OE Webex 18Oct07

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10/18/2007    17:30:29 PM    from melissaH to All Attendees:
Hiya,been absent from all the hullaballoo recently. wow.
10/18/2007    17:31:08 PM    from Midori Harris to All Attendees:
indeed
10/18/2007    17:33:09 PM    from John Day-Richter to All Attendees:
Hi, all. Sorry I'm late.
10/18/2007    17:33:23 PM    from Midori Harris to All Participants:
hi
10/18/2007    17:33:33 PM    from melissaH to All Attendees:
	hi john!

10/18/2007    17:33:42 PM    from melissaH to All Participants:
hi john again!
10/18/2007    17:34:05 PM    from John Day-Richter to All Participants:
	I also apologize for the lack of a new release - my evening was 
taken up by an evening in the emergency room with my beloved, which, 
luckily, turned out to be nothing.
10/18/2007    17:34:13 PM    from Midori Harris to All Participants:
whew!
10/18/2007    17:34:14 PM    from Erika to All Participants:
	Hi John!

10/18/2007    17:34:23 PM    from melissaH to All Participants:
oh dear!
10/18/2007    17:34:54 PM    from John Day-Richter to All Participants:
	But, on the plus side, I saw a vivid illustration of what 
happens when you skateboard with a beer, and then fall over onto your 
beer.
10/18/2007    17:35:01 PM    from John Day-Richter to All Participants:
	It's not pretty.
10/18/2007    17:35:18 PM    from Jen Deegan to All Participants:
I guess that wasn't what happened to your wife?
10/18/2007    17:35:33 PM    from John Day-Richter to All Participants:
	Similar, but with polo ponies.
10/18/2007    17:35:39 PM    from Jen Deegan to All Participants:
wow!
10/18/2007    17:35:41 PM    from Jen Deegan to All Participants:
classy
10/18/2007    17:35:57 PM    from Midori Harris to All Participants:
she skateboarded with a polo pony?
10/18/2007    17:35:59 PM    from melissaH to All Participants:
we are going to miss you john
10/18/2007    17:36:23 PM    from Midori Harris to All Participants:
hey! some of us are still in denial here, ok?
10/18/2007    17:36:33 PM    from Tanya Berardini to All Participants:
	hello!
10/18/2007    17:36:41 PM    from Tanya Berardini to All Participants:
	Who is in denial?
10/18/2007    17:36:45 PM    from John Day-Richter to All Participants:
	Hello, Tanya.
10/18/2007    17:36:47 PM    from melissaH to All Participants:
oh right..... google who?
10/18/2007    17:36:50 PM    from Tanya Berardini to All Participants:
	It's not just a river in Egypt, you know.
10/18/2007    17:37:00 PM    from John Day-Richter to All Participants:
	Midori - she thinks that Golden Girls is going to come back on 
the air.
10/18/2007    17:37:22 PM    from John Day-Richter to All Participants:
	Anyway -
10/18/2007    17:37:38 PM    from Midori Harris to All Participants:
I said denial, not schizophrenia ...
10/18/2007    17:37:49 PM    from John Day-Richter to All Participants:
	I'll give a brief summary of what I've gotten done this week:
10/18/2007    17:38:06 PM    from John Day-Richter to All Participants:
	OBO-Edit has been broken into 3 projects:
10/18/2007    17:38:13 PM    from John Day-Richter to All Participants:
	org.bbop
10/18/2007    17:38:15 PM    from John Day-Richter to All Participants:
	org.obo
10/18/2007    17:38:17 PM    from John Day-Richter to All Participants:
	org.oboedit
10/18/2007    17:38:44 PM    from John Day-Richter to All Participants:
	Each of which now has its own subversion repository on 
sourceforge.
10/18/2007    17:39:10 PM    from John Day-Richter to All Participants:
	This means that future developers can use the ontology 
loading/editing stuff (from org.obo) without having to load the OBO-Edit 
gui stuff.
