https://wiki.geneontology.org/index.php?title=OE_Webex_18Oct07&feed=atom&action=historyOE Webex 18Oct07 - Revision history2024-03-29T04:54:38ZRevision history for this page on the wikiMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=OE_Webex_18Oct07&diff=52753&oldid=prevGail at 22:34, 30 June 20142014-06-30T22:34:07Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>10/18/2007 17:30:29 PM from melissaH to All Attendees:</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>10/18/2007 17:30:29 PM from melissaH to All Attendees:</div></td></tr>
</table>Gailhttps://wiki.geneontology.org/index.php?title=OE_Webex_18Oct07&diff=14649&oldid=prevMidori: New page: <pre> 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...2008-08-05T16:24:39Z<p>New page: <pre> 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...</p>
<p><b>New page</b></p><div><pre><br />
10/18/2007 17:30:29 PM from melissaH to All Attendees:<br />
Hiya,been absent from all the hullaballoo recently. wow.<br />
10/18/2007 17:31:08 PM from Midori Harris to All Attendees:<br />
indeed<br />
10/18/2007 17:33:09 PM from John Day-Richter to All Attendees:<br />
Hi, all. Sorry I'm late.<br />
10/18/2007 17:33:23 PM from Midori Harris to All Participants:<br />
hi<br />
10/18/2007 17:33:33 PM from melissaH to All Attendees:<br />
hi john!<br />
<br />
10/18/2007 17:33:42 PM from melissaH to All Participants:<br />
hi john again!<br />
10/18/2007 17:34:05 PM from John Day-Richter to All Participants:<br />
I also apologize for the lack of a new release - my evening was <br />
taken up by an evening in the emergency room with my beloved, which, <br />
luckily, turned out to be nothing.<br />
10/18/2007 17:34:13 PM from Midori Harris to All Participants:<br />
whew!<br />
10/18/2007 17:34:14 PM from Erika to All Participants:<br />
Hi John!<br />
<br />
10/18/2007 17:34:23 PM from melissaH to All Participants:<br />
oh dear!<br />
10/18/2007 17:34:54 PM from John Day-Richter to All Participants:<br />
But, on the plus side, I saw a vivid illustration of what <br />
happens when you skateboard with a beer, and then fall over onto your <br />
beer.<br />
10/18/2007 17:35:01 PM from John Day-Richter to All Participants:<br />
It's not pretty.<br />
10/18/2007 17:35:18 PM from Jen Deegan to All Participants:<br />
I guess that wasn't what happened to your wife?<br />
10/18/2007 17:35:33 PM from John Day-Richter to All Participants:<br />
Similar, but with polo ponies.<br />
10/18/2007 17:35:39 PM from Jen Deegan to All Participants:<br />
wow!<br />
10/18/2007 17:35:41 PM from Jen Deegan to All Participants:<br />
classy<br />
10/18/2007 17:35:57 PM from Midori Harris to All Participants:<br />
she skateboarded with a polo pony?<br />
10/18/2007 17:35:59 PM from melissaH to All Participants:<br />
we are going to miss you john<br />
10/18/2007 17:36:23 PM from Midori Harris to All Participants:<br />
hey! some of us are still in denial here, ok?<br />
10/18/2007 17:36:33 PM from Tanya Berardini to All Participants:<br />
hello!<br />
10/18/2007 17:36:41 PM from Tanya Berardini to All Participants:<br />
Who is in denial?<br />
10/18/2007 17:36:45 PM from John Day-Richter to All Participants:<br />
Hello, Tanya.<br />
10/18/2007 17:36:47 PM from melissaH to All Participants:<br />
oh right..... google who?<br />
10/18/2007 17:36:50 PM from Tanya Berardini to All Participants:<br />
It's not just a river in Egypt, you know.<br />
10/18/2007 17:37:00 PM from John Day-Richter to All Participants:<br />
Midori - she thinks that Golden Girls is going to come back on <br />
the air.<br />
10/18/2007 17:37:22 PM from John Day-Richter to All Participants:<br />
Anyway -<br />
10/18/2007 17:37:38 PM from Midori Harris to All Participants:<br />
I said denial, not schizophrenia ...<br />
10/18/2007 17:37:49 PM from John Day-Richter to All Participants:<br />
I'll give a brief summary of what I've gotten done this week:<br />
10/18/2007 17:38:06 PM from John Day-Richter to All Participants:<br />
OBO-Edit has been broken into 3 projects:<br />
10/18/2007 17:38:13 PM from John Day-Richter to All Participants:<br />
org.bbop<br />
10/18/2007 17:38:15 PM from John Day-Richter to All Participants:<br />
