josephwb pg_2832Crassulaceae
21:28 josephwb ot_155Aulacorhynchus
21:28 josephwb pg_2926Palaeognathae
21:28 josephwb pg_2906Aquilegia
21:29 josephwb pg_2710Metazoa
21:29 josephwb pg_264Coursetia
21:29 josephwb pg_446Cercospora
21:29 kcranstn josephwb, please stop
21:29 josephwb pg_2879Bryophyta
21:29 josephwb pg_57Podalyrieae
21:29 josephwb pg_216Hedera
21:29 josephwb pg_32Valerianella
21:29 josephwb pg_340Neotyphodium
21:29 josephwb pg_1849Formicidae
21:29 josephwb pg_267Ateleia
21:29 josephwb pg_2656Primates
21:29 josephwb pg_1974Polygonaceae
21:29 josephwb pg_312Excavata
21:29 josephwb ot_168Pteropus
21:29 josephwb pg_448
21:29 josephwb pg_2591Parulidae
21:29 josephwb ot_139Threskiornithidae
21:29 josephwb pg_723Triticum
21:29 josephwb pg_2741Catarrhini
21:29 josephwb pg_1343Hexactinella
21:29 josephwb pg_2077Podalyria
21:29 josephwb pg_650Meliaceae
21:29 josephwb pg_1450Huperzia
21:29 josephwb pg_75Apioideae
21:29 josephwb pg_412Coniferophyta
21:29 josephwb pg_761Drosera
21:29 josephwb pg_2165Dryopteris
21:29 josephwb pg_2688Rodentia
21:29 josephwb pg_447Aurapex
21:29 josephwb pg_1268Anthocerotophyta
21:29 josephwb pg_2608Saxifragales
21:29 josephwb pg_2587Cetacea
21:29 josephwb ot_154Ramphastidae
21:29 josephwb pg_1411Catasetinae
21:29 josephwb pg_926Rosaceae
21:29 josephwb pg_473Salmacisia
21:29 josephwb pg_1473Dryopteridaceae
21:29 josephwb pg_2143Kentropyx
21:29 josephwb ot_162Prioniturus
21:29 josephwb pg_1842Oxalis
21:30 josephwb pg_275Celastraceae
21:30 josephwb pg_2553Euglenophyceae
21:30 josephwb pg_2594Diptera
21:30 josephwb pg_271Polygalaceae
21:30 josephwb pg_1646
21:30 josephwb pg_1094Sarcostemma
21:30 josephwb pg_399Parmeliaceae
21:30 josephwb pg_1337Endopterygota
21:30 josephwb pg_1408Orchidaceae
21:30 josephwb pg_402Aspergillus
21:30 josephwb pg_1761Scleractinia
21:30 josephwb pg_2004Cyrtandra
21:30 josephwb pg_2833Metatheria
21:30 josephwb pg_292Papilionoideae
21:30 josephwb pg_2841Sparganium
21:30 josephwb pg_2625Utricularia
21:30 josephwb pg_1796Typhlatya
21:30 josephwb pg_1409Orchidaceae
21:30 josephwb pg_2044Orobanchaceae
21:30 josephwb pg_375Colletotrichum
21:30 josephwb pg_594
21:30 josephwb pg_2671Caridina
21:30 josephwb pg_2598Boraginaceae
21:30 josephwb pg_1103Bignonieae
21:30 josephwb pg_394Cucumis
21:30 josephwb pg_2901Thalictrum
21:30 josephwb pg_2068Osedax
21:30 josephwb pg_2866Anseriformes
21:30 josephwb pg_901Meryta
21:30 josephwb pg_2057
21:30 josephwb pg_2807Alpheidae
21:30 josephwb ot_178Hirundinidae
21:30 josephwb pg_576Alocasia
21:30 josephwb ot_176Tachycineta
21:30 josephwb pg_1786Hydrozoa
21:30 josephwb pg_349Retiboletus
21:30 josephwb pg_1570Asteraceae
21:30 josephwb pg_2573Archosauria
21:30 josephwb pg_1131Saxifragaceae
21:30 josephwb pg_2593Dermaptera
21:31 josephwb pg_1133Rosales
21:31 josephwb ot_149Todidae
21:31 josephwb pg_1600Primates
21:31 josephwb ot_137Sulidae
21:31 josephwb pg_2689Lupinus
21:31 josephwb fewer missing than i anticipated
21:31 josephwb oh, that was for kcranstn, but she is knot here
21:31 kcranstn I am here. Can you put those in the spreadsheet rather than spamming irc? ;)
21:32 kcranstn nice to see how few are un-annotated
21:35 josephwb gah! who is working on the spreadsheet?
