WPWG-20080325-transcript

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(08:30:51 AM) gwg: pourquoi? travaille sur les choses dans la maison/jardin?
(08:30:59 AM) gwg: ou sur le travail?
(08:31:11 AM) pascale: sur le travail :(

(08:31:33 AM) Logging started. Future messages in this conversation will be logged.
(08:31:49 AM) gwg: ah non!
(08:32:16 AM) gwg: tu as trop de choses a faire, c'est obvieux (pardonnez mon francais)
(08:32:31 AM) pascale: j'aime bien obvieux, tres joli

(08:32:53 AM) gwg: mais peut-etre c'est la prix qu'on droit payer si on veux etre un PI!
(08:33:56 AM) pascale: tres drole
(08:34:09 AM) gwg: est-ce que tu sais quand tu vas acheter les billets pour SLC?
(08:34:43 AM) pascale: cette semaine j'espere

(08:35:13 AM) pascale: j'aessaie de planifier une combinaison avec Chicago, mais je pense que je devrai faire 2 voyages
(08:35:38 AM) gwg: oui, moi aussi... j'ai trop de choses a faire, et je n'ai pas travaillee cette weekend!
(08:35:46 AM) gwg: ah non, c'est dommage...
(08:36:07 AM) gwg: quand est-ce que tu dois aller a Chicago?

(08:36:39 AM) pascale: c'est le probleme... je ne suis pas encore sure des dates
(08:37:03 AM) gwg: ah non! (encore une fois)
(08:38:15 AM) gwg: peut-etre tu peux avoir des vacances entre le rendezvous de GO et le rendezvous a Chicago?
(08:38:31 AM) pascale: peut-etre...

(08:38:49 AM) pascale: (I hope Seth and Ben like the French lesson ;)
(08:39:07 AM) gwg: tu peux hitchhike a Chicago - tu ne dois pas reserver les billets!
(08:39:31 AM) gwg: (I hope Seth and Ben aren't paying any attention to my French if so...)
(08:39:41 AM) pascale: bonne idee, j'aurais du te consolter avant!

(08:39:46 AM) pascale: (consulter)
(08:40:14 AM) gwg: J'ai toujours beaucoup de bonnes idees!
(08:41:27 AM) gwg: ou est tout le monde?
(08:41:52 AM) pascale: are we meeting? or just amelia and I chatting?

(08:42:00 AM) pascale: (not that I am not having a great time...)
(08:42:03 AM) sjcarbon: I sent out another email, but does anybody know the whereabouts of Mary, Val, and Chris?
(08:42:15 AM) sjcarbon: Any others that I'm missing?
(08:42:18 AM) gwg: I know Jane is supposedly coming - but she'll be late

(08:42:32 AM) pascale: Val said she wont come anymore I thought
(08:42:35 AM) gwg: Eurie?
(08:42:48 AM) ben: Rama is out
(08:44:19 AM) sjcarbon: Ah well, I guess we can go ahead and start--probably not that many new people will arrive.

(08:44:37 AM) sjcarbon: On the agenda:
(08:44:43 AM) pascale: so I am the one tester against 3 developers?
(08:44:50 AM) sjcarbon: we win!
(08:44:55 AM) pascale: I know!!

(08:44:56 AM) gwg: muahahahaha!
(08:45:11 AM) pascale: this is really scary
(08:45:37 AM) gwg: I'll be gentle... can't speak for Seth or Ben, tho ;)
(08:45:53 AM) ben: I will switch sides for you Pascale...

