OE Webex 5Feb08

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02/05/2008    09:42:08 AM    from David OS to All Participants:	:(
02/05/2008    09:42:15 AM    from Nomi Harris to All Participants:	That was the first time WebEx died on me!
02/05/2008    09:42:20 AM    from Nomi Harris to All Participants:	I guess I've been lucky so far!
02/05/2008    09:42:22 AM    from Jen Deegan to All Participants:	no problem :-)

02/05/2008    09:42:33 AM    from Nomi Harris to All Participants:	Anyway, Jen, did you stick the regulates into your ontology by hand?
02/05/2008    09:43:12 AM    from Nomi Harris to All Participants:	Hello?
02/05/2008    09:43:40 AM    from Jen Deegan to All Participants:	the first time I did, but this time I chose it from the list

02/05/2008    09:43:40 AM    from midori to All Participants:	OK, changed to built-in icons and they're all still showing up.
02/05/2008    09:43:57 AM    from Jen Deegan to All Participants:	what term are you looking at?

02/05/2008    09:44:09 AM    from Nomi Harris to All Participants:	Are you two co-located, Jen and midori?
02/05/2008    09:44:14 AM    from midori to All Participants:	yes
02/05/2008    09:44:24 AM    from midori to All Participants:	(I'm looking at some metabolism terms ...)
02/05/2008    09:44:26 AM    from Nomi Harris to All Participants:	So maybe you can work together and figure out why it's not showing up for Jen?
02/05/2008    09:45:12 AM    from Jen Deegan to All Participants:	we're workign on it

02/05/2008    09:45:20 AM    from Nomi Harris to All Participants:	Ok.
02/05/2008    09:45:27 AM    from Nomi Harris to All Participants:	I've been trying to figure out the sub-selection bug.
02/05/2008    09:45:45 AM    from midori to All Participants:	argh. that one's gly.
02/05/2008    09:45:52 AM    from midori to All Participants:	... ugly (like my typing)
02/05/2008    09:46:06 AM    from Nomi Harris to All Participants:	I'm confused about what's happening.  For some reason, when it considers its candidates for what's currently the subselection, it doesn't always consider everything that's selected.
02/05/2008    09:46:12 AM    from Nomi Harris to All Participants:	Sometimes it leaves out some of the items.
02/05/2008    09:46:20 AM    from Nomi Harris to All Participants:	But I'm not sure why that's happening.
02/05/2008    09:46:24 AM    from Nomi Harris to All Participants:	I will continue investigating.
02/05/2008    09:46:42 AM    from Nomi Harris to All Participants:	Meanwhile, I'm also trying to track down memory leaks in OE2 that may be causing it to run out of memory sometimes.
02/05/2008    09:46:49 AM    from Nomi Harris to All Participants:	Have you guys had it run out of memory?
02/05/2008    09:47:00 AM    from Erika to All Participants:	sometimes

02/05/2008    09:47:16 AM    from Nomi Harris to All Participants:	I added a memory-checking thread that should warn you if you're almost out of memory.
02/05/2008    09:47:18 AM    from Jen Deegan to All Participants:	I have trouble with it running slowly

02/05/2008    09:47:21 AM    from Nomi Harris to All Participants:	Of course at that point it may already be too late to save.
02/05/2008    09:47:31 AM    from Nomi Harris to All Participants:	The running slowly could be a symptom of running out of memory.
02/05/2008    09:47:36 AM    from midori to All Participants:	I haven't seen the low-memory warning in beta29 yet, but I've certainly had symptoms consistent with out-of-memory  in several betas
02/05/2008    09:47:39 AM    from David OS to All Participants:	Only if runining on my puny latop.  OK on a mac with 2G ram.
02/05/2008    09:48:15 AM    from Nomi Harris to All Participants:	There's also evidence that there are components that are doing stuff even when they're not showing, which could be contributing to the slowness.
02/05/2008    09:48:41 AM    from Erika to All Participants:	It happend to me when I load three ontology at the same time.OE run out of memory