10/18/2007    17:39:33 PM    from Midori Harris to All Participants:
nice
10/18/2007    17:39:42 PM    from John Day-Richter to All Participants:
	In other news, I've been experimenting with other ways of 
engineering the reasoner.
10/18/2007    17:39:47 PM    from Midori Harris to All Participants:
(tho not something I'll rush out and use)
10/18/2007    17:40:25 PM    from John Day-Richter to All Participants:
	While conducting those experiments, I tested a prototype 
reasoner against our tried and true reasoner, to make sure it was giving 
the correct answers.
10/18/2007    17:40:44 PM    from John Day-Richter to All Participants:
	I was shocked to discover that the tried-and-true reasoner was 
NOT giving (wholly) correct answers, and the prototype was!
10/18/2007    17:41:04 PM    from Tanya Berardini to All Participants:
	urk
10/18/2007    17:41:05 PM    from Midori Harris to All Participants:
oh my.
10/18/2007    17:41:20 PM    from John Day-Richter to All Participants:
	It turns out that the current reasoner architecture always 
infers the right links, but it doesn't infer every possible explanation 
for those links.
10/18/2007    17:41:26 PM    from melissaH to All Participants:
hey-suess.
10/18/2007    17:41:43 PM    from John Day-Richter to All Participants:
	This is important, because the explanations are used to do fast 
link deletion while the reasoner is running.
10/18/2007    17:41:56 PM    from John Day-Richter to All Participants:
	So the old reasoner may exhibit incorrect incremental link 
deletion.
10/18/2007    17:42:41 PM    from John Day-Richter to All Participants:
	Trouble is, the new reasoner design is slower to start up, and 
(initially) used more memory.
10/18/2007    17:43:28 PM    from Erika to All Participants:
	oh no! 
more memory! This is the time for me to buy a new machine 
10/18/2007    17:43:31 PM    from John Day-Richter to All Participants:
	I mentioned this conundrum on the developer mailing lists, and 
Jen and Midori mentioned that OBO-Edit tends to run worse with the 
reasoner on as it is, with symptoms consistent with nearly-maxed-out 
memory conditions.
10/18/2007    17:43:47 PM    from John Day-Richter to All Participants:
	Jen was really alarmed at the idea that the reasoner would use 
even more memory.
10/18/2007    17:44:12 PM    from John Day-Richter to All Participants:
	Yesterday, I decided to see exactly how much more speed & memory 
use I could get out of the reasoner.
10/18/2007    17:44:16 PM    from John Day-Richter to All Participants:
	And there's good news!
10/18/2007    17:44:19 PM    from Midori Harris to All Participants:
The symptoms were very different from the 1.x reasoner slowness.
10/18/2007    17:44:51 PM    from John Day-Richter to All Participants:
	The new reasoner is still slower than the old reasoner, but it's 
only about 3 times slower (as opposed to 10 times slower in the initial 
version) and it uses much LESS memory.
10/18/2007    17:45:28 PM    from John Day-Richter to All Participants:
	And you can turn on a memory save feature where it runs about 
30% slower still, but uses even less memory.
10/18/2007    17:46:18 PM    from John Day-Richter to All Participants:
	And realize that the slower/faster language only refers to the 
initial startup time of the reasoner. Once it's running, new edits are 
incorporated in under 1 second.
10/18/2007    17:46:27 PM    from John Day-Richter to All Participants:
	So that's the reasoner stuff.
10/18/2007    17:47:23 PM    from Midori Harris to All Participants:
<applause>
10/18/2007    17:47:51 PM    from John Day-Richter to All Participants:
	Finally, in the course of fixing a bug related to text editing 
dbxrefs and synonyms, I realized that the simplest, best way to deal 
with the problem is to tear out some old legacy stuff from OBO-Edit 1.1 
and replace it entirely with shiny new bbop.org
10/18/2007    17:47:55 PM    from John Day-Richter to All Participants:
	components.