org.obo<br />
10/18/2007 17:38:17 PM from John Day-Richter to All Participants:<br />
org.oboedit<br />
10/18/2007 17:38:44 PM from John Day-Richter to All Participants:<br />
Each of which now has its own subversion repository on <br />
sourceforge.<br />
10/18/2007 17:39:10 PM from John Day-Richter to All Participants:<br />
This means that future developers can use the ontology <br />
loading/editing stuff (from org.obo) without having to load the OBO-Edit <br />
gui stuff.<br />
10/18/2007 17:39:33 PM from Midori Harris to All Participants:<br />
nice<br />
10/18/2007 17:39:42 PM from John Day-Richter to All Participants:<br />
In other news, I've been experimenting with other ways of <br />
engineering the reasoner.<br />
10/18/2007 17:39:47 PM from Midori Harris to All Participants:<br />
(tho not something I'll rush out and use)<br />
10/18/2007 17:40:25 PM from John Day-Richter to All Participants:<br />
While conducting those experiments, I tested a prototype <br />
reasoner against our tried and true reasoner, to make sure it was giving <br />
the correct answers.<br />
10/18/2007 17:40:44 PM from John Day-Richter to All Participants:<br />
I was shocked to discover that the tried-and-true reasoner was <br />
NOT giving (wholly) correct answers, and the prototype was!<br />
10/18/2007 17:41:04 PM from Tanya Berardini to All Participants:<br />
urk<br />
10/18/2007 17:41:05 PM from Midori Harris to All Participants:<br />
oh my.<br />
10/18/2007 17:41:20 PM from John Day-Richter to All Participants:<br />
It turns out that the current reasoner architecture always <br />
infers the right links, but it doesn't infer every possible explanation <br />
for those links.<br />
10/18/2007 17:41:26 PM from melissaH to All Participants:<br />
hey-suess.<br />
10/18/2007 17:41:43 PM from John Day-Richter to All Participants:<br />
This is important, because the explanations are used to do fast <br />
link deletion while the reasoner is running.<br />
10/18/2007 17:41:56 PM from John Day-Richter to All Participants:<br />
So the old reasoner may exhibit incorrect incremental link <br />
deletion.<br />
10/18/2007 17:42:41 PM from John Day-Richter to All Participants:<br />
Trouble is, the new reasoner design is slower to start up, and <br />
(initially) used more memory.<br />
10/18/2007 17:43:28 PM from Erika to All Participants:<br />
oh no! <br />
more memory! This is the time for me to buy a new machine <br />
10/18/2007 17:43:31 PM from John Day-Richter to All Participants:<br />
I mentioned this conundrum on the developer mailing lists, and <br />
Jen and Midori mentioned that OBO-Edit tends to run worse with the <br />
reasoner on as it is, with symptoms consistent with nearly-maxed-out <br />
memory conditions.<br />
10/18/2007 17:43:47 PM from John Day-Richter to All Participants:<br />
Jen was really alarmed at the idea that the reasoner would use <br />
even more memory.<br />
10/18/2007 17:44:12 PM from John Day-Richter to All Participants:<br />
Yesterday, I decided to see exactly how much more speed & memory <br />
use I could get out of the reasoner.<br />
10/18/2007 17:44:16 PM from John Day-Richter to All Participants:<br />
And there's good news!<br />
10/18/2007 17:44:19 PM from Midori Harris to All Participants:<br />
The symptoms were very different from the 1.x reasoner slowness.<br />
10/18/2007 17:44:51 PM from John Day-Richter to All Participants:<br />
The new reasoner is still slower than the old reasoner, but it's <br />
only about 3 times slower (as opposed to 10 times slower in the initial <br />
version) and it uses much LESS memory.<br />
10/18/2007 17:45:28 PM from John Day-Richter to All Participants:<br />
And you can turn on a memory save feature where it runs about <br />
30% slower still, but uses even less memory.<br />
10/18/2007 17:46:18 PM from John Day-Richter to All Participants:<br />
And realize that the slower/faster language only refers to the <br />
initial startup time of the reasoner. Once it's running, new edits are <br />
incorporated in under 1 second.<br />
10/18/2007 17:46:27 PM from John Day-Richter to All Participants:<br />
