The printable version is no longer supported and may have rendering errors. Please update your browser bookmarks and please use the default browser print function instead.
05/27/2008 09:32:07 AM from midori: made it!
05/27/2008 09:32:14 AM from Nomi Harris: Yay!
05/27/2008 09:32:17 AM from Nomi Harris: Sorry about that.
05/27/2008 09:32:43 AM from Nomi Harris: Hi, Amina!
05/27/2008 09:32:47 AM from midori: hi
05/27/2008 09:33:03 AM from Amina: hi Nomi and Midori
05/27/2008 09:34:22 AM from Nomi Harris: Hi Alex
05/27/2008 09:34:53 AM from Alexander Diehl: Hi Nomi, I'll be mostly lurking, I'm afraid.
05/27/2008 09:34:59 AM from Amina: hi Ed and Alex
05/27/2008 09:34:59 AM from Nomi Harris: No problem.
05/27/2008 09:35:00 AM from Ed: Morning.
05/27/2008 09:35:01 AM from Nomi Harris: Hi Ed.
05/27/2008 09:35:15 AM from Nomi Harris: midori, do you know if Jen is coming?
05/27/2008 09:35:52 AM from midori: Not user, but I don't know of any reason why she wouldn't.
05/27/2008 09:35:59 AM from midori: er, "not sure" ...
05/27/2008 09:36:22 AM from Nomi Harris: We'll give her another minute
05/27/2008 09:38:18 AM from Nomi Harris: Ok, let's just start.
05/27/2008 09:38:19 AM from Alexander Diehl: Do people ever notice differences between the two built in reasoners. The newer one hangs in a loop for me.
05/27/2008 09:38:22 AM from Alexander Diehl: ?
05/27/2008 09:38:26 AM from Nomi Harris: The newer one is a lot slower.
05/27/2008 09:38:34 AM from midori: I haven't done much with either reasoner lately ...
05/27/2008 09:38:42 AM from Nomi Harris: John revealed the probable reason for that in a discussion last week:
05/27/2008 09:38:47 AM from Nomi Harris: the old one didn't actually work.
05/27/2008 09:38:51 AM from Alexander Diehl: It completes then OBO-Edit keeps running the processor full out.
05/27/2008 09:38:56 AM from Jen Deegan: sorry I'm late
05/27/2008 09:39:05 AM from Nomi Harris: Hi Jen!
05/27/2008 09:39:09 AM from Jen Deegan: Hi!
05/27/2008 09:39:26 AM from Alexander Diehl: The program becomes unresponsive.
05/27/2008 09:39:28 AM from Nomi Harris: Alex, the new one does often make my computer thrash, although it does complete if you have a small ontology.
05/27/2008 09:39:29 AM from Amina: Hi Jen
05/27/2008 09:39:39 AM from Jen Deegan: Hi Amina!
05/27/2008 09:39:45 AM from Nomi Harris: We know the reasoner is problematic and it's definitely high on the list to fix.
05/27/2008 09:39:51 AM from Alexander Diehl: I'm using a subset of the SO, with a limited number of terms.
05/27/2008 09:39:56 AM from Nomi Harris: However, it's not going to be a simple bug fix.
05/27/2008 09:40:07 AM from Nomi Harris: Really, a subset of the SO and it's not returning? That's odd. Can you send me the file?
05/27/2008 09:40:15 AM from Amina: Alex could you please post a bug report with details of what you were doing and the name of the dataset
05/27/2008 09:40:32 AM from Amina: o ok
05/27/2008 09:40:42 AM from Nomi Harris: Please send me and Amina the actual dataset. Often people post the name of the dataset but I'm not sure where to get one
05/27/2008 09:40:49 AM from Nomi Harris: or whether it's the same as the one they used.
05/27/2008 09:41:11 AM from Alexander Diehl: sure
05/27/2008 09:41:26 AM from Nomi Harris: Was this with b39?
05/27/2008 09:41:29 AM from Alexander Diehl: yes
05/27/2008 09:41:47 AM from Nomi Harris: midori, did you try b39? I was wondering if you liked the new menus.
05/27/2008 09:42:09 AM from midori: Downloaded and installed just minutes ago ... hang on, I'll fire it up.
05/27/2008 09:42:37 AM from Nomi Harris: When you guys get a chance, can you try the Text Editor and see if you see Erika's bug (can't commit changes)?
