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Revision as of 09:32, 30 September 2008 by Sjcarbon (talk | contribs) (New page: <font color="#8D01A6"><font size="2">(08:32:03 AM) </font><font size="3">pascale:</font></font><font size="3"> je suppose que c'est une qualite</font><br> <font size="2">(08:32:26 AM) </fo...)

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(08:32:03 AM) pascale: je suppose que c'est une qualite
(08:32:26 AM) zenbitz [hitz@c-98-210-219-14.hsd1.ca.comcast.net] entered the room.
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(08:32:39 AM) gwg: tres belle, et cetera... ;)
(08:33:31 AM) rama: hello
(08:34:06 AM) sjcarbon: morinin;
(08:34:48 AM) sjcarbon: lemme just pull up the wiki page...
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(08:36:12 AM) sjcarbon: OK...
(08:36:24 AM) sjcarbon: <a href="http://ash.lbl.gov/cgi-bin/amigo/amigo">http://ash.lbl.gov/cgi-bin/amigo/amigo</a>
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(08:36:45 AM) sjcarbon: Has everybody taken a look? <a href="http://ash.lbl.gov/cgi-bin/amigo/amigo">http://ash.lbl.gov/cgi-bin/amigo/amigo</a>
(08:36:52 AM) ben: hmm network trouble
(08:36:59 AM) ben: i mean with chat, not page
(08:37:22 AM) sjcarbon: I've added a few fixes that haven't appeared on ash yet.
(08:38:39 AM) sjcarbon: Also, I still need to run it through the w3 test stuff and fix the table styles a bit (done dirty).
(08:40:56 AM) sjcarbon: (Chris skyped me about some IRC problems.)
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(08:44:23 AM) rama: seth
(08:44:40 AM) sjcarbon: hello!
(08:44:54 AM) rama: in the mean time please refresh our minds about what specific item is going to need solid testing
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(08:45:12 AM) rama: there are lot of beta software on this 'ash' location
(08:45:33 AM) sjcarbon: Sorry--mostly beta to be ignored (for now).
(08:45:55 AM) sjcarbon: The Homolset Summary and the associated detail pages and graphs.
(08:46:08 AM) sjcarbon: <a href="http://ash.lbl.gov/cgi-bin/amigo/amigo?mode=homolset_summary">http://ash.lbl.gov/cgi-bin/amigo/amigo?mode=homolset_summary</a>
(08:46:11 AM) rama: okay thanks
(08:46:18 AM) sjcarbon: And links out from that page.
(08:46:33 AM) rama: are we really set on this big long table?
(08:46:46 AM) sjcarbon: Another way to break it up?
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(08:47:20 AM) rama: I know you have put lot of effort into this...but this is not very userfriendly
(08:47:47 AM) rama: thinking of workflow- what do you think an user will do after coming to this page?
(08:47:48 AM) pascale: why not? what do you think it should look like?
(08:48:23 AM) sjcarbon: Also remember that you can link directly from the gp-details pages to the ref genome details pages.
(08:48:32 AM) cjm2: There will be many ways that a user can get to a homolset summary - for example from a gene page
(08:48:42 AM) pascale: well in the long run it doesn't make so much sense to list *all* annotated genes, but given some selection cirteria, it's nice to be able to get some lists
(08:49:09 AM) gwg: are you going to zebra stripe the tables? It makes it a bit easier on the eye
(08:49:35 AM) sjcarbon: Still trying to figure out how without making the color thing too strange...
(08:49:36 AM) rama: for example ALG6
(08:49:55 AM) rama: there are 3 Zfin entries. It is confusing in my mind..
(08:50:24 AM) sjcarbon: yes, that is something that I'll have fixed later today...
(08:50:39 AM) rama: I understand the difference between the 3...but once you are at the bottom of the table you won't see the legend on the top and one will wonder
(08:51:04 AM) sjcarbon: i could add hover text...
(08:51:11 AM) sjcarbon: also, we were thinking about
(08:51:19 AM) sjcarbon: going back to an older version where
(08:51:35 AM) sjcarbon: there was just one symbol followed by information.
(08:53:06 AM) rama: I am not sure what is the best way to display this..we should send it out to curators and get some feedback. I could be in the minority
(08:53:21 AM) cjm2: rama - Val and I agree with you
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(08:53:32 AM) rama: okay. thanks.
(08:53:34 AM) cjm2: see my email yesterday:
(08:53:43 AM) sjcarbon: It will be a fix for later today.
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(08:53:50 AM) cjm2: -----
(08:53:51 AM) cjm2: I think it is really confusing to list the gene names multiply to indicate different types of evidence.
