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06/03/2008 09:36:45 AM from midori : I'll have to go at 6 today (PM, that is!)
06/03/2008 09:36:48 AM from Nomi Harris: Anyway, yes, let's start.
06/03/2008 09:36:59 AM from Nomi Harris: midori, I'm puzzled about your CPU-spike bug.
06/03/2008 09:37:03 AM from Nomi Harris: I hope we can find a repeatable.
06/03/2008 09:37:07 AM from Amina : Hi David
06/03/2008 09:37:13 AM from David OS : Hi Amina
06/03/2008 09:37:15 AM from Nomi Harris: I have gotten that sort of behavior with Graph Editor + Reasoner,
06/03/2008 09:37:16 AM from Amina : Hi MElissa
06/03/2008 09:37:20 AM from Nomi Harris: but you said you weren't running either of those.
06/03/2008 09:37:26 AM from melissaH : Hi there
06/03/2008 09:37:31 AM from Nomi Harris: Oh, hi, Melissa!
06/03/2008 09:37:42 AM from midori : correct. and I only noticed the spiking in the one session so far.
06/03/2008 09:37:43 AM from Nomi Harris: and Karen
06/03/2008 09:38:00 AM from Nomi Harris: I was looking at the logfile you attached, and I'm kind of puzzled about what it was doing.
06/03/2008 09:38:02 AM from Amina : hi Karen
06/03/2008 09:38:08 AM from Nomi Harris: I'll send you some thoughts/questions later.
06/03/2008 09:38:19 AM from Karen : Hi, glad to finally make it back to a meeting after a series of reasons why I missed them. Hi Amina!
06/03/2008 09:38:31 AM from Nomi Harris: David, we're looking into the filtered save problem.
06/03/2008 09:38:39 AM from midori : The log files always puzzle me, but that's because I'm a biologist, not a programmer.
06/03/2008 09:38:45 AM from melissaH : me too karen!
06/03/2008 09:38:58 AM from Nomi Harris: The log files aren't really meant for users to understand, don't worry.
06/03/2008 09:39:25 AM from Nomi Harris: About the filtered save, I'm thinking that the saving is happening on the unreasoned ontology and we need to make it save the reasoned ontology
06/03/2008 09:39:40 AM from Nomi Harris: so I'm hoping that once we figure out where that's happening it should be straightforward to fix.
06/03/2008 09:39:50 AM from Amina : Thanks for the details David - Chris and me noticed that last week too where we got similar results with the reasoner on and off
06/03/2008 09:39:56 AM from David OS : Cheers Nomi. Thought it might be somethiing like that
06/03/2008 09:40:31 AM from Nomi Harris: Jen, you're trying to add a little spanner/wrench to the GraphViz window?
06/03/2008 09:40:38 AM from Jen Deegan : yes that's right
06/03/2008 09:41:00 AM from Jen Deegan : the configuration on graphvizViewer is currently done a different way
06/03/2008 09:41:06 AM from Jen Deegan : I'm trying to standardize it
06/03/2008 09:41:06 AM from Nomi Harris: Look at oboedit/gui/tasks/DefaultGUIStartupTask.java where I added the camera icons
06/03/2008 09:41:12 AM from Nomi Harris: you should be able to borrow some of that code.
06/03/2008 09:41:25 AM from Jen Deegan : really?
06/03/2008 09:41:30 AM from Nomi Harris: Yes, I just added that on Fri
06/03/2008 09:41:33 AM from Jen Deegan : oh
06/03/2008 09:41:42 AM from Jen Deegan : I assumed it happened in the factory
06/03/2008 09:41:47 AM from Nomi Harris: Not exactly
06/03/2008 09:41:51 AM from Jen Deegan : like the question mark icon but I couldn't find it
06/03/2008 09:42:00 AM from Nomi Harris: You can look at it later and ask me questions if it's unclear
06/03/2008 09:42:06 AM from Jen Deegan : great thanks.
06/03/2008 09:42:08 AM from Nomi Harris: Not that anything in OBO-Edit is really clear. :-)
06/03/2008 09:42:13 AM from Jen Deegan : :-)
06/03/2008 09:42:16 AM from Jen Deegan : or commented
06/03/2008 09:42:37 AM from Nomi Harris: Comments are for WIMPS
06/03/2008 09:42:39 AM from Ed : Hah, c'mon comments are over rated, right? Code should be self commenting ;)
06/03/2008 09:43:07 AM from Nomi Harris: Hi Harold. Your bug with the text editing appears to be situational.
