OE Webex 17Jan08

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01/17/2008    09:30:28 AM    from Nomi Harris to All Participants:
Hello
01/17/2008    09:30:44 AM    from melissaH to All Participants:
hi there

01/17/2008    09:30:57 AM    from midori to All Participants:
hi
01/17/2008    09:31:56 AM    from Nomi Harris to All Participants:
It's too bad WebEx doesn't show the new participants the messages they 
missed before they joined the chat.
01/17/2008    09:32:01 AM    from Nomi Harris to All Participants:
If it did, we could just get started.
01/17/2008    09:33:11 AM    from Nomi Harris to All Participants:
I'll be right back, I'm getting some tea...
01/17/2008    09:33:30 AM    from melissaH to All Participants:
ok, me too.

01/17/2008    09:35:45 AM    from Nomi Harris to All Participants:
Hi, Karen
01/17/2008    09:36:01 AM    from midori to All Participants:
welcome back!
01/17/2008    09:36:03 AM    from Karen to All Participants:
	Hi Nomi
01/17/2008    09:36:07 AM    from Karen to All Participants:
	thanks
01/17/2008    09:36:11 AM    from Nomi Harris to All Participants:
Where were you?
01/17/2008    09:36:21 AM    from Karen to All Participants:
maternity leave
01/17/2008    09:36:31 AM    from Nomi Harris to All Participants:
Oh!
01/17/2008    09:37:00 AM    from Nomi Harris to All Participants:
How old is your baby?
01/17/2008    09:37:02 AM    from Karen to All Participants:
	wacky, I 
can get onto this Webex no problem, but I haven't been able to get onto 
the SGD group meeting ones, I'll have to check to see the settings - it 
complains that I don't have Windows Media player...
01/17/2008    09:37:06 AM    from Karen to All Participants:
	almost 4 
months
01/17/2008    09:37:25 AM    from Nomi Harris to All Participants:
I'm on a Mac, and it hasn't said anything about Windows Media player.
01/17/2008    09:37:35 AM    from Nomi Harris to All Participants:
I haven't had too much trouble with Webex.  It's generally worked for 
me.
01/17/2008    09:38:22 AM    from Karen to All Participants:
	yea me 
too, but when I go through the troubleshooting for the SGD meeting, 
that's the one that fails. Until recently WEbex has been great for me. 
I've hosted meetings from home and used OBO-Edit.
01/17/2008    09:38:38 AM    from Nomi Harris to All Participants:
Jennifer just emailed me that she's all by herself on the Webex
01/17/2008    09:38:49 AM    from Nomi Harris to All Participants:
She must be on a different one.  Hang on while I try to figure out 
what's going on.
01/17/2008    09:40:27 AM    from midori to All Participants:
hi again ppp
01/17/2008    09:40:28 AM    from Nomi Harris to All Participants:
I sent her the URL for this one--hopefully she'll find us soon!
01/17/2008    09:40:52 AM    from midori to All Participants:
What timing! Webex crashed just as I was typing a comment to the effect 
that I sometimes have it crash.
01/17/2008    09:40:53 AM    from melissaH to All Participants:
a belated congrats, Karen

01/17/2008    09:41:05 AM    from Nomi Harris to All Participants:
Jen made it!  Yay!
01/17/2008    09:41:06 AM    from Karen to All Participants:
	thanks 
:)
01/17/2008    09:41:06 AM    from midori to All Participants:
but I've only had trouble joining once
01/17/2008    09:41:09 AM    from Jen Deegan to All Participants:
hi

01/17/2008    09:41:25 AM    from Nomi Harris to All Participants:
Congrats from me, too!  I didn't know!
01/17/2008    09:41:36 AM    from Nomi Harris to All Participants:
Ok, this is probably everyone.
01/17/2008    09:41:45 AM    from Jen Deegan to All Participants:
tanya's on the way

01/17/2008    09:41:47 AM    from Nomi Harris to All Participants:
So, I have a sick three-year-old home with me today.
01/17/2008    09:41:58 AM    from melissaH to All Participants:
bummer, know how that goes!!

