OE Webex 28Jun07

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June 28, 2007	    10:33:17 AM	    from John Day-Richter� to All Participants:	Hi, everybody. While we wait for everyone to join, please install 2.0-beta5 on your machine (if you haven't already)
June 28, 2007	    10:34:35 AM	    from John Day-Richter� to All Participants:	Also, thanks to everyone who persuaded me not to race ahead with Java 1.6. I think the final results with this IDW package turned out a lot better in end, and with a lot less hassle.
June 28, 2007	    10:35:04 AM	    from Jane Lomax� to All Participants:	I think everyone needs to change their settings to 'all participants' or John can't see what they say
June 28, 2007	    10:35:20 AM	    from John Day-Richter� to All Participants:	That's true. As far as I know, no one has spoken besides Jane just now.
June 28, 2007	    10:35:34 AM	    from Midori Harris� to All Participants:	I've just been keeping quiet ;)
June 28, 2007	    10:35:48 AM	    from Jennifer Clark� to All Participants:	dash
June 28, 2007	    10:35:57 AM	    from Jennifer Clark� to All Participants:	I've been chattering away here

June 28, 2007	    10:36:02 AM	    from Alexander Diehl� to All Participants:	I just got a java heap error loading GO 1.2 into B5
June 28, 2007	    10:36:18 AM	    from John Day-Richter� to All Participants:	Turn up your memory settings, Alex.
June 28, 2007	    10:36:20 AM	    from Midori Harris� to All Participants:	pulldown just below the chat box
June 28, 2007	    10:36:27 AM	    from Karen R Christie� to All Participants:	thanks
June 28, 2007	    10:36:31 AM	    from Midori Harris� to All Participants:	GO loaded neatly for me
June 28, 2007	    10:36:49 AM	    from Erika� to All Participants:	Load works for me
June 28, 2007	    10:36:56 AM	    from Alexander Diehl� to All Participants:	where are the memory settings?
June 28, 2007	    10:37:15 AM	    from John Day-Richter� to All Participants:	View -> Show -> Config -> Configuration Manager
June 28, 2007	    10:37:26 AM	    from John Day-Richter� to All Participants:	When you change the settings, you need to restart OBO-Edit.
June 28, 2007	    10:37:31 AM	    from Alexander Diehl� to All Participants:	will try
June 28, 2007	    10:38:22 AM	    from Karen R Christie� to All Participants:	hmmm, it says it loaded a file, but only shows me a blank gray screen...
June 28, 2007	    10:38:49 AM	    from John Day-Richter� to All Participants:	Try going to Show -> Edit -> Ontology Editor Panel
June 28, 2007	    10:38:54 AM	    from John Day-Richter� to All Participants:	See if a new panel shows up.
June 28, 2007	    10:39:05 AM	    from Karen R Christie� to All Participants:	nope
June 28, 2007	    10:39:51 AM	    from John Day-Richter� to All Participants:	I think I need to see your error log, Karen. You might try shutting down OBO-Edit, renaming your .oboedit directory, and starting again.
June 28, 2007	    10:40:02 AM	    from Alexander Diehl� to All Participants:	I couldn't see the config window so I restarted and now I just get an empty window with the menu bar.
June 28, 2007	    10:40:09 AM	    from Karen R Christie� to All Participants:	renaming my .oboedit directory to what?
June 28, 2007	    10:40:24 AM	    from John Day-Richter� to All Participants:	Anything. Just rename it so you can get your settings back when we're done here.
June 28, 2007	    10:40:37 AM	    from John Day-Richter� to All Participants:	If OBO-Edit doesn't find a directory named ".oboedit", it starts from scratch.
June 28, 2007	    10:41:17 AM	    from John Day-Richter� to All Participants:	I'd like to do a little overview of new features while Karen does that.
June 28, 2007	    10:41:20 AM	    from John Day-Richter� to All Participants:	...
June 28, 2007	    10:41:34 AM	    from Karen R Christie� to All Participants:	I'm not sure where to find my .oboedit directory
June 28, 2007	    10:41:34 AM	    from John Day-Richter� to All Participants:	First, Quick-Fixes now work from the text editor. Observe...
June 28, 2007	    10:41:48 AM	    from John Day-Richter� to All Participants:	On Mac OS, the directory is in ~/.oboedit
June 28, 2007	    10:42:03 AM	    from John Day-Richter� to All Participants:	on windows, c:\documents & settings\<your user name>\.oboedit
June 28, 2007	    10:42:27 AM	    from John Day-Richter� to All Participants:	Anyway, if I right click a highlighted error in the text editor, a quickfix menu will appear.
June 28, 2007	    10:43:07 AM	    from John Day-Richter� to All Participants:	So that should help speed up editing.