(08:46:06 AM) pascale: thanks :)
(08:46:22 AM) sjcarbon: Now that we have teams...
(08:46:33 AM) sjcarbon: Discuss previous action items
(08:46:39 AM) sjcarbon: finish soliciting comments on new mockups

(08:46:49 AM) sjcarbon: Are they solicited?
(08:47:07 AM) gwg: only Rama replied, which was very solicitous of her...
(08:47:24 AM) pascale: I stll need to test...
(08:47:30 AM) ben: 1) all the options (browse, Blast, GO Slimmer, HELP) are all listed

(08:47:30 AM) ben: below the Search box on the main page. We did not decide on this
(08:47:30 AM) ben: layout. Since this idea did not develop much, I strongly feel we
(08:47:30 AM) ben: should go with the previous simple version.1) all the options (browse, Blast, GO Slimmer, HELP) are all listed
(08:47:30 AM) ben: below the Search box on the main page. We did not decide on this

(08:47:32 AM) ben: layout. Since this idea did not develop much, I strongly feel we
(08:47:34 AM) ben: should go with the previous simple version.
(08:47:36 AM) ben: 1) all the options (browse, Blast, GO Slimmer, HELP) are all listed
(08:47:38 AM) ben: below the Search box on the main page. We did not decide on this

(08:47:40 AM) ben: layout. Since this idea did not develop much, I strongly feel we
(08:47:42 AM) ben: should go with the previous simple version.
(08:47:44 AM) ben: 1) all the options (browse, Blast, GO Slimmer, HELP) are all listed
(08:47:46 AM) ben: below the Search box on the main page. We did not decide on this

(08:47:48 AM) ben: layout. Since this idea did not develop much, I strongly feel we
(08:47:50 AM) ben: should go with the previous simple version.
(08:47:54 AM) ben: whoa, sorry
(08:47:55 AM) pascale: maybe

(08:48:04 AM) sjcarbon: Channeling rama.
(08:48:53 AM) gwg: should I answer Rama's things here or reply to the mailing list?
(08:49:09 AM) pascale: so the previous version, you mean the menu we have with those options?
(08:49:48 AM) gwg: previous version == google-esque front page

(08:49:51 AM) sjcarbon: Amelia: Since we are intending this on going out as soon as possible, both might be good.
(08:51:12 AM) gwg: To be honest I don't think I have enough time to do all Rama's things - I think we should release the version that went out to the GO list + any minor corrections.
(08:51:40 AM) gwg: (enough time before the GO meeting, that is)
(08:51:45 AM) sjcarbon: What about just changing the front page template.

(08:51:55 AM) sjcarbon: We can do an additional release later.
(08:52:24 AM) gwg: I think there should be something with links and a bit of explanation on the front page...
(08:52:48 AM) gwg: I guess people didn't like the big fonts - those can easily be changed tho
(08:53:07 AM) gwg: (I had just been reading a web design article about big fonts - that's the only reason they're on that page!)

(08:53:10 AM) pascale: right, if it fitted in a page, that'd be nice
(08:53:33 AM) ben: I am of two minds about this.
(08:53:51 AM) gwg: Maybe the Googly box and then a little list below with the links in it?
(08:54:00 AM) ben: 1) Amelia made a bunch of changes without really asking

(08:54:14 AM) ben: 2) None of the testers complained, even though they had been up on toy for months
(08:54:32 AM) pascale: well the testers have been pretty useless (at least I have)
(08:55:06 AM) pascale: and since no one requested *anyting*, it's great Amelia dis something to try to make us react
(08:55:12 AM) gwg: you've been fine - it's just that everyone's busy!

(08:55:15 AM) ben: There is one (at least?) advantange to Amelia's front page - it certainly draws attention to the fact that there have been interface changes
(08:55:20 AM) pascale: but even the big fonts didn't work!
(08:55:41 AM) gwg: I don't have strong feelings either way on the big fonts
(08:55:51 AM) ben: I do think the word "operator" should be struck. Qualifier is indeed less correct, but that's a GOC issue, not one for use to impose

(08:57:06 AM) sjcarbon: Sorry--obofoundry.org just disappeared and I have to go and find it. BRB.
(08:57:15 AM) ben: I do have to make at least 1 change (one of the cache scripts)
(08:57:25 AM) gwg: yeah, I agree about operator
(08:59:26 AM) gwg: I think that the AmiGO version on toy:9012 should be released now - there are enough positive changes for it to replace the current AmiGO

