OE IRC 3May07

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=== IRC ===

5:25 PM

Alex_MGI has joined the channel

tberardi has joined the channel

midori: Hi, Alex. I'm not sure whether everyone's going to join this channel or use the webex chat instead.

Alex_MGI: Yeah, I just thought I would do both just to be sure.

midori: Same here.

pfey has joined the channel

5:30 PM

midori: OK, John's on the Webex chat, and says he plans to use that instead of this channel. So everyone please join the Webex meeting! I'll stay tuned here in case you have problems or questions.

tberardi: OK, I'm in the webex meeting so I'll sign off here.

tberardi has quit the server saying: Quit: tberardi

pfey: sorry - remind me what the webex channel is please?

midori: It's not a chat channel; fire up a web browser and go to the URL in the email I'm about to forward to you.

5:35 PM

pfey: ok, thanks!

=== Webex chat ===

05/03/2007    17:28:26 PM    John Day-Richter:

	I hope we're going to use WebEx chat rather than IRC this time...

05/03/2007    17:29:03 PM    Karen Eilbeck:

	Are we supposed to call the conference line?

05/03/2007    17:29:08 PM    Midori Harris:

	There are a couple of people logged into IRC, but I'll tell 'em this is where the action is.

05/03/2007    17:30:21 PM    John Day-Richter:

	I think we're not going to use the phone, since folks were interested in recording this.

05/03/2007    17:30:31 PM    John Day-Richter:

	We don't want any unrecordable side conversations

05/03/2007    17:30:58 PM    Midori Harris:

	Jen - I'm rashly assuming that it's recording ... I made John the presenter; haven't touched anything eles.

05/03/2007    17:31:07 PM    Midori Harris:

	(... else)

05/03/2007    17:32:28 PM    John Day-Richter:

	Okay, let's see if I can get this demo to work.

05/03/2007    17:32:55 PM    John Day-Richter:

	My apologies to the good people of GO, but I'm using SO for this demo, because it already has nice intersection definitions and is error-free.

05/03/2007    17:33:47 PM    Harold:

	I just lost the demo

05/03/2007    17:33:47 PM    John Day-Richter:

	There's no good way to share the screen AND chat!

05/03/2007    17:33:47 PM    Midori Harris:

	We'll try not to pout.

05/03/2007    17:34:07 PM    Harold:

	We have 10 people; I think Skype should work?

05/03/2007    17:34:07 PM    John Day-Richter:

	Can everyone else see me type while the application is up?

05/03/2007    17:34:27 PM    Harold:

	no, I  didn't see anything else

05/03/2007    17:34:31 PM    Tanya:


05/03/2007    17:34:35 PM    Karen R Christie:

	When the demo is up, that's all I see, no chat, no anything else

05/03/2007    17:34:47 PM    John Day-Richter:

	Okay, then maybe we ought to use IRC for chat.

05/03/2007    17:34:57 PM    John Day-Richter:

	We can still record the transcript.

05/03/2007    17:35:01 PM    Karen R Christie:

	maybe we should try Skype for audio

05/03/2007    17:35:01 PM    Midori Harris:

	I can only see one thing at a time (but I can toggle between them).

05/03/2007    17:35:11 PM    Tanya:

	but won't we have the same thing happen?

05/03/2007    17:35:45 PM    Jane Lomax:

	Are we on IRC too?

05/03/2007    17:36:13 PM    Midori Harris:

	Most of us are here ...

05/03/2007    17:36:13 PM    Alex:

	some of us are

05/03/2007    17:36:28 PM    Midori Harris:

	only 3 also on IRC at the moment

05/03/2007    17:36:38 PM    Alex:

	john just joined

05/03/2007    17:37:04 PM    John Day-Richter:

	With IRC, at least you have 2 windows. You can make your application sharing window smaller, or set your IRC client to "always on top"

05/03/2007    17:38:22 PM    John Day-Richter:

	Does everyone know how to switch to IRC?

05/03/2007    17:38:24 PM    Tanya:

	ok, ready

05/03/2007    17:38:30 PM    erika:

	I have some problems with IRC but you can go on with the demo and I will try to join you on IRC

05/03/2007    17:38:34 PM    John Day-Richter:

	If so, I'm going to start application sharing again.

05/03/2007    17:38:56 PM    John Day-Richter:

	Erika: Try going to http://www.fruitfly.org/oboedit_webinar and use the chat client there.

05/03/2007    17:39:10 PM    John Day-Richter:

	I'm starting application sharing...

=== IRC ===

Guest4191 has joined the channel

Guest4191 is now called jrichter

hjd_mgi has joined the channel

tberardi has joined the channel

kchris has joined the channel

karen has joined the channel

jrichter: Can everyone see OBO-Edit?