June 28, 2007	    10:43:24 AM	    from John Day-Richter� to All Participants:	Second new feature:
June 28, 2007	    10:44:13 AM	    from John Day-Richter� to All Participants:	The stderr log file is no more. I've switched to the Java logging system. Now there are 3 log files, named something like oboedit-log0.log, oboedit-log1.log, etc.
June 28, 2007	    10:44:31 AM	    from John Day-Richter� to All Participants:	The idea is that when one log file gets larger than 1 mb, it switches to the next.
June 28, 2007	    10:44:56 AM	    from John Day-Richter� to All Participants:	This should prevent the giant stderr file problem that some people have seen, and it'll make it easier for me to get useful info from the logs.
June 28, 2007	    10:45:05 AM	    from John Day-Richter� to All Participants:	If you have an error, send me all 3 log files.
June 28, 2007	    10:45:14 AM	    from John Day-Richter� to All Participants:	Third new/reinstated feature:
June 28, 2007	    10:45:22 AM	    from Midori Harris� to All Participants:	will they end up in .oboedit?
June 28, 2007	    10:45:39 AM	    from John Day-Richter� to All Participants:	Either in .oboedit or .oboedit/log. I don't remember which.


June 28, 2007	    10:45:49 AM	    from John Day-Richter� to All Participants:	Third feature: Autosave is back, with some changes.


June 28, 2007	    10:45:56 AM	    from Karen R Christie� to All Participants:	Hmmm, now it opens with a view, but gives me a bunch of java.io.ObjectInputStream errors when I try to load
June 28, 2007	    10:46:25 AM	    from John Day-Richter� to All Participants:	Make sure you're using the OBO adapter.
June 28, 2007	    10:46:50 AM	    from John Day-Richter� to All Participants:	Autosave files are now written out in OBO format, not the fragile object serialization format they used before.
June 28, 2007	    10:47:06 AM	    from Jennifer Clark� to All Participants:	that sounds good!
June 28, 2007	    10:47:28 AM	    from John Day-Richter� to All Participants:	When OBO-Edit autosaves, the program will pause, and you'll see a progress bar until the save is complete.
June 28, 2007	    10:47:36 AM	    from Karen R Christie� to All Participants:	I assume you mean the OBO flat file adaptor as opposed to the OBO Serial adaptor
June 28, 2007	    10:47:49 AM	    from John Day-Richter� to All Participants:	That's right, Karen.
June 28, 2007	    10:48:21 AM	    from John Day-Richter� to All Participants:	It's a little annoying when the autosave bar pops up, but it was the only way I could think of to prevent users from changing the ontology during the autosave and really messing things up.
June 28, 2007	    10:48:51 AM	    from John Day-Richter� to All Participants:	Final new feature: Notice that there are some new icons on some of the title bars.
June 28, 2007	    10:48:52 AM	    from Karen R Christie� to All Participants:	OK, now it looked like it loaded, but it has given me a 'Java heap space' Load error
June 28, 2007	    10:48:59 AM	    from Jennifer Clark� to All Participants:	that's how other applications do it so we're used to it
June 28, 2007	    10:49:02 AM	    from John Day-Richter� to All Participants:	Karen - up the memory, and you're ready to go.