So that's the reasoner stuff.<br />
10/18/2007 17:47:23 PM from Midori Harris to All Participants:<br />
<applause><br />
10/18/2007 17:47:51 PM from John Day-Richter to All Participants:<br />
Finally, in the course of fixing a bug related to text editing <br />
dbxrefs and synonyms, I realized that the simplest, best way to deal <br />
with the problem is to tear out some old legacy stuff from OBO-Edit 1.1 <br />
and replace it entirely with shiny new bbop.org<br />
10/18/2007 17:47:55 PM from John Day-Richter to All Participants:<br />
components.<br />
10/18/2007 17:48:35 PM from John Day-Richter to All Participants:<br />
So that's taking longer than I thought.<br />
10/18/2007 17:48:38 PM from John Day-Richter to All Participants:<br />
End of summary.<br />
10/18/2007 17:49:59 PM from Midori Harris to All Participants:<br />
we seem to be speechless<br />
10/18/2007 17:50:15 PM from Tanya Berardini to All Participants:<br />
awestruck<br />
10/18/2007 17:50:33 PM from melissaH to All Participants:<br />
seeing stars<br />
10/18/2007 17:50:43 PM from John Day-Richter to All Participants:<br />
Has everyone been updating the wiki with their testing tasks?<br />
10/18/2007 17:50:49 PM from Jen Deegan to All Participants:<br />
yes<br />
10/18/2007 17:50:56 PM from Midori Harris to All Participants:<br />
I have<br />
10/18/2007 17:51:10 PM from John Day-Richter to All Participants:<br />
Jen, there was a mysterious bug report from you today...<br />
10/18/2007 17:51:13 PM from melissaH to All Participants:<br />
I am out of date... been out of town. tell me what you want me to do....<br />
<br />
10/18/2007 17:51:15 PM from Tanya Berardini to All Participants:<br />
<guilt> no </guilt><br />
10/18/2007 17:51:37 PM from John Day-Richter to All Participants:<br />
Jen - you said that the graph viewer should "show the path to <br />
root". It does that.<br />
10/18/2007 17:51:45 PM from John Day-Richter to All Participants:<br />
But only if the reasoner is on.<br />
10/18/2007 17:51:47 PM from Jen Deegan to All Participants:<br />
does it?<br />
10/18/2007 17:51:49 PM from Jen Deegan to All Participants:<br />
oh<br />
10/18/2007 17:52:02 PM from Jen Deegan to All Participants:<br />
so I should bug test with the reasoner on then<br />
10/18/2007 17:52:06 PM from Jen Deegan to All Participants:<br />
I didn't know that<br />
10/18/2007 17:52:08 PM from Jen Deegan to All Participants:<br />
thanks<br />
10/18/2007 17:52:09 PM from John Day-Richter to All Participants:<br />
I think that in the next release, I'm going to switch to the new <br />
reasoner, and turn it on by default.<br />
10/18/2007 17:52:14 PM from Midori Harris to All Participants:<br />
I have a question:<br />
10/18/2007 17:52:16 PM from Jen Deegan to All Participants:<br />
eek!<br />
10/18/2007 17:52:25 PM from Midori Harris to All Participants:<br />
(not about the reasoner directly) ...<br />
10/18/2007 17:52:26 PM from John Day-Richter to All Participants:<br />
In a perfect world, "no reasoner" mode won't even be available <br />
in the OBO-Edit 2 release.<br />
10/18/2007 17:52:30 PM from John Day-Richter to All Participants:<br />
Go ahead, Midori.<br />
10/18/2007 17:52:48 PM from Midori Harris to All Participants:<br />
In the shiny new search system, how does one search for redundant <br />
relationships?<br />
10/18/2007 17:53:10 PM from John Day-Richter to All Participants:<br />
Good question!<br />
10/18/2007 17:53:23 PM from Midori Harris to All Participants:<br />
I try<br />
10/18/2007 17:53:24 PM from John Day-Richter to All Participants:<br />
That merits some thoughtful discussion.<br />
10/18/2007 17:53:44 PM from John Day-Richter to All Participants:<br />
See, everyone HATED the old "link search" options, and never <br />
used them.<br />
10/18/2007 17:53:57 PM from John Day-Richter to All Participants:<br />
But this is exactly what you need to find redundant <br />
relationships.<br />
10/18/2007 17:54:33 PM from John Day-Richter to All Participants:<br />
But, for simplicity, I don't even present a link searching <br />
component right now, so there's no way to do it.<br />
10/18/2007 17:54:38 PM from Midori Harris to All Participants:<br />