05/27/2008 09:42:41 AM from Nomi Harris: I haven't been able to reproduce it.
05/27/2008 09:42:53 AM from midori: I could swear the text editor worked in b38 ...
05/27/2008 09:43:09 AM from Jen Deegan: is that witht he commit button or autocommit?
05/27/2008 09:43:16 AM from Nomi Harris: Commit button.
05/27/2008 09:43:20 AM from midori: works with commit button for me
05/27/2008 09:43:23 AM from Nomi Harris: Me too.
05/27/2008 09:43:40 AM from midori: (b38, that is; waiting for b39 to start up)
05/27/2008 09:43:49 AM from Nomi Harris: I'll suggest that she wipe her config directory and try again.
05/27/2008 09:44:00 AM from Nomi Harris: (BTW, there is now a button to let you do that from the Config Manager)
05/27/2008 09:44:14 AM from Nomi Harris: Does it really take that long to start up, midori?
05/27/2008 09:44:39 AM from Jen Deegan: commit works for me.
05/27/2008 09:45:22 AM from midori: did this time; might be the other stuff I have running, since it was slower than usual. I'l lsquawk if it persists in taking so long.
05/27/2008 09:45:40 AM from Nomi Harris: For me, the startup time has not changed.
05/27/2008 09:45:53 AM from Nomi Harris: Are you running any Office programs? Those make everything slow down on my mac.
05/27/2008 09:46:01 AM from Nomi Harris: (Word, Powerpoint, Excel)
05/27/2008 09:46:02 AM from Alexander Diehl: Startup time seems normal to me.
05/27/2008 09:46:02 AM from midori: text editor working fine with commit button
05/27/2008 09:46:13 AM from Nomi Harris: Good. So Erika must have just gotten in some weird state.
05/27/2008 09:46:31 AM from midori: i don't even have any MS software on this machine :)
05/27/2008 09:46:31 AM from Jen Deegan: is she on linux?
05/27/2008 09:47:09 AM from midori: but I have got two web browsers, gnucash, four terminal windows ... too much infor mation!
05/27/2008 09:47:18 AM from Nomi Harris: Yes, she's on linux.
05/27/2008 09:47:29 AM from Nomi Harris: (Erika, that is.)
05/27/2008 09:47:32 AM from Jen Deegan: is anybody able to test on linux?
05/27/2008 09:47:45 AM from Jen Deegan: I don't have a linux setup just now
05/27/2008 09:47:54 AM from Nomi Harris: Amina has linux.
05/27/2008 09:47:59 AM from Jen Deegan: great
05/27/2008 09:48:33 AM from Amina: I'm on the mac right now so i cant demo
05/27/2008 09:48:39 AM from midori: just quit & restarted b39 ... second startup at least as fast as ever
05/27/2008 09:48:41 AM from Alexander Diehl: (BTW, reasoning over the full SO with new reasoner and it doesn't get past 1% at all. The Computer is running full out with fans blowing, one processor maxed. It could be the SO itself, of course) )
05/27/2008 09:48:41 AM from Amina: but it works for me
05/27/2008 09:48:44 AM from Nomi Harris: Amina couldn't run WebEx on linux.
05/27/2008 09:49:03 AM from Nomi Harris: Alex, I'm pretty sure I've successfully reasoned over SO. I'll look into it.
05/27/2008 09:49:07 AM from Nomi Harris: Maybe you need more memory.
05/27/2008 09:49:25 AM from Alexander Diehl: I am getting older, it's true.
05/27/2008 09:49:32 AM from Nomi Harris: :-)
05/27/2008 09:49:34 AM from Alexander Diehl: (@ GB)
05/27/2008 09:49:37 AM from Nomi Harris: Hey, speaking of memory,
05/27/2008 09:49:41 AM from Amina: I tried so some test cases with the SO file.. new reasoner works for me
05/27/2008 09:49:41 AM from Alexander Diehl: (2 GB)
05/27/2008 09:49:44 AM from midori: what were we talking about ?? ;)
05/27/2008 09:49:54 AM from Nomi Harris: have others noticed that the OBO flat file loader is not remembering what you loaded last?
05/27/2008 09:50:07 AM from Nomi Harris: At some point, that stopped working for me.