June 28, 2007	    10:49:21 AM	    from John Day-Richter� to All Participants:	(Sorry about all the trouble - it comes from starting with a brand-new config)
June 28, 2007	    10:49:28 AM	    from Karen R Christie� to All Participants:	how?
June 28, 2007	    10:49:51 AM	    from John Day-Richter� to All Participants:	Use the configuration manager: View -> Show -> Config -> Configuration Manager
June 28, 2007	    10:49:58 AM	    from John Day-Richter� to All Participants:	Then restart.
June 28, 2007	    10:50:13 AM	    from Alexander Diehl� to All Participants:	It worked for me.
June 28, 2007	    10:50:30 AM	    from Jane Lomax� to All Participants:	my configuration manager doesn't appear for some reason
June 28, 2007	    10:50:52 AM	    from Midori Harris� to All Participants:	am I the only one who just had the thing work right away? ;)
June 28, 2007	    10:50:56 AM	    from Karen R Christie� to All Participants:	It appears to let me select it from the menu, but then nothing happens
June 28, 2007	    10:51:00 AM	    from John Day-Richter� to All Participants:	Are you sure it hasn't appeared as a tab somewhere on your screen?
June 28, 2007	    10:51:02 AM	    from Jennifer Clark� to All Participants:	no it was fine for me
June 28, 2007	    10:51:07 AM	    from Jane Lomax� to All Participants:	likewise
June 28, 2007	    10:51:20 AM	    from Jane Lomax� to All Participants:	(to karen i mean)
June 28, 2007	    10:51:40 AM	    from Alexander Diehl� to All Participants:	it appeared in the lower right corner for me of the OBO-edit window.
June 28, 2007	    10:51:57 AM	    from Erika� to All Participants:	I have the config panel very small near the Ontology editor panel
June 28, 2007	    10:52:00 AM	    from Alexander Diehl� to All Participants:	lower-left I mean
June 28, 2007	    10:52:10 AM	    from John Day-Richter� to All Participants:	(while we wait) There are two new title bar buttons on the ontology editor panel. One looks like a little globe. That toggles between global/local selection.
June 28, 2007	    10:52:21 AM	    from Karen R Christie� to All Participants:	there is no new tab anywhere in OBO-Edit and no pop up windows anywhere
June 28, 2007	    10:52:33 AM	    from Jane Lomax� to All Participants:	i'm running 1.101 at the same time - perhaps that's causing a problem?
June 28, 2007	    10:52:55 AM	    from John Day-Richter� to All Participants:	Perhaps... but not terrible likely. I think I'm going to need to see error logs from the people who are having problems.
June 28, 2007	    10:53:30 AM	    from Jennifer Clark� to All Participants:	have you tried calling up the graph editor or something?
June 28, 2007	    10:53:36 AM	    from Jennifer Clark� to All Participants:	mine is blank until I do that
June 28, 2007	    10:53:53 AM	    from John Day-Richter� to All Participants:	One last thing to try: You can disable the reasoner (Show -> Reasoner -> Reasoner Manager) and try loading GO again. If that doesn't work, I'll just do the demo and we'll work this out later.
June 28, 2007	    10:54:48 AM	    from Karen R Christie� to All Participants:	why don't we work it out later, I can't get to the REsoner Manager either, and even getting the menus to show is terribly slow
June 28, 2007	    10:55:07 AM	    from Jane Lomax� to All Participants:	can't get the reasoner manager either
June 28, 2007	    10:55:16 AM	    from John Day-Richter� to All Participants:	Uh oh. That kind of problem should be fixed. Is anyone else having big slowdown problems?
June 28, 2007	    10:55:32 AM	    from Jennifer Clark� to All Participants:	only with the reasoner on
June 28, 2007	    10:55:44 AM	    from Erika� to All Participants:	I can't see The Reasoner
June 28, 2007	    10:55:54 AM	    from Jane Lomax� to All Participants:	speed's okay for me
June 28, 2007	    10:56:00 AM	    from Erika� to All Participants:	I get a large grey window
June 28, 2007	    10:56:04 AM	    from Midori Harris� to All Participants:	I haven't tried anything other than layout stuff ... that's all been fine so far. I can see the reasoner manager, config manager, etc.
June 28, 2007	    10:56:20 AM	    from Midori Harris� to All Participants:	Speed of that is fine.
June 28, 2007	    10:56:42 AM	    from Alexander Diehl� to All Participants:	I can get the reasoner manager.
June 28, 2007	    10:56:45 AM	    from John Day-Richter� to All Participants:	I'll bet that these "missing window" and slowdown problems are memory related. I'll see what I can do about getting OBO-Edit to use all available memory in the next release. I think Java 1.5 can do that.
June 28, 2007	    10:57:06 AM	    from John Day-Richter� to All Participants:	Then we can do away with this ridiculous memory settings nonsense once and for all.
June 28, 2007	    10:57:13 AM	    from Alexander Diehl� to All Participants:	I set memory to 512M
June 28, 2007	    10:57:25 AM	    from John Day-Richter� to All Participants:	With GO and the reasoner, you might need quite a bit more.
June 28, 2007	    10:57:28 AM	    from Midori Harris� to All Participants:	me too ... 512M
June 28, 2007	    10:57:40 AM	    from John Day-Richter� to All Participants:	Anyway, I'll get on with this graph editor demo then.