(08:53:51 AM) cjm2: I tend to agree
(08:53:51 AM) cjm2: Seth previously had this such the gene was only listed once. He will temporarily restore the previous display so we can compare.
(08:53:51 AM) cjm2: The confusion is compounded in the case of WB because they are providing annotations to both genes and gene products, meaning you see things such as eat-6 and EAT-6. Not a lot we can do about this until the data is fixed.
(08:53:52 AM) ben: I keep getting booted...
(08:53:53 AM) cjm2: ----
(08:54:06 AM) cjm2: (email snippet)
(08:54:06 AM) pascale: I wonder also how that table is sorted?
(08:54:29 AM) sjcarbon: That has been fixed, but is not showing up on ash yet.
(08:54:41 AM) sjcarbon: Alphabetical on my local (fixed) machine.
(08:54:57 AM) cjm2: Seth: I notice the sort option is now gone.
(08:55:22 AM) cjm2: Previously there was an option to sort by either high-information content terms or terms that are deep in the graph
(08:55:34 AM) cjm2: sorry ignore me
(08:55:44 AM) cjm2: that's on the individual homolset pages, doh!
(08:56:26 AM) ben: I suppose I don't need to point out that the images are gynormous, and don't always load properly.
(08:56:42 AM) sjcarbon: The SVGs or the PNGs?
(08:57:41 AM) rama: we talked about this before i think- about showing one ontology at a time.
(08:58:32 AM) sjcarbon: So for each set, six images? Also, won't the ontologies be blending soon?
(08:59:11 AM) rama: also rather than saying svg |png can we say ontology view or something explicit
(08:59:23 AM) rama: many people arent' familiar with what svg and png means
(08:59:41 AM) sjcarbon: yes, maybe interactive and static instead?
(08:59:42 AM) ben: both
(08:59:46 AM) cjm2: Seth - we can still opt to display each ontology individually even if wehave links between them
(09:00:11 AM) sjcarbon: ben - they work for me, can you give an example of one that fails for you?
(09:01:06 AM) cjm2: rama: what do you think are good labels? how about "static" image vs "navigable/zoomable" image?
(09:01:42 AM) ben: set 240/PNG- phenotype is that it drew a pic, spun and thrashed (I had a huge number of apps open, btw), then just didn't quite finish drawing.
(09:01:58 AM) ben: I did start force quitting stuff I wasn't using
(09:02:46 AM) cjm2: Perhaps there could be some warning for large images?
(09:02:53 AM) rama: how about - ontology view (static | dynamic)
(09:03:39 AM) sjcarbon: ben - the PNG itself seems fine, but it did take bunches of memory to initially load.
(09:03:47 AM) pascale: or graphical view?
(09:03:48 AM) sjcarbon: A warning would be good.
(09:03:57 AM) rama: graphical view works for me
(09:05:52 AM) rama: graphical view (static | zoomable/dynamic)- does that sound good?
(09:06:39 AM) sjcarbon: static vs. interactive makes it more obvious to me, but we can fiddle with the words as we go...
(09:06:50 AM) rama: i like interactive. nice.
(09:06:54 AM) pascale: me too
(09:07:35 AM) ben: I will reload the image and see.
(09:07:50 AM) sjcarbon: Thanks.
(09:08:50 AM) ben: I have a 2x2Ghz intel mac, with 1.5Gb of RAM
(09:09:17 AM) gwg: monitor size?
(09:09:19 AM) ben: PNG might eventually load... but I think most users are going call "fail" after a little while.
(09:09:23 AM) sjcarbon: Sounds more or less like mine.
(09:09:49 AM) sjcarbon: Hmmm...I could try shrinking them a bit.
(09:09:55 AM) ben: it's a macbook pro, what like 13"? Not the huge one.
(09:10:04 AM) ben: Lower the resolution?
(09:10:29 AM) ben: this pic is 12735x7173
(09:10:29 AM) sjcarbon: Yeah, that should get the bit count down.
(09:11:08 AM) sjcarbon: Maybe try and see if I can get other things limited as well...
(09:11:23 AM) ben: it is a 15", 1440x900. I guess the big one is 17"
(09:11:36 AM) sjcarbon: I'll see what I can do and get back to the group.
(09:12:46 AM) cjm2: Some indication of size of the graph would be useful also to given an indication of how widely distributed annotations are for particular homolsets
(09:13:13 AM) sjcarbon: a node count?
(09:13:31 AM) cjm2: Would it be overloading the table too much to show the total number of annotated nodes (incl transitive) for each homolset?
(09:13:50 AM) sjcarbon: That was something people hated previously.
(09:13:52 AM) ben: ok , it stopped loading after about 5 min, still has the bottom part of the graph cut off.
(09:13:59 AM) sjcarbon: Safari?