10/18/2007    17:48:35 PM    from John Day-Richter to All Participants:
	So that's taking longer than I thought.
10/18/2007    17:48:38 PM    from John Day-Richter to All Participants:
	End of summary.
10/18/2007    17:49:59 PM    from Midori Harris to All Participants:
we seem to be speechless
10/18/2007    17:50:15 PM    from Tanya Berardini to All Participants:
	awestruck
10/18/2007    17:50:33 PM    from melissaH to All Participants:
seeing stars
10/18/2007    17:50:43 PM    from John Day-Richter to All Participants:
	Has everyone been updating the wiki with their testing tasks?
10/18/2007    17:50:49 PM    from Jen Deegan to All Participants:
yes
10/18/2007    17:50:56 PM    from Midori Harris to All Participants:
I have
10/18/2007    17:51:10 PM    from John Day-Richter to All Participants:
	Jen, there was a mysterious bug report from you today...
10/18/2007    17:51:13 PM    from melissaH to All Participants:
I am out of date... been out of town. tell me what you want me to do....

10/18/2007    17:51:15 PM    from Tanya Berardini to All Participants:
	<guilt> no </guilt>
10/18/2007    17:51:37 PM    from John Day-Richter to All Participants:
	Jen - you said that the graph viewer should "show the path to 
root". It does that.
10/18/2007    17:51:45 PM    from John Day-Richter to All Participants:
	But only if the reasoner is on.
10/18/2007    17:51:47 PM    from Jen Deegan to All Participants:
does it?
10/18/2007    17:51:49 PM    from Jen Deegan to All Participants:
oh
10/18/2007    17:52:02 PM    from Jen Deegan to All Participants:
so I should bug test with the reasoner on then
10/18/2007    17:52:06 PM    from Jen Deegan to All Participants:
I didn't know  that
10/18/2007    17:52:08 PM    from Jen Deegan to All Participants:
thanks
10/18/2007    17:52:09 PM    from John Day-Richter to All Participants:
	I think that in the next release, I'm going to switch to the new 
reasoner, and turn it on by default.
10/18/2007    17:52:14 PM    from Midori Harris to All Participants:
I have a question:
10/18/2007    17:52:16 PM    from Jen Deegan to All Participants:
eek!
10/18/2007    17:52:25 PM    from Midori Harris to All Participants:
(not about the reasoner directly) ...
10/18/2007    17:52:26 PM    from John Day-Richter to All Participants:
	In a perfect world, "no reasoner" mode won't even be available 
in the OBO-Edit 2 release.
10/18/2007    17:52:30 PM    from John Day-Richter to All Participants:
	Go ahead, Midori.
10/18/2007    17:52:48 PM    from Midori Harris to All Participants:
In the shiny new search system, how does one search for redundant 
relationships?
10/18/2007    17:53:10 PM    from John Day-Richter to All Participants:
	Good question!
10/18/2007    17:53:23 PM    from Midori Harris to All Participants:
I try
10/18/2007    17:53:24 PM    from John Day-Richter to All Participants:
	That merits some thoughtful discussion.
10/18/2007    17:53:44 PM    from John Day-Richter to All Participants:
	See, everyone HATED the old "link search" options, and never 
used them.
10/18/2007    17:53:57 PM    from John Day-Richter to All Participants:
	But this is exactly what you need to find redundant 
relationships.
10/18/2007    17:54:33 PM    from John Day-Richter to All Participants:
	But, for simplicity, I don't even present a link searching 
component right now, so there's no way to do it.
10/18/2007    17:54:38 PM    from Midori Harris to All Participants:
That's what I used ... in fact, it was the only thing I ever did use the 
link filter for.
10/18/2007    17:54:58 PM    from Midori Harris to All Participants:
Well, at lesat I can take comfort in not feeling stupid --
10/18/2007    17:55:01 PM    from John Day-Richter to All Participants:
	So I can think of two ways of dealing with this -
10/18/2007    17:55:01 PM    from Jen Deegan to All Participants:
I only realised how they worked from the reading the developer docs
10/18/2007    17:55:08 PM    from Midori Harris to All Participants:
there was nothing staring me in the face.