June 28, 2007	    10:57:47 AM	    from Midori Harris� to All Participants:	reasoner's off at the moment ...
June 28, 2007	    10:57:52 AM	    from Midori Harris� to All Participants:	yes, go ahead
June 28, 2007	    10:57:59 AM	    from Erika� to All Participants:	Reasoner works nw for me
June 28, 2007	    10:58:04 AM	    from John Day-Richter� to All Participants:	Oh, one more new feature - single-click now selects.
June 28, 2007	    10:58:10 AM	    from Jennifer Clark� to All Participants:	yay!
June 28, 2007	    10:58:12 AM	    from Midori Harris� to All Participants:	yay!!!
June 28, 2007	    10:58:20 AM	    from John Day-Richter� to All Participants:	Okay, the demo:
June 28, 2007	    10:58:23 AM	    from Midori Harris� to All Participants:	On the topic of new features: we have a tracker full of feature requests! Some may be addressed, and otheres rendered moot/out-of-date, by what's already in 2.0, but I wouldn't know which ones.
June 28, 2007	    10:58:41 AM	    from Midori Harris� to All Participants:	We should come back to them after the dome.
June 28, 2007	    10:58:51 AM	    from John Day-Richter� to All Participants:	I'm cleaning house on new requests and OBO-Edit 1.1 bugs today and tomorrow.
June 28, 2007	    10:59:15 AM	    from John Day-Richter� to All Participants:	Demo: Currently, I've got both ontology editing panels in global selection mode. When I select something in one panel, it's selected in both.
June 28, 2007	    11:00:04 AM	    from Midori Harris� to All Participants:	Webexx crashed on me. What'd I miss? <sigh>
June 28, 2007	    11:00:26 AM	    from John Day-Richter� to All Participants:	When a term is clicked in the graph editor, it becomes "focused". The graph editor will usually take steps to keep the focused term in view.
June 28, 2007	    11:00:59 AM	    from John Day-Richter� to All Participants:	What it does depends on the "bounds guarantor" setting (I'm taking applications for a different name for this).
June 28, 2007	    11:01:16 AM	    from John Day-Richter� to All Participants:	If you press V in the Graph Editor, it switches the bounds guarantor setting.
June 28, 2007	    11:01:24 AM	    from Karen R Christie� to All Participants:	You'll need to explain what it does before I can even suggest something
June 28, 2007	    11:01:41 AM	    from Midori Harris� to All Participants:	I saw it, and I don't know what just happened!
June 28, 2007	    11:01:56 AM	    from John Day-Richter� to All Participants:	There are 3 bounds guarantor settings:
June 28, 2007	    11:02:16 AM	    from John Day-Richter� to All Participants:	"Pan to focused": when a term is focused, put it in the middle of the screen
June 28, 2007	    11:02:35 AM	    from John Day-Richter� to All Participants:	"Zoom to focused": when a term is focused, put it in the middle of the screen and zoom in as far as you can.
June 28, 2007	    11:02:57 AM	    from John Day-Richter� to All Participants:	"Zoom to all": When the screen bounds change, zoom out to show all the currently expanded terms.
June 28, 2007	    11:03:12 AM	    from Erika� to All Participants:	I can't see the V 
June 28, 2007	    11:03:14 AM	    from John Day-Richter� to All Participants:	We're in "zoom to all mode" now. Watch what happens when I make more terms visible.
June 28, 2007	    11:03:25 AM	    from John Day-Richter� to All Participants:	(Erika - press the V key on your keyboard)
June 28, 2007	    11:03:32 AM	    from Erika� to All Participants:	thanks
June 28, 2007	    11:03:59 AM	    from John Day-Richter� to All Participants:	It keeps zooming a little further out each time I show a new term.
June 28, 2007	    11:04:45 AM	    from John Day-Richter� to All Participants:	I can still use the normal pan and zoom controls, but when the screen bounds change, I'll get zoomed out again.
June 28, 2007	    11:04:47 AM	    from Alexander Diehl� to All Participants:	can you control the zoom level incrementally.
June 28, 2007	    11:04:53 AM	    from Karen R Christie� to All Participants:	Webex crashed on me, what was the 3rd setting of the obnoxiously named thing?
June 28, 2007	    11:05:07 AM	    from John Day-Richter� to All Participants:	"Zoom to all", the current mode.