That's what I used ... in fact, it was the only thing I ever did use the <br />
link filter for.<br />
10/18/2007 17:54:58 PM from Midori Harris to All Participants:<br />
Well, at lesat I can take comfort in not feeling stupid --<br />
10/18/2007 17:55:01 PM from John Day-Richter to All Participants:<br />
So I can think of two ways of dealing with this -<br />
10/18/2007 17:55:01 PM from Jen Deegan to All Participants:<br />
I only realised how they worked from the reading the developer docs<br />
10/18/2007 17:55:08 PM from Midori Harris to All Participants:<br />
there was nothing staring me in the face.<br />
10/18/2007 17:55:39 PM from John Day-Richter to All Participants:<br />
I can add a "Link Search" option to the View -> Search menu, <br />
that presents a search control just like the one you see by default, but <br />
has link-centric options...<br />
10/18/2007 17:56:08 PM from John Day-Richter to All Participants:<br />
Or I can leave things as they are, and add a "has redundant <br />
parents" search criterion to the term search panel.<br />
10/18/2007 17:56:35 PM from Midori Harris to All Participants:<br />
I still don't know whether I would ever search links for anything other <br />
than redundant relationships, so the second option would meet my present <br />
needs.<br />
10/18/2007 17:56:42 PM from John Day-Richter to All Participants:<br />
And, of course, now that I've typed that, it seems fairly <br />
obvious I should do both.<br />
10/18/2007 17:57:01 PM from Tanya Berardini to All Participants:<br />
Are there other reasons one might want to use the link search?<br />
<br />
10/18/2007 17:57:12 PM from John Day-Richter to All Participants:<br />
Absolutely. Link searches let you:<br />
10/18/2007 17:57:14 PM from Tanya Berardini to All Participants:<br />
If not, it may just be more confusing to have the first option <br />
present.<br />
10/18/2007 17:57:22 PM from John Day-Richter to All Participants:<br />
* find implied links<br />
10/18/2007 17:57:27 PM from John Day-Richter to All Participants:<br />
* find links of a certain type<br />
10/18/2007 17:57:41 PM from John Day-Richter to All Participants:<br />
* find links with certain type properties (like transitive <br />
links)<br />
10/18/2007 17:58:00 PM from John Day-Richter to All Participants:<br />
* find links in a certain namespace (which will become very <br />
important when we start creating cross product files)<br />
10/18/2007 17:58:02 PM from Tanya Berardini to All Participants:<br />
ok<br />
10/18/2007 17:58:03 PM from Tanya Berardini to All Participants:<br />
ok<br />
10/18/2007 17:58:03 PM from Tanya Berardini to All Participants:<br />
ok<br />
10/18/2007 17:58:06 PM from Tanya Berardini to All Participants:<br />
v. useful<br />
10/18/2007 17:58:08 PM from John Day-Richter to All Participants:<br />
and other cool stuff.<br />
10/18/2007 17:58:09 PM from Tanya Berardini to All Participants:<br />
:)<br />
10/18/2007 17:58:11 PM from Jen Deegan to All Participants:<br />
I found the link thing much more intuitive after reading the developer <br />
docs on the wiki. I could post the url.<br />
10/18/2007 17:58:39 PM from Tanya Berardini to All Participants:<br />
Maybe it should go in the users (user's -didn't we have this <br />
discussion?) guide as well.<br />
10/18/2007 17:58:40 PM from John Day-Richter to All Participants:<br />
Another idea:<br />
10/18/2007 17:58:57 PM from John Day-Richter to All Participants:<br />
What if we add context-dependent help to each component?<br />
10/18/2007 17:59:12 PM from Tanya Berardini to All Participants:<br />
That would be cool.<br />
10/18/2007 17:59:15 PM from Jen Deegan to All Participants:<br />
that would be good<br />
10/18/2007 17:59:17 PM from Midori Harris to All Participants:<br />
wow<br />
10/18/2007 17:59:26 PM from Tanya Berardini to All Participants:<br />
Cause who wants to read the manual anyway?<br />
10/18/2007 17:59:28 PM from John Day-Richter to All Participants:<br />
Like we add a little question mark next to the little black <br />
icons at the top of each component. When you click the question mark it <br />
goes right to the relevant documentation page.<br />