5:40 PM

kchris: yes, I can see it, and also my IRC window

midori: Most of it ... but there's a yellow blob where (I presume) your IRC client window is.

karen: I see part of it and a yello box

Alex_MGI: Yes I can see both now.

jrichter: I'll try to keep my irc client in the lower left corner, since not much is going on down there right now.

midori: That works ... the yellow box is there but out of the way of the fun.

hjd_mgi: I have squre blob cutting out bottom of dag view

jrichter: Okay, let the demo begin!

jrichter: We're looking at the new Graph editing view right now.

midori: Pay no attention to the man behind the yellow blob ...

jrichter: Solid lines are curator-asserted links. Dotted lines are reasoner-inferred links.

jrichter: OBO-Edit always draws every reasoner-inferred link between the visible terms.

jrichter: Let's say we want to see the children of "genomic island"

jrichter: I'll expand the children by hovering over the controls at the bottom of "genomic island" and clicking the "expand children" box.

jrichter: I just panned the screen back to the middle by clicking and dragging on empty space with the left mouse button.

jrichter: Notice that transposable_element_gene has a thick blue outline. That's because it's the current selection.

j-lo has joined the channel

jrichter: I can click on other terms to focus them, but the selection doesn't change unless I double-click.

jrichter: This is one of the most noticeable changes in OBO-Edit 2.0 - double-click selects.

jclark has joined the channel

5:45 PM

midori: I hope I don't end up hating that ...

jrichter: I made this change because OBO-Edit's behavior relies heavily on what's currently selected, and I was shocked at how sensitive a complex operation can be to an errant mouse click.

jrichter: Don't worry Midori, the selection isn't as important as it used to be, anyway...

jrichter: While I've got "transposable_element_gene" selected, let's look at the new graphical dag viewer...

jrichter: Notice that there are two graphs, one for part_of and one for is_a. If this term had relationships with other types, those types would be shown too.

jrichter: People are sometimes confused by this display initially.

tberardi: would you have a third (etc) panel?

jrichter: Yup.

Alex_MGI: This is great, but I worry about screen real estate.

jrichter: Alex: Did I mention you can zoom?

kchris: Yea, I'm wondering how this will scale if we have more relationship types

Alex_MGI: Wow

tberardi: what's the magic zoom button?

jrichter: Note that by default it only shows transitive types, so it's not that bad.

jrichter: Right-click and drag to zoom in and out.

tberardi: cool

jrichter: Anyway, a lot of people see this and say "Why are there is_a links in the part_of view"?

5:50 PM

jrichter: That's because the part_of view is showing all the TERMS to which the selected term has a part_of relationship. Then OBO-Edit goes and draws the relationships between those terms, whatever the type.

jrichter: So transposable_element_gene is part of all those terms because of the single part_of relationship between transposable_element_gene and transposable_element.

Alex_MGI: That should be quite useful.

jrichter: BTW: The toolbars at the top won't be there in the final version. The toolbar only works in editing mode.

jrichter: Anyway, back to the editing mode...

jrichter: Actually, before I do that, any questions so far?

jrichter: Okay, good. Moving on.

jrichter: The graphical editor is designed to work like Photoshop or Illustrator. You use the drawing tools at the top to edit.

jrichter: The first tool is the Picker tool.

jrichter: This tool allows you to edit via drag and drop, just like the term editor panel that we know and love.

jrichter: When you drop, it shows you a menu asking what that drop operation should mean.

5:55 PM

midori: Will it have the keystroke modifiers that I know, love, and use all the time?

jrichter: (For you coders out there, that menu calls the same libraries as the term editor panel menu, so its easy to debug)

jrichter: Here's a little problem...

jrichter: I've changed OBO-Edit 2.0 to use real drag and drop, so you can drag out of OBO-Edit to other applications (like Phenote).

jrichter: Unfortunately, during a system drag and drop operation, Java doesn't log keyboard events.

jrichter: So you have to press your modifier key BEFORE you start to drag.

jrichter: There is absolutely nothing I can do about this. But we want real drag and drop, because it'll let us drag and drop between windows in OBO-Edit, and other nifty things we couldn't do before with my hacky system.

Alex_MGI: Can this be configurable so that if you never need to D and D to another application it behaves as before?

midori: OK ... I'm sure I'll get that through my head by trial & error. And I'll be happy as long as I can still use the modifiers at all.

jrichter: You still need D and D for inter-window dragging.

Alex_MGI: okay

jrichter: Here's where things get interesting...

midori wonders if she'll need a dodecahedral die to edit ...

jrichter dons the +1 cloak of dorkiness

jrichter: The next tool is the "Draw Link" tool.

