WPWG-20090324-transcript

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(08:22:06 AM) pascale [pascale@dhcp-165-124-223-159.nubic.northwestern.edu] entered the room.
(08:22:11 AM) pascale: hi Seth
(08:22:44 AM) sjcarbon: hey, how are you doing?

(08:23:32 AM) pascale: not bad, you ?
(08:23:40 AM) gwg [gwg@plutonium.lbl.gov] entered the room.
(08:23:51 AM) gwg: eh, bonjour!
(08:23:54 AM) sjcarbon: hanging in there.

(08:24:24 AM) gwg: are you still ill, or feeling better?
(08:24:26 AM) pascale: I was wondering- if I send you a GAF file, can you load that in the GO database to make that figure for the paper?
(08:24:53 AM) sjcarbon: pascale: for the graph display?
(08:25:07 AM) pascale: I think everyone has now done the annotations but they are not all in the GO database yet
(08:25:09 AM) pascale: yes

(08:25:35 AM) sjcarbon: gwg: better-ish
(08:25:48 AM) pascale: oh ! you've been sick a long time!
(08:26:08 AM) sjcarbon: pascale: there is some special database stuff done in addition to the information in the GAF file
(08:26:20 AM) sjcarbon: but that doesn't mean it can't be done by hand.
(08:26:27 AM) sjcarbon: how big would it be?

(08:26:53 AM) sjcarbon: (actually, the homolset information is pulled from a different source...)
(08:28:21 AM) pascale: in terms of size: there are about 5 new genes that have now been annotated: I think from zebra fish, chicken and plant
(08:29:50 AM) sjcarbon: so this a large file? more than a few hundred lines?
(08:30:27 AM) pascale: no I dont think so- it's more like 5 lines per gene, so I would say less than 40-50 lines
(08:30:45 AM) rama [rama@cider.Stanford.EDU] entered the room.

(08:30:52 AM) sjcarbon: ah! that I might just be able to do by hand...
(08:31:04 AM) sjcarbon: could you skype me the file?
(08:31:05 AM) pascale: unless I get all annotations for the 12 ref genomes in a single file? Or could you just superimpose that extra data on the existing one?
(08:31:27 AM) pascale: I will look for the data and skype or email you later
(08:31:32 AM) rama: hello

(08:31:35 AM) pascale: hi Rama
(08:32:30 AM) sjcarbon: ideally, if you could get all of the information that you want displayed in one file, i should be able to rig something up.
(08:32:42 AM) pascale: ok then
(08:32:50 AM) rama: what are you talking about?
(08:33:10 AM) rama: (if I don't need to know it is okay!)

(08:33:17 AM) sjcarbon: sorry, getting the RG viewer to display an image that's not currently loaded into the database.
(08:33:36 AM) irc [cjm@yuri.lbl.gov] entered the room.
(08:33:51 AM) irc: hi yall
(08:33:51 AM) sjcarbon: pascale: i'll probably have a skype presence most of the day, but i may be gone for stretches.

(08:33:57 AM) pascale: ok
(08:34:06 AM) rama: irc- what is your name?
(08:34:31 AM) sjcarbon: irc is cjm
(08:35:03 AM) sjcarbon: pascale: just send it and i'll pick it up at some point.
(08:35:06 AM) rama: okay. thanks

(08:35:22 AM) irc: oh sorry, i can never remember how to work irc --chris
(08:36:51 AM) rama: Seth, can you query for ref.genome data using GOOSE yet?
(08:36:52 AM) irc: are we all ready to sign off on the release?
(08:37:08 AM) rama: sign -off on the release?
(08:37:13 AM) sjcarbon: let's just wait a couple more minutes for stragglers. mostly i just wanted to clarify (if necessary) the coverage that people are going to give for AmiGO testing, and then get time expectations from people.

(08:37:13 AM) irc: the refg data has been in the db for a while
(08:37:16 AM) rama: I just started testing y'day
(08:37:42 AM) sjcarbon: (sorry started typing my last message a while back...)
(08:39:30 AM) sjcarbon: <a href="http://wiki.geneontology.org/index.php/Web_Presence_Working_Group:_Testing_Guide">http://wiki.geneontology.org/index.php/Web_Presence_Working_Group:_Testing_Guide</a>
(08:39:30 AM) sjcarbon: kinda moot since most people aren't here...

