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  • Jan 13 20:38

    jimallman on improved-collection-editor

    layout tweak (compare)

  • Jan 13 20:30

    jimallman on development

    more cleanup Merge branch 'improved-collecti… (compare)

  • Jan 13 20:30

    jimallman on improved-collection-editor

    more cleanup (compare)

  • Jan 13 20:26

    jimallman on development

    margin fix Merge branch 'improved-collecti… (compare)

  • Jan 13 20:26

    jimallman on improved-collection-editor

    margin fix (compare)

  • Jan 13 20:22

    jimallman on development

    more form cleanup Merge branch 'improved-collecti… (compare)

  • Jan 13 20:21

    jimallman on improved-collection-editor

    more form cleanup (compare)

  • Jan 13 20:13

    jimallman on development

    add-tree cleanup Merge branch 'improved-collecti… (compare)

  • Jan 13 20:13

    jimallman on improved-collection-editor

    add-tree cleanup (compare)

  • Jan 13 19:50

    jimallman on development

    Shuffle add-tree UI in full-pag… Merge branch 'improved-collecti… (compare)

  • Jan 13 19:50

    jimallman on improved-collection-editor

    Shuffle add-tree UI in full-pag… (compare)

  • Jan 13 05:45

    jimallman on development

    cleanup of unwanted buttons Merge branch 'improved-collecti… (compare)

  • Jan 13 05:44

    jimallman on improved-collection-editor

    cleanup of unwanted buttons (compare)

  • Jan 12 22:44

    jimallman on development

    fix for combined HTML Merge branch 'improved-collecti… (compare)

  • Jan 12 22:43

    jimallman on improved-collection-editor

    fix for combined HTML (compare)

  • Jan 12 22:16

    jimallman on development

    cosmetic cleanup of tree commen… Merge branch 'improved-collecti… (compare)

  • Jan 12 22:16

    jimallman on improved-collection-editor

    cosmetic cleanup of tree commen… (compare)

  • Jan 12 18:26

    jimallman on development

    Cleanup of read-only tree displ… Merge branch 'improved-collecti… (compare)

  • Jan 12 18:25

    jimallman on improved-collection-editor

    Cleanup of read-only tree displ… (compare)

  • Jan 07 00:45

    bredelings on track-implied-splits

    Just keep all the solutions, by… Rename c1 and c2 to split_comp … Simplify component-merging logi… (compare)

Mark T. Holder
@mtholder
I'm going to deploy a branch of peyotl-for-phylesystem-api onto devtree (hopefully, this won't step on @jimallman 's toes. (or anyone elses'))
Mark T. Holder
@mtholder
sort-of got phylesystem-api working with the script-managed trees option using: https://github.com/OpenTreeOfLife/phylesystem-0
nm.
still rejecting that study.
I had to edit the opentree-shared.conf on devapi to replace ot56 with devphylesystemapi in order to get the forwarding to work.
that may mean that I should have been updating the server name on devphylesystemapi rather the confs ondevapi
Benjamin Redelings
@bredelings
@LunaSare OK, I think you can try conflict on ot_1876 against api again.
The first fix wasn't.
After checking with valgrind, it looks like this one is better.
Luna Luisa Sanchez Reyes
@LunaSare

@LunaSare Cool, that is helpful. I think I just need to debug this locally, as it appears to be a "heisenbug" -- i.e. a bug that appears only when you are not looking at it.

Agh, that’s annoying… I’m glad it is not a “schroedinbug”, that one sounds way scarier tbh

After checking with valgrind, it looks like this one is better.

That’s great @bredelings. I’ll try conflict again then 🙊

Benjamin Redelings
@bredelings
Great, please do.
Luna Luisa Sanchez Reyes
@LunaSare
Yay, it’s working!
Mark T. Holder
@mtholder
OK. @jimallman I finally have the phylesystem-api on dev returning a nexson blob for https://devtree.opentreeoflife.org/curator/study/view/tt_217 , but I think that it is not the nexson blob the JS was expecting.
I can try to diagnose, but you might find it faster than I do
Jim Allman
@jimallman
no worries, i'm sure it's failing some kind of client-side validation (or code that presumes too much).
Matt
@mjy

Greetings tree-folk. Just popping in to note that we've started work on this repo, that was discussed a long time ago: https://github.com/SpeciesFileGroup/otu_mapping_widget. In essence we're stealing your OTU->Name widget and trying to make it generic, because we need a nearly identical interface.

I'd love to have your feedback on what worked and didn't, what you didn't have time to work on but would have like to have, etc. In theory the interface we build will be software agnostic, hopefully utlimately pluggable into your tools if it becomes useful.