6:00 PM

jrichter: Please pardon the nonsensical edit, but lets say we want to create a part_of link between transposable_element_gene and engineered_gene.

jrichter: We select part_of from the dropdown list at the top...

jrichter: And then we just draw the new link!

tberardi is off to other meeting, sorry! It's just getting exciting!

midori: and overheat webex ...

tberardi has quit the server saying: Quit: 

jrichter: Sorry about the blip there, it actually was the debugger showing me a useless message.

jrichter: Watch what happens if I select more than one term and then use the link drawing tool.

kchris: that's cool 

jrichter: You can create many links at once that way.

Alex_MGI: Can you create a term initially as unlinked, then connect it?

jrichter: Yes!

pfey: really cool

jrichter: And you can create links between things that aren't even part of the current selection.

Alex_MGI: The curtain always draws shut during the magic!

jrichter: I'm going to restart this so that doesn't happen (I need to shutdown the debugger to do it)

6:05 PM

jrichter: One other thing to notice: the graphical editor's selection can be linked to the term editor panel selection.

jrichter: Notice that it didn't show the whole path, just the link I selected. Hopefully, this will keep the graphs from getting needlessly cluttered.

jrichter: It's showing the implied link region -is_a-> Sequence_Ontology.

jrichter: Before, you'd need to look at the explanation plugin to see how the reasoner came up with that.

kchris: can you expand the graph view if you need/want to see more?

jrichter: But now, you can right click on the implied link to do just that!

jrichter: I was having mouse issues, but voila.

Alex_MGI: (is that black box a relationship type?)

jrichter: Yeah. Right now I've only defined icons for is_a and part of. If we zoom in, we can see that the link in question is...

jrichter: has_quality

Alex_MGI: I see

jrichter: The link color is matched to the relationship type to help with this, but you'll be able to define custom icons for any relationship type. And there will be mouseover tooltips.

6:10 PM

jrichter: Next tool: "Draw term"

jrichter: Lets say we want to add a new child to engineered_region...

jrichter: Hmm... looks like this one isn't enabled at the moment. Sorry.

midori: that's how we know this is a software demo

jrichter: When you click a term with this tool, it will add a new child (when enabled).

jrichter: If you click empty space, it adds a new root.

jrichter: I also know that the "erase" tool isn't yet enabled (but it's pretty clear how that should work), so we'll move right to the text edit tool.

jrichter: Let's edit the text of "located_sequence_feature"

jrichter: The screen isn't yet updating name changes correctly, but you saw how the interface works.

jrichter: You click the term you want to edit, and the editor appears right in the middle of the screen. You do your edits, and when you press Ctrl+Enter or mouse out of the editor, your changes are committed.

jrichter: In the final version, there will also be tools for merge, split and clone.

6:15 PM

jrichter: Sorry about the roughness of this code: I was pulled off graphical editor development at the beginning of the week for another urgent demo, so this isn't as polished as it would have been.

midori: keep you down to earth :P

jrichter: But I hope you can see how graphical editing (in general) works.

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Alex_MGI: Will you be able to make X-products by having two ontologies opened up side-by-side in the graphical view?

pfey: yes, look really great Jonh

jrichter: All the ontologies appear in one graph anyway, so yes.

jrichter: Any other comments/questions? If we have time, I can demo the thing I was working on instead of this. (this is of interest to you X-product people out there who weren't at the Chebi meeting this morning)

Alex_MGI: Excellent

hjd_mgi has joined the channel

jclark: might it be possible to switch to the webex chat window? Erika can't access the oboedit channel so is watching the demo without the commentary.

jrichter: If we do that, no one will be able to see the commentary, right?

jclark: yes we can all se it

j-lo: right!

j-lo: not at the same time as the demo though

Alex_MGI: I can.

jclark: you just don't look at the demo in full screen mode

karen: great work John. Since I saw the XP thing this morning already, I'm gonna split :o)

jclark: me too

kchris: actually, now that I've made the demo portion not full screen, I can see the Webex chat at the same time too

karen has quit the server saying: Quit: karen

jrichter: Okay, let's switch back to webex.

6:20 PM

Alex_MGI: Will someone join the two chat transcripts then?

jclark: yes

midori: I'll save this one as usual.

hjd_mgi: I can't seem to get back to the demo screen AND have chat on same screen; However, I have two questions

hjd_mgi: 1. The graph viewer is integrated, and not dependent upon graphiz

hjd_mgi: 2. WIll it be possible to edit the text in the boxes directly

=== Webex chat ===

05/03/2007    18:19:55 PM    Petra Fey:

	testing it out

05/03/2007    18:20:41 PM    John Day-Richter:

	The other thing I'd like to demonstrate is the new intersections editor.

05/03/2007    18:20:54 PM    Jen Clark:

	can you all see this?

05/03/2007    18:21:09 PM    Petra Fey:

	my demo screen is gone

05/03/2007    18:21:16 PM    John Day-Richter:

	I shut down demo mode for a sec.