(08:40:01 AM) rama: we shd add some example queries relevant to ref-genomes on the GOOSE pulldown
(08:40:12 AM) rama: I am totally digressing- sorry
(08:40:20 AM) sjcarbon: no, that's fine.
(08:40:29 AM) sjcarbon: have any favorites?
(08:40:58 AM) rama: i can send you a list over email

(08:41:33 AM) rama: the schema diagram should be updated too.
(08:42:51 AM) sjcarbon: okay.
(08:42:51 AM) sjcarbon: chris, isn't the schema diagram stuff auto-generated?
(08:43:20 AM) eurie [eurie@brix.Stanford.EDU] entered the room.

(08:44:56 AM) rama: Seth- when do you want testing comments by?
(08:46:05 AM) sjcarbon: sooner would be better, naturally. however the initial idea was to give a weeks' warning and then have a week of testing. unfortunately, that week of testing now falls on the GO meeting.
(08:46:45 AM) irc: seth - yes
(08:47:31 AM) rama: we will do our best to get comments in by Friday
(08:47:37 AM) sjcarbon: i'm not sure if people would appreciate the extra pressure right before a meeting...so i'd say the week after for commment.

(08:47:51 AM) sjcarbon: oops, never mind my last message then ;)
(08:47:56 AM) rama: do we have a release date set? also, are we going to talk about this/do a demo at the GOC meeting?
(08:49:01 AM) sjcarbon: release date is as soon as everybody checks off their section and ben switches the server (that usually is pretty fast).
(08:49:01 AM) sjcarbon: most of the stuff was talked about at the last meeting.
(08:49:03 AM) rama: are we planning to release this with a link to AmiGO Beta?

(08:49:25 AM) sjcarbon: if nobody finds it offensive.
(08:50:00 AM) sjcarbon: the idea was to give people semi-dependable access to new features as they are rolled out and tested.
(08:50:06 AM) rama: I see. It might still be worth it to briefly talk about this at this meeting.
(08:50:19 AM) sjcarbon: also to get more feedback during the development process.
(08:50:23 AM) sjcarbon: sure.

(08:50:48 AM) sjcarbon: would be like to have a split out group at some point to do this in the general meeting?
(08:50:52 AM) rama: I was not sure what I was going to get by clicking on the beta. IT goes to the wiki page and then one has to click on the link
(08:51:26 AM) sjcarbon: the wiki should have a clear explanation. if not, we can change that.
(08:51:40 AM) sjcarbon: <a href="http://wiki.geneontology.org/index.php/AmiGO_Beta">http://wiki.geneontology.org/index.php/AmiGO_Beta</a>
(08:51:51 AM) rama: may be some notes on the wiki about new cool features in beta will help

(08:52:09 AM) rama: the wiki currently only lists the caveats of a beta software.
(08:52:37 AM) rama: sorry- if i am digressing again. Seth, please go ahead with your agenda
(08:52:39 AM) sjcarbon: certainly. however, right now, the testing amigo and the beta amigo are the same thing.
(08:53:43 AM) rama: in that case, i think we should remove the link.
(08:55:21 AM) sjcarbon: yes, but as soon as the meeting is done, we'll be building new features on again and they will soon diverge. also, I don't want to bother Ben too much about reinstalling in that case.

(08:55:46 AM) sjcarbon: are other people not liking the "beta link"?
(08:55:57 AM) gwg: i've got to go now - will check the transcript late
(08:56:00 AM) gwg: r
(08:56:02 AM) gwg left the room (quit: Quit: Goodbye cruel world!).