June 28, 2007	    11:05:54 AM	    from John Day-Richter� to All Participants:	Normally, you're going to want to use "pan to focused node". "Zoom to all" is useful if you want to see a big overview of the ontology.
June 28, 2007	    11:06:16 AM	    from John Day-Richter� to All Participants:	You can pan around the screen by left clicking on empty space and dragging.
June 28, 2007	    11:06:36 AM	    from John Day-Richter� to All Participants:	You zoom in and out by right-clicking and dragging.
June 28, 2007	    11:06:50 AM	    from Alexander Diehl� to All Participants:	got it.
June 28, 2007	    11:06:57 AM	    from John Day-Richter� to All Participants:	You can select terms by clicking their box.
June 28, 2007	    11:07:16 AM	    from John Day-Richter� to All Participants:	And you can select links by clicking the little box with the icon in it.
June 28, 2007	    11:07:48 AM	    from John Day-Richter� to All Participants:	This is one of the big differences between the graph editor and the ontology editor. You can select links and terms independently.
June 28, 2007	    11:08:32 AM	    from Jennifer Clark� to All Participants:	I think I managed to delete the root nodes earlier without deleting their children.
June 28, 2007	    11:09:07 AM	    from John Day-Richter� to All Participants:	Yeah - delete works differently in the graph editor, because it's not a big deal if you create orphans in the graph view.
June 28, 2007	    11:09:50 AM	    from John Day-Richter� to All Participants:	Some areas of the graph view will show a tooltip if you mouse over them.
June 28, 2007	    11:11:02 AM	    from John Day-Richter� to All Participants:	Note that if you have the reasoner turned on, the link tooltips will explain why a link is being shown.
June 28, 2007	    11:11:24 AM	    from John Day-Richter� to All Participants:	Some links are displayed with dotted lines. These are links that have been inferred by the reasoner.
June 28, 2007	    11:11:27 AM	    from John Day-Richter� to All Participants:	OBO-Edit will always draw ALL the links between the visible terms, including ones implied by the reasoner. That's why there are a lot of implied links back to the root right now.
June 28, 2007	    11:13:08 AM	    from John Day-Richter� to All Participants:	Questions so far? If not, I'll move on to how to expand and collapse nodes.
June 28, 2007	    11:13:50 AM	    from John Day-Richter� to All Participants:	Okay, moving on.
June 28, 2007	    11:14:03 AM	    from John Day-Richter� to All Participants:	There are several ways to control what's visible on the screen.
June 28, 2007	    11:14:23 AM	    from John Day-Richter� to All Participants:	The little bars at the bottom of each term box represent all the children of a node.
June 28, 2007	    11:14:36 AM	    from Midori Harris� to All Participants:	they're awfully tiny ...
June 28, 2007	    11:14:43 AM	    from John Day-Richter� to All Participants:	We can tweak that.
June 28, 2007	    11:14:47 AM	    from John Day-Richter� to All Participants:	Of course, you can always zoom in.
June 28, 2007	    11:15:44 AM	    from John Day-Richter� to All Participants:	Note that the little blue bar is made up of many tiny bars. Each bar is an expand/hide control for a particular link. If you mouse over a bar, a tooltip will tell you the associated link.
June 28, 2007	    11:16:07 AM	    from John Day-Richter� to All Participants:	I clicked the bar, so the link was shown.
June 28, 2007	    11:16:17 AM	    from Midori Harris� to All Participants:	(wooo ... gotta work on my zoom control ...)
June 28, 2007	    11:16:53 AM	    from John Day-Richter� to All Participants:	It's hard to see because of the link in the way, but notice that one of the blue bars at the bottom of substitution has changed color.
June 28, 2007	    11:17:01 AM	    from Karen R Christie� to All Participants:	yea, if each little bar is going to control something different, I agree with Midori that a little bigger would be good
June 28, 2007	    11:18:16 AM	    from John Day-Richter� to All Participants:	I can work on that. And maybe we'll decide that this whole concept is a little hard to use, and we'll go with something different. We're in uncharted UI territory here, so this is going to require a lot of tweaking.


