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(08:36:46 AM) sjcarbon: sorry i'm late
(08:36:48 AM) gwg: wow, spooky!
(08:36:55 AM) sjcarbon: i tried calling in--forgot

(08:36:56 AM) pascale: very spooky
(08:37:16 AM) ben: yes, it's like amelia knows where he is or something
(08:37:33 AM) eurie [eurie@brix.Stanford.EDU] entered the room.
(08:37:58 AM) eurie: sorry i'm late

(08:38:09 AM) rama: no worries
(08:39:23 AM) rama: we are waiting for?
(08:39:56 AM) sjcarbon: val?
(08:40:10 AM) sjcarbon: dong hui?

(08:40:30 AM) sjcarbon: and chris...but i think he might be in san diego
(08:40:34 AM) rama: Mary too
(08:41:46 AM) sjcarbon: a couple more minutes, then we'll start. i'll email a reminder.
(08:44:29 AM) rama: shall we?

(08:45:05 AM) sjcarbon: ok, let's go...
(08:45:36 AM) sjcarbon: the first thing is the term enrichment tool.
(08:45:59 AM) sjcarbon: i;ve gotten feedback on it from rama; anybody else?
(08:46:20 AM) ben: i commented

(08:46:41 AM) rama: FYI- I can come up with some descriptive text for the top, for both tools
(08:46:50 AM) sjcarbon: wonderful!
(08:47:22 AM) sjcarbon: ben, i think i only got notes from you on the slimmer
(08:47:23 AM) sjcarbon: .

(08:47:36 AM) eurie: i do agree with ben and rama's comments about having a new page for the results
(08:47:48 AM) sjcarbon: ok, i'll change this.
(08:47:52 AM) eurie: On a small screen, it's not obvious that there are results at the bottom of the page
(08:48:13 AM) sjcarbon: or would a note at the top be sufficient?

(08:48:27 AM) ben: I am not sure we need a NEW page... but at least we need the results at the top, or otherwise make it obvious there ARE results
(08:49:01 AM) gwg: I'm not sure that it is necessary to show all the input on the results page - the first thing that the user should see is the results
(08:49:04 AM) rama: I would want to see a new page load. Note isn't sufficient
(08:50:12 AM) sjcarbon: 2 for clearly a new page. anybody else?

(08:50:29 AM) sjcarbon: otherwise, i'll just go with the new page.
(08:50:42 AM) eurie: switching the order would be fine - results first and then input at the bottom of the page. but new page is good too
(08:50:59 AM) ***gwg is for a new page - my tangential comment was supposed to mean that
(08:52:01 AM) sjcarbon: does anybody not want to see the controls anywhere?

(08:53:04 AM) ben: I think having the controls there is OK for people who eschew the 'back' button... especially if they want to tweak a parameter or filter or something
(08:53:17 AM) eurie: i don't feel strongly about whether the inputs are listed on the results page or not. it might be nice not to have to use the "back" button
(08:53:27 AM) eurie: oh, what ben said.

(08:53:50 AM) sjcarbon: any control haters?
(08:54:06 AM) gwg: or control freaks?
(08:54:53 AM) sjcarbon: nobody will admit it?
(08:54:58 AM) sjcarbon: ACTION ITEM:

(08:55:06 AM) sjcarbon: move results to the top.
(08:55:37 AM) rama: sounds good
(08:56:07 AM) sjcarbon: this item will cover both the slimmer and term enrichment.
(08:57:06 AM) sjcarbon: does anybody (besides rama and ben) have any term enrichment specific comments?

(08:57:22 AM) sjcarbon: if not, we can talk about some of those comments.
(08:58:10 AM) sjcarbon: rama, do you find the wording on this iteration clearer than the last?
(08:58:45 AM) rama: i am checking.
(08:59:50 AM) rama: clearer than the last. thanks. I am sure others will have better ways of saying it

(08:59:58 AM) rama: http://toy.lbl.gov:9002/cgi-bin/amigo/term_enrichment
(09:00:03 AM) sjcarbon: thanks!
(09:00:11 AM) sjcarbon: what do people think of the text?
(09:00:27 AM) rama: we are talking about the wording on the top of the Input box and under Enter your background set

(09:02:27 AM) pascale: Do we need to say 'cut and paste? Seems like the blue insytructions are sufficient
(09:03:14 AM) ben: needed to distinguish cut-and-paste from upload
(09:03:28 AM) sjcarbon: i would agree with that.
(09:03:44 AM) sjcarbon: looks prettier too.

(09:03:51 AM) pascale: well 'enter' seems to distinguish from 'upload'
(09:03:58 AM) pascale: ok!
(09:04:19 AM) ben: yes, you could cut the phrase "cut and paste". I don't really care either way

(09:04:36 AM) rama: Enter will do
(09:04:42 AM) pascale: sure
(09:05:56 AM) sjcarbon: I know this is fiddly stuff, but how about "Input"?