02/05/2008    09:49:04 AM    from Nomi Harris to All Participants:	You're looking at all three together, not sequentially?
02/05/2008    09:49:25 AM    from Erika to All Participants:	mmm! unfortunately three together

02/05/2008    09:49:47 AM    from Nomi Harris to All Participants:	Hmm.  I'm not sure that fixing memory leaks will help that much, since you have them all in memory at the same time.
02/05/2008    09:50:27 AM    from Nomi Harris to All Participants:	What happens with memory leaks is that when you load a new ontology, OE may still have dangling references to the old one, so it doesn't reclaim that memory, and after a while you run out.
02/05/2008    09:50:46 AM    from Nomi Harris to All Participants:	This used to happen in Apollo before Mark Gibson fixed the memory leaks.
02/05/2008    09:51:09 AM    from Erika to All Participants:	oh, I understand!...an other case was when I selected too many terms to be showed in DAG viewer

02/05/2008    09:51:21 AM    from Nomi Harris to All Participants:	The DAG viewer seems to be problematic in various ways.
02/05/2008    09:51:47 AM    from Nomi Harris to All Participants:	I haven't tried loading multiple ontologies at the same time--how do you even do that?
02/05/2008    09:51:56 AM    from Erika to All Participants:	Load terms

02/05/2008    09:52:06 AM    from Erika to All Participants:	and then select more than one file

02/05/2008    09:52:18 AM    from Erika to All Participants:	I usually work with CheBI and GO

02/05/2008    09:52:26 AM    from Erika to All Participants:	or Plant ontology and GO

02/05/2008    09:52:33 AM    from Nomi Harris to All Participants:	I'll have to try that.
02/05/2008    09:52:35 AM    from David OS to All Participants:	Ahhh - Chebi's pretty huge.
02/05/2008    09:52:41 AM    from Erika to All Participants:	yes!

02/05/2008    09:53:45 AM    from midori to All Participants:	Meanwhile, we've solved the icon problem -- Jen and I had different files loaded!
02/05/2008    09:54:01 AM    from Nomi Harris to All Participants:	Different ontology files?
02/05/2008    09:54:17 AM    from midori to All Participants:	long story ...
02/05/2008    09:54:27 AM    from Nomi Harris to All Participants:	Ok, glad you got it straightened out.
02/05/2008    09:54:49 AM    from Nomi Harris to All Participants:	So the top priority bugs are still slowness/memory problems and sub-selection, right?
02/05/2008    09:54:55 AM    from Jen Deegan to All Participants:	I have an icon question

02/05/2008    09:54:57 AM    from Nomi Harris to All Participants:	Any other ones on that must-fix-before-public-release list?
02/05/2008    09:55:02 AM    from Nomi Harris to All Participants:	Yes, Jen, what's your icon question?
02/05/2008    09:55:09 AM    from Jen Deegan to All Participants:	do you know how the icon size is set?

02/05/2008    09:55:15 AM    from Jen Deegan to All Participants:	is it be the sidth or height or what?

02/05/2008    09:55:23 AM    from Jen Deegan to All Participants:	width, that was

02/05/2008    09:55:33 AM    from Nomi Harris to All Participants:	Hmm, I don't know.  I can check later and let you know.  Why?
02/05/2008    09:56:03 AM    from Jen Deegan to All Participants:	some of mine are different sizes from other and the is_a and part_of ones look neater because they are square and the same size with a nice background

02/05/2008    09:56:07 AM    from midori to All Participants:	Oughta fix, #1: sub-selection (but you knew that)
02/05/2008    09:56:27 AM    from Jen Deegan to All Participants:	would be better if R ones were also square with nice background

