WPWG-20091123-transcript

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  • Tuesday November 24 2009, 08:29 -
  • j-lo has joined the room

Ben: hi there!

sjcarbon: mornin!

Ben: I am chatting from my phone, so my net access is a little limited

  • cjm has joined the room

sjcarbon: no problem.

sjcarbon: let's just give it until 8:35, then we can start.

  • rama has joined the room

rama: Hello,

rama: Good morning

sjcarbon: mornin!

sjcarbon: rama - we're just giving it another three minutes.

sjcarbon: two now.

rama: Sure

rama: we are waiting for?

rama: Amelia?

rama: Val, pascale may be?

Ben: I should tell chris that I use his code in go-prepare-release.pl to torture job candidates


  • 08:34 -
  • gwg has joined the room

cjm: good morning.

gwg: Hello, sorry I'm late!

cjm: I am simultaneously on the OE call

sjcarbon: no problem.

gwg: whoa, multitask-o-rama!

j-lo: please send them my apologies, not going to try doing both!

sjcarbon: let's get rockin!

rama: Seth- if i need a new feature on AmiGO, should i put it on SF or the Wiki?

sjcarbon: SF

sjcarbon: definitely SF.

rama: okay. thanks.

sjcarbon: there is always the possibility that things on the wiki might go undiscovered

sjcarbon: first off, nice to meet you Kalpana!

rama: hmm

rama: she went to get water i think

j-lo: heh!

sjcarbon: moving on then...

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sjcarbon: I wanted to see if anybody here still needed/wanted google accounts to view the analytics data.


  • 08:39 -

cjm: Do I have one?

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sjcarbon: i also wanted to ask ben if there was any way for us to view the main GO data.

j-lo: it's very interesting

rama: I would like one. What do I have to do? (apologies if you sent instructions and I overlooked)

sjcarbon: cjm - yes, you do.

Ben: sorry I got booted

sjcarbon: rama - you need a gmail account first, then send that information to me.

rama: hah. okay

rama: will do

Ben: what do you mean "view the main go data"?

j-lo: seth - do you know why term finder and slimmer don't appear in the stats?

sjcarbon: ben - i noticed that there was google analytics code embedded in the main GO site.

gwg: Mike Cherry is in control of that - I emailed him and got access

sjcarbon: yes, that will be fixed once the latest fixed version of 1.7 goes public.

j-lo: ah - okay

sjcarbon: gwg - cool, thanks.

gwg: does anyone know if the wiki is also on GA?

Ben: oh sure I can ask mike to add your account to view it

sjcarbon: ben - that would be great!

sjcarbon: i'll email you my information after the meeting.

sjcarbon: amelia - the wiki seems to be free of the analytics JS.

Ben: I don't think the wiki is on ga

gwg: no, there doesn't appear to be any sign of it... it would be useful to put it on if poss, to see if people are using the wiki

sjcarbon: http://www.mediawiki.org/wiki/Extension:Google_Analytics_Integration

gwg: and to see if people outside the consortium are using the FAQ

gwg: and the AmiGO manual, etc.

j-lo: that would be great


  • 08:44 -

gwg: Ben, would you be able to ask Mike about getting the wiki on GA?

Ben: Should probably attach to www.geneontology.org GA account

sjcarbon: that would be fabulous.

sjcarbon: i didn't know there was one.

gwg: (so then when we get those GO help queries where they obviously haven't read the FAQ... )

j-lo: seth, do we have an agenda? Can we talk about 1.8?

sjcarbon: yes, the agenda is on the wiki.

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sjcarbon: http://wiki.geneontology.org/index.php/WPWG-20091123

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j-lo: oops - so it is!

Ben: booted again!

sjcarbon: We finally have an easy way of doing unit/regression testing for AmiGO:

sjcarbon: http://amigo.berkeleybop.org/cgi-bin/amigo/page_test?mode=kappa_results


  • 08:49 -

rama: not sure how to interpret the results of this unit testing.

cjm: awesome!

j-lo: so this is the automatic testing?

cjm: longer file names may be more informative; e.g. te -> term_enrichment

sjcarbon: In addition to testing pages and responses in general, it can also ready certain formatted information out of the documnt and test it against expectations.

rama: thanks for implementing this testing suite Seth.

rama: very cool

sjcarbon: cjm - there are also comment fields in the test files that i should display as well.

sjcarbon: for anybody interested, the profiles are in SVN:

sjcarbon: geneontology/go-dev/amigo/testing/profiles/amigo

sjcarbon: next up...

cjm: is there a way of getting it to show the TE input page too?

cjm: be useful for context

j-lo: does it use real datasets for testing TE?

sjcarbon: cjm - not really, but if you look at the testing files, all the information is in there.