06/03/2008 09:43:15 AM from Ed : I've gotten used to comments being a debugger and break points ;)
06/03/2008 09:43:16 AM from Nomi Harris: Sometimes it nags, sometimes it just works.
06/03/2008 09:43:20 AM from Harold : my luck
06/03/2008 09:43:33 AM from Nomi Harris: Yesterday I got it to do both, so now I need to figure out what the difference was between the two sessions.
06/03/2008 09:43:40 AM from Jen Deegan : Erika says her commit bug is fixed.
06/03/2008 09:43:57 AM from Nomi Harris: It was fixed when she wiped out her config directory, right?
06/03/2008 09:44:01 AM from Jen Deegan : yes
06/03/2008 09:44:02 AM from midori : cloning is back in b39 :)
06/03/2008 09:44:18 AM from Nomi Harris: This one also seems to be somehow config-related, because when it happened to me yesterday, I got it to stop by removing my config directory.
06/03/2008 09:44:30 AM from Nomi Harris: midori, yes, that was not fixed by elves, I very consciously fixed that problem.
06/03/2008 09:45:00 AM from Nomi Harris: Has anyone else had the text editor nag them? http://sourceforge.net/tracker/index.php?func=detail&aid=1982488&group_id=36855&atid=418257
06/03/2008 09:45:18 AM from midori : th ank you for the cloning fix!
06/03/2008 09:45:39 AM from Harold : I might be the only one who prefers to have the "commit" button so I know when I make the commit
06/03/2008 09:45:41 AM from Nomi Harris: You're welcome--I was dismayed that it broke!
06/03/2008 09:45:49 AM from Nomi Harris: No, Erika has the Commit button too
06/03/2008 09:45:52 AM from midori : I think I have had the text editor nag me when I'd already committed, but hadn't quite tested enough to be sure.
06/03/2008 09:46:16 AM from Nomi Harris: Anyway, I hope to get that one fixed soon, because it's annoying when it nags!
06/03/2008 09:46:20 AM from David OS : "Has anyone else had the text editor nag them?" No, but I don't use the commit button.
06/03/2008 09:46:24 AM from midori : I use the commit button all the time, except when I'm testing autocommit.
06/03/2008 09:47:01 AM from Nomi Harris: We still have the looming issue of the Graph Editor (and possibly other components) eating memory/CPU.
06/03/2008 09:47:04 AM from Jen Deegan : I haven't used the commit button, though I usually do with group editing as 1.101 occassionally loses edits.
06/03/2008 09:47:21 AM from Nomi Harris: I must admit I'm not really sure how to address that, and am hoping Amina and Ed can work on that.
06/03/2008 09:47:53 AM from Nomi Harris: (The Graph Editor, I mean, not 1.101 losing edits)
06/03/2008 09:48:00 AM from Jen Deegan : seems good
06/03/2008 09:48:10 AM from Nomi Harris: I haven't yet found a good Java profiling tool that works on Mac
06/03/2008 09:48:28 AM from Nomi Harris: We bought JBuilder/OptimizeIt and it turned out it doesn't work on Mac (or most Linuxes)
06/03/2008 09:48:40 AM from Amina : yes sounds good.. I'm already looking into it along with the reasoner
06/03/2008 09:48:41 AM from Nomi Harris: and we still don't have a Windows machine, though our sysadmin has ordered one.
06/03/2008 09:48:49 AM from Nomi Harris: Thanks, Amina!
06/03/2008 09:49:03 AM from Ed : There's still one thing in Apollo that broke a while back (before I came on board) and I want to fix it, but I'll start looking at OBO-Edit once I've taken care of that.
06/03/2008 09:49:22 AM from Nomi Harris: That would be awesome.
06/03/2008 09:49:30 AM from Jen Deegan : thanks Ed
06/03/2008 09:49:50 AM from Nomi Harris: So I have now integrated the Term Image Display panel
06/03/2008 09:50:03 AM from Jen Deegan : great
06/03/2008 09:50:04 AM from Nomi Harris: you don't have to go through any plug-in rigamarole, it's just on the menu like the other components.
06/03/2008 09:50:17 AM from Nomi Harris: Along with it, you get a little camera icon on each component to let you save it as an image file.
06/03/2008 09:50:22 AM from Jen Deegan : I will tell Colin.
06/03/2008 09:50:30 AM from Nomi Harris: (Though personally I just use Grab to grab screenshots)
06/03/2008 09:50:49 AM from Jen Deegan : the camera is needed where images are bigger than the component
06/03/2008 09:50:57 AM from Nomi Harris: The question I have is, how are we going to assemble a nice collection of term images?