(09:14:07 AM) ben: FF2.x+
(09:14:29 AM) cjm2: ok. I tend towards information-rich displays.. perhaps this could be a power user option
(09:14:42 AM) sjcarbon: Ben - I don't suppose I could talk you into FF3+...?
(09:14:55 AM) ben:
(09:15:13 AM) sjcarbon: Cool.
(09:15:24 AM) ben: I will switch eventually.
(09:15:26 AM) pascale: but some users may have V2 still
(09:15:27 AM) sjcarbon: I'll see if there are specific issues for that as well.
(09:15:30 AM) gwg: but you won't be able to talk all the users into FF3+
(09:15:45 AM) gwg: the functionality should not be browser dependent
(09:15:54 AM) sjcarbon: Not the PNG stuff at least.
(09:16:14 AM) gwg: there may even be users with (whisper it!) IE! :o
(09:16:26 AM) ben: I would vote for a cytoscape webstart
(09:16:42 AM) ben: sure it's a 10Mb download....
(09:17:23 AM) ben: It's not that hard to do, although they have bumped a couple versions since last I tried.
(09:20:23 AM) rama: we are looking at cytoscape webstart for the png stuff?
(09:20:24 AM) sjcarbon: Is there anything else that people want to talk about before the next iteration? I'll try and see how much ground I can cover today.
(09:20:32 AM) rama: couple of questions
(09:20:50 AM) rama: 1) are you going to demo the new ref.genome views at the GOC?
(09:21:03 AM) rama: 2) are curators going to test it before the GOC?
(09:21:18 AM) sjcarbon: If you think it's test-worth, then we can.
(09:21:27 AM) sjcarbon: It would be nice...
(09:22:07 AM) rama: I think it would be useful to get the attention of the larger GOC
(09:22:34 AM) rama: because it seems like people are working on their own thing and would love to see what is going on
(09:23:08 AM) rama: it is test-worthy if you can revert it to displaying the gene name once
(09:23:23 AM) sjcarbon: one of today's projects!
(09:23:46 AM) sjcarbon: I'll see how much I can get done today, and send the URL out tonight.
(09:23:48 AM) rama: I would definitely send it to ref-genome/annotation mailing lists or just the GO mailing list
(09:23:49 AM) cjm2: great! once it's done should we send it to a wider group or the whole GO list?
(09:24:11 AM) sjcarbon: I think the (ancient) initial plan was the wider group.
(09:24:17 AM) cjm2: ok
(09:24:27 AM) sjcarbon: Although now the testing machine might be somewhat underpowered...
(09:24:28 AM) rama: ref.genome and annotations mailing list shd do
(09:24:53 AM) rama: please give specific time line for testing (please don't leave it open ended)
(09:25:06 AM) pascale: right!
(09:25:09 AM) rama: and specific questions will help
(09:25:14 AM) sjcarbon: Will do.
(09:25:19 AM) pascale: and ref genome and annotation lists are more likely to look at it seriously
(09:25:25 AM) rama: thanks
(09:25:37 AM) pascale: although it woud be good to send to the wider group as well
(09:25:48 AM) sjcarbon: Anything else today?
(09:26:02 AM) pascale: not for me
(09:26:07 AM) rama: i think we should give folks on these two mailing list 1 week time, fix bugs and then send it to wider list
(09:26:17 AM) sjcarbon: sounds good.
(09:26:22 AM) rama: what happened to the dual taxon id
(09:26:33 AM) gwg: nothing as yet
(09:26:48 AM) rama: I saw a posting by Michelle over the weekend and was reminded of that
(09:26:57 AM) ben: we no longer ignore most of them!
(09:27:06 AM) ben: sw group is going to talk about it tomorrow
(09:27:16 AM) ben: can't get them in the Db at the moment.
(09:27:31 AM) rama: okay. thanks.
(09:27:43 AM) sjcarbon: Anything else?
(09:27:48 AM) rama: they are in the DB i think
(09:28:05 AM) rama: i don't know for sure
(09:28:33 AM) sjcarbon: Going once...
(09:28:43 AM) sjcarbon: Going twice...
(09:28:43 AM) rama: Action item?
(09:28:47 AM) sjcarbon: Yes?
(09:29:38 AM) rama: send the ref. genome stuff for testing to the 2 mailing lists
(09:29:46 AM) rama: thats all from me. thanks all. bye
(09:29:57 AM) pascale: bye
(09:29:59 AM) sjcarbon: After y'all take another look. Yes. Added.
(09:30:00 AM) pascale left the room.
(09:30:02 AM) sjcarbon: Bye!
(09:30:07 AM) rama: bye
(09:30:10 AM) rama left the room (quit: Quit: Computer goes to sleep!).