01/17/2008    09:42:01 AM    from midori to All Participants:
Tanya just asked if it's worth her showing up.
01/17/2008    09:42:04 AM    from Nomi Harris to All Participants:
She is currently watching Creature Comforts on my computer (while I'm 
relegated to the laptop).
01/17/2008    09:42:15 AM    from Nomi Harris to All Participants:
Tell her she doesn't have to.
01/17/2008    09:42:20 AM    from Nomi Harris to All Participants:
(Her  Tanya)
01/17/2008    09:42:28 AM    from Karen to All Participants:
Fortunately, my 3 year old is well and at daycare, and right now the 
baby is sleeping
01/17/2008    09:42:46 AM    from Jen Deegan to All Participants:
sounds good :-)

01/17/2008    09:42:48 AM    from melissaH to All Participants:
hooray!

01/17/2008    09:42:51 AM    from Nomi Harris to All Participants:
Anyway, if I suddenly fail to answer something, it's probably because I 
had to attend to my daughter.
01/17/2008    09:43:01 AM    from Jen Deegan to All Participants:
good to know

01/17/2008    09:43:12 AM    from Jen Deegan to All Participants:
john had that too so we are all organised for unexpected silences

01/17/2008    09:43:34 AM    from midori to All Participants:
gives us time to type up more long questions ;)
01/17/2008    09:43:43 AM    from Nomi Harris to All Participants:
Anyway, there's not much on the agenda today.
01/17/2008    09:43:46 AM    from Jen Deegan to All Participants:
good point

01/17/2008    09:43:52 AM    from Nomi Harris to All Participants:
Midori has set up a poll for the meeting time.
01/17/2008    09:43:57 AM    from midori to All Participants:
Is someone on transcript duty?
01/17/2008    09:44:08 AM    from midori to All Participants:
I missed a bit when webex crashed ...
01/17/2008    09:44:13 AM    from Jen Deegan to All Participants:
could I ask a question later about obsoletes?

01/17/2008    09:44:25 AM    from Nomi Harris to All Participants:
I can send out a transcript.
01/17/2008    09:44:36 AM    from Nomi Harris to All Participants:
Yes, Jen (though I don't promise to be able to answer it).
01/17/2008    09:44:40 AM    from Jen Deegan to All Participants:
:)

01/17/2008    09:44:52 AM    from Nomi Harris to All Participants:
As for the meeting time, keep in mind that I will soon be replaced by 
our new OBO-Edit developer.
01/17/2008    09:44:59 AM    from Nomi Harris to All Participants:
She is still waiting for a visa (last I heard).
01/17/2008    09:45:13 AM    from midori to All Participants:
thanks (for transcript)
01/17/2008    09:45:31 AM    from Nomi Harris to All Participants:
So it may not make much sense to worry about my schedule when deciding 
on the meeting time, since Amina will presumably have different 
constraints anyway.
01/17/2008    09:46:15 AM    from midori to All Participants:
It's easy to set up those polls, so I can do another one when Amina's 
here.
01/17/2008    09:46:26 AM    from Nomi Harris to All Participants:
The only reason I'd even change the meeting time now is so as not to 
exclude David.
01/17/2008    09:46:41 AM    from midori to All Participants:
(OR we can just present her with the results of this one ...)
01/17/2008    09:46:52 AM    from Nomi Harris to All Participants:
I was discussing the "regulates" icon with Chris yesterday.
01/17/2008    09:47:22 AM    from Nomi Harris to All Participants:
I suggested one that he liked, with a circle that has an arched arrow 
(suggestive of some sort of regulatory network) and an R.
01/17/2008    09:47:31 AM    from Nomi Harris to All Participants:
Oh, here's midori again.  Sorry Webex is not working well for you today.
01/17/2008    09:47:45 AM    from Jen Deegan to All Participants:
that sounds nice

01/17/2008    09:47:45 AM    from midori to All Participants:
wow, two crashes in 15 minutes ... don't think I've had that happen 
before!
01/17/2008    09:48:01 AM    from melissaH to All Participants:
there are two of you now!