21:35 kcranstn anonymous random animal?
21:37 josephwb yes
21:37 josephwb i am trying to paste in sorted data
21:37 kcranstn sure the sort order is the same?
21:37 josephwb it was. but they keep resorting it!
21:38 josephwb maybe dail.
21:39 josephwb i just want to sort by curation link (= by study id), paste, and sort back by priority
21:39 kcranstn try the chat?
21:39 josephwb they are not signed in
21:40 kcranstn throw it in a different sheet and we can update later when no one is editing
21:40 kcranstn different worksheet in the same spreadsheet
21:40 jimallman as a sometime anonymous animal, i believe sending an invitation is the key to seeing a user’s proper name
21:41 kcranstn lemme test that
21:42 kcranstn do you use you ibang address for gdocs?
21:42 josephwb i guess i will just wait
21:42 josephwb maybe romina
21:42 jimallman kcranstn: yes
21:43 kcranstn try accessing https://docs.google.com/spreadsheets/d/11T7O2Yre9SB3l1viokGlUsO3LVh3wgjf8_FEQHieXy0/edit#gid=947887154
21:43 kcranstn once you get that
21:43 jimallman i’m there...
21:43 kcranstn anonymous snake!
21:44 josephwb python
21:44 kcranstn python, to be specific
21:44 jimallman i just typed a comment there: “noice"
21:44 josephwb anywho, i've got most focal clades
21:44 jimallman and i am in fact logged into google (name in upper right)
21:44 kcranstn I created a new tab in that doc
21:44 kcranstn for the focal clades
21:45 josephwb ok
21:45 kcranstn what do you mean by proper invite? better than the one I just sent?
21:45 * jimallman just left the doc, in case you want to try sending me an invitation
21:45 kcranstn I did
21:46 kcranstn email slower than irc
21:46 jimallman oh, checking now.. (doh!0
21:46 jimallman clicked, looking for the doc again
21:47 jimallman i’m back in the doc, clicking your old link above… any change?
21:47 josephwb i see you now
21:47 kcranstn Jim Allman!
21:47 kcranstn you can no longer hide behind your randomly-assigned icon
21:48 jimallman drat!
21:49 jimallman let’s taunt Anonymous Hedgehog in the chat. maybe we can see his/her name!
21:50 jimallman (or maybe it’s me in a second browser. moooohahaha!
21:50 jimallman )
21:58 josephwb curator uses "Tree type", but nexson uses "curatedType"
21:58 josephwb i don't like "curatedType"
21:59 kcranstn for what property?
21:59 josephwb tree inference method
21:59 josephwb can we change that?
22:00 kcranstn I think there will be more than just this to discuss once we add more tree metadata
22:00 kcranstn will require changes to validation, UI, etc
22:00 josephwb right
22:00 josephwb don't know how this slipped by towodo, tho.
22:01 josephwb he likes things to have precise meaning
22:02 josephwb in which repo would i file an issue for this?
22:02 kcranstn I was just wondering the same thing
22:03 kcranstn is the validation code in peyotl or phylesystem-ape?
22:03 kcranstn api
22:03 josephwb i believe the  former
22:03 kcranstn put it there - we can always move it
22:04 josephwb pmidford2: do you know? you are our nexson guru.
22:05 pmidford2 <josephwb> not so much since we stopped using phylografter
22:06 josephwb ok, thanks.
22:06 pmidford2 But I know peyotl does do a lot of validation
22:06 josephwb jimallman: you must know what performs the nexson validation?
22:06 jimallman peyotl
22:06 josephwb i am pretty sure it is peyotl too
22:06 josephwb wee. thanks for the confimation.
22:07 josephwb can we think of that as where the nexson specification lives too?
22:08 josephwb gah. i will just put it in the opentree repo since it touches multiple tools
22:21 pmidford2 The formal NexSON specification is currently at https://github.com/OpenTreeOfLife/phylesystem-api/wiki/NexSON (not the same place as Mark's validator).  I think this is part of the source of the confusion <josephwb> may have had.
23:03 ilbot3 joined #opentreeoflife
23:03 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today

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