10/18/2007 17:59:38 PM from Tanya Berardini to All Participants:<br />
Yup, yup, yup.<br />
10/18/2007 18:00:03 PM from Tanya Berardini to All Participants:<br />
Might get a little glyph ridden but might not.<br />
10/18/2007 18:00:32 PM from Tanya Berardini to All Participants:<br />
Argh. Got to run to next meeting. Will catch up with <br />
transcript.<br />
10/18/2007 18:00:36 PM from John Day-Richter to All Participants:<br />
There's a lot of room for extra glyphs right now, and a question <br />
mark would have the advantage of being immediately comprehensible.<br />
10/18/2007 18:00:40 PM from John Day-Richter to All Participants:<br />
Bye Tanya.<br />
10/18/2007 18:00:41 PM from Tanya Berardini to All Participants:<br />
Bye<br />
10/18/2007 18:00:44 PM from Midori Harris to All Participants:<br />
The question mark is widely recognized, tho, so won't add too much <br />
clutter.<br />
10/18/2007 18:00:45 PM from Midori Harris to All Participants:<br />
bye!<br />
10/18/2007 18:01:12 PM from John Day-Richter to All Participants:<br />
I had another bug report question, hold on...<br />
10/18/2007 18:01:47 PM from Midori Harris to All Participants:<br />
(I was just saying goodbye to tanya, not leaving)<br />
10/18/2007 18:01:48 PM from John Day-Richter to All Participants:<br />
Oh, never mind. The bug I was looking at was one we discussed at <br />
office hours.<br />
10/18/2007 18:02:37 PM from John Day-Richter to All Participants:<br />
Okay, last issue I wanted to talk about:<br />
10/18/2007 18:02:52 PM from John Day-Richter to All Participants:<br />
I want to kill the GraphViz component and not resurrect it.<br />
10/18/2007 18:03:02 PM from John Day-Richter to All Participants:<br />
It's too much work to port over, IMHO.<br />
10/18/2007 18:03:25 PM from Midori Harris to All Participants:<br />
I'll miss it, but you've explained why it oughta go and I can't really <br />
argue.<br />
10/18/2007 18:03:34 PM from Jen Deegan to All Participants:<br />
I think if we could save pics of the graph dag view it would probably be <br />
fine<br />
10/18/2007 18:03:50 PM from John Day-Richter to All Participants:<br />
But a dedicated coder could easily port it as a plugin. I <br />
suspect that Jen could do it if she had copious free time.<br />
10/18/2007 18:04:04 PM from Jen Deegan to All Participants:<br />
I think you may be over estimating my skills<br />
10/18/2007 18:04:15 PM from Jen Deegan to All Participants:<br />
or my free time<br />
10/18/2007 18:04:20 PM from Jen Deegan to All Participants:<br />
:-)<br />
10/18/2007 18:04:26 PM from John Day-Richter to All Participants:<br />
Ah, I take the second point.<br />
10/18/2007 18:04:35 PM from Jen Deegan to All Participants:<br />
ta :-)<br />
10/18/2007 18:04:44 PM from Jen Deegan to All Participants:<br />
I think the graph dag viewer will do it<br />
10/18/2007 18:04:48 PM from John Day-Richter to All Participants:<br />
Anyway, the need for this thing should be significantly reduced <br />
when I add rendering the the graph viewer.<br />
10/18/2007 18:04:57 PM from Jen Deegan to All Participants:<br />
once we get the nack of it<br />
10/18/2007 18:05:01 PM from Jen Deegan to All Participants:<br />
what'sthat<br />
10/18/2007 18:05:09 PM from John Day-Richter to All Participants:<br />
?<br />
10/18/2007 18:05:16 PM from Jen Deegan to All Participants:<br />
what's rendering the graph viewr<br />
10/18/2007 18:05:41 PM from Jen Deegan to All Participants:<br />
you mean colouring bits?<br />
10/18/2007 18:05:55 PM from Jen Deegan to All Participants:<br />
john got kicked out<br />
10/18/2007 18:06:02 PM from Jen Deegan to All Participants:<br />
he says he'll be back<br />
10/18/2007 18:06:36 PM from John Day-Richter to All Participants:<br />
As I was saying before the crash - the graph editor will allow <br />
renderers. They're actually pretty easy to add, I just haven't gotten <br />
around to it.<br />
10/18/2007 18:06:53 PM from Jen Deegan to All Participants:<br />
so colouring terms?<br />
10/18/2007 18:07:09 PM from John Day-Richter to All Participants:<br />
Coloring terms, backgrounds, maybe even controlling the box <br />