(09:00:48 AM) gwg: there are still some small annoying stupid things to clear up with sort-by-qualifier version that people were testing, and I don't think I have enough time to get them done before the GO meet
(09:00:55 AM) pascale: that seems true; although I wish I had tested more...
(09:01:08 AM) ben: what is the diff between what is on toy and what is on goweb-dev?
(09:01:18 AM) pascale: sure, but people wont agree about that any time soon, so I wouldn't worry about it

(09:01:21 AM) gwg: I am off next week and the week after, and I also have to organize my visa and moving my life over to the US!
(09:01:52 AM) sjcarbon: Sorry--found it. Hiding in corner.
(09:01:57 AM) gwg: I believe they're probably v. similar if not the same?
(09:02:23 AM) gwg: I haven't committed the changes I've made for the sort-by-qualifier version into cvs

(09:03:02 AM) sjcarbon: Ben, the only changes about what is currently tagged on what is on the goweb-dev should be the regulates fixes.
(09:03:22 AM) sjcarbon: Let me try that again in English.
(09:04:29 AM) sjcarbon: The only changes between what is currently tagged "amigo_1_5_RC3" and what is on the goweb-dev should be the fixes that make regulates work properly. (I'd have to check the logs to make sure though.)

(09:05:13 AM) gwg: I updated the images to the new regulates ones used in OBO-Edit
(09:05:30 AM) sjcarbon: They look good?
(09:05:52 AM) gwg: Yep, not too bad!
(09:06:01 AM) sjcarbon: Cool.

(09:06:16 AM) ben: OK, I will update goweb-dev with RC3 today.
(09:07:14 AM) sjcarbon: How about an RC4 with the corrected icons--right after the chat--if there's no problem.
(09:08:01 AM) ben: OK RC4. I won't be able to do it until this afternoon though.
(09:08:09 AM) sjcarbon: No problem.

(09:08:33 AM) sjcarbon: I'll email you all when it's tagged.
(09:08:47 AM) gwg: This is what I suggest: tomorrow I will compare my AmiGO files with what's in GO SF cvs, and if there are any other simple things which can be committed, I will do that. Tomorrow morning (for you) we can do a final check and release rc4
(09:09:27 AM) gwg: It won't have any of the sort-by-operator stuff, but there will be a couple of little things that Rama suggested which I implemented
(09:09:53 AM) sjcarbon: I don't know if we have time anymore--regulates goes up on the 28th and it must be up by then. If anything needs fixes, there will be problems.

(09:10:07 AM) sjcarbon: We can work on a release soon after though.
(09:10:16 AM) gwg: OK, sure
(09:10:40 AM) gwg: they weren't major things - it's just I have stuff on straight after work so I can't do it now :S
(09:11:21 AM) sjcarbon: I'm sure we'll have another release before the meeting.

(09:12:09 AM) gwg: with the new installer, releases should be easier and they won't be a big deal like they were with the old version!
(09:12:41 AM) j-lo [jane@cpc1-cmbg1-0-0-cust325.cmbg.cable.ntl.com] entered the room.
(09:12:50 AM) gwg: ms. Lopez!
(09:13:01 AM) j-lo: hiya - sorry i'm so late

(09:13:14 AM) j-lo: did i miss the meeting entire;y?
(09:13:27 AM) gwg: well, it's still going on... just about ;)
(09:13:41 AM) sjcarbon: We have to make new teams now though...
(09:13:58 AM) gwg: hmmmm... unless someone plays for both teams?

(09:14:34 AM) sjcarbon: We were just discussing the details behind getting this release out and what gets in under the wire.
(09:14:52 AM) j-lo: have we got a date?
(09:15:17 AM) sjcarbon: Up on the 28th--there are bug fixes necessary for the regulates relation.
(09:15:29 AM) j-lo: excellent!

