OE Webex 3Jun08

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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