10/18/2007    17:55:39 PM    from John Day-Richter to All Participants:
	I can add a "Link Search" option to the View -> Search menu, 
that presents a search control just like the one you see by default, but 
has link-centric options...
10/18/2007    17:56:08 PM    from John Day-Richter to All Participants:
	Or I can leave things as they are, and add a "has redundant 
parents" search criterion to the term search panel.
10/18/2007    17:56:35 PM    from Midori Harris to All Participants:
I still don't know whether I would ever search links for anything other 
than redundant relationships, so the second option would meet my present 
needs.
10/18/2007    17:56:42 PM    from John Day-Richter to All Participants:
	And, of course, now that I've typed that, it seems fairly 
obvious I should do both.
10/18/2007    17:57:01 PM    from Tanya Berardini to All Participants:
	Are there other reasons one might want to use the link search?

10/18/2007    17:57:12 PM    from John Day-Richter to All Participants:
	Absolutely. Link searches let you:
10/18/2007    17:57:14 PM    from Tanya Berardini to All Participants:
	If not, it may just be more confusing to have the first option 
present.
10/18/2007    17:57:22 PM    from John Day-Richter to All Participants:
	* find implied links
10/18/2007    17:57:27 PM    from John Day-Richter to All Participants:
	* find links of a certain type
10/18/2007    17:57:41 PM    from John Day-Richter to All Participants:
	* find links with certain type properties (like transitive 
links)
10/18/2007    17:58:00 PM    from John Day-Richter to All Participants:
	* find links in a certain namespace (which will become very 
important when we start creating cross product files)
10/18/2007    17:58:02 PM    from Tanya Berardini to All Participants:
	ok
10/18/2007    17:58:03 PM    from Tanya Berardini to All Participants:
	ok
10/18/2007    17:58:03 PM    from Tanya Berardini to All Participants:
	ok
10/18/2007    17:58:06 PM    from Tanya Berardini to All Participants:
	v. useful
10/18/2007    17:58:08 PM    from John Day-Richter to All Participants:
	and other cool stuff.
10/18/2007    17:58:09 PM    from Tanya Berardini to All Participants:
	:)
10/18/2007    17:58:11 PM    from Jen Deegan to All Participants:
I found the link thing much more intuitive after reading the developer 
docs on the wiki. I could post the url.
10/18/2007    17:58:39 PM    from Tanya Berardini to All Participants:
	Maybe it should go in the users (user's -didn't we have this 
discussion?) guide as well.
10/18/2007    17:58:40 PM    from John Day-Richter to All Participants:
	Another idea:
10/18/2007    17:58:57 PM    from John Day-Richter to All Participants:
	What if we add context-dependent help to each component?
10/18/2007    17:59:12 PM    from Tanya Berardini to All Participants:
	That would be cool.
10/18/2007    17:59:15 PM    from Jen Deegan to All Participants:
that would be good
10/18/2007    17:59:17 PM    from Midori Harris to All Participants:
wow
10/18/2007    17:59:26 PM    from Tanya Berardini to All Participants:
	Cause who wants to read the manual anyway?
10/18/2007    17:59:28 PM    from John Day-Richter to All Participants:
	Like we add a little question mark next to the little black 
icons at the top of each component. When you click the question mark it 
goes right to the relevant documentation page.
10/18/2007    17:59:38 PM    from Tanya Berardini to All Participants:
	Yup, yup, yup.
10/18/2007    18:00:03 PM    from Tanya Berardini to All Participants:
	Might get a little glyph ridden but might not.
10/18/2007    18:00:32 PM    from Tanya Berardini to All Participants:
	Argh.  Got to run to next meeting.  Will catch up with 
transcript.
10/18/2007    18:00:36 PM    from John Day-Richter to All Participants:
	There's a lot of room for extra glyphs right now, and a question 
mark would have the advantage of being immediately comprehensible.