(09:15:43 AM) sjcarbon: I'm excited!
(09:16:04 AM) j-lo: me too - the users are going to love it!
(09:16:17 AM) sjcarbon: I hope so.
(09:16:47 AM) sjcarbon: Anything else we need on this topic?

(09:16:50 AM) gwg: ...until they find a load of bugs ;)
(09:17:03 AM) sjcarbon: (sshhh!)
(09:17:13 AM) ben: OK then...
(09:17:24 AM) gwg: excellent!

(09:18:16 AM) j-lo: btw - this meeting doesn't clash with OE meeting - I had my time zones/daylight saving all mixed up apparently. OE meeting is directly after this one.
(09:18:41 AM) sjcarbon: That gives us just ten minutes then.
(09:18:50 AM) sjcarbon: Next agenda item.
(09:19:01 AM) sjcarbon: Everybody! Let's test AmiGO!

(09:19:12 AM) sjcarbon: Always a good thing.
(09:19:36 AM) sjcarbon: Ben will have a new version up this afternoon, and we'll annouce on the list when it's up.
(09:19:41 AM) pascale: yep!
(09:19:52 AM) j-lo: Will do. Do bugs go to the list or in the tracker?

(09:20:34 AM) j-lo: (not that there'll be any of course)
(09:20:37 AM) sjcarbon: List will be faster but both are good.
(09:21:06 AM) sjcarbon: Hopefully there'll be no showstoppers.
(09:21:49 AM) sjcarbon: Next agenda item:

(09:21:58 AM) sjcarbon: preview of live ref genome graphs
(09:22:43 AM) sjcarbon: I'd like to start getting feedback on what should be shown and what features are wanted (if possible). Is this the right place, or should I be bugging the ref genome list?
(09:23:06 AM) gwg: definitely bug the ref genome list about it
(09:23:10 AM) pascale: right

(09:23:14 AM) ben: The graphs seem too big to be useful
(09:23:20 AM) sjcarbon: They zoom.
(09:23:40 AM) gwg: I don't know if there are any others on this list who aren't on the ref genomes list... J-Lo, are you on the ref genomes list?
(09:25:20 AM) pascale: I haven't figured out how to view the ref genomes graphs on amigo?

(09:25:40 AM) ben: well.. maybe my SVG software sucks, but I think they can be improved
(09:26:12 AM) sjcarbon: There is some testing stuff at: <a href="http://berkeleybop.org/alpha/amigo/amigo">http://berkeleybop.org/alpha/amigo/amigo</a>
(09:26:23 AM) sjcarbon: ben: what are you using?
(09:26:25 AM) j-lo: no, i'm not

(09:28:30 AM) gwg: you should sign up, it's wikkid
(09:29:23 AM) gwg: hello?
(09:30:04 AM) pascale: seth, can you order the gene list alphabetically?
(09:30:33 AM) sjcarbon: yes, they is an option at the top of the summary page...are you looking at the summary page?

(09:30:51 AM) sjcarbon: I'll switch the default over to that.
(09:30:53 AM) pascale: I see- it's by number or orthologs, ok
(09:31:02 AM) sjcarbon: it was useful for testing.
(09:31:08 AM) sjcarbon: that way.

(09:31:13 AM) pascale: well it'd be nice to be able to rank be different columns (if possible)
(09:31:16 AM) pascale: sure, right
(09:31:28 AM) pascale: send to ref genomes, we'll comment
(09:31:30 AM) ben left the room (quit: Ping timeout).

(09:31:37 AM) sjcarbon: okey-dokey.
(09:31:44 AM) pascale: we can put that in the agenda for the next meeting
(09:31:53 AM) pascale: if you (an anyone else) want to attend
(09:31:53 AM) sjcarbon: that'd be great.