06/03/2008 09:51:09 AM from Nomi Harris: Ah, I see, Jen.
06/03/2008 09:51:12 AM from Jen Deegan : we just need a few examples don't we?
06/03/2008 09:51:23 AM from Karen : what do you mean 'term images'?
06/03/2008 09:51:37 AM from Nomi Harris: Like if you click on the term 'mitochondrion', it shows a picture of a mitochondrion.
06/03/2008 09:51:45 AM from Nomi Harris: The images are linked via GO ID
06/03/2008 09:52:03 AM from Jen Deegan : it's very good for chemical ontologies so they can show structures.
06/03/2008 09:52:11 AM from Harold : I think there will be a lot of terms that will be image-less, especially in process
06/03/2008 09:52:24 AM from Karen : How much of GO do you envisage this being appropriate for?
06/03/2008 09:52:29 AM from David OS : There are some great movies of Drosophila developmental processes
06/03/2008 09:52:32 AM from Nomi Harris: Mostly the cellular component
06/03/2008 09:52:39 AM from Nomi Harris: Yes, we were talking about movies yesterday
06/03/2008 09:52:43 AM from Jen Deegan : I don't think we were planning to use it were we?
06/03/2008 09:52:49 AM from Nomi Harris: I'm not sure about showing movies *in* OE, though that would certainly be cool
06/03/2008 09:53:02 AM from Jen Deegan : it was Alex and Colin that wanted it.
06/03/2008 09:53:04 AM from Nomi Harris: but I put on the tracker an item to let OE talk to your browser
06/03/2008 09:53:21 AM from Nomi Harris: and then it could point your browser at an URL that would show a movie.
06/03/2008 09:53:54 AM from Nomi Harris: The usefulness of the Term Image display will depend on getting images for terms
06/03/2008 09:53:59 AM from Karen : Oh, makes sense for Alex and Colin, thanks :)
06/03/2008 09:54:12 AM from Nomi Harris: We're envisioning eventually having an URL that serves term images
06/03/2008 09:54:29 AM from David OS : So - I've been linking to images, but by using IDs in the Definition reference field. Might be worth me looking at doing them like this though.
06/03/2008 09:54:30 AM from Jen Deegan : We could add some examples for that one ontology that comes loaded with oboedit if that would help.
06/03/2008 09:54:34 AM from Nomi Harris: e.g. http://geneontology.org/image.pl?id=GO_0000536
06/03/2008 09:54:41 AM from Nomi Harris: would return an image for that GO term
06/03/2008 09:54:56 AM from Nomi Harris: David, yes, definitely./
06/03/2008 09:55:07 AM from Ed : Nomi, take a look at src/java/edu/stanford/ejalbert/BrowserLauncher.java in Apollo. It should work for lauching the web browser independent of OS.
06/03/2008 09:55:07 AM from Harold : Is there a public repository of relevant images?
06/03/2008 09:55:08 AM from Nomi Harris: Jen, yes, that would be great, but make sure you have permission to reproduce the images.
06/03/2008 09:55:14 AM from Nomi Harris: We don't want to end up in Copyright Prison.
06/03/2008 09:55:25 AM from David OS : Preumably we're talking about a repository for GO relevant images here. COuld be v.large if all OBO...?
06/03/2008 09:55:35 AM from Harold : I have a similar problem getting images for lectures
06/03/2008 09:55:37 AM from Jen Deegan : I'm not sure we want to spend a huge amount of time on this.
06/03/2008 09:55:38 AM from Nomi Harris: (Though, as someone pointed out, there'd be great music-making in that prison, since all musicians end up illegally photocopying music at some point)
06/03/2008 09:55:40 AM from melissaH : yes, i was wondering if this would slow things down.
06/03/2008 09:55:55 AM from Nomi Harris: Slow down OE running time or suck developer/curator time?
06/03/2008 09:56:01 AM from Jen Deegan : maybe Alex would like to look at it as he is keen on the component?
06/03/2008 09:56:13 AM from Nomi Harris: Anyway, I agree we shouldn't spend a huge amount of time on this.
06/03/2008 09:56:13 AM from Jen Deegan : develop/curator time
06/03/2008 09:56:17 AM from melissaH : well, both I guess!
06/03/2008 09:56:17 AM from midori : and he isn't here ;)
06/03/2008 09:56:21 AM from Nomi Harris: I just wanted to mention it so that people who are interested know about it.