02/05/2008    09:56:28 AM    from midori to All Participants:	Oughta fix, #2: right-click editing bug has reappeared; new SF item today
02/05/2008    09:56:44 AM    from Nomi Harris to All Participants:	Reappeared!  It went away for a while?
02/05/2008    09:56:57 AM    from Nomi Harris to All Participants:	I can't imagine what I've changed that would have affected that.
02/05/2008    09:57:50 AM    from midori to All Participants:	yup. and I can't think of anything either ... would it be worthwhile for me to go back and figure out which betas do and don't have it working?
02/05/2008    09:58:10 AM    from Nomi Harris to All Participants:	If that's easy for you to do, that would be useful info.
02/05/2008    09:58:34 AM    from midori to All Participants:	A bit tedious, but not difficult, so if it'll help, ok.
02/05/2008    09:58:59 AM    from Nomi Harris to All Participants:	Tell you what, I'll try to do it myself, assuming I can recreate the bug in the current version.
02/05/2008    09:59:09 AM    from Nomi Harris to All Participants:	If I can't, I'll let you know.
02/05/2008    09:59:23 AM    from Nomi Harris to All Participants:	I'm still mystified about why I have to click twice to see the selected thing in the Text Editor and you don't.
02/05/2008    09:59:23 AM    from midori to All Participants:	ok
02/05/2008    09:59:29 AM    from midori to All Participants:	me too
02/05/2008    10:00:10 AM    from Nomi Harris to All Participants:	I hope I can fix sub-selection.  The whole selection process is pretty complicated.
02/05/2008    10:00:14 AM    from midori to All Participants:	I've tried Mac installer and platform-independent; Mac OS X 10.4.11; PowerPC ...
02/05/2008    10:00:44 AM    from Nomi Harris to All Participants:	I wish I could look over your shoulder.  Any trips to California in your near future?
02/05/2008    10:01:04 AM    from midori to All Participants:	nope ...
02/05/2008    10:01:19 AM    from midori to All Participants:	would webex app sharing help at all?
02/05/2008    10:01:25 AM    from Nomi Harris to All Participants:	Hey, that's a good idea!
02/05/2008    10:01:41 AM    from Nomi Harris to All Participants:	Maybe when we're done with the official meeting, midori can hang around and we can try it?
02/05/2008    10:02:13 AM    from midori to All Participants:	OK; I can be here for about another half hour from now.
02/05/2008    10:02:29 AM    from Nomi Harris to All Participants:	Are we pretty much done now?
02/05/2008    10:02:32 AM    from Nomi Harris to All Participants:	Any other issues?
02/05/2008    10:02:43 AM    from Jen Deegan to All Participants:	hi

02/05/2008    10:02:48 AM    from midori to All Participants:	I've done a tiny bit of documentation today ...
02/05/2008    10:02:53 AM    from Jen Deegan to All Participants:	I have just tried making an icon that is the same width as height

02/05/2008    10:03:06 AM    from Jen Deegan to All Participants:	and it gets the left hand side chopped odff in oboedit

02/05/2008    10:03:09 AM    from Jen Deegan to All Participants:	off

02/05/2008    10:03:18 AM    from Jen Deegan to All Participants:	isn't that a bit weird

02/05/2008    10:03:27 AM    from Wasila to All Participants:	(have to run to a meeting -- will attend next week - bye!)
02/05/2008    10:03:45 AM    from Nomi Harris to All Participants:	(Bye, Wasila)   I don't know how it constrains the icons.  Send me that one and I will investigate.
02/05/2008    10:03:48 AM    from David OS to All Participants:	Bye Wasila
02/05/2008    10:05:29 AM    from Jen Deegan to All Participants:	thanks, will do

02/05/2008    10:05:48 AM    from Nomi Harris to All Participants:	Ok, bye everyone except midori?
02/05/2008    10:06:04 AM    from Erika to All Participants:	Thanks Nomi. Bye everybody!