01/17/2008    09:48:03 AM    from Nomi Harris to All Participants:
Anyway, I made a rough mockup of it, and I think one of the more 
graphically gifted group members might try to work on it.
01/17/2008    09:48:05 AM    from Jen Deegan to All Participants:
the icon will have to be very small in oboedit 12 point font so there 
may not be room for much detail

01/17/2008    09:48:13 AM    from midori to All Participants:
I'll catch what I missed in the transcript.
01/17/2008    09:48:21 AM    from Nomi Harris to All Participants:
We've been busy this week with a grant proposal (due tomorrow-ack!).
01/17/2008    09:48:21 AM    from Jen Deegan to All Participants:
oooo

01/17/2008    09:48:30 AM    from Nomi Harris to All Participants:
It's mostly for PATO.
01/17/2008    09:48:30 AM    from midori to All Participants:
good luck!
01/17/2008    09:48:35 AM    from Jen Deegan to All Participants:
yes good luck

01/17/2008    09:48:58 AM    from Nomi Harris to All Participants:
Suzi's the one who needs the good wishes.  I imagine she's pulling a few 
all-nighters this week.
01/17/2008    09:49:15 AM    from melissaH to All Participants:
lemme know if there's anything we can do to help here at zfin

01/17/2008    09:49:17 AM    from Nomi Harris to All Participants:
Anyway, I have been editing the grant this week and haven't really done 
any OBO-Editing.
01/17/2008    09:49:31 AM    from Nomi Harris to All Participants:
Thanks, melissa--I don't think there's time for any outside help, 
unfortunately.
01/17/2008    09:49:35 AM    from Nomi Harris to All Participants:
You know how it is; it always comes down to the wire.
01/17/2008    09:49:36 AM    from Jen Deegan to All Participants:
if you don't have any things shall we ask questions?

01/17/2008    09:49:41 AM    from Nomi Harris to All Participants:
Sure.
01/17/2008    09:49:49 AM    from Jen Deegan to All Participants:
I have a question about obsoletes

01/17/2008    09:49:56 AM    from Jen Deegan to All Participants:
it is a long one.

01/17/2008    09:50:05 AM    from Jen Deegan to All Participants:
you know how we add consider and replaced_by tags

01/17/2008    09:50:09 AM    from Jen Deegan to All Participants:
to obsolete terms

01/17/2008    09:50:13 AM    from Nomi Harris to All Participants:
Yes
01/17/2008    09:50:21 AM    from Jen Deegan to All Participants:
and I thought that oboedit automtically generated the comment part that 
says

01/17/2008    09:50:37 AM    from Jen Deegan to All Participants:
to update annotations please use term [name]

01/17/2008    09:50:41 AM    from Jen Deegan to All Participants:
with id [id]

01/17/2008    09:50:52 AM    from Jen Deegan to All Participants:
but I just tired it and the comment is not autogenerated

01/17/2008    09:51:03 AM    from Jen Deegan to All Participants:
it only generates when I run the file through obo2obo

01/17/2008    09:51:09 AM    from midori to All Participants:
what did you do (specifically)?
01/17/2008    09:51:21 AM    from Nomi Harris to All Participants:
Huh.  So it sounds like it might be something obo2obo puts in?
01/17/2008    09:51:33 AM    from Jen Deegan to All Participants:
I obsoleted a term and added the replaced_by tags and then I saved the 
file and looked at the stanza

01/17/2008    09:51:50 AM    from Jen Deegan to All Participants:
but if I run obo2obo I have to add the writecomments flag to make it 
happen

01/17/2008    09:51:56 AM    from midori to All Participants:
Jen - that's what should happen.
01/17/2008    09:52:07 AM    from Jen Deegan to All Participants:
would we not want the comment no?

01/17/2008    09:52:25 AM    from midori to All Participants:
Nomi- these comments result from using obo2obo with the writecommen 
option.
01/17/2008    09:52:29 AM    from Jen Deegan to All Participants:
yes

01/17/2008    09:52:35 AM    from Jen Deegan to All Participants:
but do we not want them then?

01/17/2008    09:53:00 AM    from midori to All Participants:
Jen - No, we agreed a while back that it would be redundant to have 
comments if we had the consider and replaced_by tags.
01/17/2008    09:53:06 AM    from Jen Deegan to All Participants:
oh okay

01/17/2008    09:53:14 AM    from Jen Deegan to All Participants:
I'll be quiet then. :-)

01/17/2008    09:53:25 AM    from Nomi Harris to All Participants:
Any other questions?
01/17/2008    09:53:59 AM    from Nomi Harris to All Participants:
It sounds like the 1.2-enabled obomerge is working.
01/17/2008    09:54:05 AM    from melissaH to All Participants:
When does Amina start should her visa go through?