06/03/2008 09:56:33 AM from Jen Deegan : It's great that the component is in though
06/03/2008 09:56:36 AM from Nomi Harris: I will announce it in the next release so Alex can check it out.
06/03/2008 09:56:39 AM from Jen Deegan : thanks for that
06/03/2008 09:56:41 AM from David OS : So - right now does it simply save a file linkeing term IDs to images?
06/03/2008 09:56:53 AM from Nomi Harris: No, it doesn't save it, it loads it. You supply the image files.
06/03/2008 09:57:13 AM from Nomi Harris: They are named by their IDs, e.g. GO_00001234.jpg
06/03/2008 09:57:32 AM from Nomi Harris: Right now I have three sample image files
06/03/2008 09:57:33 AM from David OS : Ahhh - so you can only have on image per term.
06/03/2008 09:57:42 AM from Nomi Harris: One image file per term.
06/03/2008 09:57:52 AM from David OS : good point
06/03/2008 09:57:53 AM from Nomi Harris: There could be multiple pictures stuck together in that file.
06/03/2008 09:57:55 AM from Jen Deegan : or one composite image
06/03/2008 09:57:58 AM from Nomi Harris: Right.
06/03/2008 09:58:06 AM from Nomi Harris: Or, maybe someday, a movie.
06/03/2008 09:58:16 AM from Nomi Harris: But although that would be fun to work on, it's probably not high priority.
06/03/2008 09:58:40 AM from Jen Deegan : Anything else we need to discuss? time is short
06/03/2008 09:59:07 AM from Nomi Harris: I didn't have any other agenda items today. Anyone else?
06/03/2008 09:59:22 AM from midori : nothing from me yet ... I want to do more testing but don't know when ...
06/03/2008 10:00:03 AM from Nomi Harris: Shall we adjourn?
06/03/2008 10:00:10 AM from midori : ok
06/03/2008 10:00:12 AM from Jen Deegan : we should mention documentation week again
06/03/2008 10:00:12 AM from Nomi Harris: We can meet next week. The week after (June 17) I will be away.
06/03/2008 10:00:14 AM from Harold : yah
06/03/2008 10:00:14 AM from Jen Deegan : before we go
06/03/2008 10:00:20 AM from Nomi Harris: Ok
06/03/2008 10:00:21 AM from Jen Deegan : week of 30th June
06/03/2008 10:00:30 AM from Jen Deegan : we all write some help guide text
06/03/2008 10:00:47 AM from Nomi Harris: I will try to do a Documentation Week
06/03/2008 10:00:49 AM from Nomi Harris: the week before that
06/03/2008 10:00:54 AM from Jen Deegan : volunteers needed!
06/03/2008 10:00:58 AM from Nomi Harris: so you can all check on June 30 what still needs to be completed.
06/03/2008 10:01:09 AM from Jen Deegan : I'm on cross prodcuts
06/03/2008 10:01:12 AM from Nomi Harris: I am also putting in skeleton pages for some of the new components
06/03/2008 10:01:20 AM from Jen Deegan : great
06/03/2008 10:01:25 AM from Nomi Harris: so that you can just fill in content and not worry about linking in the new pages
06/03/2008 10:01:29 AM from Jen Deegan : thanks.
06/03/2008 10:01:39 AM from Nomi Harris: Thanks for volunteering for cross products, Jen.
06/03/2008 10:01:42 AM from Nomi Harris: We can talk more about this next time.
06/03/2008 10:01:47 AM from Jen Deegan : shall we wrap up so Midori can get her train.
06/03/2008 10:01:48 AM from David OS : Some movies for GO dev process terms: http://flymove.uni-muenster.de/
06/03/2008 10:01:50 AM from Nomi Harris: Thanks for coming today, everyone.
06/03/2008 10:02:01 AM from Nomi Harris: Bye!
06/03/2008 10:02:01 AM from Jen Deegan : thanks for all the work Nomi and Amina
06/03/2008 10:02:03 AM from Jen Deegan : bye
06/03/2008 10:02:04 AM from midori : see you next week, then
06/03/2008 10:02:05 AM from Harold : yes
06/03/2008 10:02:07 AM from midori : bye
06/03/2008 10:02:13 AM from Karen : bye
06/03/2008 10:02:17 AM from Jen Deegan : Nomi and Amina, shall we discuss call times?
06/03/2008 10:02:24 AM from David OS : Cheers - see you next time.
06/03/2008 10:02:27 AM from Nomi Harris: Ok
06/03/2008 10:02:27 AM from Amina : bye everyone... Jen: yes