10/18/2007    18:00:40 PM    from John Day-Richter to All Participants:
	Bye Tanya.
10/18/2007    18:00:41 PM    from Tanya Berardini to All Participants:
	Bye
10/18/2007    18:00:44 PM    from Midori Harris to All Participants:
The question mark is widely recognized, tho, so won't add too much 
clutter.
10/18/2007    18:00:45 PM    from Midori Harris to All Participants:
bye!
10/18/2007    18:01:12 PM    from John Day-Richter to All Participants:
	I had another bug report question, hold on...
10/18/2007    18:01:47 PM    from Midori Harris to All Participants:
(I was just saying goodbye to tanya, not leaving)
10/18/2007    18:01:48 PM    from John Day-Richter to All Participants:
	Oh, never mind. The bug I was looking at was one we discussed at 
office hours.
10/18/2007    18:02:37 PM    from John Day-Richter to All Participants:
	Okay, last issue I wanted to talk about:
10/18/2007    18:02:52 PM    from John Day-Richter to All Participants:
	I want to kill the GraphViz component and not resurrect it.
10/18/2007    18:03:02 PM    from John Day-Richter to All Participants:
	It's too much work to port over, IMHO.
10/18/2007    18:03:25 PM    from Midori Harris to All Participants:
I'll miss it, but you've explained why it oughta go and I can't really 
argue.
10/18/2007    18:03:34 PM    from Jen Deegan to All Participants:
I think if we could save pics of the graph dag view it would probably be 
fine
10/18/2007    18:03:50 PM    from John Day-Richter to All Participants:
	But a dedicated coder could easily port it as a plugin. I 
suspect that Jen could do it if she had copious free time.
10/18/2007    18:04:04 PM    from Jen Deegan to All Participants:
I think you may be over estimating my skills
10/18/2007    18:04:15 PM    from Jen Deegan to All Participants:
or my free time
10/18/2007    18:04:20 PM    from Jen Deegan to All Participants:
:-)
10/18/2007    18:04:26 PM    from John Day-Richter to All Participants:
	Ah, I take the second point.
10/18/2007    18:04:35 PM    from Jen Deegan to All Participants:
ta :-)
10/18/2007    18:04:44 PM    from Jen Deegan to All Participants:
I think the graph dag viewer will do it
10/18/2007    18:04:48 PM    from John Day-Richter to All Participants:
	Anyway, the need for this thing should be significantly reduced 
when I add rendering the the graph viewer.
10/18/2007    18:04:57 PM    from Jen Deegan to All Participants:
once we get the nack of it
10/18/2007    18:05:01 PM    from Jen Deegan to All Participants:
what'sthat
10/18/2007    18:05:09 PM    from John Day-Richter to All Participants:
	?
10/18/2007    18:05:16 PM    from Jen Deegan to All Participants:
what's rendering the graph viewr
10/18/2007    18:05:41 PM    from Jen Deegan to All Participants:
you mean colouring bits?
10/18/2007    18:05:55 PM    from Jen Deegan to All Participants:
john got kicked out
10/18/2007    18:06:02 PM    from Jen Deegan to All Participants:
he says he'll be back
10/18/2007    18:06:36 PM    from John Day-Richter to All Participants:
	As I was saying before the crash - the graph editor will allow 
renderers. They're actually pretty easy to add, I just haven't gotten 
around to it.
10/18/2007    18:06:53 PM    from Jen Deegan to All Participants:
so colouring terms?
10/18/2007    18:07:09 PM    from John Day-Richter to All Participants:
	Coloring terms, backgrounds, maybe even controlling the box 
shape.
10/18/2007    18:07:15 PM    from Jen Deegan to All Participants:
cool!
10/18/2007    18:07:30 PM    from Jen Deegan to All Participants:
and saving the picture to a file
10/18/2007    18:07:35 PM    from John Day-Richter to All Participants:
	Also, I don't know if anyone noticed, but if you right click in 
the graph editor, there's a "Save as SVG" option at the bottom of the 
right click menu.