05/27/2008 09:50:14 AM from Jen Deegan: mine is
05/27/2008 09:50:19 AM from midori: it just did remember for me, between my two b39 starts
05/27/2008 09:50:25 AM from Nomi Harris: So yours offers you the path of the last file you loaded?
05/27/2008 09:50:39 AM from midori: yup
05/27/2008 09:50:42 AM from Jen Deegan: yes
05/27/2008 09:50:43 AM from Alexander Diehl: I think mine is remembering.
05/27/2008 09:50:47 AM from Nomi Harris: Hmm. I wonder why it's not with me.
05/27/2008 09:51:05 AM from Nomi Harris: Guess I need to remove my oboeditbeta again
05/27/2008 09:51:05 AM from midori: at long last, one of the special personalized bugs has bit you!
05/27/2008 09:51:17 AM from Nomi Harris: Oh, I get plenty of personalized bugs!
05/27/2008 09:51:24 AM from Nomi Harris: I'm special, too!
05/27/2008 09:51:31 AM from Jen Deegan: Congratulations!
05/27/2008 09:51:49 AM from Amina: alex I'll test the new reasoner with the SO dataset again... 2GB should be sufficient
05/27/2008 09:51:55 AM from Nomi Harris: By the way, "oboeditbeta" is no longer .oboeditbeta. It's now in a different place on different operating systems.
05/27/2008 09:52:16 AM from Nomi Harris: I have mixed feelings about this, but it was the consensus decision.
05/27/2008 09:52:18 AM from Jen Deegan: Yes that is working fine for me
05/27/2008 09:52:28 AM from Nomi Harris: Did it offer to copy over your old .oboeditbeta files?
05/27/2008 09:52:33 AM from Jen Deegan: yes
05/27/2008 09:52:38 AM from Jen Deegan: even in eclipse
05/27/2008 09:52:40 AM from midori: So + new reasoner made it to 53% quickly for me, but has been stucj there for a couple minutes (and counting)
05/27/2008 09:52:52 AM from Alexander Diehl: I copied the .oboeditbeta preference when the program asked about it, can I trash the .oboeditbeta directory now?
05/27/2008 09:53:01 AM from Nomi Harris: Yes
05/27/2008 09:53:16 AM from Nomi Harris: In fact, that's a good idea, so you don't accidentally get confused and look at the old config files there
05/27/2008 09:53:24 AM from Nomi Harris: when they are no longer being used by OE.
05/27/2008 09:53:32 AM from Alexander Diehl: (I had to force quit OE to get back good responsiveness -- never got past 1%)
05/27/2008 09:53:47 AM from Nomi Harris: That's not so good.
05/27/2008 09:53:53 AM from Nomi Harris: We'll investigate.
05/27/2008 09:54:17 AM from Nomi Harris: Maybe at some point Ed can take a look at the reasoner.
05/27/2008 09:54:17 AM from Amina: yes this is reasoner bug week!
05/27/2008 09:54:28 AM from Alexander Diehl: I'll send the files I'm using. I just downloaded SO last week again, but could also try a new copy.
05/27/2008 09:54:40 AM from midori: still 53% ...
05/27/2008 09:54:51 AM from Nomi Harris: I'd also try quitting some of your other applications that use a lot of memory
05/27/2008 09:54:59 AM from midori: (not the most up-to-date SO ...)
05/27/2008 09:55:11 AM from Nomi Harris: such as web browsers, Eclipse, any drawing programs (Photoshop, etc)
05/27/2008 09:55:57 AM from Alexander Diehl: Of course, I often need to be referencing things in other programs when I am using OE, so running it by itself is not the nest solution.
05/27/2008 09:56:02 AM from Amina: my second test its stuck at 3%
05/27/2008 09:56:04 AM from Alexander Diehl: best
05/27/2008 09:56:07 AM from Nomi Harris: Sure, I agree
05/27/2008 09:56:13 AM from Nomi Harris: We definitely need to fix the reasoner.
05/27/2008 09:56:22 AM from Nomi Harris: I'm just suggesting ways you might try right now to see if it can complete.
05/27/2008 09:56:30 AM from Amina: I'll look into it today
05/27/2008 09:56:35 AM from Ed: Yeah, I'll take a look at the reasoner. I'll also look at any memory leaks.