01/17/2008    09:54:06 AM    from Jen Deegan to All Participants:
yes it's great thanks

01/17/2008    09:54:07 AM    from midori to All Participants:
The comments were a stopgap measure for the days before we had the tags; 
we regenerate them for the OBO v1.0 file precisely because that file 
doesn't have the tags ... which in turn is so the tags don't break 
things.
01/17/2008    09:54:17 AM    from Nomi Harris to All Participants:
The (minor) issues Jen reported with obomerge are not 1.2-specific.
01/17/2008    09:54:27 AM    from Jen Deegan to All Participants:
yes I see

01/17/2008    09:54:31 AM    from Nomi Harris to All Participants:
Melissa, once Amina has the visa, she will start ASAP.
01/17/2008    09:54:49 AM    from Jen Deegan to All Participants:
the 1.2 thing is great, thanks for that Nomi.

01/17/2008    09:54:57 AM    from Nomi Harris to All Participants:
My pleasure.
01/17/2008    09:55:13 AM    from Nomi Harris to All Participants:
I wish I could do more to help you guys, but Suzi has me on other 
projects.
01/17/2008    09:55:20 AM    from Jen Deegan to All Participants:
that's play

01/17/2008    09:55:23 AM    from Jen Deegan to All Participants:
I mean okay

01/17/2008    09:55:25 AM    from Jen Deegan to All Participants:
:-)

01/17/2008    09:55:30 AM    from melissaH to All Participants:
i liked play better....

01/17/2008    09:55:33 AM    from Jen Deegan to All Participants:
should we discuss testing tasks?

01/17/2008    09:55:37 AM    from Nomi Harris to All Participants:
Yes
01/17/2008    09:55:39 AM    from Jen Deegan to All Participants:
so we are ready for amina?

01/17/2008    09:55:41 AM    from melissaH to All Participants:
yes, thanks for all you've done nomi, no worries

01/17/2008    09:55:59 AM    from Nomi Harris to All Participants:
Amina will have plenty to do, don't worry about that!
01/17/2008    09:56:05 AM    from Jen Deegan to All Participants:
that's good then

01/17/2008    09:56:14 AM    from Jen Deegan to All Participants:
shoudl we co-ordinate something amongst ourselves?

01/17/2008    09:56:26 AM    from Nomi Harris to All Participants:
I hope to do some more work on the user documentation soon.
01/17/2008    09:56:37 AM    from Jen Deegan to All Participants:
are there any show-stopping bugs that prevent testing?

01/17/2008    09:56:45 AM    from Nomi Harris to All Participants:
Jen, I don't think it's pressing to do more systematic testing at this 
point,
01/17/2008    09:56:46 AM    from Jen Deegan to All Participants:
like the save mechanism or anything?

01/17/2008    09:56:49 AM    from midori to All Participants:
<sigh> it could be the network at home this time ... it was completely 
FUBAR yesterday
01/17/2008    09:56:57 AM    from Nomi Harris to All Participants:
as there are already enough bugs to keep Amina busy for months.
01/17/2008    09:57:03 AM    from Jen Deegan to All Participants:
oh ok

01/17/2008    09:57:12 AM    from Jen Deegan to All Participants:
I guess we could write docs then?

01/17/2008    09:57:17 AM    from Nomi Harris to All Participants:
The problem I've noticed with the save is the one I posted to SF
01/17/2008    09:57:34 AM    from Jen Deegan to All Participants:
is there any point our doing anything about oboedit 2 just now?

