Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-02-12

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

All times shown according to UTC.

Time Nick Message
00:01 josephwb joined #opentreeoflife
00:36 jar joined #opentreeoflife
00:47 dukeleto joined #opentreeoflife
01:17 towodo joined #opentreeoflife
01:17 towodo dukeleto, git help?
01:47 towodo dukeleto, never mind, figured it out (looking at wrong repo)
01:55 josephwb joined #opentreeoflife
01:56 mtholder joined #opentreeoflife
02:05 kcranstn joined #opentreeoflife
02:31 kcranstn joined #opentreeoflife
02:38 kcranstn joined #opentreeoflife
03:04 kcranstn joined #opentreeoflife
04:06 kcranstn joined #opentreeoflife
04:18 josephwb joined #opentreeoflife
04:44 mtholder joined #opentreeoflife
06:07 kcranstn joined #opentreeoflife
11:40 josephwb joined #opentreeoflife
12:03 josephwb joined #opentreeoflife
12:40 kcranstn joined #opentreeoflife
12:57 josephwb joined #opentreeoflife
13:50 josephwb joined #opentreeoflife
14:24 towodo joined #opentreeoflife
14:32 blackrim joined #opentreeoflife
14:33 blackrim towodo: you are seeing the bits about taxonomy from Laura and Dail?
14:33 blackrim oops, just saw your email
14:33 towodo looking now
14:34 towodo I thought I responded. I don't know what the priority is. Are these must-fix-before-publication? As I said I look to you & Karen for priority guidance when it comes to microbe work, which is going to be a huge time sink
14:35 blackrim towodo: agreed. the message I got from Laura over the call last week were that they weren't priority, but then Dail's last message that I added you on the reply to said it was priority
14:35 towodo It doesn't help that they never answer my questions
14:35 blackrim I am happy to write some scripts to get some of these things IDed, but I can't do it until after my seminar tomorrow
14:39 towodo I think I know how to fix problem 2: snip out 'incertae sedis' taxa that have no siblings
14:39 towodo problem 1 is a simple script to provide a list for their review
14:39 blackrim right
14:39 towodo problem 3 cannot be done automatically, i think.  with some painful scripting i could make a list of candidates
14:41 towodo problem 4 is things that can't be done with the patch system, i would have to use the new one, but they are all pretty easy
14:41 towodo i just haven't made any of this a priority
14:42 blackrim I can't imagine that adding things at this point is a big prioriry. I am going to (after seminar) do some synth on Laura's trees to see where the major problems are. That might help prioritize
14:45 kcranstn joined #opentreeoflife
14:48 kcranstn impressed that Dail figured out how to initiate a pull request
14:49 josephwb Happy Darwin Day, Y'All.
15:13 kcranstn joined #opentreeoflife
15:13 blackrim joined #opentreeoflife
15:13 blackrim towodo: how many species are in silva before we process it? can't seem to find that info
15:28 towodo back again now, i'll answer. what do you mean by 'species' - tips?
15:28 blackrim yeah that works
15:28 blackrim names would also be fine if that is easier
15:29 towodo 73479 rows in the taxonomy.tsv file...
15:30 blackrim ok, tht is fine (smaller than I thought but that is because you cut things out I suppose
15:31 towodo 67715 I think is the number of tips I think
15:31 towodo 479726 total accessions, but I map them to ncbi taxa, yielding a much smaller number
15:31 towodo (as described in my writeup in google docs)
15:32 blackrim yeah. thanks!
15:32 towodo I think this information is in one of the files in the log/ directory in the reference-taxonomy repo
15:43 kcranstn joined #opentreeoflife
15:48 blackrim aha, looking at my slides I wanted the 479726 so we are good. thanks
15:48 towodo that's silva version 115. the one on their site is 117
15:49 blackrim well, i ain't changin it. lyx is forever
15:49 josephwb1 joined #opentreeoflife
15:49 towodo of course, just wanted you to know
15:50 towodo I haven't been refreshing any of our sources, to avoid disruption as publication nears
15:50 blackrim thanks. also, i am going to do some demos (just of the d3 trees) so hopefully that will be stable for one day
16:02 mtholder joined #opentreeoflife
16:03 kcranstn hey mtholder: you going to be at the all-hands tomorrow?
16:06 mtholder i think so..
16:07 kcranstn we are projected to have a "historically significant" ice storm tonight
16:07 mtholder that could mean "snow"
16:08 kcranstn could
16:08 mtholder Yes. I will be on the call.
16:08 kcranstn but trying to plan for loss of power
16:08 mtholder ugh to that.
16:08 kcranstn ok, if I can't make it can you start the call (I will send out a message asking people to add you to contacts if that is the case)
16:09 mtholder surely there is some form of chicken-based electricity generator you can purchase. I guess you'd still have to become your own ISP to make the call.
16:09 mtholder FWIW I just put up a couple GSoC thoughts. I could mentor or (preferred) co-mentor either. Only 1 is OT-specific.
16:10 mtholder And yes I can start the call.
16:10 josephwb1 This looks pretty slick: http://www.wellcome.ac.uk/stellent/groups/corporatesite/@msh_publishing_group/documents/web_document/wtd026042.pdf
16:11 kcranstn thanks, mtholder! (for the call and for gsoc)
16:25 kcranstn we don't prune out things that are strains from ncbi, do we?
16:31 mtholder joined #opentreeoflife
16:59 dukeleto joined #opentreeoflife
17:56 dukeleto joined #opentreeoflife
18:25 towodo joined #opentreeoflife
19:00 towodo kcranstn, we don't prune anything out of NCBI
19:01 towodo NCBI taxonomy is not a comprehensive source of strains. it's very spotty
19:40 jar joined #opentreeoflife
20:34 towodo joined #opentreeoflife
20:37 dukeleto Github webhooks (post-receive hooks) just got a lot nicer and easier to use: https://github.com/blog/1778-webhooks-level-up
20:52 mtholder left #opentreeoflife
21:00 kcranstn joined #opentreeoflife
21:04 dukeleto joined #opentreeoflife
22:29 dukeleto joined #opentreeoflife

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