05/27/2008 09:56:37 AM from Alexander Diehl: Sure, I understand.
05/27/2008 09:56:42 AM from Nomi Harris: Besides the reasoner, are there other bugs that are particularly bugging you this week?
05/27/2008 09:56:46 AM from Nomi Harris: Thanks, Ed.
05/27/2008 09:57:02 AM from Nomi Harris: Did you find a good tool for finding memory leaks?
05/27/2008 09:57:36 AM from Ed: I'm thinking that for now, I'll just use the builtin Java tools for memory profiling.
05/27/2008 09:57:54 AM from Tanya Berardini: sorry I'm so very late (commuting issues)
05/27/2008 09:57:58 AM from Ed: There are some tricks you can use to help spot memory leaks, although it might not be enough (in which case I'll have to find a more rigorous tool).
05/27/2008 09:58:12 AM from Nomi Harris: That's ok, Tanya.
05/27/2008 09:58:21 AM from Nomi Harris: Did you try the new menus in b39?
05/27/2008 09:58:54 AM from Ed: And I figured that the fastest solution once I locate the memory issues is to use weak references.
05/27/2008 09:58:55 AM from Tanya Berardini: no
05/27/2008 09:58:58 AM from midori: yes, just one or two. Nice.
05/27/2008 09:59:00 AM from Tanya Berardini: just downloaded the beta
05/27/2008 09:59:13 AM from Alexander Diehl: yes (to the menus)
05/27/2008 09:59:30 AM from Ed: Or soft references. I'll have to analyze if that leaked memory is really never accessed again.
05/27/2008 09:59:33 AM from Nomi Harris: Good. I like the new menus--it's nice not having to hold the mouse down so much.
05/27/2008 10:00:02 AM from Amina: sounds good Ed let me know if I can help
05/27/2008 10:00:16 AM from Nomi Harris: Anything else to discuss today?
05/27/2008 10:00:33 AM from Amina: I had some questions for David -
05/27/2008 10:00:42 AM from Amina: I couldnt reproduce his reasoner bugs
05/27/2008 10:00:43 AM from Nomi Harris: David's not here, though.
05/27/2008 10:00:55 AM from Nomi Harris: I couldn't reproduce them, either.
05/27/2008 10:00:57 AM from Nomi Harris: He might be out of town.
05/27/2008 10:00:59 AM from Jen Deegan: If anybody wants to have a shot of the obomerge feature I'd be keen to hear bug reports.
05/27/2008 10:01:06 AM from Amina: yeah.. I was wondering if anyone else could
05/27/2008 10:01:29 AM from Alexander Diehl: By the way, at the NIAID Cell Ontology workshop two weeks ago, people really loved the OBO_Edit graph editor display.
05/27/2008 10:01:44 AM from Nomi Harris: Buggy though it is?
05/27/2008 10:02:10 AM from Jen Deegan: Colin Batchelor at the RSc was also enthusing to me about it.
05/27/2008 10:02:21 AM from Alexander Diehl: We didn't hit any bugs, but we were not editing with the graph editor, just displaying terms with it.
05/27/2008 10:03:06 AM from Jen Deegan: Colin is also keen on the image plugin that Alex reminded us of the other week
05/27/2008 10:03:19 AM from Jen Deegan: for displaying chemical structures
05/27/2008 10:03:28 AM from Nomi Harris: Is there any reason not to just add the image plugin to the standard distribution?
05/27/2008 10:03:36 AM from Nomi Harris: Why did John make it a plugin and not just part of OE2?
05/27/2008 10:03:45 AM from Alexander Diehl: I use all the time for that myself. And I set one of the other attendee up with the image plugin too.
05/27/2008 10:03:52 AM from Jen Deegan: I think it would be good to add it
05/27/2008 10:04:19 AM from Nomi Harris: I think I'll do that for the next release.
05/27/2008 10:04:27 AM from Alexander Diehl: I think John didn't want it to slow down the release of OE2 -- but that is a moot point now.
05/27/2008 10:04:30 AM from Nomi Harris: We should get some images to include with it, to show what it does.
05/27/2008 10:04:30 AM from midori: Nomi - I think it's just that it was experimental, not that it couldn't or shouldn't eventually become a component.
05/27/2008 10:04:44 AM from Nomi Harris: Well, it probably has bugs, but so do other useful components.