shape.<br />
10/18/2007 18:07:15 PM from Jen Deegan to All Participants:<br />
cool!<br />
10/18/2007 18:07:30 PM from Jen Deegan to All Participants:<br />
and saving the picture to a file<br />
10/18/2007 18:07:35 PM from John Day-Richter to All Participants:<br />
Also, I don't know if anyone noticed, but if you right click in <br />
the graph editor, there's a "Save as SVG" option at the bottom of the <br />
right click menu.<br />
10/18/2007 18:07:43 PM from Jen Deegan to All Participants:<br />
great!<br />
10/18/2007 18:08:04 PM from Jen Deegan to All Participants:<br />
will this apply tot he graph dag viewer too?<br />
10/18/2007 18:08:09 PM from John Day-Richter to All Participants:<br />
I'll add the file formats we really want in the next release - <br />
that was kind of an experiment.<br />
10/18/2007 18:08:25 PM from John Day-Richter to All Participants:<br />
Yeah - there will be rendering/image saving in the graph dag <br />
viewer too.<br />
10/18/2007 18:08:31 PM from Jen Deegan to All Participants:<br />
excellent!<br />
10/18/2007 18:08:42 PM from Jen Deegan to All Participants:<br />
in that case we should be fine without the graphviz plugin<br />
10/18/2007 18:09:29 PM from John Day-Richter to All Participants:<br />
Anyone else have anything they want to talk about?<br />
10/18/2007 18:10:06 PM from Jen Deegan to All Participants:<br />
I guess if we have done a load of bug testing we just wait for you to <br />
get to our bug reports?<br />
10/18/2007 18:10:16 PM from Jen Deegan to All Participants:<br />
no sense producng more yet?<br />
10/18/2007 18:10:40 PM from Midori Harris to All Participants:<br />
When's the next release out? If it's just a day or two, I'll wait for it <br />
before doing more testing.<br />
10/18/2007 18:10:59 PM from John Day-Richter to All Participants:<br />
Well, the more bugs I know about the better, since we want fast <br />
turnaround times. But I hope to have a release out by Friday night.<br />
10/18/2007 18:11:22 PM from Midori Harris to All Participants:<br />
I'll wait, then, because I'm taking tomorrow afternoon off.<br />
10/18/2007 18:11:25 PM from John Day-Richter to All Participants:<br />
So don't waste too much time bug testing if you've got lots of <br />
bug reports out on your current testing area.<br />
10/18/2007 18:11:26 PM from Jen Deegan to All Participants:<br />
Actually I can try the various graph things witht he reasonder on so <br />
I'll do that<br />
10/18/2007 18:11:39 PM from Midori Harris to All Participants:<br />
back in the saddle on monday<br />
10/18/2007 18:11:50 PM from John Day-Richter to All Participants:<br />
That's a good idea. The reasoner is an essential part of <br />
OBO-Edit 2. I really want it on most of the time<br />
10/18/2007 18:12:02 PM from hurdle to All Participants:<br />
hi everyone; betterr late then never I guess<br />
10/18/2007 18:12:07 PM from Jen Deegan to All Participants:<br />
how do we describe reasoner bugs?<br />
10/18/2007 18:12:19 PM from Jen Deegan to All Participants:<br />
if it just makes things slow do we say that?<br />
10/18/2007 18:12:44 PM from John Day-Richter to All Participants:<br />
You probably won't know you're looking at a reasoner bug most of <br />
the time, but if you just notice worse performance in general, report <br />
that.<br />
10/18/2007 18:12:54 PM from John Day-Richter to All Participants:<br />
It would help if you could talk about what form the bad <br />
performance took.<br />
10/18/2007 18:12:55 PM from Jen Deegan to All Participants:<br />
ok <br />
10/18/2007 18:13:01 PM from Jen Deegan to All Participants:<br />
sure<br />
10/18/2007 18:13:06 PM from Jen Deegan to All Participants:<br />
I will time things<br />
10/18/2007 18:13:21 PM from John Day-Richter to All Participants:<br />
If you're running into problems like that, also see what happens <br />
if you turn off other applications on your machine.<br />
10/18/2007 18:13:25 PM from hurdle to All Participants:<br />
I've noticed that in using it OE for just searches, it appears to get <br />
slower and slower and I do more and more searches<br />
10/18/2007 18:13:49 PM from Jen Deegan to All Participants:<br />