(09:06:15 AM) sjcarbon: "enter" twice in a row seems odd to me.
(09:06:24 AM) eurie: Input sounds good to me
(09:06:31 AM) pascale: I was lloking at the BLAST page-- sems like it would be more user friendly is both interfaces had the same phrasing- whichever you prefer

(09:06:32 AM) pascale: http://amigo.geneontology.org/cgi-bin/gost/gost.cgi
(09:07:30 AM) sjcarbon: the inputs seem a little different to me. anybody else?
(09:07:54 AM) gwg: Just a general comment about the results format - I think it would be better to have a summary of what was entered, rather than having the whole form recapitulated. I think that users are likely to keep their original query set; they might want to change the threshold settings and the results options, but I think that changing the background set should be classed as a new query (i.e. they have to click on 'Term Enrichment' again)
(09:08:17 AM) ben: agree with gwg

(09:09:09 AM) sjcarbon: i think a summary, without a way of changing it, is a bit odd.
(09:09:58 AM) sjcarbon: anybody else?
(09:10:39 AM) rama: agree with gwg as well.
(09:10:52 AM) gwg: just spotted another issue - I was looking for the gene product 'fuzzy onions', but the TE tells me that it can't find 'onions'. Is this a search parser thing?

(09:11:29 AM) pascale: I think if you put the result son top ten maybe it's fine. The problem is right now you hit 'results' and you get the same page, it seems like nothing has happenned
(09:12:21 AM) ***gwg agrees with Pascale
(09:13:09 AM) sjcarbon: action item above.
(09:13:27 AM) gwg: re: my comment about the results format / summary, what I would do is to have something like

(09:14:01 AM) pascale: yes-- this was to follow up on the summary vs full query on the results page. I was saying fixing #1 might automatically fix #2
(09:14:06 AM) gwg: Gene product set: gp1, gp2, gp3 and xxx more OR name of the file that the user uploaded
(09:14:37 AM) gwg: Background set: gp1, gp2, gp3 and xxx more OR file name OR database + filter
(09:15:05 AM) gwg: threshold filters: [details of threshold filters]

(09:15:17 AM) gwg: then have the results
(09:15:54 AM) gwg: then have options like 'Perform this query again with different threshold settings' or 'change output format' or something like that
(09:16:37 AM) sjcarbon: i'd prefer either just using the back button or giving the users full access to everything.
(09:16:42 AM) pascale: another question: are we

(09:16:48 AM) sjcarbon: the middle seems like an odd place.
(09:17:00 AM) eurie: I agree with seth
(09:17:11 AM) gwg: although I don't do term enrichment stuff in my day-to-day work, if I did, I think that I would be likely to change the filters and the output, but use the same input as before
(09:17:18 AM) pascale: going to have a small sentence like 'this tools allows to view which terms are enriched in two different sets of ...'

(09:17:35 AM) pascale: (this was suppose to start with "are we going to...")
(09:17:46 AM) gwg: we should definitely have an introduction to what the tool does
(09:18:01 AM) gwg: currently you would need to know what term enrichment means to be able to use it

(09:18:20 AM) sjcarbon: rama was going to get text for us.
(09:18:28 AM) gwg: I think maybe a couple of sentences and a link for further reading if people are still mystified
(09:18:36 AM) pascale: great
(09:18:50 AM) rama: yes i will send it around via email

(09:19:16 AM) sjcarbon: great!
(09:19:59 AM) sjcarbon: we have about ten minutes left, i'd like to see whether people have have a chance to look at the app note?
(09:20:37 AM) sjcarbon: or have had a chance?
(09:20:46 AM) pascale: not in detail- but it seems like the amigo WG is the OBO wg?

(09:20:47 AM) ben: not yet
(09:20:51 AM) rama: Can you post the outstanding questions for these two tools on the mailing list, so that people can comment?
(09:21:08 AM) rama: I haven't looked at the app.note. sorry.
(09:21:19 AM) sjcarbon: no problem--will send it out after the meeting/

(09:21:24 AM) gwg: I haven't yet either - sorry! :(
(09:21:26 AM) rama: AmiGO wg is the user advocacy?
(09:21:35 AM) sjcarbon: Web Presence.
(09:21:46 AM) rama: yeah, thanks seth.

(09:21:54 AM) rama: Pascale, what did you mean?
(09:22:12 AM) pascale: I look at the list of names
(09:22:30 AM) rama: ho, yes, I saw that too. copy paste
(09:22:34 AM) pascale: :)

(09:23:13 AM) sjcarbon: d'oh!
(09:23:26 AM) sjcarbon: i'll change that and send around a fresh copy.
(09:25:11 AM) sjcarbon: we have about five minutes left--anything that anybody wants to bring up?
(09:25:49 AM) sjcarbon: complaints, hopes, dreams?

(09:26:01 AM) pascale: well there's only 5 minutes ...
(09:26:05 AM) gwg: Could I take this opportunity to ask people to check things are OK with the main AmiGO stuff, currently to be found at http://toy.lbl.gov:9006/cgi-bin/new-amigo/search.cgi
(09:26:10 AM) rama: there are still some questions in the email.
(09:26:24 AM) rama: about the two tools

(09:26:45 AM) sjcarbon: rama, since it's only five minutes, what do you think is most important?
(09:27:59 AM) rama: I can't tell which one is most important. Guess, one of us can summarize and send a list of questions?
(09:28:22 AM) rama: I think your reply to my long list of comments got buried.
(09:28:31 AM) sjcarbon: i'll summarize and send out.

(09:28:36 AM) rama: okay. thanks.
(09:29:14 AM) sjcarbon: anything else? shall we wrap up?
(09:29:32 AM) rama: sure
(09:29:49 AM) sjcarbon: ok, thanks everyone!

(09:29:52 AM) ben: ok bye!
(09:29:54 AM) ben left the room.
(09:29:56 AM) pascale: ok
(09:29:56 AM) eurie: bye

(09:30:02 AM) pascale left the room (quit: Quit).