June 28, 2007	    11:19:00 AM	    from John Day-Richter� to All Participants:	As you expand child links, the expanded links move to the right side of the link meter and become transparent.

June 28, 2007	    11:19:18 AM	    from John Day-Richter� to All Participants:	This way, you get a rough sense of what percentage of child nodes are currently visible.
June 28, 2007	    11:19:25 AM	    from John Day-Richter� to All Participants:	Take a look at region, for example.
June 28, 2007	    11:19:29 AM	    from Midori Harris� to All Participants:	the "link meter" is the row of teensy blue boxes?
June 28, 2007	    11:19:34 AM	    from John Day-Richter� to All Participants:	Yeah.
June 28, 2007	    11:19:47 AM	    from John Day-Richter� to All Participants:	You can tell right away that most of region's children are still hidden, because the bar is mostly blue.
June 28, 2007	    11:20:03 AM	    from John Day-Richter� to All Participants:	But all of sequence_variant's children are currently visible, because the bar is mostly clear.
June 28, 2007	    11:20:20 AM	    from John Day-Richter� to All Participants:	Actually, totally clear, not mostly clear.
June 28, 2007	    11:20:43 AM	    from John Day-Richter� to All Participants:	Every node has a link meter for it's parent links too.
June 28, 2007	    11:21:20 AM	    from John Day-Richter� to All Participants:	You don't have to expand/collapse children link by link. If you mouse over the link meter (and you're zoomed in close enough), some more control fade into view.
June 28, 2007	    11:21:24 AM	    from Jennifer Clark� to All Participants:	I could see this working best when used with the normal editing window
June 28, 2007	    11:21:33 AM	    from Jennifer Clark� to All Participants:	asking it to do all the editing seems a lot
June 28, 2007	    11:22:05 AM	    from John Day-Richter� to All Participants:	The two views do work together, but we should do our best to fix the problems with this view as far as we possibly can.
June 28, 2007	    11:22:20 AM	    from Jennifer Clark� to All Participants:	it might be easier to find the terms you want in the normal dag window and then use the graph for e.g. deleting links
June 28, 2007	    11:22:40 AM	    from Jennifer Clark� to All Participants:	I don't think content meeting people would be too chuffed if I zoom around too much while they're watching
June 28, 2007	    11:22:55 AM	    from Jennifer Clark� to All Participants:	I'm just trying to think round how we can use this to best effect
June 28, 2007	    11:23:06 AM	    from Jennifer Clark� to All Participants:	is that the sort of thing you want us to think about?
June 28, 2007	    11:23:07 AM	    from John Day-Richter� to All Participants:	Note that you don't have to use these controls at all.
June 28, 2007	    11:23:13 AM	    from Jennifer Clark� to All Participants:	oh righty
June 28, 2007	    11:23:16 AM	    from Jennifer Clark� to All Participants:	good point
June 28, 2007	    11:23:18 AM	    from John Day-Richter� to All Participants:	(Yes it is, Jen)
June 28, 2007	    11:23:20 AM	    from Jennifer Clark� to All Participants:	great
June 28, 2007	    11:23:28 AM	    from Jennifer Clark� to All Participants:	I'll have a play and see what I can come up with
June 28, 2007	    11:23:36 AM	    from John Day-Richter� to All Participants:	You can control what's visible via the right-click menu too.
June 28, 2007	    11:24:32 AM	    from Wacek� to All Participants:	:)
June 28, 2007	    11:25:13 AM	    from John Day-Richter� to All Participants:	The right-click menu has a LOT of options to give you fine control of what's visible. Many of these options interact with the reasoner.
June 28, 2007	    11:25:47 AM	    from Jennifer Clark� to All Participants:	might it be more practical to think of this GUI in terms of google maps rather than our usual editor?
June 28, 2007	    11:26:08 AM	    from Midori Harris� to All Participants:	wha' ...?
June 28, 2007	    11:26:11 AM	    from Jennifer Clark� to All Participants:	you could have that little zoom bar at the top right with the steps on it
June 28, 2007	    11:26:20 AM	    from Jennifer Clark� to All Participants:	left I mean
June 28, 2007	    11:26:35 AM	    from Jennifer Clark� to All Participants:	do you know what I mean?
June 28, 2007	    11:26:45 AM	    from John Day-Richter� to All Participants:	That would be very simple to add. I could also add a little overview map in the bottom right that shows a fully zoomed-out view of the current graph.
June 28, 2007	    11:26:55 AM	    from Jennifer Clark� to All Participants:	that would be very nice
June 28, 2007	    11:27:13 AM	    from Wacek� to All Participants:	shows and allow to navigate it
June 28, 2007	    11:27:18 AM	    from Jennifer Clark� to All Participants:	then we could get a rough idea of ho much we would be sooming out if we click a setp
June 28, 2007	    11:27:31 AM	    from Jennifer Clark� to All Participants:	rather than just smoothly zooming
June 28, 2007	    11:27:46 AM	    from Alexander Diehl� to All Participants:	Could we add "post-it" notes to terms that could remind us of things we mean to do (stored separately of course?
June 28, 2007	    11:28:02 AM	    from Jennifer Clark� to All Participants:	I think you would do that in the def field. 
June 28, 2007	    11:28:05 AM	    from Jennifer Clark� to All Participants:	that's what I do now
June 28, 2007	    11:28:10 AM	    from John Day-Richter� to All Participants:	That's a great idea! Let's add that to the feature requests.