10/18/2007    18:07:43 PM    from Jen Deegan to All Participants:
great!
10/18/2007    18:08:04 PM    from Jen Deegan to All Participants:
will this apply tot he graph dag viewer too?
10/18/2007    18:08:09 PM    from John Day-Richter to All Participants:
	I'll add the file formats we really want in the next release - 
that was kind of an experiment.
10/18/2007    18:08:25 PM    from John Day-Richter to All Participants:
	Yeah - there will be rendering/image saving in the graph dag 
viewer too.
10/18/2007    18:08:31 PM    from Jen Deegan to All Participants:
excellent!
10/18/2007    18:08:42 PM    from Jen Deegan to All Participants:
in that case we should be fine without the graphviz plugin
10/18/2007    18:09:29 PM    from John Day-Richter to All Participants:
	Anyone else have anything they want to talk about?
10/18/2007    18:10:06 PM    from Jen Deegan to All Participants:
I guess if we have done a load of bug testing we just wait for you to 
get to our bug reports?
10/18/2007    18:10:16 PM    from Jen Deegan to All Participants:
no sense producng more yet?
10/18/2007    18:10:40 PM    from Midori Harris to All Participants:
When's the next release out? If it's just a day or two, I'll wait for it 
before doing more testing.
10/18/2007    18:10:59 PM    from John Day-Richter to All Participants:
	Well, the more bugs I know about the better, since we want fast 
turnaround times. But I hope to have a release out by Friday night.
10/18/2007    18:11:22 PM    from Midori Harris to All Participants:
I'll wait, then, because I'm taking tomorrow afternoon off.
10/18/2007    18:11:25 PM    from John Day-Richter to All Participants:
	So don't waste too much time bug testing if you've got lots of 
bug reports out on your current testing area.
10/18/2007    18:11:26 PM    from Jen Deegan to All Participants:
Actually I can try the various graph things witht he reasonder on so 
I'll do that
10/18/2007    18:11:39 PM    from Midori Harris to All Participants:
back in the saddle on monday
10/18/2007    18:11:50 PM    from John Day-Richter to All Participants:
	That's a good idea. The reasoner is an essential part of 
OBO-Edit 2. I really want it on most of the time
10/18/2007    18:12:02 PM    from hurdle to All Participants:
hi everyone; betterr late then never I guess
10/18/2007    18:12:07 PM    from Jen Deegan to All Participants:
how do we describe reasoner bugs?
10/18/2007    18:12:19 PM    from Jen Deegan to All Participants:
if it just makes things slow do we say that?
10/18/2007    18:12:44 PM    from John Day-Richter to All Participants:
	You probably won't know you're looking at a reasoner bug most of 
the time, but if you just notice worse performance in general, report 
that.
10/18/2007    18:12:54 PM    from John Day-Richter to All Participants:
	It would help if you could talk about what form the bad 
performance took.
10/18/2007    18:12:55 PM    from Jen Deegan to All Participants:
ok 
10/18/2007    18:13:01 PM    from Jen Deegan to All Participants:
sure
10/18/2007    18:13:06 PM    from Jen Deegan to All Participants:
I will time things
10/18/2007    18:13:21 PM    from John Day-Richter to All Participants:
	If you're running into problems like that, also see what happens 
if you turn off other applications on your machine.
10/18/2007    18:13:25 PM    from hurdle to All Participants:
I've noticed that in using it OE for just searches, it appears to get 
slower and slower and I do more and more searches
10/18/2007    18:13:49 PM    from Jen Deegan to All Participants:
sometime the form is that the music I'm listening to on my machine skips 
bits when I run the reasoner:-)
10/18/2007    18:13:56 PM    from Chris Mungall to All Participants:
Jen: if you describe the sequence of operations, we can make a benchmark 
specifically for that
10/18/2007    18:14:03 PM    from Jen Deegan to All Participants:
ok :-)
10/18/2007    18:14:07 PM    from hurdle to All Participants:
IF I  the n close and restart, it is ok again.