05/27/2008 10:04:55 AM from Alexander Diehl: I haven't seen a bug yet.
05/27/2008 10:04:57 AM from Nomi Harris: Do you guys have some good term images I could include?
05/27/2008 10:04:58 AM from Jen Deegan: it comes with two images I think
05/27/2008 10:05:03 AM from midori: if it's included, we might remember to test it ...
05/27/2008 10:05:15 AM from Jen Deegan: I haven't seen any bugs
05/27/2008 10:05:20 AM from Nomi Harris: I'll include it in the next release.
05/27/2008 10:05:29 AM from Nomi Harris: By the way, I'll be away the week of June 14.
05/27/2008 10:05:29 AM from Alexander Diehl: Great
05/27/2008 10:05:32 AM from Jen Deegan: great :-)
05/27/2008 10:05:48 AM from Alexander Diehl: (great to the image plugin)
05/27/2008 10:05:58 AM from Nomi Harris: Ah. I was wondering why it was great that I would be away. :-)
05/27/2008 10:06:05 AM from Jen Deegan: I think the instructions are on the wiki but not the help guide
05/27/2008 10:06:21 AM from Jen Deegan: I'll just look for them
05/27/2008 10:06:24 AM from Nomi Harris: The instructions are for installing the plugin.
05/27/2008 10:06:40 AM from Nomi Harris: They won't be necessary when I include it with the distribution.
05/27/2008 10:06:50 AM from Nomi Harris: We'll need a help page for the image plugin.
05/27/2008 10:06:54 AM from Jen Deegan: http://wiki.geneontology.org/index.php/OBO-Edit:_Installing_the_Term_Image_Plugin
05/27/2008 10:07:03 AM from Nomi Harris: Speaking of which, some of the component help pages are pretty minimal, e.g. the one for the Graph Editor
05/27/2008 10:07:04 AM from Jen Deegan: that's what I mean
05/27/2008 10:07:27 AM from Jen Deegan: we need to do a blitz when people have time
05/27/2008 10:07:37 AM from Jen Deegan: we take a topic each until they are all done
05/27/2008 10:07:52 AM from Nomi Harris: I did some work on the help pages last week, but need to do more.
05/27/2008 10:08:08 AM from Jen Deegan: the image plugin instructions on the wiki I meant are the ones about how to add images
05/27/2008 10:08:09 AM from Nomi Harris: Do you forsee a time coming up when you might be able to spend some time working on them?
05/27/2008 10:08:37 AM from Jen Deegan: my priorities can be changed :-)
05/27/2008 10:08:46 AM from Jen Deegan: Midori what do you think?
05/27/2008 10:08:55 AM from midori: july and august don't look too bad for me
05/27/2008 10:09:04 AM from Jen Deegan: me neither
05/27/2008 10:09:25 AM from Nomi Harris: But June is bad?
05/27/2008 10:09:54 AM from Jen Deegan: June is not awful for me either
05/27/2008 10:10:25 AM from Nomi Harris: If you decide to do extensive work on any help pages, just email the group to alert them so no one else works on those pages.
05/27/2008 10:10:38 AM from midori: june is getting full ... I have to work on the protease activity terms, which fills me with dread. But ifhat goes better than I expect, the end of June may become available.
05/27/2008 10:10:42 AM from Jen Deegan: I think it would be best if the whole group was mobilized about the same time
05/27/2008 10:10:54 AM from Jen Deegan: that is how we did it last time and it worked well
05/27/2008 10:11:03 AM from Jen Deegan: if we leave it to people to find time things will nto happen
05/27/2008 10:11:05 AM from Nomi Harris: Possibly, but I don't think that's a requirement if it's going to make it hard to find a time.
05/27/2008 10:11:12 AM from Jen Deegan: true
05/27/2008 10:11:23 AM from Nomi Harris: So should we just designate a "help write documentation" week?
05/27/2008 10:11:30 AM from Jen Deegan: yes
05/27/2008 10:11:35 AM from Jen Deegan: then we will find loads of bugs too
05/27/2008 10:11:46 AM from Nomi Harris: Week of June 30th?
05/27/2008 10:11:51 AM from Jen Deegan: fine by me
05/27/2008 10:11:57 AM from midori: We can do more documentation weeks if not enough people make the first one to get it all done.