June 28, 2007	    11:28:27 AM	    from John Day-Richter� to All Participants:	It'd make a good plugin.
June 28, 2007	    11:28:39 AM	    from Wacek� to All Participants:	are there graph layouts other than the hierarchical available?
June 28, 2007	    11:28:48 AM	    from Jennifer Clark� to All Participants:	would that field have to go in the obo format?
June 28, 2007	    11:28:51 AM	    from Midori Harris� to All Participants:	Speaking of which, did my earlier comment about the feature requests get through?
June 28, 2007	    11:28:53 AM	    from Alexander Diehl� to All Participants:	These notes could be indicated by a little icon in the graphical view and elsewhere and expanded for viewing.
June 28, 2007	    11:29:04 AM	    from Midori Harris� to All Participants:	(I sent it just when webex crashed.)
June 28, 2007	    11:29:12 AM	    from Jennifer Clark� to All Participants:	not sure, what was it?
June 28, 2007	    11:29:23 AM	    from John Day-Richter� to All Participants:	Midori - it did, I'm working on going through these and bug reports today and tomorrow.
June 28, 2007	    11:29:30 AM	    from Midori Harris� to All Participants:	must not've arrived then ;)
June 28, 2007	    11:29:39 AM	    from Midori Harris� to All Participants:	(oops, never mind)
June 28, 2007	    11:29:46 AM	    from John Day-Richter� to All Participants:	Anyway, I think you won't need to do as much expanding of children in this view as you do in the current view.
June 28, 2007	    11:29:53 AM	    from Midori Harris� to All Participants:	John -- excellent.
June 28, 2007	    11:30:03 AM	    from John Day-Richter� to All Participants:	Let me show you a little more of how this can be used in concert with the existing editor panel.
June 28, 2007	    11:30:09 AM	    from Midori Harris� to All Participants:	(about the trackers, that is)
June 28, 2007	    11:30:46 AM	    from John Day-Richter� to All Participants:	If you drag a term from another panel onto empty space in the graph editor, the new term will appear in the graph panel.
June 28, 2007	    11:31:19 AM	    from John Day-Richter� to All Participants:	You can use this to build a view that just shows the terms you want to work with.
June 28, 2007	    11:31:45 AM	    from John Day-Richter� to All Participants:	You can also get the reasoner to help you.
June 28, 2007	    11:32:11 AM	    from John Day-Richter� to All Participants:	There's a dotted line between binding_site and nuclease_binding_site. I can ask the reasoner to show me all the links that went into that inference.
June 28, 2007	    11:32:41 AM	    from Midori Harris� to All Participants:	kicked out again ...
June 28, 2007	    11:32:53 AM	    from John Day-Richter� to All Participants:	Via the right-click menu, but there seems to be a little problem with it right now.
June 28, 2007	    11:33:11 AM	    from John Day-Richter� to All Participants:	We're out of time, but if people want to stay 10 more minutes, I'll show the new graph editing tools.
June 28, 2007	    11:33:39 AM	    from John Day-Richter� to All Participants:	So far, I've just been using the "pick" tool.
June 28, 2007	    11:33:52 AM	    from John Day-Richter� to All Participants:	If I want to add new links, I can use the "Draw link" tool.
June 28, 2007	    11:33:55 AM	    from Midori Harris� to All Participants:	Editing tools sound pretty important ... any chance of a review like last week's?
June 28, 2007	    11:34:15 AM	    from John Day-Richter� to All Participants:	If you want, we can do this again next week instead of going on now.
June 28, 2007	    11:34:29 AM	    from John Day-Richter� to All Participants:	That could give me time to add some new feature requests too.
June 28, 2007	    11:34:33 AM	    from Jennifer Clark� to All Participants:	that might be better. We've covered a lot of ground
June 28, 2007	    11:35:05 AM	    from John Day-Richter� to All Participants:	Hey, before we go, make sure to read the Wiki article I wrote about options for building a new complex filter editor!
June 28, 2007	    11:35:17 AM	    from Karen R Christie� to All Participants:	and maybe by then we can work out the memory issues, or whatever, so that I can actually play with it instead of just watch
June 28, 2007	    11:35:26 AM	    from Midori Harris� to All Participants:	I did, and I thought it would make excellent wg meeting fodder.
June 28, 2007	    11:35:42 AM	    from John Day-Richter� to All Participants:	Anyone who couldn't get OBO-Edit to work right, please send me their log files.
June 28, 2007	    11:36:05 AM	    from Midori Harris� to All Participants:	So another webex/chat in a week? Mostly graph editing, part2?
June 28, 2007	    11:36:13 AM	    from John Day-Richter� to All Participants:	Okay, let's meet again next week. Maybe we'll change the format of WG meetings so that the first 30 mins is discussion, and the second 30 minutes is demo.
June 28, 2007	    11:36:24 AM	    from Jennifer Clark� to All Participants:	seems good
June 28, 2007	    11:36:33 AM	    from Midori Harris� to All Participants:	fine with me
June 28, 2007	    11:37:10 AM	    from John Day-Richter� to All Participants:	If people can't meet this frequently, I understand. Feel free to miss a meeting if you need to, and just hope we don't discuss something you care deeply about.
June 28, 2007	    11:37:23 AM	    from Jennifer Clark� to All Participants:	shall we start recording?
June 28, 2007	    11:37:28 AM	    from Jennifer Clark� to All Participants:	this is important stuff