10/18/2007    18:14:23 PM    from John Day-Richter to All Participants:
	And if you can't get a consistent script, it means that your 
machine memory is just maxed out.
10/18/2007    18:14:43 PM    from John Day-Richter to All Participants:
	The only recourse is to shut down big memory hog applications 
like, say, iTunes or something.
10/18/2007    18:15:07 PM    from Jen Deegan to All Participants:
what's a consistent script?
10/18/2007    18:15:44 PM    from John Day-Richter to All Participants:
	You know - 1) open gene_ontology_edit.obo 2) copy 
cellular_component to molecular_function 3) notice blue screen
10/18/2007    18:16:07 PM    from Jen Deegan to All Participants:
oh I see
10/18/2007    18:16:22 PM    from Jen Deegan to All Participants:
the thing is I never usuall have other things running
10/18/2007    18:16:32 PM    from Jen Deegan to All Participants:
so there's not anything I can shut down
10/18/2007    18:16:37 PM    from John Day-Richter to All Participants:
	Zounds!
10/18/2007    18:16:48 PM    from Jen Deegan to All Participants:
I need webex and skype
10/18/2007    18:16:50 PM    from John Day-Richter to All Participants:
	Hopefully the new reasoner prototype will do a little better for 
you.
10/18/2007    18:16:51 PM    from Jen Deegan to All Participants:
so they are on
10/18/2007    18:17:01 PM    from Jen Deegan to All Participants:
but that's it
10/18/2007    18:18:01 PM    from John Day-Richter to All Participants:
	Now I'm anxious to get this new release out to see how the 
reasoner behaves for people.
10/18/2007    18:18:05 PM    from Midori Harris to All Participants:
some browsers can eat memory, especially if they've been running for a 
while
10/18/2007    18:18:33 PM    from John Day-Richter to All Participants:
	Harold - how many searches do you have to do before you notice 
the slowdown?
10/18/2007    18:18:40 PM    from John Day-Richter to All Participants:
	And has anyone else seen this?
10/18/2007    18:19:10 PM    from Jen Deegan to All Participants:
I rarely use it as it is very slow
10/18/2007    18:19:11 PM    from hurdle to All Participants:
oh, about I'd say 10-15; I use it for searching for terms to annotate
10/18/2007    18:19:19 PM    from Midori Harris to All Participants:
I have ... it's one aspect of the general "things don't work" that we 
talked about yesterday.
10/18/2007    18:19:37 PM    from Jen Deegan to All Participants:
oddly, on my mac I can work with the reasoner just fine
10/18/2007    18:19:44 PM    from Jen Deegan to All Participants:
it's the windows machine that struggles
10/18/2007    18:19:46 PM    from Midori Harris to All Participants:
For me it's pretty variable, possibly because I've been doing varying 
numbers of other things besides searches.
10/18/2007    18:20:03 PM    from John Day-Richter to All Participants:
	So, just to be clear, the bug is "searches grow progressively 
slower when the reasoner is on?"
10/18/2007    18:20:25 PM    from hurdle to All Participants:
Not sure; will have to check but if the reasoner is on by default, yes
10/18/2007    18:20:30 PM    from Midori Harris to All Participants:
for me , yes.
10/18/2007    18:20:42 PM    from Erika to All Participants:
	for me 
too!
10/18/2007    18:20:46 PM    from John Day-Richter to All Participants:
	Ah, so the bug is "searches grow progressively slower always"
10/18/2007    18:20:59 PM    from Jen Deegan to All Participants:
for me it's just that when I look for redundant links things get slow
10/18/2007    18:21:02 PM    from hurdle to All Participants:
so it would seem
10/18/2007    18:21:15 PM    from hurdle to All Participants:
but that "redundant " thing now has me wondering
10/18/2007    18:21:26 PM    from Jen Deegan to All Participants:
that's the only time I use the reasoner
10/18/2007    18:21:27 PM    from Midori Harris to All Participants:
hmmm, I haven't done much with the reasoner off ... so can't shed light
10/18/2007    18:21:56 PM    from John Day-Richter to All Participants:
	Is the affect more pronounced when your searches return lots of 
results?