(09:32:06 AM) ben [hitz@c-98-210-219-14.hsd1.ca.comcast.net] entered the room.
(09:32:13 AM) sjcarbon: i'm always lurking at least.
(09:32:28 AM) ben: sorry my interwebs tube just broke
(09:32:44 AM) sjcarbon: we're at time--is there anything else before we wrap up?

(09:32:57 AM) pascale: not really for me
(09:32:58 AM) ben: I just use Firefox to view the SVG
(09:33:19 AM) pascale: I see nothing in firefox, just lines, can't scroll enough to see anything
(09:33:40 AM) sjcarbon: pascale: which one?

(09:34:38 AM) pascale: 2.0.0.12 on XP. it works better on my other computer with vista
(09:34:51 AM) pascale: so I will not comment until I have a proper look at it!
(09:34:56 AM) sjcarbon: which graph were you looking at?
(09:35:20 AM) sjcarbon: there is a known bug with graphviz that I need to crush on a case-by-case basis.

(09:35:32 AM) sjcarbon: Or is this with all of the graphs?
(09:35:33 AM) pascale: ok
(09:35:42 AM) pascale: probably not
(09:35:45 AM) ben: I have just been looking at MSH6... it's not responsive enough to be useful.

(09:35:53 AM) pascale: I got a better one now
(09:35:55 AM) ben: that may be the server
(09:36:06 AM) pascale: slc22a13
(09:36:13 AM) ben: also, what zooms? Remember I have a stupid 1 button mac mouse...

(09:36:41 AM) sjcarbon: ben: 2-finger slide or ctrl-a/ctrl-z
(09:36:48 AM) pascale: right, I was able to zoom with my mouse,
(09:37:02 AM) pascale: oh! I tried ctrl + crtl -
(09:38:46 AM) sjcarbon: Instructions:

(09:38:49 AM) sjcarbon: <a href="http://wiki.geneontology.org/index.php/RG:_Software#Summary_and_Graph_Views">http://wiki.geneontology.org/index.php/RG:_Software#Summary_and_Graph_Views</a>
(09:39:04 AM) gwg: holy crap, that reminds me - the help docs are out of date for AmiGO!
(09:39:25 AM) ben: oh, it's just super slow and backwards (scroll towards you makes it smaller)
(09:40:01 AM) sjcarbon: ben: I'm still working on different speed-ups.

(09:40:34 AM) sjcarbon: gwg: it should all be linked through the wiki now so we can roll it out just by copying it over.
(09:41:07 AM) gwg: I haven't updated any of the docs, tho :o
(09:41:22 AM) sjcarbon: I've been working on it a bit in the inbetween times.
(09:41:35 AM) ben: I think you are going to have to go with a more heavyweight client to handle the larger graphs. A java applet or webstart... maybe I am wrong though.

(09:42:44 AM) sjcarbon: I have a fix in mind, but it probably won't be ready for the first iteration. We can always fall back on a cronned pre-generation too.
(09:42:57 AM) pascale: sure
(09:43:12 AM) sjcarbon: We can go into more detail on the software group.
(09:43:23 AM) sjcarbon: Time's up! Anything else?

(09:43:38 AM) pascale: what woud be nice would be if more info appeared as you zoomed. initially you could see the GO term, maybe whether the annotations are EXP or ISS
(09:43:51 AM) pascale: and then as you zoom you;d see more details like gene names
(09:44:03 AM) pascale: I am ready to go for lunch!
(09:44:15 AM) gwg: you go girl!

(09:44:29 AM) pascale: :)
(09:44:47 AM) gwg: bon appetit!
(09:44:52 AM) pascale: ref genome meeting is April 8
(09:45:30 AM) pascale: talk to you soon

(09:45:34 AM) pascale left the room (quit: Quit).
(09:45:42 AM) sjcarbon: See y'all later.
(09:46:15 AM) gwg: see yas!
(09:46:16 AM) ben: bye

(09:46:20 AM) sjcarbon: bye!
(09:46:23 AM) gwg left the room.