(08:56:36 AM) rama: no problem in that case. I thought that link was was distracting
(08:57:19 AM) pascale: I think the beta link is okay if it does allow people to check out new features- however going to the wiki seems odd? Why not go to beta directly?
(08:57:19 AM) sjcarbon: i tried a couple of ways to balance visibility and usefulness.
(08:57:20 AM) irc: I love having the link to the beta, but Rama is correct, it's
(08:57:51 AM) irc: a link to a beta from a production website should go to a beta for the *next* release

(08:58:07 AM) irc: in this case, as soon as 1.6 goes live we have no beta
(08:58:22 AM) irc: we either change the beta wiki page to "come back soon!"
(08:59:00 AM) irc: or add some configuration such that we can flip a switch with the live 1.6 such that it will show the beta link when we have 1.7 beta ready
(08:59:09 AM) sjcarbon: the link will just go to the most recent update i've done on our testing servers.

(08:59:47 AM) sjcarbon: ah! right, it also exposes things like the lucene tests and other very early things.
(09:00:17 AM) sjcarbon: and other things that may be extant in the 1.6 codebase, but not exposed.
(09:00:19 AM) irc: ok, I guess we can get away with call this a beta then
(09:00:32 AM) irc: (a 1.7 beta that is)
(09:01:24 AM) sjcarbon: just call it AmiGO labs? or is that too derivative?

(09:01:33 AM) irc: The generic AmiGO beta web page should have a link to the wiki page for v n+1 as soon as v n is released
(09:02:52 AM) rama: I actually like AmiGO labs
(09:02:57 AM) irc: something like labs is perhaps better as it does not commit to a stage in the release cycle
(09:03:12 AM) sjcarbon: if we're also trialling features that may or may not exist in a release labs would be better.
(09:03:16 AM) rama: tells users that some development/experimentation is going on

(09:03:37 AM) irc: the wiki page for version n+1 woul state whether it was in alpha/beta state, and this could be changed simply by editing the wiki page
(09:04:03 AM) irc: so the link from the production amigo might be better called 'test new features' or something
(09:04:37 AM) sjcarbon: new features sounds production-ready/useable.
(09:04:44 AM) sjcarbon: to me anyways.
(09:04:46 AM) rama: i agree with Seth

(09:04:50 AM) irc: ok
(09:05:06 AM) rama: also i think the AmiGO labs link shouldn't be in the tool bar?
(09:05:25 AM) rama: may be move it down to the lower bar, left side?
(09:05:53 AM) sjcarbon: in the footer area?
(09:06:01 AM) rama: yes (thanks!)

(09:07:01 AM) sjcarbon: i can try a mock-up of that and will send a link out later today to the group.
(09:08:36 AM) irc: but this shouldn't hold up the release
(09:08:41 AM) rama: sure
(09:08:45 AM) rama: i agree
(09:08:51 AM) sjcarbon: no, this will just be a template change.

(09:09:21 AM) sjcarbon: could be done after release too.
(09:09:39 AM) rama: cool. We shd all divy up the Help pages and update them.
(09:10:00 AM) rama: it is on the wiki- so can be done independently
(09:10:38 AM) sjcarbon: maybe people could start with what they're testing?
(09:10:53 AM) rama: okay.

(09:11:09 AM) rama: anything else?
(09:11:13 AM) sjcarbon: i'll send links out to the group.
(09:11:15 AM) gwg [gwg@plutonium.lbl.gov] entered the room.
(09:11:33 AM) sjcarbon: i think i'm covered.

(09:11:43 AM) sjcarbon: anybody else?
(09:12:43 AM) sjcarbon: ...that's a no then...
(09:13:09 AM) sjcarbon: okay, thanks everybody!
(09:13:09 AM) sjcarbon: (and chris, do you have a minute afterwards?)
(09:13:13 AM) pascale: nothing for me- I think the ref genome stuff is fine

(09:13:20 AM) sjcarbon: cool.
(09:13:23 AM) irc: yep
(09:13:26 AM) rama: thanks. yes, the ref.genome stuff is cool.
(09:13:35 AM) rama: awesome job.
(09:13:35 AM) rama: bye

(09:13:35 AM) pascale: bye
(09:13:38 AM) sjcarbon: my pleasure.
(09:13:38 AM) gwg left the room (quit: Quit: Goodbye cruel world!).
(09:13:38 AM) pascale left the room (quit: Quit).
(09:13:40 AM) sjcarbon: bye.