  • 08:54 -

sjcarbon: jane - yes it does.

sjcarbon: should be able to do anything a user can.

j-lo: cool

sjcarbon: umm...lemme see...

sjcarbon: i'll do the "official" 1.7 announcement once the newest goweb-dev version goes to production.

sjcarbon: i think we got of of the serious bugs.

Ben: We'll do that today

sjcarbon: cool, thanks!

sjcarbon: also, we've started the wiki for 1.8:

sjcarbon: http://wiki.geneontology.org/index.php/AmiGO_1_8

j-lo: is there any sort of priority listing for the new features?

sjcarbon: not as of yet.

sjcarbon: just trying to see where we are.


  • 09:00 -

rama: Revisiting the Ref.genome displays should be moved up i feel

j-lo: can I vote for redo of tree view?

rama: yes, I will vote for the tree view also

gwg: moi aussi!

sjcarbon: there will also be the order of difficulty to consider too as we go.

rama: sure

sjcarbon: but it looks like people have tired of the tree.

sjcarbon: to the axe it wil go.

sjcarbon: we can talk more about this at the next AHWG, but hopefully this will give us a place to start.

Ben: having a simple refgenome view might be more important for grant renewal

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santista: hi

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cjm: The current RefG display will become rapidly outdated. We'll want to show more species, show the phylo tree like PAINT, etc.

Ben: I think such a thing will be brought up at refg call

sjcarbon: i'll make sure to start lurking again.


  • 09:05 -

rama: yes, we (amiGO) have to be more in sync with the ref.genome stuff

j-lo: I have to go in a minute - can we discuss the news stuff quickly?

sjcarbon: sure.

j-lo: I think it's going okay

j-lo: no-one except the news people actually adds stuff

j-lo: but that's alright

sjcarbon: i've had to field a fair number of queries from news editors who were having problems.

j-lo: oh right!

sjcarbon: has everybody had a chance at the rotation yet?

j-lo: GOC people?

sjcarbon: yeah.

j-lo: not yet - we're on to the 3rd

j-lo: we have 112 folowers on twitter!

sjcarbon: okay. i was just wondering if a more formal tutorial might be useful? some people seem to get it immediately, but other people have a little trouble.

rama: who are the news editors- should any of us be on the rotation (SGD folks I mean)

j-lo: eurie - but she's not on the rotation

j-lo: she got exemption

j-lo: maybe - shall I ask?

rama: I can take over that responsibility from our end

j-lo: sure!

rama: J-lo- we can talk off-line about that.

j-lo: yep - sure

rama: one more thing- about answering go_help emails

j-lo: yep


  • 09:11 -

rama: recently I saw some emails forwarded to the mailing list, not sure who answered them.

rama: Can we have some protocol?

j-lo: it's the responsibility of the person on the gohelp rota tom chase it up

rama: (to the webpresence WG)

rama: I see. okay. then all good

j-lo: but you're right - I think a couple may have slipped past last week

j-lo: I'll ask Jen - she was on last week

rama: in any case, whoever is responding, can you please cc the WPWG mailing list so we all know what the answer is

j-lo: seth - tutorial might be good

sjcarbon: !?

j-lo: rama - yes, definitely

rama: tutorial fo?

j-lo: sorry - replying to you from several minutes ago!

j-lo: "okay. i was just wondering if a more formal tutorial might be useful? some people seem to get it immediately, but other people have a little trouble."

sjcarbon: yes! okay! i was worried that maybe people were having trouble with email...

rama: is this about the news editing stuff

sjcarbon: yeah.

rama: I can use a tutorial

sjcarbon: are you on the news list?

rama: i don't think so

j-lo: sorry - I have to go - lets finish this by email

sjcarbon: okay, see you later.

rama: no worries..i will follow with J-lo on this stuff

rama: btw, I will start a SF on the Tree View thing

sjcarbon: okay, thanks.

rama: J-lo please add your comments to that.

rama: (all for 1.8)


  • 09:16 -

sjcarbon: (and 1.8 for all)

rama: haha

sjcarbon: i think we covered most of the agenda items. does anybody have anything else?

rama: Seth-Chris-GWG- wondering if you were planning to come down to Stanford in Dec?

sjcarbon: no plans yet, but it sounds good.

rama: If not Dec, early Jan

sjcarbon: we'll work something out.

rama: we will come up with an agenda so that we can make sure time spent is productive etc

gwg: I'd been planning to go to England for xmas, but maybe Stanford would be a better choice!

sjcarbon: no problem, we can probably take care of that on the hub list.

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rama: I don't have anything else to add

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sjcarbon: okay, everybody else good?

rama: bye

rama: happy thanksgiving

sjcarbon: okay, see y'all

sjcarbon: to you too!

Kalpana: bye everyone. Seth, Sorry I missed your greeting, had stepped out briefly.

Ben: bye

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