10/18/2007    18:22:08 PM    from Jen Deegan to All Participants:
is information from 1.101 pertinent as well as 2?
10/18/2007    18:22:20 PM    from John Day-Richter to All Participants:
	No, 2 does things totally differently.
10/18/2007    18:22:24 PM    from Jen Deegan to All Participants:
oh
10/18/2007    18:22:28 PM    from Jen Deegan to All Participants:
I have only tried 1.101
10/18/2007    18:22:29 PM    from Midori Harris to All Participants:
yes! (to John's question)
10/18/2007    18:22:30 PM    from hurdle to All Participants:
Will elaborate: the searches I most do is to s set where I load6 
ontologies, including the GO, MA, EC, CE, EMAP, and one of my own (ATTC 
lines)
10/18/2007    18:22:38 PM    from hurdle to All Participants:
I don't havethe probelm in 1.101
10/18/2007    18:22:59 PM    from John Day-Richter to All Participants:
	Hmm... I'm going to run and look something up quickly. I'll be 
right back -
10/18/2007    18:23:26 PM    from hurdle to All Participants:
sorry about the typing; something is not quite write with my keyboard 
skin today
10/18/2007    18:23:31 PM    from hurdle to All Participants:
right
10/18/2007    18:23:37 PM    from hurdle to All Participants:
or my breain
10/18/2007    18:23:40 PM    from hurdle to All Participants:
brain
10/18/2007    18:24:50 PM    from John Day-Richter to All Participants:
	Aha!
10/18/2007    18:25:09 PM    from John Day-Richter to All Participants:
	I see evidence that OBO-Edit might be thoughtfully caching the 
results of every single query.
10/18/2007    18:25:20 PM    from hurdle to All Participants:
ahh
10/18/2007    18:25:23 PM    from Jen Deegan to All Participants:
that is very thoughtful
10/18/2007    18:25:37 PM    from John Day-Richter to All Participants:
	Especially if the thought is "let's uselessly waste memory".
10/18/2007    18:25:56 PM    from John Day-Richter to All Participants:
	I'll do some more experiments to confirm this, but turning this 
off might be the solution.
10/18/2007    18:27:42 PM    from John Day-Richter to All Participants:
	Anyway, shall we disperse?
10/18/2007    18:28:03 PM    from hurdle to All Participants:
I'm melting....
10/18/2007    18:28:03 PM    from Midori Harris to All Participants:
and ride off into the sunset?
10/18/2007    18:28:52 PM    from John Day-Richter to All Participants:
	Farewell my little corn flowers, I got other towns to save.
10/18/2007    18:28:57 PM    from John Day-Richter to All Participants:
	See you at office hours.
10/18/2007    18:29:00 PM    from Jen Deegan to All Participants:
byeeeeee
10/18/2007    18:29:01 PM    from hurdle to All Participants:
happy trails
10/18/2007    18:29:06 PM    from Erika to All Participants:
	Thanks 
John!
10/18/2007    18:29:12 PM    from Erika to All Participants:
	Bye all!

10/18/2007    18:29:13 PM    from Midori Harris to All Participants:
bum-ba-dee-da ...
10/18/2007    18:29:23 PM    from John Day-Richter to All Participants:
	Can a non-crashed participant distribute the minutes?
10/18/2007    18:29:35 PM    from Midori Harris to All Participants:
ok
10/18/2007    18:29:40 PM    from John Day-Richter to All Participants:
	Bye all.
10/18/2007    18:29:42 PM    from melissaH to All Participants:
bye!
10/18/2007    18:29:50 PM    from Midori Harris to All Participants:
bye