05/27/2008 10:12:03 AM from Nomi Harris: Although that Fri is the 4th of July
05/27/2008 10:12:07 AM from Nomi Harris: which is of course a big holiday in the US
05/27/2008 10:12:09 AM from midori: week of June 30th probably OK for me ...
05/27/2008 10:12:11 AM from Tanya Berardini: (I'm off that week, sorry)
05/27/2008 10:12:17 AM from Jen Deegan: we could do the previous week?
05/27/2008 10:12:26 AM from Nomi Harris: Does that work for you, midori?
05/27/2008 10:12:32 AM from midori: less promising for me, but go ahead if it's ok for the rest
05/27/2008 10:12:32 AM from Nomi Harris: The sooner the better
05/27/2008 10:12:40 AM from Tanya Berardini: (but I'm really just a minor contributor)
05/27/2008 10:12:44 AM from midori: I'll chip in if I can,
05/27/2008 10:12:57 AM from Jen Deegan: is the week of the 30th better then?
05/27/2008 10:13:10 AM from Jen Deegan: I can get on to Karen and ask for a cross prodcuts demo
05/27/2008 10:13:21 AM from Jen Deegan: then I'd be able to document it
05/27/2008 10:13:38 AM from Nomi Harris: Chris wrote a powerpoint about cross products, have you seen it?
05/27/2008 10:13:40 AM from midori: for me, yes, but there's only one of me. We haven't heard from very many people yet ...
05/27/2008 10:13:51 AM from Jen Deegan: Not sure.
05/27/2008 10:13:53 AM from Jen Deegan: true
05/27/2008 10:14:01 AM from Jen Deegan: have they wandered off?
05/27/2008 10:14:06 AM from Tanya Berardini: hmmm ppt about xps?
05/27/2008 10:14:09 AM from Tanya Berardini: I don't think I've seen it.
05/27/2008 10:14:15 AM from midori: I've seen various ppts from Chris that deal with xps, so maybe
05/27/2008 10:14:15 AM from Alexander Diehl: I am moving back to the US at the end of June, which limits my availability for a while.
05/27/2008 10:14:15 AM from Jen Deegan: could you forward it?
05/27/2008 10:14:27 AM from Jen Deegan: good luck with the move
05/27/2008 10:14:28 AM from Nomi Harris: I'll forward it to you, Jen.
05/27/2008 10:14:30 AM from Tanya Berardini: or maybe it's on the GO tutorial site?
05/27/2008 10:14:30 AM from Jen Deegan: ta
05/27/2008 10:14:33 AM from Alexander Diehl: thanks
05/27/2008 10:14:36 AM from Nomi Harris: I'm not sure he wanted it distributed widely.
05/27/2008 10:14:37 AM from Tanya Berardini: can you forward to me as well, please
05/27/2008 10:14:52 AM from Nomi Harris: I'll ask Chris if it's ok.
05/27/2008 10:14:54 AM from Tanya Berardini: ok
05/27/2008 10:14:54 AM from Nomi Harris: He's not in yet today.
05/27/2008 10:14:55 AM from Jen Deegan: the main thing is to find out how oboedit2 does cross prodcuts.
05/27/2008 10:14:58 AM from Jen Deegan: I can get that from karen
05/27/2008 10:15:01 AM from midori: yes
05/27/2008 10:15:01 AM from Amina: plz fwd it to me too Nomi
05/27/2008 10:15:55 AM from Nomi Harris: Ok, anything else today?
05/27/2008 10:15:58 AM from Jen Deegan: nope
05/27/2008 10:16:11 AM from Nomi Harris: Thanks for coming, sorry about the bad WebEx meeting URL
05/27/2008 10:16:23 AM from Alexander Diehl: thanks, bye
05/27/2008 10:16:24 AM from Nomi Harris: Should we meet next week?
05/27/2008 10:16:32 AM from Jen Deegan: yes please :-)
05/27/2008 10:16:42 AM from Nomi Harris: Ok.
05/27/2008 10:16:48 AM from Nomi Harris: Bye!
05/27/2008 10:16:54 AM from Jen Deegan: bye!
05/27/2008 10:16:54 AM from Amina: bye everyone
05/27/2008 10:16:56 AM from Ed: Alrighty, see you guys next week.
05/27/2008 10:16:59 AM from midori: bye