sometime the form is that the music I'm listening to on my machine skips <br />
bits when I run the reasoner:-)<br />
10/18/2007 18:13:56 PM from Chris Mungall to All Participants:<br />
Jen: if you describe the sequence of operations, we can make a benchmark <br />
specifically for that<br />
10/18/2007 18:14:03 PM from Jen Deegan to All Participants:<br />
ok :-)<br />
10/18/2007 18:14:07 PM from hurdle to All Participants:<br />
IF I the n close and restart, it is ok again.<br />
10/18/2007 18:14:23 PM from John Day-Richter to All Participants:<br />
And if you can't get a consistent script, it means that your <br />
machine memory is just maxed out.<br />
10/18/2007 18:14:43 PM from John Day-Richter to All Participants:<br />
The only recourse is to shut down big memory hog applications <br />
like, say, iTunes or something.<br />
10/18/2007 18:15:07 PM from Jen Deegan to All Participants:<br />
what's a consistent script?<br />
10/18/2007 18:15:44 PM from John Day-Richter to All Participants:<br />
You know - 1) open gene_ontology_edit.obo 2) copy <br />
cellular_component to molecular_function 3) notice blue screen<br />
10/18/2007 18:16:07 PM from Jen Deegan to All Participants:<br />
oh I see<br />
10/18/2007 18:16:22 PM from Jen Deegan to All Participants:<br />
the thing is I never usuall have other things running<br />
10/18/2007 18:16:32 PM from Jen Deegan to All Participants:<br />
so there's not anything I can shut down<br />
10/18/2007 18:16:37 PM from John Day-Richter to All Participants:<br />
Zounds!<br />
10/18/2007 18:16:48 PM from Jen Deegan to All Participants:<br />
I need webex and skype<br />
10/18/2007 18:16:50 PM from John Day-Richter to All Participants:<br />
Hopefully the new reasoner prototype will do a little better for <br />
you.<br />
10/18/2007 18:16:51 PM from Jen Deegan to All Participants:<br />
so they are on<br />
10/18/2007 18:17:01 PM from Jen Deegan to All Participants:<br />
but that's it<br />
10/18/2007 18:18:01 PM from John Day-Richter to All Participants:<br />
Now I'm anxious to get this new release out to see how the <br />
reasoner behaves for people.<br />
10/18/2007 18:18:05 PM from Midori Harris to All Participants:<br />
some browsers can eat memory, especially if they've been running for a <br />
while<br />
10/18/2007 18:18:33 PM from John Day-Richter to All Participants:<br />
Harold - how many searches do you have to do before you notice <br />
the slowdown?<br />
10/18/2007 18:18:40 PM from John Day-Richter to All Participants:<br />
And has anyone else seen this?<br />
10/18/2007 18:19:10 PM from Jen Deegan to All Participants:<br />
I rarely use it as it is very slow<br />
10/18/2007 18:19:11 PM from hurdle to All Participants:<br />
oh, about I'd say 10-15; I use it for searching for terms to annotate<br />
10/18/2007 18:19:19 PM from Midori Harris to All Participants:<br />
I have ... it's one aspect of the general "things don't work" that we <br />
talked about yesterday.<br />
10/18/2007 18:19:37 PM from Jen Deegan to All Participants:<br />
oddly, on my mac I can work with the reasoner just fine<br />
10/18/2007 18:19:44 PM from Jen Deegan to All Participants:<br />
it's the windows machine that struggles<br />
10/18/2007 18:19:46 PM from Midori Harris to All Participants:<br />
For me it's pretty variable, possibly because I've been doing varying <br />
numbers of other things besides searches.<br />
10/18/2007 18:20:03 PM from John Day-Richter to All Participants:<br />
So, just to be clear, the bug is "searches grow progressively <br />
slower when the reasoner is on?"<br />
10/18/2007 18:20:25 PM from hurdle to All Participants:<br />
Not sure; will have to check but if the reasoner is on by default, yes<br />
10/18/2007 18:20:30 PM from Midori Harris to All Participants:<br />
for me , yes.<br />
10/18/2007 18:20:42 PM from Erika to All Participants:<br />
for me <br />
too!<br />
10/18/2007 18:20:46 PM from John Day-Richter to All Participants:<br />
Ah, so the bug is "searches grow progressively slower always"<br />
10/18/2007 18:20:59 PM from Jen Deegan to All Participants:<br />
for me it's just that when I look for redundant links things get slow<br />