June 28, 2007	    11:37:42 AM	    from John Day-Richter� to All Participants:	Let's try recording next week.
June 28, 2007	    11:37:45 AM	    from Chris Mungall� to All Participants:	yes, can we have recordings of all webex mtgs
June 28, 2007	    11:37:50 AM	    from Midori Harris� to All Participants:	People tend not to mind catching up via transcripts (hint, hint) ... recordings can help too.
June 28, 2007	    11:37:59 AM	    from John Day-Richter� to All Participants:	<grimace>

June 28, 2007	    11:38:00 AM	    from Jennifer Clark� to All Participants:	we can have both
June 28, 2007	    11:38:00 AM	    from John Day-Richter� to All Participants:	Hey, one last idea!
June 28, 2007	    11:38:04 AM	    from Jennifer Clark� to All Participants:	jus transcript
June 28, 2007	    11:38:10 AM	    from Jennifer Clark� to All Participants:	or transcript and demo
June 28, 2007	    11:38:17 AM	    from Chris Mungall� to All Participants:	t+d
June 28, 2007	    11:38:26 AM	    from Jennifer Clark� to All Participants:	yes?
June 28, 2007	    11:38:42 AM	    from John Day-Richter� to All Participants:	How would people feel if I held "office hours" once a week? I'd have a webex meeting where people could ask questions, and use the application sharing feature of WebEx to show me what's going wrong with their installation of OBO-Edit.
June 28, 2007	    11:38:54 AM	    from Midori Harris� to All Participants:	that sounds excellent!
June 28, 2007	    11:39:00 AM	    from Chris Mungall� to All Participants:	++
June 28, 2007	    11:39:01 AM	    from Jennifer Clark� to All Participants:	yes sounds good
June 28, 2007	    11:39:02 AM	    from Erika� to All Participants:	fantastic
June 28, 2007	    11:39:18 AM	    from Jennifer Clark� to All Participants:	chris was that to me?

June 28, 2007	    11:39:23 AM	    from Jennifer Clark� to All Participants:	yes I can tell yoou
June 28, 2007	    11:39:35 AM	    from Jennifer Clark� to All Participants:	oh sorry, I mean chris yes I can tell you how to record
June 28, 2007	    11:39:46 AM	    from John Day-Richter� to All Participants:	How about Friday mornings at 9AM Pacific?
June 28, 2007	    11:39:59 AM	    from Jennifer Clark� to All Participants:	what is that best?
June 28, 2007	    11:40:00 AM	    from Midori Harris� to All Participants:	ok, I gotta go. See you next week, and thanks!
June 28, 2007	    11:40:04 AM	    from Jennifer Clark� to All Participants:	bst

June 28, 2007	    11:40:14 AM	    from Jennifer Clark� to All Participants:	isn't that friday evening in our place?
June 28, 2007	    11:40:17 AM	    from Jennifer Clark� to All Participants:	we might be busy then
June 28, 2007	    11:40:18 AM	    from Midori Harris� to All Participants:	9AM PDT = 5 PM BST
June 28, 2007	    11:40:21 AM	    from Erika� to All Participants:	yes Jen
June 28, 2007	    11:40:26 AM	    from Erika� to All Participants:	here it is 6 pm
June 28, 2007	    11:40:29 AM	    from Jennifer Clark� to All Participants:	that's maybe not so good
June 28, 2007	    11:40:35 AM	    from Jennifer Clark� to All Participants:	monday is better
June 28, 2007	    11:40:36 AM	    from Midori Harris� to All Participants:	bye!
June 28, 2007	    11:40:37 AM	    from Karen R Christie� to All Participants:	they'll be an hour, so I'll at least be able to make it by the second half hour?
June 28, 2007	    11:40:39 AM	    from Jennifer Clark� to All Participants:	bye
June 28, 2007	    11:40:46 AM	    from Jennifer Clark� to All Participants:	seems good
June 28, 2007	    11:40:59 AM	    from John Day-Richter� to All Participants:	Yeah, Friday might not work well. Okay, let's do Monday at 9:00 PST.
June 28, 2007	    11:41:07 AM	    from Jennifer Clark� to All Participants:	great
June 28, 2007	    11:41:18 AM	    from Erika� to All Participants:	Maybe on Monday people arrive at work later
June 28, 2007	    11:41:34 AM	    from John Day-Richter� to All Participants:	And Karen, you can show up whenever you want.
June 28, 2007	    11:41:43 AM	    from Jane Lomax� to All Participants:	John - I just sent you the log files, but only found two
June 28, 2007	    11:41:49 AM	    from John Day-Richter� to All Participants:	If people have pressing needs, we can always schedule one of these at some other time.
June 28, 2007	    11:41:56 AM	    from John Day-Richter� to All Participants:	Jane - that's okay, there won't always be 3.
June 28, 2007	    11:41:56 AM	    from Karen R Christie� to All Participants:	I only had 1 log file, but I've just sent it
June 28, 2007	    11:42:08 AM	    from John Day-Richter� to All Participants:	Thanks everyone. See some of you Monday.
June 28, 2007	    11:42:16 AM	    from Jane Lomax� to All Participants:	bye!
June 28, 2007	    11:42:16 AM	    from Erika� to All Participants:	thanks John

June 28, 2007	    11:42:22 AM	    from Erika� to All Participants:	bye guys

June 28, 2007	    11:42:25 AM	    from Jennifer Clark� to All Participants:	bye

June 28, 2007	    11:42:28 AM	    from Karen R Christie� to All Participants:	bye