02/05/2008    10:06:08 AM    from Nomi Harris to All Participants:	See you all next Tues.
02/05/2008    10:06:32 AM    from Jen Deegan to All Participants:	cheerio :-)

02/05/2008    10:06:48 AM    from David OS to All Participants:	OK. See you next week.  Back to editing next week so may have more to report. D
02/05/2008    10:07:12 AM    from Nomi Harris to All Participants:	Could you see that?
02/05/2008    10:07:25 AM    from Nomi Harris to All Participants:	Oh, did Karen just join?  Hi, Karen!
02/05/2008    10:07:52 AM    from midori to All Participants:	yes, I saw your OBO-Edit. Should I look for something specific?
02/05/2008    10:08:00 AM    from midori to All Participants:	(& hi Karen)
02/05/2008    10:08:09 AM    from Nomi Harris to All Participants:	Could you see me select a relation and click on it?
02/05/2008    10:08:26 AM    from Nomi Harris to All Participants:	The first one I clicked, nothing showed up in the Text Editor.  The second one did.
02/05/2008    10:08:32 AM    from Nomi Harris to All Participants:	Should I do it again?
02/05/2008    10:08:51 AM    from midori to All Participants:	yes please! things can go by pretty fast when sharing ...
02/05/2008    10:08:56 AM    from Nomi Harris to All Participants:	Ok!
02/05/2008    10:09:12 AM    from Karen Christie to All Participants:	Sorry I missed the meeting, had a doctor's appt, thought I'd check if it was still going, but I see that most people have logged out, so I'm assuming it's over
02/05/2008    10:09:40 AM    from Nomi Harris to All Participants:	Yes, it's basically over--I'm working with midori to try to figure out why we see different behavior in the Text Editor
02/05/2008    10:09:45 AM    from Nomi Harris to All Participants:	Did you see it that time?
02/05/2008    10:09:47 AM    from midori to All Participants:	It's just me and Nomi trying to figure out why she has a bug and I don't.
02/05/2008    10:10:16 AM    from Karen Christie to All Participants:	OK, till next week., bye
02/05/2008    10:10:20 AM    from midori to All Participants:	Yes, got it. That's definitely not happening to me.
02/05/2008    10:10:24 AM    from Nomi Harris to All Participants:	So weird!
02/05/2008    10:10:24 AM    from midori to All Participants:	bye Karen
02/05/2008    10:10:37 AM    from Nomi Harris to All Participants:	I wonder if we have some difference in our preferences/config?
02/05/2008    10:10:48 AM    from midori to All Participants:	I could show you mine .. but it's probably pretty easy to imagine.
02/05/2008    10:10:55 AM    from Nomi Harris to All Participants:	You saw what I meant, right?  I'm not dreaming?
02/05/2008    10:10:58 AM    from midori to All Participants:	(my obo-edit behavior, that is)
02/05/2008    10:11:11 AM    from Nomi Harris to All Participants:	Right, I assume yours works the way it should--you choose a term, it shows up in the Text Editor.
02/05/2008    10:11:23 AM    from midori to All Participants:	I did see it -- I'm convinced it's happening to you. And yep, mine's working.
02/05/2008    10:11:39 AM    from Nomi Harris to All Participants:	So weird.
02/05/2008    10:11:43 AM    from midori to All Participants:	Soooo ... what's different??
02/05/2008    10:11:48 AM    from Nomi Harris to All Participants:	Can you zip up your .oboeditbeta and send it to me?
02/05/2008    10:11:56 AM    from midori to All Participants:	sure
02/05/2008    10:12:02 AM    from Nomi Harris to All Participants:	Note that I had not loaded an ontology yet.  But I see the same behavior if I do.
02/05/2008    10:12:14 AM    from Nomi Harris to All Participants:	It also ignores my first selection when I switch between a class and a relation.
02/05/2008    10:12:37 AM    from Nomi Harris to All Participants:	I would be happy if this is *not* in fact a bug and I just have something configured strangely!
02/05/2008    10:12:45 AM    from Nomi Harris to All Participants:	The sub-selection bug is bad enough!
02/05/2008    10:12:50 AM    from midori to All Participants:	LIkewise, mine works with or without a file loaded.
02/05/2008    10:13:15 AM    from Nomi Harris to All Participants:	Ok, send me your .oboeditbeta zip file.  I can't think what else to try.
02/05/2008    10:13:45 AM    from Nomi Harris to All Participants:	Bye?
02/05/2008    10:14:21 AM    from midori to All Participants:	ok, bye
02/05/2008    10:14:28 AM    from Nomi Harris to All Participants:	See you later.