05/03/2007    18:21:21 PM    Petra Fey:

	ah ok

05/03/2007    18:21:22 PM    John Day-Richter:

	I can't type and demo at the same time.

05/03/2007    18:21:38 PM    Jen Clark:

	I can imagine that's hard

05/03/2007    18:21:54 PM    John Day-Richter:

	No, I mean its just not possible in the webex client.

05/03/2007    18:22:00 PM    Jen Clark:

	oh I see. 

05/03/2007    18:22:03 PM    Jen Clark:

	never mind then

05/03/2007    18:22:11 PM    Harold:

	1. The graph viewer is integrated, and not dependent upon graphiz

2. WIll it be possible to edit the text in the boxes directly

05/03/2007    18:22:13 PM    Jen Clark:


05/03/2007    18:22:30 PM    erika:

	Sorry to bother you but I found a way to see John desktop and also the chat window

05/03/2007    18:22:32 PM    John Day-Richter:

	1 - Yes! I stole and adapted some graph layout code from QuickGO. GraphViz is no longer required

05/03/2007    18:22:54 PM    John Day-Richter:

	2 - I'll probably always have to pop up the regular text editor, but I can make it look more integrated.

05/03/2007    18:23:25 PM    John Day-Richter:

	(Piccolo, the snazzy toolkit that draws the pictures, has horrible text editing abilities)

05/03/2007    18:24:17 PM    John Day-Richter:

	Anyway, lets quickly look that the intersection editor, because even if you don't use intersections, it contains concepts that are going to be used in other parts of OBO-Edit 2.0.

05/03/2007    18:24:51 PM    John Day-Richter:

	When I bring up the intersection editor, you'll see a list of all the intersection terms in SO. When I double click one, an editor will appear where I double-clicked.

05/03/2007    18:25:13 PM    Petra Fey:

	I still don't seee the graphics

05/03/2007    18:25:22 PM    Karen R Christie:

	me neither

05/03/2007    18:25:23 PM    John Day-Richter:

	Hold on. I'm describing it first.

05/03/2007    18:25:58 PM    John Day-Richter:

	Note the auto-complete features as I type in the text boxes, and realize that I'm navigating without using the mouse at all, just keystrokes.

05/03/2007    18:26:02 PM    John Day-Richter:

	Okay, here we go..

05/03/2007    18:26:24 PM    Petra Fey:


05/03/2007    18:27:47 PM    John Day-Richter:

	It was hard to tell what was going on at the end there, but when I finished my edits and pressed enter, I jumped right into editing mode for the next item in the list.

05/03/2007    18:28:49 PM    John Day-Richter:

	I was thinking we might want to use something like this for a bulk-editing mode in OBO-Edit. You could drop a bunch of terms into a blank list, and then use an editor to quickly move through the list, automatically loading the next item when you finish editing the current item.

05/03/2007    18:29:30 PM    Midori Harris:

	Where would the list come from, and would it have to be in some particular format?

05/03/2007    18:29:52 PM    John Day-Richter:

	No, no. You could drop in search results, or your current selection, or whatever.

05/03/2007    18:31:01 PM    John Day-Richter:

	It looks like we're out of time. Any final thoughts before we part?

05/03/2007    18:31:08 PM    John Day-Richter:

	Interface suggestions are always welcome...

05/03/2007    18:31:23 PM    Jen Clark:

	I'll try to figure out how to chat and demo at the same time before next meeting.

05/03/2007    18:31:32 PM    John Day-Richter:


05/03/2007    18:31:34 PM    erika:

	I found the way

05/03/2007    18:31:44 PM    Midori Harris:

	We'll probably have both questions and suggestions when we try it out ourselves.

05/03/2007    18:32:00 PM    Karen R Christie:

	I just had one question, unrelated to the demo, is there any reason GO should not switch from 1.100 to 1.101? there aren't any corresponding file format changes, so I've no objection.

05/03/2007    18:32:36 PM    Midori Harris:

	No reason not to switch a GO-editing perspective ...

05/03/2007    18:32:42 PM    John Day-Richter:

	No reason. As far as OBO-Edit gui users are concerned, there is absolutely no difference between the two. It only effects command-line utilities.

05/03/2007    18:33:10 PM    Karen R Christie:

	and there was a problem in 1.100, so 1.101 is better from that perspective

05/03/2007    18:33:11 PM    John Day-Richter:

	Affects, not Effects! Help me, I'm dumb!

05/03/2007    18:34:08 PM    John Day-Richter:

	Will the relevant people initiate the switchover process?

05/03/2007    18:34:12 PM    Midori Harris:

	I gotta run ... Jen, I've saved the IRC transcript; tomorrow I'm happy to merge if you can save this chat.

05/03/2007    18:34:20 PM    Jen Clark:

	I'll save this one then