10/18/2007 18:21:02 PM from hurdle to All Participants:<br />
so it would seem<br />
10/18/2007 18:21:15 PM from hurdle to All Participants:<br />
but that "redundant " thing now has me wondering<br />
10/18/2007 18:21:26 PM from Jen Deegan to All Participants:<br />
that's the only time I use the reasoner<br />
10/18/2007 18:21:27 PM from Midori Harris to All Participants:<br />
hmmm, I haven't done much with the reasoner off ... so can't shed light<br />
10/18/2007 18:21:56 PM from John Day-Richter to All Participants:<br />
Is the affect more pronounced when your searches return lots of <br />
results?<br />
10/18/2007 18:22:08 PM from Jen Deegan to All Participants:<br />
is information from 1.101 pertinent as well as 2?<br />
10/18/2007 18:22:20 PM from John Day-Richter to All Participants:<br />
No, 2 does things totally differently.<br />
10/18/2007 18:22:24 PM from Jen Deegan to All Participants:<br />
oh<br />
10/18/2007 18:22:28 PM from Jen Deegan to All Participants:<br />
I have only tried 1.101<br />
10/18/2007 18:22:29 PM from Midori Harris to All Participants:<br />
yes! (to John's question)<br />
10/18/2007 18:22:30 PM from hurdle to All Participants:<br />
Will elaborate: the searches I most do is to s set where I load6 <br />
ontologies, including the GO, MA, EC, CE, EMAP, and one of my own (ATTC <br />
lines)<br />
10/18/2007 18:22:38 PM from hurdle to All Participants:<br />
I don't havethe probelm in 1.101<br />
10/18/2007 18:22:59 PM from John Day-Richter to All Participants:<br />
Hmm... I'm going to run and look something up quickly. I'll be <br />
right back -<br />
10/18/2007 18:23:26 PM from hurdle to All Participants:<br />
sorry about the typing; something is not quite write with my keyboard <br />
skin today<br />
10/18/2007 18:23:31 PM from hurdle to All Participants:<br />
right<br />
10/18/2007 18:23:37 PM from hurdle to All Participants:<br />
or my breain<br />
10/18/2007 18:23:40 PM from hurdle to All Participants:<br />
brain<br />
10/18/2007 18:24:50 PM from John Day-Richter to All Participants:<br />
Aha!<br />
10/18/2007 18:25:09 PM from John Day-Richter to All Participants:<br />
I see evidence that OBO-Edit might be thoughtfully caching the <br />
results of every single query.<br />
10/18/2007 18:25:20 PM from hurdle to All Participants:<br />
ahh<br />
10/18/2007 18:25:23 PM from Jen Deegan to All Participants:<br />
that is very thoughtful<br />
10/18/2007 18:25:37 PM from John Day-Richter to All Participants:<br />
Especially if the thought is "let's uselessly waste memory".<br />
10/18/2007 18:25:56 PM from John Day-Richter to All Participants:<br />
I'll do some more experiments to confirm this, but turning this <br />
off might be the solution.<br />
10/18/2007 18:27:42 PM from John Day-Richter to All Participants:<br />
Anyway, shall we disperse?<br />
10/18/2007 18:28:03 PM from hurdle to All Participants:<br />
I'm melting....<br />
10/18/2007 18:28:03 PM from Midori Harris to All Participants:<br />
and ride off into the sunset?<br />
10/18/2007 18:28:52 PM from John Day-Richter to All Participants:<br />
Farewell my little corn flowers, I got other towns to save.<br />
10/18/2007 18:28:57 PM from John Day-Richter to All Participants:<br />
See you at office hours.<br />
10/18/2007 18:29:00 PM from Jen Deegan to All Participants:<br />
byeeeeee<br />
10/18/2007 18:29:01 PM from hurdle to All Participants:<br />
happy trails<br />
10/18/2007 18:29:06 PM from Erika to All Participants:<br />
Thanks <br />
John!<br />
10/18/2007 18:29:12 PM from Erika to All Participants:<br />
Bye all!<br />
<br />
10/18/2007 18:29:13 PM from Midori Harris to All Participants:<br />
bum-ba-dee-da ...<br />
10/18/2007 18:29:23 PM from John Day-Richter to All Participants:<br />
Can a non-crashed participant distribute the minutes?<br />
10/18/2007 18:29:35 PM from Midori Harris to All Participants:<br />
ok<br />
10/18/2007 18:29:40 PM from John Day-Richter to All Participants:<br />
Bye all.<br />
10/18/2007 18:29:42 PM from melissaH to All Participants:<br />
bye!<br />
10/18/2007 18:29:50 PM from Midori Harris to All Participants:<br />
bye<br />
</pre></div>Midori