01/17/2008    09:57:40 AM    from Nomi Harris to All Participants:
where the error-checking window also creates a vestigial window that 
steals the focus.
01/17/2008    09:57:41 AM    from midori to All Participants:
to the extent that we can work around the bugs, yes, I think we could 
document
01/17/2008    09:57:47 AM    from Jen Deegan to All Participants:
ok

01/17/2008    09:58:09 AM    from Jen Deegan to All Participants:
I wonder what is missing in the docs

01/17/2008    09:58:10 AM    from Nomi Harris to All Participants:
Jen, were you using OE2 for the sole purpose of testing and reporting 
bugs?
01/17/2008    09:58:17 AM    from Nomi Harris to All Participants:
It's not actually useful to you right now?
01/17/2008    09:58:19 AM    from Jen Deegan to All Participants:
I'm not using it at all just now

01/17/2008    09:58:25 AM    from midori to All Participants:
I haven't been making OE2 a very high priority  lately
01/17/2008    09:58:30 AM    from Nomi Harris to All Participants:
Fair enough.
01/17/2008    09:58:33 AM    from melissaH to All Participants:
me neither, sorry

01/17/2008    09:58:40 AM    from Jen Deegan to All Participants:
I haven't got to the stage where I'm editing with it yet

01/17/2008    09:58:49 AM    from Jen Deegan to All Participants:
once I am at that stage it's much easier to test

01/17/2008    09:59:01 AM    from Nomi Harris to All Participants:
I think the testing can be a background task for you.
01/17/2008    09:59:16 AM    from Jen Deegan to All Participants:
However, I guess we need it released before we can release the regulates 
relationship don't we?

01/17/2008    09:59:31 AM    from midori to All Participants:
I do think it needs some bug-fixing, and I hope Amina will find ways to 
improve performance on non-state-of-the-art hardware
01/17/2008    09:59:40 AM    from Nomi Harris to All Participants:
What do you mean by "release" the regulates relationship?
01/17/2008    09:59:42 AM    from midori to All Participants:
Jen - I don't think so ... unless I'm missing something.
01/17/2008    10:00:00 AM    from Karen to All Participants:
	Is OE2 
required before we can release the regulates relationship?
01/17/2008    10:00:00 AM    from Nomi Harris to All Participants:
It definitely needs both bug-fixing and performance improvement, midori.
01/17/2008    10:00:00 AM    from Jen Deegan to All Participants:
it was the cross-products bit I wondered about

01/17/2008    10:00:34 AM    from Jen Deegan to All Participants:
for the intersection relationships

01/17/2008    10:00:34 AM    from midori to All Participants:
It'll be easier to do the cros-products in OE2, but they can be cerated 
and manipulated in OE1.
01/17/2008    10:00:34 AM    from Jen Deegan to All Participants:
really?

01/17/2008    10:00:34 AM    from Jen Deegan to All Participants:
ok

01/17/2008    10:00:34 AM    from midori to All Participants:
Try out the cross-product editor. :)
01/17/2008    10:00:34 AM    from Jen Deegan to All Participants:
does that bit work then?

01/17/2008    10:00:34 AM    from Jen Deegan to All Participants:
will do

01/17/2008    10:00:34 AM    from Jen Deegan to All Participants:
I thought it didn't work from what chris said

01/17/2008    10:00:37 AM    from Nomi Harris to All Participants:
That's why I don't think it's crucial to do more testing now.  There are 
already enough known bugs and issues to be fixed.  If the bug list were 
empty, then we'd want more thorough testing to make sure we'd got 
everything.
01/17/2008    10:00:39 AM    from Jen Deegan to All Participants:
I'll have a go

01/17/2008    10:00:53 AM    from Jen Deegan to All Participants:
so docs I guess then...

01/17/2008    10:01:10 AM    from midori to All Participants:
Karen tested it (with the reasoner ON, no less), in the run-up to OE1 
release. That level of pain shouldn't go to waste!
01/17/2008    10:01:12 AM    from Nomi Harris to All Participants:
Yes, docs are definitely important.
01/17/2008    10:01:22 AM    from Jen Deegan to All Participants:
good-oh

01/17/2008    10:01:29 AM    from Jen Deegan to All Participants:
shall we divy up tasks?

