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