Jim Allman
@jimallman
Hi @mjy ! Have you tried our bulk-TNRS tool? This uses the same UI as we do for per-study OTU mapping, but it loads and saves all work in ZIP archives. Most useful for mapping entire sets of OTU labels that follow a particular lab's or project's nomenclature.
As with most of our webapps, it was built using the web2py framework, but almost all of the logic here is client-side JS, plus calls to existing OpenTree APIs. You can follow that traffic and see how we bundle arguments using in-browser dev tools, e.g. the Network tab in Google Chrome.
Jim Allman
@jimallman
oh, here's a well-hidden README to help with testing and re-use of the TNRS code.
Matt
@mjy
Thanks @jimallman. Have not tried. We're really trying to just focus on the resolution bit, not how or what is being resolved. For example we could configure the same widget to map People to People. It's really the UI/UX of matching two columns (that have hooks for external things), and a hook to say "I'm done" (then externally trigger the Zip creation, or the batch upload, or the batch update etc... all that external bit is seperate).
I'll definitely checkout the bulk tool- definitely sounds like similar concepts.
Yan Wong
@hyanwong
I guess you must have noticed that Homo sapiens is marked as extinct on the current OpenTree?
There is presumably an issue for that somewhere.
Jim Allman
@jimallman
yes, this is definitely a Known Issue:
OpenTreeOfLife/feedback#480
Yan Wong
@hyanwong
:thumbsup: :skull:
Yan Wong
@hyanwong
If anyone is interested, we have just preprinted a paper on how OneZoom works, and interacts with the OpenTree. It's at https://www.biorxiv.org/content/10.1101/2020.10.14.323055v1 - do let me know if you think anything needs changing, and whether we have done justice to the OpenTree efforts! It was quite hard to squeeze it all in to the required length, so there's a fair bit of the description in the supporting material PDF.
Yan Wong
@hyanwong
I just noticed a new sp. that is presumably a good test of name length constraints, both in code and display. But it won't be in OpenTree yet: https://scientistseessquirrel.wordpress.com/2020/10/20/a-new-and-unfortunate-record-the-longest-latin-name/
Mark T. Holder
@mtholder
Awesome. according to https://www.curioustaxonomy.net/word/longShort.html the longest genus is Kimmeridgebrachypteraeschnidium. But I doubt that anyone has mistaken a myxobacterium for a fossil dragonfly, so we don't have to worry about it being moved to that genus.
Yan Wong
@hyanwong
What's the formal name for a completely unbalanced, ladder-like topology? I seem to remember there is something, and it isn't "ladder tree"?
Chris Meacham
@MrNewick
Mark T. Holder
@mtholder
"pectinate" is also used.
Chris Meacham
@MrNewick
Yes, that's right.
Yan Wong
@hyanwong
"pectinate" was what I was thinking of, but actually "comb" is a little more visual. Thanks!
It was surprisingly hard to google for.
Yan Wong
@hyanwong
I have another phylogenetic question to which someone like @mtholder might know the answer - I hope people don't mind me asking here (I'm happy to take it to personal chat, but I know that other phylo folk hang around here too). Say I have a tree of 10 subspecies of brown bear, and 10 subspecies of polar bear. I want to know if the polar bears are essentially monophyletically nested within the browns (or indeed if there is reciprocal monophyly). But I don't mind if one or two of the polars are not-quite monophyletically nested. Are there standard metrics which measure this "degree of monophyly"? I thought one possibility would be to take the set of induced trees containing all possible mixes of "2 polars + 1 brown" and count up the number in which the polars are not sisters, comparing it to a sensible null model (which I guess would be equiprobable topologies, although I do have the issue that there may be polytomies in the tree).
I'm just after some pointers to papers or standard metrics, really.
Mark T. Holder
@mtholder
sorry. i just saw this... you might want to look at the genealogical sorting index https://doi.org/10.1002/9780471650126.dob0929 that is usually for measures of the extent to which gene trees agree with a species tree. but it might be interesting to treat the subspecies tree as if it were a gene tree and calculate gsi on the 2 species tree.
Your thought about looking at the fraction of rooted triples that yield monophyly seems like a good one to me.
@hyanwong ^
Yan Wong
@hyanwong
Thanks Mark. Very useful. Hope all's well with OpenTree folk in the US.
Yan Wong
@hyanwong
Also, @mtholder - do you know if the idea of looking for monophyly in rooted triples is a used and published method?
Mark T. Holder
@mtholder
not for this purpose, @hyanwong . It's very similar to the Concordance Factors (fraction of each split for an unrooted 4-taxon case) used as the key summary in SNaQ (Solis-Lemus, Yang, and Ane) or in ASTRAL. But the focus there is estimating a species tree, not saying something species status.
Yan Wong
@hyanwong
Thanks. We might have a super snazzy way of calculating this in a scalable way over a genome - will keep you posted.
Emily Jane McTavish
@snacktavish
Jim Allman
@jimallman
:confetti_ball:
Mark T. Holder
@mtholder
updating the SSL certs right now. I was supposed to do that earlier this week, but I forgot... there have been some distractions this week..
Mark T. Holder
@mtholder
certs updated. Remind me to tell you on the call next week how I did finally remember