01/17/2008    10:01:45 AM    from melissaH to All Participants:
I did too. earlier versions had strange results, but my most recent 
testing (some few months back)looked good

01/17/2008    10:01:51 AM    from midori to All Participants:
It's just hugely improved in OE2, apparently (but I haven't tried it 
myself).
01/17/2008    10:02:30 AM    from Jen Deegan to All Participants:
shall we look at the doc list? 
http://wiki.geneontology.org/index.php/OBO-Edit:_Help_document_OBO-Edit_2

01/17/2008    10:03:15 AM    from Nomi Harris to All Participants:
Has anyone noticed any significant new features that are not on that 
list?
01/17/2008    10:03:36 AM    from Nomi Harris to All Participants:
Does someone want to write about how to customize the layout?
01/17/2008    10:03:52 AM    from Jen Deegan to All Participants:
I can do that

01/17/2008    10:03:56 AM    from Nomi Harris to All Participants:
Great!
01/17/2008    10:04:05 AM    from Jen Deegan to All Participants:
it's just dragging bits around isn't it?

01/17/2008    10:04:10 AM    from Jen Deegan to All Participants:
Is there any other secret?

01/17/2008    10:04:23 AM    from Nomi Harris to All Participants:
I'm not sure...
01/17/2008    10:04:50 AM    from Nomi Harris to All Participants:
If it's really that straightforward, maybe I should do that one and you 
can work on some of the more complicated editing functionality, Jen.
01/17/2008    10:05:04 AM    from Jen Deegan to All Participants:
darn...

01/17/2008    10:05:19 AM    from Jen Deegan to All Participants:
anything particular in mind?

01/17/2008    10:05:33 AM    from Nomi Harris to All Participants:
I don't know--whatever's still on the list that hasn't been done.
01/17/2008    10:05:34 AM    from midori to All Participants:
One thing that needs doing is to go through the old parts and update 
things that are affected by new features.
01/17/2008    10:05:44 AM    from Nomi Harris to All Participants:
Yes, I was just going to say I'm going to do some of that.
01/17/2008    10:06:04 AM    from Nomi Harris to All Participants:
But there are parts I don't understand well, so maybe you can take on 
those, ok?
01/17/2008    10:06:07 AM    from Jen Deegan to All Participants:
I'll have a look round and see what there is

01/17/2008    10:06:15 AM    from Nomi Harris to All Participants:
Thanks.
01/17/2008    10:06:19 AM    from melissaH to All Participants:
I'll try to do the same...

01/17/2008    10:06:24 AM    from midori to All Participants:
I'm specifically thinking of the places where filtering can be used - 
Jen might be interested in that since she did the new-search 
documentation.
01/17/2008    10:06:25 AM    from Jen Deegan to All Participants:
I'd be interested to learn the cross product plugin

01/17/2008    10:06:29 AM    from Jen Deegan to All Participants:
shall I try that?

01/17/2008    10:06:29 AM    from Nomi Harris to All Participants:
I won't be able to do much on this for a few days.
01/17/2008    10:06:44 AM    from Nomi Harris to All Participants:
But I will try to allocate some time for it next week.
01/17/2008    10:06:49 AM    from Nomi Harris to All Participants:
Jen, yes, that would be great.
01/17/2008    10:07:01 AM    from Jen Deegan to All Participants:
great, that would be useful for me too

01/17/2008    10:07:03 AM    from Nomi Harris to All Participants:
Are we done?
01/17/2008    10:07:12 AM    from midori to All Participants:
I don't have anything else ...
01/17/2008    10:07:31 AM    from Jen Deegan to All Participants:
for the meeting?

01/17/2008    10:07:31 AM    from Nomi Harris to All Participants:
I will look at the poll results and suggest some possible meeting times.
01/17/2008    10:07:39 AM    from Jen Deegan to All Participants:
ok

01/17/2008    10:07:41 AM    from midori to All Participants:
.. except that if there's a meeting next week I probably won't make it.
01/17/2008    10:07:46 AM    from Jen Deegan to All Participants:
ok

01/17/2008    10:07:46 AM    from Nomi Harris to All Participants:
We can skip next week.
01/17/2008    10:07:59 AM    from Nomi Harris to All Participants:
Bye, all?
01/17/2008    10:08:02 AM    from Jen Deegan to All Participants:
bye then

01/17/2008    10:08:12 AM    from melissaH to All Participants:
ok with me, bye!

01/17/2008    10:08:17 AM    from midori to All Participants:
bye!